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Open Sustainable Technology

Recent Releases of Open Sustainable Technology Projects

xgcm - v0.10.0

What's Changed

New Contributors

Full Changelog: https://github.com/xgcm/xgcm/compare/v0.9.0...v0.10.0

Climate Change - Climate Data Processing and Analysis - Python
Published by hdrake 1 day ago

PlantCV - PlantCV v4.11.3

What's Changed

New Contributors

Full Changelog: https://github.com/danforthcenter/plantcv/compare/v4.11.2...v4.11.3

Biosphere - Plants and Vegetation - Python
Published by nfahlgren 3 days ago

cellpy - v1.0.4a4

What's Changed

Full Changelog: https://github.com/jepegit/cellpy/compare/v1.0.4a3...v1.0.4a4

Energy Storage - Battery - Python
Published by jepegit 3 days ago

CoralNet-Toolbox - v1.0.3

Full Changelog: https://github.com/Jordan-Pierce/CoralNet-Toolbox/compare/v1.0.2...v1.0.3

Biosphere - Marine Life and Fishery - Python
Published by Jordan-Pierce 5 days ago

CairnOpen - Cairn 6.0.0

Non exhaustive list of modifications:

[Core]

  • Refactoring of EnergyVector: split into ElectricalCarrier and MaterialCarrier (with type Mass or Energy). A script update_v5.4_v6.0.py is included to migrate existing studies and ensure compatibility.
  • EnergyVector: improve management of atomic composition for MaterialCarrier, with support for user-defined inputs.
  • EnergyVector: add support for time-varying parameters (e.g., LHV/PCI, atomic composition, etc.).
  • Renaming Parameters and Indicators: renaming of certain parameters (Grey… -> Embodied…, …Constant -> …Offset) and indicators for clarity and consistency. Use the script update_v5.4_v6.0.py to migrate existing studies and ensure compatibility.
  • Profiling tool: new class allowing automatic measurement of execution time and memory usage, with data export for each run.
  • Sizing of converters: improve sizing based on Weight and consistency checks; removal of unused Pmin variables when minPower = 0.
  • Minimum capacity logic: extended to Compressor and Pipeline models.
  • Compressor: add an option to manually specify electrical consumption.
  • MultiConverter: users can now define upper limits on inputs/outputs via a CSV file.
  • VariableOpex at the port level: users can now define VariableOpex at the port level.
  • TecEcoAnalysis: removal of the Range parameter.
  • Multi-threading: add support for multi-thread execution of Parametric Study.
  • Logging: clean and improve log display.
  • Developer tools: add a model template for developers creating new components.
  • Code quality: general code cleanup, refactoring, and minor fixes.

[API]

  • Add a function to perform a Parametric Study.
  • Add an Import Group function: import_group(json: string)
  • Support for timeseries in dataframe format via the API: add_df_timeseries(problem: OptimProblem, timeSeries: pd.DataFrame)
  • Support for user comments via the API.
  • Add an attribute to know the energy vector associated with a bus: bus.carrier

[GUI]

  • The GUI now retrieves all necessary data (variables, indicators, ports, units, etc.) directly from the API, removing the dependency on Model.json.
  • Improve and centralized font sizes in the interface.
  • Add units in the results windows.
  • Fix display issues related to Parametric Study (progress bar, etc.).
  • Add support for exporting a single component or a selection of components (in addition to the existing group export).

Energy Systems - Energy System Modeling Frameworks - HTML
Published by stephanie-crevon 5 days ago

echoSMs -

  • update documentation
  • update descriptions in datastore schema
  • add geometric shape to datastore schema (unions of spheroids and bent cylinders)
  • add a license property to the datastore schema
  • prototype datastore server address is now available as echosms.DATASTORE_URI
  • adjust some datastore schema property values to match relevant ICES vocabularies
  • miscellaneous bug fixes

Biosphere - Marine Life and Fishery - Python
Published by github-actions[bot] 5 days ago

icechunk - v2.1.1

What's Changed

Full Changelog: https://github.com/earth-mover/icechunk/compare/v2.1.0...v2.1.1

Climate Change - Climate Data Standards - Rust
Published by paraseba 5 days ago

CoralNet-Toolbox - v1.0.2

Full Changelog: https://github.com/Jordan-Pierce/CoralNet-Toolbox/compare/v1.0.1...v1.0.2

Biosphere - Marine Life and Fishery - Python
Published by Jordan-Pierce 6 days ago

cellpy - v1.0.4a3

What's Changed

Full Changelog: https://github.com/jepegit/cellpy/compare/v1.0.4a2...v1.0.4a3

Energy Storage - Battery - Python
Published by jepegit 6 days ago

CoralNet-Toolbox - v1.0.1

Full Changelog: https://github.com/Jordan-Pierce/CoralNet-Toolbox/compare/v1.0.0...v1.0.1

Biosphere - Marine Life and Fishery - Python
Published by Jordan-Pierce 7 days ago

openfoodnetwork - v5.7.2 Gratin Dauphinois

What's Changed

API changes ⚠️

Experimental features for testing 🚧

Technical changes 🛠️

Dependencies 📦

Full Changelog: https://github.com/openfoodfoundation/openfoodnetwork/compare/v5.7.1...v5.7.2

Gratin dauphinois is a French gratin of sliced raw potatoes baked in cream, from the Dauphiné region in south-eastern France.

Consumption - Agriculture and Nutrition - Ruby
Published by rioug 7 days ago

PowerIO - v0.6.3

  • Arrow matrix axes (#234): the C ABI Arrow export gains a table catalog and
    dense matrix axis maps. pio_to_arrow exposes matrix_bus and
    matrix_branch axis tables alongside the ybus, incidence, bprime, and
    bdoubleprime COO tables, which carry powerio.row_axis / powerio.col_axis
    schema metadata so a consumer maps dense matrix rows and incidence columns
    back to source bus and branch rows. Matrix rows are labeled with the
    matrix_bus axis, which stays correct when 3-winding transformer star-point
    lowering expands the bus set past the handle bus order.
  • FDPF matrices (#234): bprime / bdoubleprime follow MATPOWER makeB
    semantics, with self-loop handling and asymmetric Matrix Market writes pinned
    by Rust, C ABI, and Python coverage.
  • Summary JSON (#234): the C ABI exposes balanced (pio_summary_json) and
    distribution summary JSON, so a binding can render network summaries without
    materializing the full model payload.
  • Matrix Arrow export (#234): the numeric matrix export path fills Julia-owned
    buffers directly for the copy-free fast path.

What's Changed

Full Changelog: https://github.com/eigenergy/powerio/compare/v0.6.2...v0.6.3

Energy Systems - Energy Data Accessibility and Integration - Rust
Published by github-actions[bot] 7 days ago

cfdm - 1.13.2.1

2026-07-06

What's Changed

Full Changelog: https://github.com/NCAS-CMS/cfdm/compare/v1.13.2.0...v1.13.2.1

Climate Change - Climate Data Standards - Python
Published by sadielbartholomew 8 days ago

goat - v2.4.45 Bugfix Release

This release is a maintenance update addressing various issues identified since the 2.4.44 release. It does not introduce any new major features, but focuses solely on improving stability and reliability.

What's Changed

Full Changelog: https://github.com/plan4better/goat/compare/v2.4.44...v2.4.45

Consumption - Mobility and Transportation - TypeScript
Published by majkshkurti 9 days ago

PowerIO - v0.6.2

  • Normalization (#210): angle bound clamping now keeps every repaired branch
    interval ordered. One sided intervals wholly outside the supported window are
    widened to the configured pad instead of producing angmin > angmax; Rust,
    C ABI, and Python normalize option coverage pin the behavior.
  • Binding coverage (#185): the already shipped study block and distribution
    graph projection now have C ABI and Python accessors. The remaining geo
    binding symbols stay in the v0.6.3 follow through.
  • BMOPF diagnostics (#219): distribution conversions now carry structured
    diagnostics alongside warning strings, and transformer export losses expose
    stable EMIT.BMOPF.* codes for downstream tests and capability checks.
  • BMOPF transformer fidelity (#214, #215, #216, #217): OpenDSS fixed
    transformer taps, center tap convention fields, delta_wye leakage referral,
    and n_winding delta_roll now export directly in BMOPF form with regression
    coverage against schema valid output and unaffected fixture byte identity.
  • BMOPF source fidelity (#218): per phase OpenDSS voltage sources on the same
    bus merge into one BMOPF voltage_source when their phase angles are
    coherent; ambiguous, bounded, priced, or conflicting source banks stay split
    with warnings.
  • Distribution capabilities (#213): the C ABI dist feature exposes
    pio_dist_capabilities_json, reporting the six BMOPF fidelity flags that
    PowerIO.jl and downstream tools can probe at runtime.
  • Geographic fields (#180): balanced and distribution models now share typed
    GeoMeta / Location JSON shapes. Network.geo, Bus.location,
    DistNetwork.geo, and DistBus.location are optional and omitted when
    absent. OpenDSS Buscoords and BMOPF longitude/latitude sideloads promote into
    typed bus locations; OpenDSS writes a Buscoords sidecar when locations are
    present, while BMOPF longitude/latitude output remains opt in and only emits
    declared geographic coordinates.
  • .pio.json model JSON: the balanced and multiconductor payload schema
    versions move from 1.0.0 to 1.1.0 for the additive geographic fields.
    The package metadata schema, C ABI version, and Python package surface stay
    in the 0.6 compatibility band.
  • JSON strategy: .pio.json docs now state that it is PowerIO's compiled
    artifact, not a case format; payload schemas are for validating model JSON
    inside .pio.json documents; powerio-json remains supported, is deprecated
    for CLI file handoffs, and is no longer shown in the PR conversion matrix.

What's Changed

Full Changelog: https://github.com/eigenergy/powerio/compare/v0.6.1...v0.6.2

Energy Systems - Energy Data Accessibility and Integration - Rust
Published by github-actions[bot] 9 days ago

PowerIO - v0.6.1

  • CI: added wasm32 coverage for the core Rust crates (#186), external BMOPF
    JSON Schema validation for emitted distribution documents (#192), and
    generated .pio.json / model JSON schema drift checks (#178).
  • Distribution fidelity (#197): OpenDSS and BMOPF writers preserve transformer
    winding voltage bases, no load admittance, tap settings, neutral impedances,
    and multi winding transformer structure. Roundtripped OpenDSS decks now run
    through a solve oracle that checks voltage agreement, load voltage model
    behavior, and neutral return handling.
  • Distribution DER mapping (#197): typed IBR and control profile data now round
    trips through OpenDSS PVSystem / Generator / InvControl and BMOPF
    ibr / control_profile records, with warnings for unsupported control
    details.
  • .pio.json documents (#181, #193): added the study block for replayable
    balanced model edits, materialization helpers, deterministic uid stamping,
    and balanced reader warnings as structured .pio.json diagnostics.
  • Normalization (#188): added an opt-in angle bound clamp pass with Rust, C ABI,
    and Python entry points; existing normalization behavior is unchanged.
  • Distribution graph projection (#182): added a bus and terminal graph view for
    DistNetwork, including transformers, open switches, and terminal metadata.
  • Matrix bindings (#190): added Arrow C ABI matrix exports as COO triplet tables
    for Ybus, incidence, B', and B'', with C and Python golden coverage.
  • Sensitivities (#8): added sparse and iterative PTDF/LODF export paths with
    drop tolerance metadata, while retaining the dense path as the small case
    oracle.
  • Documentation (#191): standardized released docs, READMEs, and crate metadata
    around .pio.json document, model JSON, and metadata terminology.
    powerio-py continues to inherit the workspace version; no separate Python
    version bump is needed.

What's Changed

Full Changelog: https://github.com/eigenergy/powerio/compare/v0.6.0...v0.6.1

Energy Systems - Energy Data Accessibility and Integration - Rust
Published by github-actions[bot] 10 days ago

PowerIO - v0.6.0

  • Breaking (#175): ElementRef.row is Option<usize>, the honest form of the
    0.5.1 wire semantics. None addresses by identity alone (refs built with
    by_source_uid); the private wire-presence shim (wire_row()) is gone, and
    row itself says whether the wire carried one. The .pio.json wire format
    is unchanged. The other break collected in #175, keyed-object addressing for
    multiconductor operating point updates, needs design and moves to the 1.0
    window (#196).
  • C ABI: the package payload extraction inverses land as additive symbols (no
    ABI version change; probe the symbols like the other feature surfaces):
    pio_package_to_balanced_network and pio_package_to_multiconductor_network
    materialize an owned network handle from a parsed .pio.json package handle,
    the inverses of the pio_package_from_* constructors. A handle built from a
    payload retains no source text, so a same-format write is a fresh
    serialization rather than a byte-exact echo; the multiconductor payload's
    parse warnings ride along.
  • C ABI: pio_to_json / pio_from_json are the function form of the balanced
    model JSON (byte identical to the powerio-json writer); the format token
    remains as a compatibility alias for file based workflows. This is the
    additive half of #194; retiring the token waits for 1.0.
  • C ABI: pio_dist_to_json / pio_dist_from_json serialize a distribution
    handle to its model JSON and back in one call each: the same object a
    .pio.json document carries under model.multiconductor_network, without
    the surrounding document. Bindings materialize element tables with this
    instead of building a throwaway package; it is not a case format (the
    converter, CLI, and inference do not know it), so BMOPF JSON remains the
    distribution JSON exchanged with other tools.
  • C ABI: pio_classify_str classifies in-memory JSON by the same top level
    markers the transmission parser's .json sniffing uses, and recognizes
    .pio.json envelopes: transmission:<format>, distribution:<format>,
    package, ambiguous, or unknown, size-then-fill. Bindings can route a
    bare .json before choosing a parser instead of matching error text.
  • The JSON classifier reports a .pio.json envelope as its own outcome
    (routing::JsonClass), so every consumer handles it: the CLI, the Python
    readers, and the Python classify_json_text now name the package surface
    for an envelope instead of a generic cannot-infer error (or, for the Python
    string reader, a MATPOWER syntax error). Envelope detection requires
    model_kind to be balanced or multiconductor, so a case document
    carrying those key names with other values still classifies as a case, and
    classification parses the document once.
  • Directed errors at the transmission boundary: a .dss path, a distribution
    from token (dss/pmd/bmopf), and a .pio.json envelope handed to the
    balanced parser now name the surface that reads them instead of a generic
    unknown-format message.

What's Changed

Full Changelog: https://github.com/eigenergy/powerio/compare/v0.5.1...v0.6.0

Energy Systems - Energy Data Accessibility and Integration - Rust
Published by github-actions[bot] 10 days ago

PowerIO - v0.5.1

The .pio.json payload schema is declared and versioned independently of the envelope (payload_schema, payload_schema_version; envelope schema_version 0.1.1). Payload rows carry stable uid identities. Operating point updates resolve by identity, a present row is a consistency check, and unknown identities are rejected at materialization and by validation. Packages from 0.5.0 read unchanged.

Python table dicts expose uid. No C ABI signature changes. Docs are restructured and served at https://powerio.dev.

Details in CHANGELOG.md.

Energy Systems - Energy Data Accessibility and Integration - Rust
Published by samtalki 11 days ago

Breeze.jl - v0.7.2

Breeze v0.7.2

Diff since v0.7.1

Merged pull requests:

  • Adaptive implicit vertical advection for all variables (anelastic SSP-RK3) (#809) (@glwagner)
  • Reland "Acoustic substep: kernel-launch reduction, per-stage substeps, cleanup" (#821) (@giordano)
  • Support adaptive implicit vertical advection with the acoustic substepper (including terrain) (#826) (@glwagner)
  • Update Project.toml (#828) (@glwagner)

Atmosphere - Atmospheric Composition and Dynamics - Julia
Published by github-actions[bot] 11 days ago

cellpy - v1.0.4a2

Retry bootstrap alpha after fixing release.yml (UV_NO_SOURCES for the full test job).

v1.0.4a1 GitHub release was created but PyPI publish did not run (test job failed on editable cellpycore path).

Install: pip install cellpy==1.0.4a2 or pip install cellpy --pre

Energy Storage - Battery - Python
Published by jepegit 11 days ago

cellpy - v1.0.4a1

First alpha on the automated GitHub release → PyPI pipeline.

Install: pip install cellpy==1.0.4a1 or pip install cellpy --pre

See HISTORY.md for highlights. Bootstrap release to verify trusted publishing before stable v1.0.4.

Energy Storage - Battery - Python
Published by jepegit 11 days ago

nomenclature - v0.31.0

What's Changed

Full Changelog: https://github.com/IAMconsortium/nomenclature/compare/v0.30.2...v0.31.0

Climate Change - Integrated Assessment and Climate Policy - Python
Published by phackstock 11 days ago

ClimateMatch Academy - v1.6.0

What's Changed

Full Changelog: https://github.com/neuromatch/climate-course-content/compare/v1.5.2...v1.6.0

Sustainable Development - Education - Jupyter Notebook
Published by iamzoltan 11 days ago

Econobis - Release 5.4.1.3

Verbetering gebruikerscontext in queue jobs
De gebruikerscontext wordt nu bij de start van diverse queue jobs expliciet opnieuw ingesteld. Deze wijziging is doorgevoerd naar aanleiding van een onderzoek naar incidenteel leeg terugkomende ontvangers bij groepsmails en zorgt ervoor dat autorisaties tijdens de uitvoering van jobs correct worden toegepast.

Energy Systems - Energy Markets - JavaScript
Published by Mosmania 12 days ago

mregions2 - v1.1.3

New maintainer @MichelleKGV

Hydrosphere - Ocean and Hydrology Data Access - R
Published by bart-v 12 days ago

MARIO - v1.0.3

MARIO v1.0.3

New features

EMERGING-E parser

  • parse_emerging now supports the variant="E" (EMERGING-E) bundle, parsing the power-disaggregated table (146 sectors, with electricity split into 14 generation sub-sectors) from EMERGING_E_<year>.mat.
  • A sibling label workbook is auto-detected, with fallback to a packaged EMERGING-E sector classification. Use labels_path= to override detection.
  • CO₂ projection: when only the standard EMERGING_CO2_<year> companion is available, the 7 fuel rows of the aggregated electricity sector are projected onto the EMERGING-E generation sub-sectors through a fixed fuel-to-technology mapping. Use co2_path= to point to a specific companion file.

Matrix-specific export — Database.export

  • Added Database.export(matrices, scenarios=..., format="csv"|"txt"|"parquet", split="scenario"|"matrix", include_meta=False, **meta_overrides), which writes selected matrices as flat long-format files with Scenario, Matrix, Unit and Value columns.
  • Flow matrices carry the numerator unit; coefficient and exploded matrices (f_ex, m_ex, p_ex and SUT variants) carry the numerator/denominator ratio.
  • Output can be split one-per-scenario or one-per-matrix, with an optional metadata header (one row per scenario, or key/value metadata in the parquet schema). release_date and other metadata fields can be supplied at export time.
  • A filters argument restricts exported rows to selected axis labels, e.g. filters={"Satellite account": ["CO2"]}. Keys may be suffixed with _from/_to to target a single side.
  • In one-per-matrix mode, a flow and its coefficient (Z/z) no longer collide on case-insensitive filesystems: the coefficient token is doubled (zz).

Documentation and packaging

  • Added the API reference page for Database.export and updated the export methods overview.
  • Aligned the documentation version string to 1.0.3.
  • Updated installation notes: Python 3.11, 3.12 and 3.13 are supported; Python 3.14 is not supported yet (the numpy==2.1.1 pin has no wheel for 3.14 and the source build fails).

Compatibility

  • Requires Python 3.11–3.13.
  • No breaking changes since v1.0.2.

Full changelog: https://github.com/it-is-me-mario/MARIO/compare/v1.0.2...v1.0.3

Industrial Ecology - Input Output Model - Python
Published by LorenzoRinaldi 12 days ago

Iceberg Tracking Beacon - Version 4.1.0

This release focuses on improving GNSS position reliability using a median-based approach to reduce the impact of outliers. Several minor improvements have also been made to improve reliability.

GNSS

  • Added median-based GNSS position calculation to improve robustness against outliers.
  • Improved position validity handling, no-fix reporting, and no-data sentinels.
  • Simplified RTC syncing with epoch plausibility checks and directionless GNSS time correction.

Iridium

  • Simplified ring buffer transmission logic for queued MO-SBD messages.
  • Improved RockBLOCK sleep compatibility for v3.D and earlier hardware revisions.

IMU

  • Simplified IMU power handling and corrected pin peripheral ordering.

Miscellaneous

  • Improved floating-point math and sensor handling.
  • Added no-data sentinels for missing sensor values.
  • Added a short delay after watchdog resets.
  • Removed legacy variables and improved inline documentation.

Cryosphere - Glacier and Ice Sheets - C++
Published by adamgarbo 12 days ago

goat - v2.4.44 Bugfix Release

This release is a maintenance update addressing various issues identified since the 2.4.43 release. It does not introduce any new major features, but focuses solely on improving stability and reliability.

What's Changed

Full Changelog: https://github.com/plan4better/goat/compare/v2.4.43...v2.4.44

Consumption - Mobility and Transportation - TypeScript
Published by majkshkurti 12 days ago

Breeze.jl - v0.7.1

Breeze v0.7.1

Diff since v0.7.0

What's Changed

Full Changelog: https://github.com/NumericalEarth/Breeze.jl/compare/v0.7.0...v0.7.1

Atmosphere - Atmospheric Composition and Dynamics - Julia
Published by github-actions[bot] 12 days ago

Breeze.jl - v0.7.0

Breeze v0.7.0

Diff since v0.6.0

Breaking changes

  • Convert CompressibleEquations to MPAS-style dry-density (ρᵈ) evolution

    Prognose dry-air density ρᵈ instead of total density, following the MPAS-A dry-coupled formulation. dynamics_density now returns ρᵈ — the coupling density that weights the flux variables (momentum ρu = ρᵈu, thermodynamic ρθ = ρᵈθ), divides velocity/θ, and is advanced by continuity. The total air density ρ = ρᵈ + Σρˣ is a diagnosed field (total_air_density, stored on the dynamics) used wherever total mass enters the physics: moisture mass-fraction recovery, scalar/water advection carriers, the equation of state, buoyancy, and saturation.

Closed issues:

  • Substepping with terrain-following coordinates: implementation plan (#673)
  • Possible bug in bulk drag formulation when using filtered veloctites (#698)
  • ZeroMomentCloudMicrophysics loses latent warming on rain-out — root cause, the compressible-core constraint, and two paths forward (#772)
  • Reactant raise=true: cannot raise vector<2xf64> gas-constant llvm.mlir.constant to stablehlo (acoustic_wave AD example) (#796)
  • NaNs & Floating point exception following Reactant@0.2.267 (#801)

What's Changed

Full Changelog: https://github.com/NumericalEarth/Breeze.jl/compare/v0.6.0...v0.7.0

Atmosphere - Atmospheric Composition and Dynamics - Julia
Published by github-actions[bot] 12 days ago

OpenLand - OpenLand 1.0.4

Bug Fixes

  • fixed global variable binding issue: resolved CRAN NOTE "no visible binding for global variable 'changes'" by properly declaring changes as a global variable used in dplyr operations. This ensures compatibility with current dplyr releases where the deprecated dplyr::changes() function is completely removed (@DavisVaughan, #13)

New Features

  • implemented .openland_try_download_and_load_rda() function for graceful dataset loading with informative error messages
  • enhanced dataset availability checks in vignette and examples with automatic error recovery

Natural Resources - Soil and Land - R
Published by reginalexavier 12 days ago

PowerIO - v0.5.0

  • powerio-pkg: NetworkPackage is the one package type name (CompilerPackage
    is gone); the Julia binding already leads with NetworkPackage. The .pio.json
    format is unchanged.
  • Python API: the seven module level package_* functions are replaced by the
    powerio.Package handle class, which parses the envelope once and exposes
    model_kind, operating_points(), materialize_operating_point(),
    as_balanced()/as_multiconductor(), validate(), validation(),
    diagnostics(), and the multiconductor to balanced preflight and lowering.
  • .pio.json operating points: the per point label and duration_hours fields
    are gone; time_axis.labels and time_axis.duration_hours (indexed by
    points[].index) are the one source of truth. Readers ignore the old fields.
  • Transmission formats: added GOC3 JSON input and Surge JSON read and write paths.
    GOC3 packages lift source time series into .pio.json operating_points,
    and package APIs can materialize one point into a static package.
  • GOC3 reader fixes: branches with additional_shunt keep the line charging
    (b/2 per terminal added to the extra shunts, per the GO Challenge 3
    formulation); ta_lb/ta_ub map to an ActiveFlow transformer control
    range instead of fabricating angmin/angmax bus angle limits; producers
    and consumers honor initial_status.on_status like every other record type;
    object form section keys sort under a total order (mixed numeric and non
    numeric keys no longer risk a sort panic).
  • powerio-pkg: GOC3 operating point extraction now consumes the parser's own
    document walking (device_rows, section, cost_at shared through a
    bridge), so update row indices match the payload by construction, including
    devices without a uid. A failed extraction attaches a
    READ.GOC3.OPERATING_POINTS_DROPPED diagnostic instead of silently
    producing a static only package. Materialized packages clear package_id
    (the parent id lives in origin.parent_package_id).
  • PSS/E .raw: revision aware record layouts for v34/v35 transformer winding
    lines (twelve ratings, NODE), v35 generator records (NREG, BASLOD),
    and v35 switched shunts (NREG, per block status triples), on both read and
    write; the 2W/3W transformer split accepts float form K fields. The
    case14_v34.raw/case14_v35.raw fixtures are regenerated in the genuine
    layouts.
  • PSLF .epc writer: parallel loads and shunts on one bus get distinct ids
    (extras["id"] preferred, positional fallback); the reader captures load,
    shunt, and SVD ids into extras["id"] so they survive cross format writes.
  • PowerWorld .pwb: the table location search runs under a work budget, so a
    crafted file fails with a read error instead of pinning a core for hours.
  • Surge JSON writer warns when named branch rating sets are dropped, like every
    other lossy writer.
  • Writing a read only format (goc3-json) returns the new
    Error::WriteUnsupported instead of a misleading UnknownFormat.
  • C ABI: the panic guard now covers index construction in the parse entry
    points; pio_package_validate documents its exclusive access requirement
    (the one non const entry point) and the header preamble scopes the
    concurrent read guarantee accordingly; PioDistNetwork gains the same
    compile time Send + Sync assertion as the other handles.
  • SourceFormat::name() is the one source format name mapping; the package,
    CLI, and Python copies are gone.

What's Changed

Full Changelog: https://github.com/eigenergy/powerio/compare/v0.4.0...v0.5.0

Energy Systems - Energy Data Accessibility and Integration - Rust
Published by github-actions[bot] 12 days ago

rdtools - Version 3.2.0

What's Changed

Full Changelog: https://github.com/NatLabRockies/rdtools/compare/3.1.1...3.2.0

Renewable Energy - Photovoltaics and Solar Energy - Python
Published by martin-springer 12 days ago

cGENIE.muffin - Bialik_et_al.SciAdv.2026

Bialik et al. ('The “warm, sluggish ocean” - a critical reevaluation')

Climate Change - Earth and Climate Modeling - Propeller Spin
Published by derpycode 13 days ago

PowSyBl Open Load Flow - v2.3.0

Labels correspond the associated described change.

  • Deprecated indicates that some methods were deprecated;
  • Breaking Change indicates a breaking change which could impact all users;
  • Test Data Change indicates a change in the simulation results that may affect existing tests in your application;
  • Parameter Change indicates a new parameter, a new parameter default or a new parameter usage;

📜 Release notes

Dependencies

  • Bump powsybl-core version to 7.3.0 (#1392, #1448) Breaking Change Breaking changes are mentioned in the powsyble-core 7.3.0 migration guide
  • Migrate to powsybl-parent v29 and fix code to follow new Checkstyle rules (#1439)

Load flow

  • Enable loadflow for ACDC networks with several synchronous components (#1390)

Robustness and accuracy

  • Fix DC nodes voltage initialization in ACDC load flow (#1406)
  • Option to disallow Non-Linear Shunt Compensator section zero (#1419) Parameter Change This can be done using parameter allowNonLinearShuntZeroSection (default value keeps the previous behavior)
  • Fix JSON update of Security and Sensitivity Parameters extensions (#1410) Test Data Change Tests using JSON parameters import can change
  • Fix DC Load Flow running slack distribution for epsilon mismatch (#1389) Test Data Change Slack distribution in reports may be impacted
  • Throw exception when having DcSwitch with non zero resistance (#1447) (before introduction in a future release)

Security Analysis

  • Fix state monitors in security analysis with operator strategies (#1420) Test Data Change
  • Add version and parameters logging for Security and Sensitivity Analysis Providers (#1400)

Sensitivity Analysis

  • Support preventive actions in DC sensitivity analysis (#1383)
  • Support generator and load actions in DC sensitivity analysis (#1425)
  • Support SHUNT_COMPENSATOR_SUSCEPTANCE variable type in AC Sensitivity Analysis (#1396)
  • Support BRANCH_RESISTANCE, BRANCH_REACTANCE and BRANCH_ADMITTANCE variable types in AC Sensitivity Analysis (#1438)
  • Support SVC_PILOT_POINT_TARGET_VOLTAGE variable type in AC Sensitivity Analysis (#1444)
  • Use lowImpedanceThreshold parameter in Sensitivity analysis (and add warning logs for unsupported parameters) (#1411) Test Data Change Sensitivity analysis that did not take into account this parameter before can have different results
  • Fix PST action in DC sensitivity analysis (#1418) Test Data Change

Performance

  • Add support of network cache for DC load flow (#1386): the fast restart feature can be used to avoid reloading the network for multiple load flow computations with a network that has only minor changes
  • Fast restart: Add support of active power update of Load, LCC, VSC and BoundaryLine (#1427)
  • Incremental Transformer Voltage Control: filter insensitive controllers from the regulation in order to avoid additional unecessary outer loops iterations (#1417)
  • Filtering monitored results in N-1 state result to limit memory usage (#1398) this can be used through the new SecurityAnalysis parameter modifiedMonitoredElementsParameters Parameter Change
  • Remove redundant outer loop executions at load flow ending (#1414)

Documentation

  • Improve documentation with links for parameters (#1381, #1428)
  • Add documentation link to core documentation for simulations details (#1445)
  • Update documentation dependencies (#1426)

Developper

  • Remove powsybl-loadflow-results-completion dependency (#1387)
  • Add contributing and security references to the readme (#1382)
  • Add common config for tests (to change MatrixFactory in all tests) (#1403)
  • Refactor network cache to allow future extension of fast restart to sensitivity analysis (#1421)
  • Fix ComponentMode parameter having category "None" instead of "Performance" (#1435)
  • Remove use of deprecated LimitViolation() constructor (#1443)

Energy Systems - Energy System Modeling Frameworks - Java
Published by SylvestreSakti 13 days ago

CoopCycle - v5.2.7

Full Changelog: https://github.com/coopcycle/coopcycle-web/compare/v5.2.6...v5.2.7

Consumption - Mobility and Transportation - PHP
Published by alexsegura 13 days ago

CoopCycle - v5.3.0-beta3

Full Changelog: https://github.com/coopcycle/coopcycle-web/compare/v5.3.0-beta2...v5.3.0-beta3

Consumption - Mobility and Transportation - PHP
Published by alexsegura 13 days ago

CoopCycle - v5.3.0-beta2

Full Changelog: https://github.com/coopcycle/coopcycle-web/compare/v5.3.0-beta1...v5.3.0-beta2

Consumption - Mobility and Transportation - PHP
Published by alexsegura 13 days ago

CoopCycle - v5.2.6

What's changed

  • Fix invoicing exporting JSON instead of CSV.

Full Changelog: https://github.com/coopcycle/coopcycle-web/compare/v5.2.5...v5.2.6

Consumption - Mobility and Transportation - PHP
Published by alexsegura 13 days ago

Hydrocron - 1.10.0a1

What's Changed

Full Changelog: https://github.com/podaac/hydrocron/compare/1.9.0a8...1.10.0a1

Hydrosphere - Ocean and Hydrology Data Access - Python
Published by github-actions[bot] 13 days ago

Open Sustainable Technology - OpenSustain.tech-2026-07

Automated monthly release of projects and organizations listed at OpenSustain.tech and enriched by metadata released by ecosyste.ms

Included files:

  • opensustain-tech-projects-OpenSustain.tech-monthly-release-2026-07.csv
  • opensustain-tech-organizations-OpenSustain.tech-monthly-release-2026-07.csv

Sustainable Development - Knowledge Platforms
Published by github-actions[bot] 13 days ago

scout - v1.2.3 (2026-06-30)

What's New

  • Update all baseline data to reflect AEO 2026 definitions and projections. (#613)
  • Refactor unit testing suite for ecm_prep module. (#605)
  • Refactor handling of linked cooling costs in ecm_prep. (#622)
  • Refactor run.py and ecm_prep.py for performance improvement (#618)
  • Fix bugs in measure attribute initialization and data reporting. (#616, #617)

Consumption - Buildings and Heating - Python
Published by rHorsey 13 days ago

Ecoscope - v2.16.2

What's Changed

Other Changes

Full Changelog: https://github.com/wildlife-dynamics/ecoscope/compare/v2.16.1...v2.16.2

Biosphere - Conservation and Restoration - Python
Published by github-actions[bot] 14 days ago

CoopCycle - v5.2.5

What's changed

  • Allow pausing & resuming recurrence rules.

Full Changelog: https://github.com/coopcycle/coopcycle-web/compare/v5.2.4...v5.2.5

Consumption - Mobility and Transportation - PHP
Published by alexsegura 14 days ago

Deadtrees.earth - v2026.06.30

What's Changed

Other Changes

Full Changelog: https://github.com/Deadwood-ai/deadtrees/compare/v2026.06.29...v2026.06.30

Biosphere - Forest Remote Sensing - TypeScript
Published by github-actions[bot] 14 days ago

PowerIO - v0.4.0

  • powerio-pkg: .pio.json reads now enforce the envelope compatibility rule:
    same major schema_version values load, while incompatible major versions
    fail before payload use. The mdBook schema page documents the rule.
  • powerio-pkg: balanced package output now emits source maps for stable bus,
    load, shunt, branch, and generator fields; validation diagnostics attach the
    matching source reference where a map exists. Format folded fields use
    mapping kinds such as split, and defaulted fields are not marked as exact
    source fields.
  • Converter tests now compare stable per element values across writable legacy
    formats, not only counts and totals. PSLF export now warns when transformer
    charging admittance is dropped.
  • powerio-dist BMOPF: OpenDSS fixed P/Q generators now emit as BMOPF
    generator.* entries with pinned P/Q bounds instead of negative load.*
    entries. The old negative load warning is gone; generators without source
    costs keep the existing cost 0 warning.
  • Python API: removed the one release powerio.Case and
    powerio.dist.DistCase compatibility aliases. Use powerio.Network /
    powerio.BalancedNetwork and powerio.dist.MulticonductorNetwork /
    powerio.dist.DistNetwork.
  • No C ABI rename in this migration slice: PIO_ABI_VERSION stays 4 and
    PIO_DIST_ABI_VERSION stays 1.

What's Changed

Full Changelog: https://github.com/eigenergy/powerio/compare/v0.3.3...v0.4.0

Energy Systems - Energy Data Accessibility and Integration - Rust
Published by github-actions[bot] 14 days ago

ADRIA.jl - ADRIAanalysis-v0.1.0

ADRIAanalysis ADRIAanalysis-v0.1.0

ADRIAanalysis v0.1.0: Release Notes

Overview

ADRIAanalysis is a new Julia sub-package that provides post-simulation analysis tools
for ADRIA (Adaptive Reef Intervention Approaches) results. It was extracted from the core
ADRIA package into a standalone package to keep the main package lean, reduce
time-to-first-execution (TTFX), and allow optional heavy dependencies to load only when
needed.

What's Included

Sensitivity Analysis (ADRIAanalysis.sensitivity)

  • pawn: Moment-independent global sensitivity analysis using the
    Kolmogorov-Smirnov statistic. Returns a summary DataFrame of
    min/mean/median/max/std/cv across binned factor samples.
  • tsa: Temporal Sensitivity Analysis: applies PAWN at each time step to reveal
    how driver importance evolves over time.
  • rsa: Regional Sensitivity Analysis using the Anderson-Darling test to identify
    factor ranges associated with behavioural vs. non-behavioural scenarios.
  • outcome_map: Maps desirable outcomes to discretized factor space, with
    bootstrapped confidence intervals, to identify which input ranges reliably produce
    target outputs.
  • convergence: Assesses how sensitivity indices stabilize as sample size grows,
    supporting confidence in results with limited runs.

Scenario Classification

  • target_clusters: Classifies scenario clusters into target / non-target groups
    based on outcome temporal variability.
  • find_scenarios: Selects scenarios from cluster assignments using user-supplied
    filter functions; works with 2D and 3D outcome arrays.
  • scenario_clusters: Converts cluster assignment vectors into a Dict mapping
    cluster IDs to BitVector masks for downstream filtering.
  • screen_scenarios: Rule-based scenario screening: returns indices of scenarios
    satisfying a normalized criterion across all output columns.

Pareto & Robustness Analysis

  • find_pareto_optimal: Identifies Pareto-optimal scenarios across multiple RCP
    climate scenarios.
  • find_robust: Filters Pareto-optimal scenarios by an additional user-defined
    robustness rule.

Data Envelopment Analysis

  • data_envelopment_analysis: Wraps DataEnvelopmentAnalysis.jl to benchmark
    scenario efficiency against a frontier (CRS/VRS/FDH models, input- or
    output-oriented). Returns a DEAResult with efficiency scores and peer groups.

Feature Engineering

  • feature_set: Assembles a cleaned feature DataFrame from a ResultSet,
    including DHW statistics, deployment indicators, and coral volumes. Automatically
    removes constant and highly correlated columns for use in downstream ML workflows.

Interpretable Rule Extraction (optional extension)

ADRIAanalysisRulesExt activates when both SIRUS.jl and MLJ.jl are loaded:

  • cluster_rules: Fits a SIRUS classifier to scenario clusters and returns the
    top-N interpretable decision rules.
  • rules: Converts raw SIRUS.StableRules to the Rule struct.
  • print_rules: Pretty-prints rules as human-readable if/else conditions.

Architecture & Design

Aspect Detail
Package type Standalone sub-package under ADRIAanalysis/
ADRIA compat 0.16, 0.17
Julia requirement ≥ 1.11
Optional extension ADRIAanalysisRulesExt (requires MLJ + SIRUS)
Array backend YAXArrays for labelled multi-dimensional outputs

MLJ and SIRUS are declared as weak dependencies. The package loads and functions
normally without them. Rule extraction stubs error with a clear message if the extension
is not active, guarding against silent missing-dependency failures.

Merged pull requests:

  • CompatHelper: add new compat entry for CSV at version 0.10, (keep existing compat) (#2) (@github-actions[bot])
  • CompatHelper: add new compat entry for ModelingToolkit at version 8, (keep existing compat) (#3) (@github-actions[bot])
  • CompatHelper: add new compat entry for Compose at version 0.9, (keep existing compat) (#4) (@github-actions[bot])
  • CompatHelper: add new compat entry for BlackBoxOptim at version 0.6, (keep existing compat) (#5) (@github-actions[bot])
  • CompatHelper: add new compat entry for IJulia at version 1, (keep existing compat) (#6) (@github-actions[bot])
  • CompatHelper: add new compat entry for MATLAB at version 0.8, (keep existing compat) (#7) (@github-actions[bot])
  • CompatHelper: add new compat entry for ProfileView at version 1, (keep existing compat) (#8) (@github-actions[bot])
  • CompatHelper: add new compat entry for DataFrames at version 1, (keep existing compat) (#9) (@github-actions[bot])
  • CompatHelper: add new compat entry for Graphs at version 1, (keep existing compat) (#10) (@github-actions[bot])
  • CompatHelper: add new compat entry for StaticArrays at version 1, (keep existing compat) (#11) (@github-actions[bot])
  • CompatHelper: add new compat entry for ModelParameters at version 0.3, (keep existing compat) (#12) (@github-actions[bot])
  • CompatHelper: add new compat entry for Setfield at version 0.8, (keep existing compat) (#13) (@github-actions[bot])
  • CompatHelper: add new compat entry for WinRPM at version 1, (keep existing compat) (#14) (@github-actions[bot])
  • CompatHelper: add new compat entry for BenchmarkTools at version 1, (keep existing compat) (#15) (@github-actions[bot])
  • CompatHelper: add new compat entry for Plots at version 1, (keep existing compat) (#16) (@github-actions[bot])
  • CompatHelper: add new compat entry for DifferentialEquations at version 7, (keep existing compat) (#17) (@github-actions[bot])
  • CompatHelper: add new compat entry for OrdinaryDiffEq at version 6, (keep existing compat) (#18) (@github-actions[bot])
  • CompatHelper: add new compat entry for GraphPlot at version 0.5, (keep existing compat) (#19) (@github-actions[bot])
  • CompatHelper: add new compat entry for GeoDataFrames at version 0.2, (keep existing compat) (#20) (@github-actions[bot])
  • CompatHelper: add new compat entry for ProgressMeter at version 1, (keep existing compat) (#67) (@github-actions[bot])
  • CompatHelper: bump compat for Setfield to 1, (keep existing compat) (#72) (@github-actions[bot])
  • CompatHelper: add new compat entry for GR at version 0.64, (keep existing compat) (#73) (@github-actions[bot])
  • CompatHelper: add new compat entry for CpuId at version 0.3, (keep existing compat) (#74) (@github-actions[bot])
  • Site population cap (#76) (@ConnectedSystems)
  • Adding new total_cover function to RCI calculation (#80) (@Rosejoycrocker)
  • Changes to support site level metrics (#84) (@ConnectedSystems)
  • Changes to scaling for MCDA criteria (site capacity) (attempts to address #79) (#85) (@Rosejoycrocker)
  • Relative cover input to RCI be relative to the sites max coral cover? (#89) (@ConnectedSystems)
  • Scenario focused metrics (#93) (@ConnectedSystems)
  • More appropriate indication of cluster-wide outcomes (#97) (@ConnectedSystems)
  • Address TODO: Extract non-coral parameters to reduce memory use (#105) (@ConnectedSystems)
  • Ensure proportional adjustment of coral cover remain in bounds (#106) (@ConnectedSystems)
  • Expand docstring for proportional_adjustment() for clarity (#107) (@ConnectedSystems)
  • Address small Shelter Volume outcomes (#91) (#108) (@ConnectedSystems)
  • Unguided selection (#112) (@ConnectedSystems)
  • Sysimage builder (#115) (@ConnectedSystems)
  • Fix log scaling error in MCDA coral cover criteria (#117) (@Rosejoycrocker)
  • Detailed docstrings added + shading matrix function added (#118) (@Rosejoycrocker)
  • Environmental data layer component for ADRIA ecosystem model (#120) (@ConnectedSystems)
  • Fixes small issue introduced by compartmentalising SE and SH matrix creation (#122) (@Rosejoycrocker)
  • Adding function to generate csv summary result set (#125) (@Rosejoycrocker)
  • Fixes typos which were not picked up in previous PR (#126) (@Rosejoycrocker)
  • Include PowerBI post processing file in module (#131) (@ConnectedSystems)
  • Fixes for recruitment issue (#137) (@ConnectedSystems)
  • Fix site ranking log (#140) (@ConnectedSystems)
  • Correct simplified settler cover calculation (#141) (@ConnectedSystems)
  • Fixes undefined absolute_site_coral_cover (#142) (@Rosejoycrocker)
  • Remove tf from simulation constants (#143) (@ConnectedSystems)
  • Fixes missed tf definition (#144) (@Rosejoycrocker)
  • Distributes seeded corals at selected sites according to space available (#145) (@Rosejoycrocker)
  • Add timeframe datapackage property (#147) (@ConnectedSystems)
  • Adds function to distribute seeded corals at selected sites according to space available (addresses #146) (#148) (@Rosejoycrocker)
  • Update bleaching mortality model (#149) (@ConnectedSystems)
  • CompatHelper: bump compat for PkgVersion to 0.3, (keep existing compat) (#150) (@github-actions[bot])
  • Additional metrics for site rank analysis (#153) (@ConnectedSystems)
  • Applying depth offset to align with IPMF (#154) (@ConnectedSystems)
  • Add copy of model spec to ResultSet (#155) (@ConnectedSystems)
  • Add incoming and outgoing connectivity ranks and criteria (#156) (@ConnectedSystems)
  • Adds function to find top n sites in result set for each scenario (#159) (@Rosejoycrocker)
  • Adding coral cover area criteria in terms of absolute coral cover (#160) (@Rosejoycrocker)
  • Miscellaneous changes to clean up code (#161) (@ConnectedSystems)
  • Mix normalisation bug in MCDA (#162) (@Rosejoycrocker)
  • Support runs across multiple RCPs (#163) (@ConnectedSystems)
  • Scenario relative cover metric to return cluster wide values (#164) (@ConnectedSystems)
  • Fixes to ODE formulation and indexing (#165) (@Rosejoycrocker)
  • CompatHelper: add new compat entry for Distributions at version 0.25, (keep existing compat) (#166) (@github-actions[bot])
  • Changes to top_N_sites rank metric (#167) (@ConnectedSystems)
  • Support extraction of geometry data from inconsistent column names (#169) (@ConnectedSystems)
  • Robustness metrics (#172) (@ConnectedSystems)
  • Replace bleaching resistance with uncertain bleaching sensitivity (#174) (@ConnectedSystems)
  • Incorporation of zoning criteria in MCDA (#175) (@Rosejoycrocker)
  • Add sampling methods (#176) (@ConnectedSystems)
  • Spread site selection (#180) (@ConnectedSystems)
  • Add dhw summary statistics to ResultSet (#181) (@Rosejoycrocker)
  • Corrections to assignment of growth rates and tests for coral_spec() parameters (#183) (@Rosejoycrocker)
  • Coral model adjustments (#184) (@ConnectedSystems)
  • Switch to netCDF (#185) (@ConnectedSystems)
  • Correct connectivity alignment (#186) (@ConnectedSystems)
  • Update example domain with netCDF format datacubes (#187) (@ConnectedSystems)
  • Changes to support Multi-Objective Optimization (#188) (@ConnectedSystems)
  • Tentative support for Multi-Objective Robust Optimization (#189) (@ConnectedSystems)
  • Bug fix for ODE + change to definition of basal area (#190) (@Rosejoycrocker)
  • Consolidate site area calcs #170 (#191) (@ConnectedSystems)
  • Performance changes (#192) (@ConnectedSystems)
  • Reorganize data loading functions (#193) (@ConnectedSystems)
  • Adjust coral wave mortalities following recommendation by Ken (#195) (@Rosejoycrocker)
  • Adding within size class growth for size class 6 back in for ODE and adjusting within size class growth rates (#196) (@Rosejoycrocker)
  • Connectivity update (#197) (@ConnectedSystems)
  • Add distance sorting to MCDA (#198) (@Rosejoycrocker)
  • Update metrics (#199) (@ConnectedSystems)
  • Updated background mortality values (#201) (@ConnectedSystems)
  • Minor changes to get visualizations working for v0.4.2 (#202) (@ConnectedSystems)
  • v0.4.2 dev merge (#203) (@ConnectedSystems)
  • CompatHelper: add new compat entry for GeoInterface at version 1, (keep existing compat) (#206) (@github-actions[bot])
  • CompatHelper: add new compat entry for RelocatableFolders at version 1, (keep existing compat) (#207) (@github-actions[bot])
  • CompatHelper: add new compat entry for Surrogates at version 6, (keep existing compat) (#208) (@github-actions[bot])
  • CompatHelper: add new compat entry for FileIO at version 1, (keep existing compat) (#209) (@github-actions[bot])
  • CompatHelper: add new compat entry for DecisionTree at version 0.11, (keep existing compat) (#210) (@github-actions[bot])
  • CompatHelper: add new compat entry for Distances at version 0.10, (keep existing compat) (#211) (@github-actions[bot])
  • CompatHelper: add new compat entry for Combinatorics at version 1, (keep existing compat) (#212) (@github-actions[bot])
  • CompatHelper: add new compat entry for BlackBoxOptim at version 0.6, (keep existing compat) (#213) (@github-actions[bot])
  • CompatHelper: add new compat entry for SnoopPrecompile at version 1, (keep existing compat) (#214) (@github-actions[bot])
  • CompatHelper: add new compat entry for Bootstrap at version 2, (keep existing compat) (#215) (@github-actions[bot])
  • CompatHelper: add new compat entry for HypothesisTests at version 0.10, (keep existing compat) (#216) (@github-actions[bot])
  • CompatHelper: add new compat entry for GeoFormatTypes at version 0.4, (keep existing compat) (#217) (@github-actions[bot])
  • CompatHelper: add new compat entry for NCDatasets at version 0.12, (keep existing compat) (#218) (@github-actions[bot])
  • CompatHelper: add new compat entry for GLMakie at version 0.7, (keep existing compat) (#219) (@github-actions[bot])
  • CompatHelper: add new compat entry for GeoMakie at version 0.4, (keep existing compat) (#220) (@github-actions[bot])
  • Adjust rankings to match site reordering due to distance sorting (#224) (@Rosejoycrocker)
  • Add depth column to MCDA decision matrix to be used in seeding and shading decision matrices (#225) (@Rosejoycrocker)
  • Remove additional weighting that is no longer needed (#227) (@ConnectedSystems)
  • Re-order site data by unique site id column to align logged site ids (#228) (@ConnectedSystems)
  • CompatHelper: bump compat for GLMakie to 0.8, (keep existing compat) (#233) (@github-actions[bot])
  • v0.4.3 merge (#241) (@ConnectedSystems)
  • Initial documentation build (#244) (@ConnectedSystems)
  • Add support for Regional Sensitivity Analysis (RSA) (#258) (@ConnectedSystems)
  • Merge v0.4.4-dev (#259) (@ConnectedSystems)
  • Add temporal sensitivity analyses based on the PAWN method (#261) (@ConnectedSystems)
  • Metric restructure (#262) (@ConnectedSystems)
  • CompatHelper: bump compat for ArchGDAL to 0.10, (keep existing compat) (#263) (@github-actions[bot])
  • v0.4.4-dev.1 (#266) (@ConnectedSystems)
  • Add parameter name and description to model specification (#273) (@ConnectedSystems)
  • Adjust coral growth rate for size class 6 (#274) (@ConnectedSystems)
  • Remove references to Input Set (#275) (@ConnectedSystems)
  • Fix: calculate distance between sites (#276) (@ConnectedSystems)
  • Simplify display of model spec (#278) (@ConnectedSystems)
  • Parametric ResultSet (#279) (@ConnectedSystems)
  • Consolidate normalize (#280) (@ConnectedSystems)
  • Changes to site selection functions (#282) (@Rosejoycrocker)
  • Changes to address bug in site_selection example (addresses issue #285 ) (#286) (@Rosejoycrocker)
  • Consolidate Named array types to use NamedDims+AxisKeys (#287) (@ConnectedSystems)
  • Reduce allocations in load_domain() (#288) (@ConnectedSystems)
  • Add criteria parameter which indicates whether distance sorting is used. (#290) (@Rosejoycrocker)
  • Add function n_locations() to determine number of sites/reefs/clusters (#291) (@ConnectedSystems)
  • Miscellaneous cleanup (#293) (@ConnectedSystems)
  • Fix bug causing implausible juvenile indicator values (#294) (@ConnectedSystems)
  • Adjust samples when use of distance thresholds is turned off (#295) (@ConnectedSystems)
  • CompatHelper: add new compat entry for AxisKeys at version 0.2, (keep existing compat) (#297) (@github-actions[bot])
  • Additional safety checks for sampling (#298) (@ConnectedSystems)
  • Adds sampler which can sample only parameters needed for site selection (#299) (@Rosejoycrocker)
  • Adds function which calculates sites selection frequency for a set of provided samples (#301) (@Rosejoycrocker)
  • Fix error mapping continous samples to discrete values (#305) (@ConnectedSystems)
  • Adjust shelter volume to remove hardcoded index and leverage NamedDimsArray (#306) (@ConnectedSystems)
  • Fix initial slice potentially not including lowest value (#307) (@ConnectedSystems)
  • Clean up Project.toml + Precompile (#309) (@ConnectedSystems)
  • Correct issue with size of NamedDims array for storing ranks in run_site_selection() (#310) (@Rosejoycrocker)
  • Initial indicative visualization (#318) (@ConnectedSystems)
  • Fix function extension issues (#319) (@ConnectedSystems)
  • Better check for constancy in RSA (#320) (@ConnectedSystems)
  • Update exploration tool to latest ADRIA API (#321) (@ConnectedSystems)
  • Additional docs for Domain/ResultSets (#322) (@ConnectedSystems)
  • Add capability to fix factors in place (#325) (@ConnectedSystems)
  • Initial ReefMod interface and functionality (#326) (@ConnectedSystems)
  • Move n_adapt from Intervention component to Coral component (#332) (@ConnectedSystems)
  • Update use of functions due to new import approach (#334) (@ConnectedSystems)
  • Migrate from SnoopPrecompile to PrecompileTools (#335) (@timholy)
  • Add planning horizon factor (#336) (@ConnectedSystems)
  • Replace use of area attribute/field with call to function site_area() to ensure correct values (#337) (@ConnectedSystems)
  • Remove reference to defunct fields when making factors constant (#338) (@ConnectedSystems)
  • Fix error caused by mismatched locations (#339) (@ConnectedSystems)
  • Make use of planning horizon in sims (#340) (@ConnectedSystems)
  • Changes to support running ADRIA with external model (ReefMod Engine) data (#341) (@ConnectedSystems)
  • CompatHelper: add new compat entry for SimpleWeightedGraphs at version 1, (keep existing compat) (#343) (@github-actions[bot])
  • CompatHelper: add new compat entry for OrderedCollections at version 1, (keep existing compat) (#344) (@github-actions[bot])
  • CompatHelper: bump compat for StatsBase to 0.34, (keep existing compat) (#345) (@github-actions[bot])
  • Split ADRIA-mod domain definition (#346) (@ConnectedSystems)
  • Add GBR zones by priority (#347) (@ConnectedSystems)
  • Add option to use JMcDM functions in ADRIA site selection (#348) (@Rosejoycrocker)
  • Make Aviz into an extension package (#349) (@ConnectedSystems)
  • Exit with error if given path is not a directory (#350) (@ConnectedSystems)
  • CompatHelper: add new compat entry for Reexport at version 1, (keep existing compat) (#351) (@github-actions[bot])
  • CompatHelper: add new compat entry for ImageMagick at version 1, (keep existing compat) (#352) (@github-actions[bot])
  • Update bleaching mortality model to align with published paper (#354) (@ConnectedSystems)
  • Update scenario viz (#355) (@ConnectedSystems)
  • Add map visualization - displays k-area (#356) (@ConnectedSystems)
  • Address mismatched number of elements under certain conditions (#358) (@ConnectedSystems)
  • Remove Copras method due to erroring (#359) (@Rosejoycrocker)
  • Update documentation (#361) (@ConnectedSystems)
  • CompatHelper: add new compat entry for JMcDM at version 0.7, (keep existing compat) (#362) (@github-actions[bot])
  • CompatHelper: bump compat for HypothesisTests to 0.11, (keep existing compat) (#363) (@github-actions[bot])
  • Scenario discovery docs (#364) (@ConnectedSystems)
  • Fix: Metric errors when applied to a single simulation (#365) (@ConnectedSystems)
  • Address ranking errors in mcda outputs (#367) (@Rosejoycrocker)
  • Add temporal clustering (#370) (@Zapiano)
  • Fix incorrect type check (#371) (@Zapiano)
  • CompatHelper: add new compat entry for Clustering at version 0.15, (keep existing compat) (#372) (@github-actions[bot])
  • CompatHelper: bump compat for Zarr to 0.9, (keep existing compat) (#373) (@github-actions[bot])
  • Update time series clustering and add visualization functionality (#374) (@Zapiano)
  • Update docstrings for growth function (#375) (@ConnectedSystems)
  • Refactor run_scenarios to improve when running multiple rcps (#376) (@Zapiano)
  • Bump version number and add new author (#378) (@Zapiano)
  • Changes to number of species in ADRIA (#380) (@Rosejoycrocker)
  • Distribution-based bleaching mortality to capture natural adaptation and heritability (#381) (@ConnectedSystems)
  • Temporal clustering for spatial data (#382) (@Zapiano)
  • Remove duplicate function recruitment (#385) (@ConnectedSystems)
  • Reorganize package structure (#386) (@ConnectedSystems)
  • Consider near-term conditions with greater weight than far-future conditions (#387) (@ConnectedSystems)
  • Update release guide (#389) (@ConnectedSystems)
  • Changes to ode solver and time step for efficiency improvements (#390) (@Rosejoycrocker)
  • Add adaptive=false specification and remove tolerances (#391) (@Rosejoycrocker)
  • Scenario viz change (#393) (@ConnectedSystems)
  • CompatHelper: add new compat entry for JuliennedArrays at version 0.4, (keep existing compat) (#395) (@github-actions[bot])
  • CompatHelper: add new compat entry for FLoops at version 0.2, (keep existing compat) (#396) (@github-actions[bot])
  • Fix bug: Use wave condition for current timestep, not previous (#397) (@ConnectedSystems)
  • Update comment to reflect changes for wave condition usage (#398) (@ConnectedSystems)
  • Incorrect function being called (#400) (@ConnectedSystems)
  • Remove use of batch sizes when running parallel scenarios (#401) (@ConnectedSystems)
  • CompatHelper: bump compat for SparseArrayKit to 0.3, (keep existing compat) (#403) (@github-actions[bot])
  • Fix map display (default display when plotting Domain or ResultSet) (#407) (@ConnectedSystems)
  • Update ReefMod interface to match new species list (#408) (@Rosejoycrocker)
  • Fix excessive memory use (#405) (#409) (@ConnectedSystems)
  • Small miscellaneous changes for scenario visualizations (#412) (@ConnectedSystems)
  • Remove dependency on ImageMagick in favour of ImageIO (#414) (@ConnectedSystems)
  • Updated Reef Indices (#415) (@ConnectedSystems)
  • Fix workers crashing and leaking memory when running scenarios in parallel (#416) (@ConnectedSystems)
  • Adjustments to heritability based on feedback (#417) (@ConnectedSystems)
  • Update docstrings with missing detail (#418) (@ConnectedSystems)
  • Implement relevant struct to handle SIRUS rule extraction (#420) (@Zapiano)
  • Implement rule extracting function (#421) (@Zapiano)
  • Implement rule scatter plot function (#422) (@Zapiano)
  • Move and modify behaviour of target_cluster function (#424) (@Zapiano)
  • Fix unnecessarily squashed figure when plotting outcome map for 1 factor (#425) (@ConnectedSystems)
  • Documentation improvement (#429) (@Zapiano)
  • Fix scenario metrics with field :scenario instead of :scenarios (#430) (@Zapiano)
  • Adds a series of aggregation functions for location selection ranks (#431) (@Rosejoycrocker)
  • Fix error when running samples generated from sample_site_selection() (#432) (@Rosejoycrocker)
  • Fix time_series_clustering for variable series with k > 0 (#433) (@Zapiano)
  • Add functions for repeated tasks when performing location selection (#434) (@Rosejoycrocker)
  • Address very slow extraction of relative cover values (#435) (@ConnectedSystems)
  • Update prototype exploration UI to work with recent changes (#436) (@ConnectedSystems)
  • Incorporate settler DHW tolerances (#437) (@ConnectedSystems)
  • Fix loc_trajectory and per_loc function (#438) (@Zapiano)
  • Fix clustering map visualisation (#439) (@Zapiano)
  • Add Blue Style Guide badge to README (#441) (@Zapiano)
  • Fix duplicate x-axis values bug in viz.outcome_map() (#442) (@Rosejoycrocker)
  • Update SIRUS StableRules type (#443) (@Zapiano)
  • Fix print_rules adding & when there are two clauses (#444) (@Zapiano)
  • More updates to documentation (#446) (@ConnectedSystems)
  • Functions to plot spatial distributions of site selection frequencies (#449) (@Rosejoycrocker)
  • Miscellaneous changes to improve type infererability and precompilation times (#455) (@ConnectedSystems)
  • Changes to improve performance of PAWN sensitivity analysis (#457) (@ConnectedSystems)
  • Fix print_rules condition (#460) (@Zapiano)
  • Update ADRIA logo (#461) (@Zapiano)
  • Adjust PAWN function to support 1D matrix for convenience (#462) (@ConnectedSystems)
  • Add function to find robust scenarios across several metrics (#463) (@Zapiano)
  • Update Reef Tourism Index regression coefficient (temporary solution) (#466) (@ConnectedSystems)
  • Add new cluster_rules method that accepts BitVector or Vector{Bool} (#467) (@Zapiano)
  • Include rule_extraction.jl in viz.jl (#468) (@Zapiano)
  • Precompilation reduction (#469) (@ConnectedSystems)
  • Add option to show GBRMPA management zones (#470) (@ConnectedSystems)
  • Update sensitivity module to follow Blue style (#471) (@ConnectedSystems)
  • Update Doc mentioning blue style guide (#472) (@Zapiano)
  • Update viz.rules_scatter to accept targeted clusters (#475) (@Zapiano)
  • Deprecate run_scenarios(scens, dom, ...) (#476) (@ConnectedSystems)
  • Add Documentation Sensitivity section for Rule Induction algorithm (#477) (@Zapiano)
  • Rename time_series_clustering and ts_cluster (#478) (@Zapiano)
  • Remove locations with no space from consideration for interventions (#479) (@ConnectedSystems)
  • Adjust run_model() to only require values relative to $k$ area (#481) (@ConnectedSystems)
  • Update viz.clustered_scenarios to allow confidence interval plot (#482) (@Zapiano)
  • Consistent treatment of k area on data load (#485) (@ConnectedSystems)
  • Transform ICC from relative to absolute area to relative to k area (#486) (@ConnectedSystems)
  • Add function to alter sampling bounds on parameters to specified value. (#490) (@Rosejoycrocker)
  • Fix bug in how sensitivity.outcome_map() treats categorical variables. (#491) (@Rosejoycrocker)
  • Fix _time_labels missing last label (#496) (@Zapiano)
  • Update version number to 0.9.0 (#497) (@Rosejoycrocker)
  • Add .JuliaFormatter.toml to .gitignore (#499) (@Zapiano)
  • Refactor viz.scenario (#500) (@Zapiano)
  • CompatHelper: bump compat for SciMLBase to 2, (keep existing compat) (#504) (@github-actions[bot])
  • Add :summary option to viz.scenarios (#505) (@Zapiano)
  • Update CSV.write writeheader parameter to header (#506) (@Zapiano)
  • Fix bug causing Domain loading with RCP to error (#511) (@Rosejoycrocker)
  • Remove top_n parameter from usage (#514) (@Rosejoycrocker)
  • CompatHelper: bump compat for MLJ to 0.20, (keep existing compat) (#515) (@github-actions[bot])
  • Add support series and map binary clusters plots (#521) (@Zapiano)
  • Fix scenarios subsetting now working (#523) (@Zapiano)
  • Add interface function to query number of scenarios in result set (#527) (@ConnectedSystems)
  • Rename rs_input with scenarios (#533) (@Zapiano)
  • CompatHelper: bump compat for NCDatasets to 0.13, (keep existing compat) (#536) (@github-actions[bot])
  • Add summarize and turn per_loc and loc_trajectory into alias (#537) (@Zapiano)
  • Broadcast _check_discrete inside update_params (#539) (@Zapiano)
  • Extract call to run scenarios inside tests to external function (#540) (@Zapiano)
  • Add missing scenario analysis function definitions to analysis module (#541) (@ConnectedSystems)
  • Resolve Out-of-Memory issues when working with larger spatial areas (#542) (@ConnectedSystems)
  • Update analysis docs with recent scenarios and clusters developments (#545) (@Zapiano)
  • Fix failing test cases due to recent changes (#546) (@ConnectedSystems)
  • Changes to mcda functions to reflect coral cover being in terms of k area (#547) (@Rosejoycrocker)
  • Add ability to perform convergence analysis (#552) (@Rosejoycrocker)
  • CompatHelper: add new compat entry for TOML at version 1, (keep existing compat) (#553) (@github-actions[bot])
  • CompatHelper: add new compat entry for Statistics at version 1, (keep existing compat) (#554) (@github-actions[bot])
  • Coral cover consistently represented as relative to coral habitable area (#555) (@ConnectedSystems)
  • Avoid assuming where the RCP column is when adjusting scenario spec (#558) (@ConnectedSystems)
  • Fix integer dims reference in location_selection_frequency() (#563) (@Rosejoycrocker)
  • Fix bug due to missing default_bounds in EnvironmentalLayer and Coral model components (#569) (@Rosejoycrocker)
  • Visualizations to be agnostic to Makie backend (#570) (@ConnectedSystems)
  • Add functions used for location selection to separate decision module (#571) (@Rosejoycrocker)
  • Add separate weighting parameter for depth criteria (#573) (@Rosejoycrocker)
  • Add conversion to scientific notation (#574) (@Zapiano)
  • Fix plot map (#575) (@Zapiano)
  • Prevent test_rs() from creating tmp dir inside test/data (#576) (@Zapiano)
  • Apply blue styleguide to some files (#579) (@Zapiano)
  • Update use of progress meter to resolve deprecation warning (#581) (@ConnectedSystems)
  • Normalize sampled MCDA weights (#582) (@Rosejoycrocker)
  • Replace package NCDatasets by NetCDF (#583) (@Zapiano)
  • Implement cyclone mortality scenarios (#585) (@Zapiano)
  • CompatHelper: add new compat entry for NetCDF at version 0.11, (keep existing compat) (#588) (@github-actions[bot])
  • Fix viz.scenarios bug introduced in changes to scenario_confint! usage (#589) (@Rosejoycrocker)
  • Change approach to listing supported MCDA methods (#593) (@ConnectedSystems)
  • Remove defunct function for post processing results into power-BI friendly csv file (#594) (@Rosejoycrocker)
  • Use min-max normalisation for heat stress (#595) (@Rosejoycrocker)
  • Use min-max normalisation for heat stress (#596) (@Rosejoycrocker)
  • Handle cases where connectivity directories may be empty (#597) (@ConnectedSystems)
  • Deactivated interventions should be considered separately (#598) (@ConnectedSystems)
  • Remove list of ignored JMcDM methods (#599) (@ConnectedSystems)
  • Fix treatment of categorical factors in regional sensitivity analysis (#601) (@Rosejoycrocker)
  • Separate shading and fogging timing parameters (#602) (@Rosejoycrocker)
  • CompatHelper: bump compat for Interpolations to 0.15, (keep existing compat) (#604) (@github-actions[bot])
  • CompatHelper: add new compat entry for YAXArrays at version 0.5, (keep existing compat) (#605) (@github-actions[bot])
  • CompatHelper: add new compat entry for DimensionalData at version 0.25, (keep existing compat) (#606) (@github-actions[bot])
  • Fix proportional_adjustment vector conversion computational error (#607) (@Zapiano)
  • Add tests for figure creation (#608) (@ConnectedSystems)
  • Fix bug where cover instead of leftover space was being used in stand alone site selection (#610) (@Rosejoycrocker)
  • Add more detail regarding sequence of events (#611) (@ConnectedSystems)
  • Adjust language in architectural overview to match recent changes (#612) (@ConnectedSystems)
  • Support RSA with large sample sizes (#614) (@ConnectedSystems)
  • Attach dummy wave and cyclone data (#616) (@ConnectedSystems)
  • CompatHelper: bump compat for SIRUS to 2, (keep existing compat) (#617) (@github-actions[bot])
  • Changes to dhw and wave logs to store scenario and site means and stds (#623) (@Rosejoycrocker)
  • Fix bug introduced by SIRUS v2.0.1 (#625) (@Zapiano)
  • Add a new ten site example domain for testing (#628) (@Rosejoycrocker)
  • Fix mcda method bugs (#629) (@Rosejoycrocker)
  • Fix set_factor_bounds! out of bounds for discrete factors (#631) (@Zapiano)
  • Consolidate methods that transform factor values into sampling.jl (#632) (@ConnectedSystems)
  • Replaces distance sorting with restrictions on the number of selected locations in the same reef (#635) (@Rosejoycrocker)
  • Update factor types and their use (#636) (@ConnectedSystems)
  • Update factor definitions to use custom constructor (#637) (@ConnectedSystems)
  • Update sampling methods for newly defined factor definitions (#638) (@ConnectedSystems)
  • Update interactions with Param types across ADRIA more generally (#639) (@ConnectedSystems)
  • Address MCDA error for single locations (#640) (@ConnectedSystems)
  • Add connectivity data to result set storage (#643) (@Rosejoycrocker)
  • Changes to make ADRIA precompilable under Julia v1.10 (#646) (@ConnectedSystems)
  • Update use of Makie/GeoMakie to address deprecation errors (#647) (@ConnectedSystems)
  • Fix larval connectivity bug (#648) (@ConnectedSystems)
  • Remove examples dir issue #584 (#651) (@DanTanAtAims)
  • Speed up calculation of truncated normal mean and cdf (#652) (@DanTanAtAims)
  • Update tests for new sampling method/factor definitions (#653) (@ConnectedSystems)
  • Update factor type documentation (#654) (@ConnectedSystems)
  • Add a default size for scenario plots (#657) (@ConnectedSystems)
  • CompatHelper: add new compat entry for StatsFuns at version 1, (keep existing compat) (#658) (@github-actions[bot])
  • CompatHelper: add new compat entry for SpecialFunctions at version 2, (keep existing compat) (#659) (@github-actions[bot])
  • Fix bleaching mortality (#660) (@ConnectedSystems)
  • Clean up settler cover function to reduce confusion (#662) (@ConnectedSystems)
  • Only load up relevant RME SSP datasets (#663) (@ConnectedSystems)
  • Reset deployed-coral-risk-tol range (#664) (@ConnectedSystems)
  • Clean up scenario running methods (#665) (@ConnectedSystems)
  • Return 0 in cases where lb > ub (#666) (@ConnectedSystems)
  • Clean up use of TP matrices to align with conceptualisation of connectivity (#667) (@ConnectedSystems)
  • Adjustment to simulated events to address numerical errors (#668) (@ConnectedSystems)
  • Support updated domain structure (#669) (@ConnectedSystems)
  • Fix erroneous handling of location IDs (#671) (@ConnectedSystems)
  • Fix error in domain loading when cluster_id is already in string format (#673) (@Rosejoycrocker)
  • Add test domain for ReefModDomain type (#675) (@Rosejoycrocker)
  • Additional setup instructions for code style and formatting (#676) (@ConnectedSystems)
  • Implementation of new MCDA types (#678) (@ConnectedSystems)
  • Fix readjustment of number of slices bug in RSA (#679) (@Rosejoycrocker)
  • Fix cyclone sorting (#683) (@Zapiano)
  • removed deprecate functions and function calls (#684) (@DanTanAtAims)
  • restructured documentation image directories (#685) (@DanTanAtAims)
  • Truncated normal changes (#687) (@DanTanAtAims)
  • Allow user to set whatever bounds they wish (#688) (@ConnectedSystems)
  • Yax loaddomain (#689) (@Zapiano)
  • Switch to YAXArrays when runnin scenarios (#690) (@Zapiano)
  • Adjustments to allow loading newest Domain datasets (#691) (@ConnectedSystems)
  • Update rank metrics to use YAXArrays (#693) (@ConnectedSystems)
  • Update viz.clustering to expect AbstractMatrix (#694) (@ConnectedSystems)
  • Migrate from NamedDimsArrays to YAXArrays (#695) (@Zapiano)
  • Remove factors input from rsa() and use scenario dataframe column names instead (#696) (@Rosejoycrocker)
  • updated data loading test for migration to YAXArrays (#697) (@DanTanAtAims)
  • Further updates to scenario runs with MCDA (#698) (@ConnectedSystems)
  • Update support for standalone MCDA use (#699) (@ConnectedSystems)
  • Yax test update (#700) (@DanTanAtAims)
  • added nameddimsarray2yaxarray (#701) (@DanTanAtAims)
  • Fix error in bin size for sensitivity.outcome_map (#702) (@Rosejoycrocker)
  • Yax viz (#703) (@DanTanAtAims)
  • Yax cube tests (#704) (@DanTanAtAims)
  • Remove MKL from build process (#705) (@ConnectedSystems)
  • Reef mod matlab domain (#706) (@DanTanAtAims)
  • Yax analysis (#707) (@DanTanAtAims)
  • Migrate metrics.jl to YAXArrays (#709) (@Zapiano)
  • Yax sensitivity (#710) (@DanTanAtAims)
  • Remove GC workaround (#711) (@ConnectedSystems)
  • CompatHelper: bump compat for DimensionalData to 0.26, (keep existing compat) (#714) (@github-actions[bot])
  • Yax migration miscellaneous (#715) (@Zapiano)
  • Keep metadata in results (#716) (@ConnectedSystems)
  • Finalize update of standalone MCDA methods (#717) (@ConnectedSystems)
  • Update all tests and remove NamedDims and AxisKeys from ADRIA.jl (#718) (@Zapiano)
  • Validating MCDA methods and initial clean/update of tests (#719) (@ConnectedSystems)
  • Provide a succinct overview of MCDA (#720) (@ConnectedSystems)
  • Add support to cyclone mortality to ReefModDomain (#722) (@Zapiano)
  • Fix locations selection in ReefMod datapackage cyclone mortality loading (#723) (@Zapiano)
  • Save right intervention label at ResultSet ranks YAXArray (#724) (@Zapiano)
  • Add counterfactual minus guided/unguided diff at location level (#726) (@Zapiano)
  • Hacky support for later RME reef id list (#731) (@ConnectedSystems)
  • Add support for specifying locations (#732) (@ConnectedSystems)
  • improve load_domain docs (#733) (@arlowhite)
  • Only rank locations with available area > 0 (#734) (@ConnectedSystems)
  • Support more vector types for maps (#736) (@ConnectedSystems)
  • Clean up connectivity and centrality methods (#737) (@ConnectedSystems)
  • Additional rank methods to determine number of locations intervened on per timestep (#738) (@ConnectedSystems)
  • Collection of miscellaneous changes (#740) (@ConnectedSystems)
  • Fix bug, min. locations to select > available locations (#741) (@ConnectedSystems)
  • Connectivity viz (#742) (@DanTanAtAims)
  • CompatHelper: bump compat for DimensionalData to 0.27, (keep existing compat) (#744) (@github-actions[bot])
  • RME Result Interface (#745) (@DanTanAtAims)
  • Working example of CUDA-fied settler_cover() (#747) (@ConnectedSystems)
  • Repeat mention that the VS Code extension is being setup (#748) (@ConnectedSystems)
  • Improved support for spatial maps (#750) (@ConnectedSystems)
  • use provided centrality measures instead of defaults (#751) (@DanTanAtAims)
  • Convenience plotting method for connectivity/centralities (#752) (@ConnectedSystems)
  • Misc cleanup (coral dynamics) (#753) (@ConnectedSystems)
  • Changes to make use of expected multi-dimensional data structure (#754) (@ConnectedSystems)
  • remove hardcoded coral spec from metrics and data store (#755) (@DanTanAtAims)
  • fix initial cover block constructor (#757) (@DanTanAtAims)
  • Support plotting DHW and cyclone (mortality) scenarios (#758) (@ConnectedSystems)
  • Support deactivating environmental disturbances (#759) (@ConnectedSystems)
  • Multidimensional cover (#761) (@DanTanAtAims)
  • add range to for loop (#762) (@DanTanAtAims)
  • Visualization for taxonomy cover. (#763) (@DanTanAtAims)
  • CompatHelper: add new compat entry for Makie in [weakdeps] at version 0.21, (keep existing compat) (#764) (@github-actions[bot])
  • CompatHelper: bump compat for NetCDF to 0.12, (keep existing compat) (#765) (@github-actions[bot])
  • CompatHelper: add new compat entry for GraphMakie in [weakdeps] at version 0.5, (keep existing compat) (#766) (@github-actions[bot])
  • CompatHelper: add new compat entry for GeoMakie in [weakdeps] at version 0.6, (keep existing compat) (#767) (@github-actions[bot])
  • Change assisted adaptation to a Discrete Uniform value (#770) (@ConnectedSystems)
  • Use underlying data instead of YAXArray type (#771) (@ConnectedSystems)
  • Increase compression level for ResultSet (#772) (@ConnectedSystems)
  • Fix erroneous function call in docstrings (#773) (@ConnectedSystems)
  • Add methods to extract deployment location info (#774) (@ConnectedSystems)
  • Clean up defunct dependencies (#776) (@ConnectedSystems)
  • Fix visualization type error (#777) (@DanTanAtAims)
  • Fix mismatched function name in docstring (#778) (@ConnectedSystems)
  • constrain growth by available area (#779) (@DanTanAtAims)
  • Fix site_level dosctring (#782) (@Zapiano)
  • remove breakpoint in code (#784) (@DanTanAtAims)
  • Assortment of improvements to SIRUS and Time Series Clustering (#786) (@Zapiano)
  • Add default option to _sort_keys (#787) (@Zapiano)
  • Julia format GH workflow, format all files (#790) (@arlowhite)
  • julia-actions recommended dependabot.yml (#791) (@arlowhite)
  • Coerce to MultiPolygon instead of Polygon (#793) (@ConnectedSystems)
  • Bump julia-actions/cache from 1 to 2 (#795) (@dependabot[bot])
  • Bump julia-actions/setup-julia from 1 to 2 (#796) (@dependabot[bot])
  • Bump actions/checkout from 2 to 4 (#797) (@dependabot[bot])
  • Minor updates to geospatial functions/handling (#798) (@ConnectedSystems)
  • use apply_mortality not apply_survival (#799) (@DanTanAtAims)
  • Address tests failing due to type mismatch (scenario confint) (#801) (@ConnectedSystems)
  • Fix depth min/offset being sampled for counterfactual scenarios (#802) (@ConnectedSystems)
  • Use CoralBlox linear_extension_scale_factor (#805) (@Zapiano)
  • Implement linear extension scale factor (#806) (@Zapiano)
  • Fix add run_model method that do not require functional_groups (#807) (@Zapiano)
  • build: prototype CD integration with Provena to update model (#808) (@PeterBaker0)
  • Fix broken tests (#809) (@Zapiano)
  • update fecundity min area variable name for clarity (#810) (@eco-ben)
  • fix permutation of initial cover dimensions (#811) (@DanTanAtAims)
  • Breaks new initial_cover.nc file into size classes assuming a LogNormal distribution (#812) (@Zapiano)
  • Fix miscellaneous of broken tests (#813) (@Zapiano)
  • Fix sampling test (#814) (@Zapiano)
  • Increase release version (#815) (@DanTanAtAims)
  • Apply changes to ADRIA to make it compatible with CoralBlox model (#817) (@Zapiano)
  • CompatHelper: add new compat entry for CoralBlox at version 1, (keep existing compat) (#821) (@github-actions[bot])
  • Fix docs builder, add .git-blame-ignore-revs and document (#823) (@arlowhite)
  • fix helper dimension size error (#824) (@DanTanAtAims)
  • Add reshape to fix dimension mismatch when logging dhw tolerances (#827) (@Rosejoycrocker)
  • updates docs github action to use Julia 1.10.* (#829) (@arlowhite)
  • Remove Manifest from gitignore (#830) (@Zapiano)
  • Rename metrics :sites dimension with :locations (#831) (@Zapiano)
  • Fix docs errors (#832) (@arlowhite)
  • Fix cover loading and size class lower bound (#833) (@DanTanAtAims)
  • convert recruitment from relative area to area before use (#834) (@DanTanAtAims)
  • lowercase png extensions to fix Documenter (#837) (@arlowhite)
  • Cscape interface improvements (#838) (@ConnectedSystems)
  • feat: migrating and updating docker functionality + publish pipeline (#839) (@PeterBaker0)
  • fix: stale links in docker docs (#843) (@PeterBaker0)
  • Overly constrained argument types causing tests to fail (#844) (@ConnectedSystems)
  • feat: restore unit testing and add julia caching (#845) (@PeterBaker0)
  • fix reefmod domain load initial cover (#846) (@DanTanAtAims)
  • Add metadata to metrics YAXArrays (#847) (@Zapiano)
  • Update interface to use correct gpkg (#850) (@DanTanAtAims)
  • correct calculation of relative cover (#853) (@DanTanAtAims)
  • Speed up CScape Result Interface (#854) (@DanTanAtAims)
  • rename dimension from sites to locations (#857) (@DanTanAtAims)
  • throw more informative error message (#858) (@DanTanAtAims)
  • add scenario id to scenario dataframe (#860) (@DanTanAtAims)
  • Improve summarize performance by using mapslices (#862) (@Zapiano)
  • Viz metadata (#863) (@Zapiano)
  • Pin NetCDF.jl and Zarr.jl in order to pin DiskArrays.jl (#864) (@Zapiano)
  • Bump actions/checkout from 3 to 4 (#865) (@dependabot[bot])
  • Bump docker/login-action from 2 to 3 (#866) (@dependabot[bot])
  • Bump docker/build-push-action from 4 to 6 (#867) (@dependabot[bot])
  • Bump docker/metadata-action from 4 to 5 (#868) (@dependabot[bot])
  • Fix rule extraction to handle constant factors (#870) (@Zapiano)
  • Improvements to model performance by reducing allocations (#871) (@ConnectedSystems)
  • Julia 1.11 Manifest and Pkg update (#876) (@arlowhite)
  • Minor change for performance (#877) (@ConnectedSystems)
  • Apply CompatHelper suggestions, free NetCDF,Zarr; add & pin DiskArrays (#878) (@arlowhite)
  • LERC_jll 3 to 4, downgrade DimensionalData to 0.27.9, Julia Pkg update (#879) (@arlowhite)
  • Update code and dependencies to GeoMakie v0.7.x (#884) (@ConnectedSystems)
  • Cyclone mortalities assigned to wrong group (#888) (@DanTanAtAims)
  • DiskArrays 0.4.5, Pkg update (#889) (@arlowhite)
  • Fix StackOverflow error when plotting maps (#891) (@ConnectedSystems)
  • Add spatial visualisations for decision matrices (#893) (@Rosejoycrocker)
  • Add DEA functions and plotting to ADRIA.analysis (#896) (@Rosejoycrocker)
  • Remove duplicate rules (#899) (@Zapiano)
  • Bump codecov/codecov-action from 4 to 5 (#901) (@dependabot[bot])
  • Fix DHW scenario viz again (#903) (@ConnectedSystems)
  • Incorporate recruitment to growth constraints and cap seeding to habitable area (#906) (@DanTanAtAims)
  • Add extraction of feature set to support analyses and assessment (#907) (@ConnectedSystems)
  • Add additional convenience functions and update docstrings (#908) (@ConnectedSystems)
  • Remove defunct method seed_corals! (#909) (@ConnectedSystems)
  • Switch to logging number of coral deployed (#910) (@ConnectedSystems)
  • Add method to display all DHW scenarios for the currently set RCP/SSP (#914) (@ConnectedSystems)
  • Minor tweaks to taxa visualization (#915) (@ConnectedSystems)
  • Updated factor bounds setting method (#917) (@ConnectedSystems)
  • Minor fix on docs (#920) (@vitorhirata)
  • Pin DiskArrays to 0.4.9 (#922) (@vitorhirata)
  • Fix tests of viz/spatial and metrics/spatial (#923) (@vitorhirata)
  • Pin DiskArrays to 0.4.9 in docs Manifest and v1.11 Manifest (#924) (@vitorhirata)
  • Custom categorical distribution (#927) (@DanTanAtAims)
  • Small change to parameter description to avoid confusion (#928) (@ConnectedSystems)
  • Replace and deprecate remaining use of site_k_area (#929) (@ConnectedSystems)
  • CompatHelper: bump compat for Makie in [weakdeps] to 0.22, (keep existing compat) (#930) (@github-actions[bot])
  • CompatHelper: bump compat for DimensionalData to 0.29, (keep existing compat) (#931) (@github-actions[bot])
  • CompatHelper: bump compat for YAXArrays to 0.6, (keep existing compat) (#932) (@github-actions[bot])
  • Avoid reshape for performance (#933) (@ConnectedSystems)
  • Considering spatial dispersal of intervention locations (#934) (@ConnectedSystems)
  • Add cyclone mortality to documentation (#936) (@Zapiano)
  • Correct RCP identifier in result directory (#937) (@ConnectedSystems)
  • Remove synopsis from documentation (#938) (@Zapiano)
  • Update docs to configure Julia Formatter extension (#939) (@ConnectedSystems)
  • Fix docs build (#945) (@Zapiano)
  • CompatHelper: bump compat for JMcDM to 0.8, (keep existing compat) (#946) (@github-actions[bot])
  • Fix rounding problem, leading to coral overgrowth, when cover plus recruits fill an entire reef (#947) (@Zapiano)
  • Bump julia-actions/julia-format from 3 to 4 (#948) (@dependabot[bot])
  • Speed up timeseries clustering (#949) (@Zapiano)
  • add bin edges used in calibration to ADRIA (#950) (@DanTanAtAims)
  • Fix multiple tests (#951) (@Zapiano)
  • Changes to enable recent RME domain loading (#952) (@Zapiano)
  • CompatHelper: bump compat for Interpolations to 0.16, (keep existing compat) (#953) (@github-actions[bot])
  • Speedup bleaching (#954) (@Zapiano)
  • Add plot for single scenario stratified by size class and functional group (#955) (@Zapiano)
  • CompatHelper: bump compat for Makie in [weakdeps] to 0.23, (keep existing compat) (#956) (@github-actions[bot])
  • Update Manifest (#957) (@Zapiano)
  • CompatHelper: bump compat for Makie in [weakdeps] to 0.24, (keep existing compat) (#958) (@github-actions[bot])
  • Update calibrated factors (#960) (@Zapiano)
  • docs: minor clarification to Makie backend selection (#961) (@PeterBaker0)
  • CompatHelper: bump compat for GraphMakie in [weakdeps] to 0.6, (keep existing compat) (#964) (@github-actions[bot])
  • Fix tests prior to merging global-calib to main (#965) (@Zapiano)
  • CompatHelper: bump compat for DataStructures to 0.19, (keep existing compat) (#966) (@github-actions[bot])
  • Calibration and SA changes (#967) (@Zapiano)
  • Bump project version prior to new release (#968) (@Zapiano)
  • Fix conn data load location selection when force_single_reef is true (#970) (@Zapiano)
  • Update compatible datapackage version to 0.8.0 (#972) (@Zapiano)
  • Deactivate criteria factors when running deactivate_interventions (#973) (@Zapiano)
  • Fix _init_cover_weights dicstring (#974) (@Zapiano)
  • Specify timeframe when loading RME dhw_scens (#975) (@Zapiano)
  • Bump actions/checkout from 4 to 5 (#976) (@dependabot[bot])
  • Doc guided sampling (#977) (@Zapiano)
  • Support independent scenarios viz legend rendering (#978) (@Zapiano)
  • CompatHelper: bump compat for YAXArrays to 0.7, (keep existing compat) (#979) (@github-actions[bot])
  • CompatHelper: bump compat for MLJ to 0.21, (keep existing compat) (#981) (@github-actions[bot])
  • Refactor Reef Index Metrics (#982) (@DanTanAtAims)
  • Export bin_edges (#983) (@Zapiano)
  • CompatHelper: bump compat for JSON to 1, (keep existing compat) (#984) (@github-actions[bot])
  • Update calibrated parameter base values (#985) (@Zapiano)
  • CompatHelper: bump compat for JSON to 1, (keep existing compat) (#986) (@github-actions[bot])
  • Fix factor update bug (#988) (@ConnectedSystems)
  • Update key dependencies and bump version (#989) (@ConnectedSystems)
  • Bump project version prior to new release (#990) (@Zapiano)
  • fix: Correct growth constraint calculation in scenario.jl (#992) (@DanTanAtAims)
  • CompatHelper: bump compat for MLJ to 0.22, (keep existing compat) (#993) (@github-actions[bot])
  • CompatHelper: bump compat for SIRUS to 3, (keep existing compat) (#994) (@github-actions[bot])
  • Refactor out recruitment constraint from timestep loop (#996) (@Zapiano)
  • Remove MAT dependency (#997) (@ConnectedSystems)
  • Update GeoDataFrame handling (#998) (@ConnectedSystems)
  • Remove broadcasting to avoid intermediate allocations (#999) (@ConnectedSystems)
  • Remove intermediate array (#1000) (@ConnectedSystems)
  • fix: fix input type declaration for _render_legend (#1001) (@DanTanAtAims)
  • Initial cleanup in prep for restructure (#1002) (@ConnectedSystems)
  • Support arbitrary number of time series clusters (#1003) (@ConnectedSystems)
  • Reorganizing code structure (#1004) (@ConnectedSystems)
  • Bump actions/checkout from 5 to 6 (#1005) (@dependabot[bot])
  • Adjusted scenario sampling and default parameters (#1006) (@ConnectedSystems)
  • Refactor Spatial Data Loading and Update Input Data Handling (#1007) (@DanTanAtAims)
  • Speedups (#1008) (@DanTanAtAims)
  • Fix incorrect use of single reef idx (#1009) (@DanTanAtAims)
  • fix: Fix categorical bug where bounds are passed instead of categories (#1010) (@DanTanAtAims)
  • Improves scenario assessment workflow (#1011) (@ConnectedSystems)
  • Pin YAXArray dependency (#1013) (@ConnectedSystems)
  • Implements decision strategies (#1019) (@ConnectedSystems)
  • Mention use of shared depot paths (#1020) (@ConnectedSystems)
  • Fix single reef load and sampling (#1023) (@Zapiano)
  • Bump project version prior to new release (#1024) (@Zapiano)
  • Restrict minimum compatible Julia version to 1.11 (#1026) (@Zapiano)
  • Improve fecundity (#1027) (@Zapiano)
  • Add Allee effect (#1031) (@Zapiano)
  • Fix: All axis values were being stripped when creating new DataCube (#1033) (@ConnectedSystems)
  • Fix LTMP Taxa Cover and Metric Metadata (#1034) (@DanTanAtAims)
  • reformat with JuliaFormatter V1 (#1035) (@arlowhite)
  • Fix wrong use of reactive strategy index (#1036) (@Zapiano)
  • Fix sampling tests (and others) (#1037) (@Zapiano)
  • Update documentation project (#1038) (@Zapiano)
  • Update Julia version used in github doc build to 1.11 (#1039) (@Zapiano)
  • Extend seeding intervention to all functional groups (#1040) (@Zapiano)
  • Rename ENV variable TEST to ADRIA_TEST (#1041) (@Zapiano)
  • Remove ODE related code (and clean up) (#1042) (@Zapiano)
  • Fix fog and seed location fixing (#1043) (@Zapiano)
  • Fix fog strategy builder (#1047) (@Zapiano)
  • Limit environmental data loading to timeframe in datapackage.json (#1048) (@DanTanAtAims)
  • Use newest version of ADRIAIndicators (#1049) (@DanTanAtAims)
  • Enforce location ids in environmental data. (#1050) (@DanTanAtAims)
  • Implement moving corals intervention (#1052) (@Zapiano)
  • Allow target locations for MCB (#1053) (@Zapiano)
  • Use seeding device density to distribute seeded corals (#1056) (@Zapiano)
  • Assisted adaptation relative to recent past (#1057) (@Zapiano)
  • Update Breeder's equation usage (#1058) (@Zapiano)
  • Add min_iv_locs param specific for moving corals (#1059) (@Zapiano)
  • Add moving corals stats to feature set (#1060) (@Zapiano)
  • Add Marine Cloud Brightening with Multi-dimensional DHW NetCDFs (#1062) (@DanTanAtAims)
  • Bump codecov/codecov-action from 5 to 6 (#1063) (@dependabot[bot])
  • Bump docker/login-action from 3 to 4 (#1064) (@dependabot[bot])
  • Bump julia-actions/cache from 2 to 3 (#1065) (@dependabot[bot])

Closed issues:

  • Core functionality to be ported from ADRIA (MATLAB) (#1)
  • Pretty display for ResultSet (#68)
  • Include site area data in result set (#69)
  • Precompilation step to include dummy runs (#70)
  • Example and test data packages (#71)
  • Investigate optimizations to improve precompilation times (#75)
  • Add total coral cover metric (#77)
  • Adjust RCI to use new total coral cover (#78)
  • Investigate alternative site selection weightings for coral cover (#79)
  • Separate coral_cover() metric into individual functions (#81)
  • Switch default behaviour of ADRIA.jl to store aggregated results? (#82)
  • Use NamedDims and NamedArrays (#83)
  • Adapt siteselection() to use dMCDA to avoid code repetition (#86)
  • Shelter Volume: investigate very small values (#91)
  • Juvenile metric: investigate small values (#92)
  • Auto-adjust site offset/depth bounds on loading Domain (#94)
  • Add an additional model component for environmental layers (#95)
  • Coral evenness: Metric returns NaNs (#96)
  • Replace duplicate proportional growth constraint with single function (#99)
  • Make relative_cover() relative to site max coral cover area (k) instead of total site area (#109)
  • ADRIA specific sampling functions (#119)
  • Update result set to derive spatial data from stored geopackage (#124)
  • Distribute seeded corals acording to available space, not k (#128)
  • Exporting to PowerBI format very slow (#132)
  • Double check recruitment calculation? (#133)
  • Add scenario index to csv created by result_post_processing.jl and filter counterfactual according to dhw scenario (#136)
  • Bleaching mortality may be over-estimated (#138)
  • DHW dataset may over-represent extreme DHW trajectories (#139)
  • Refactor seeding step into its own function with tests (#146)
  • Use measure of dhw time distribution for MCDA heat stress criteria (#151)
  • Check scaling of coral real estate criteria in MCDA function and add measure of space for coral to be seeded. (#152)
  • Make shading of seeded sites user controllable (#157)
  • Metric function to extract the top N performing sites (#158)
  • Process area data on file read (#170)
  • Add support for NetCDF data files (#173)
  • Adjust MCDA functions to be more generic (#177)
  • Deprecate support for .mat files (#182)
  • Update site_selection() function in Domain.jl and use within ADRIA model site selection process to reduce replication (#194)
  • Standardize to NamedDimsArray + AxisKeys (#200)
  • Standardize relative cover metric to report values relative to k area (#204)
  • Adjust scenario input IDs for clarity (#205)
  • Use NamedDims+AxisKeys instead of matrix for MCDA decision matrices (#221)
  • Site ranks are never updated after distance sorting (#223)
  • Update the bleaching response to formally account for depth, surface shading and water quality. (#226)
  • Move natural adaptation parameter to be part of the Coral component (#229)
  • Add human-readable name to Parameter types (#230)
  • List management zones in order of preference for targeted deployment (#231)
  • Change triangular distributions to specify peak in absolute terms (#234)
  • Use Haversine instead of Euclidean distance (#236)
  • Use mean distance threshold and change in aggregate criteria value threshold instead of site by site distance threshold and top_n in distance sorting (#237)
  • Adjust definition or sampling of dist_thresh so that the value representing 'don't use distance sorting' is as likely as values representing using distance sorting (#238)
  • Investigate bounds used for coral_cover_tol (#239)
  • Set up documentation system and website (#240)
  • Consider using JMcDM (#242)
  • Register package (#245)
  • Change reference to Input Set to Domain to align with interface functions (#246)
  • Address possible double switching of RCPs (#248)
  • Make plotting functions more generic to support rapid workflows (#249)
  • Better separation of Aviz sub-system (#250)
  • Make MCDA functions generic (#252)
  • Move example scripts into documentation (#253)
  • pareto analysis (#256)
  • Regional Sensitivity Analysis (#257)
  • Temporal Sensitivity Analysis (#260)
  • Favicon for Documentation site (#265)
  • Use LTMP observations (#267)
  • Update growth rates for size class 6 (#268)
  • TagBot trigger issue (#269)
  • [Discussion] Natural adaptation (#270)
  • Release v0.4.5 (#272)
  • Separate fogging from shading (#277)
  • Possible bug in site_selection (#284)
  • Bug in site selection example (#285)
  • Scenario juvenile metric returning implausible values (?) and values > 1 (#292)
  • Create function which returns just the set of criteria values needed for MCDA (#296)
  • Re-enable tests/CI when Julia v1.9 is released (#300)
  • Connectivity data cubes (#302)
  • First conversion of model specification to DataFrame is excruciatingly slow (#303)
  • map_to_discrete() erroring due to type mismatch (#304)
  • run_site_selection() errors out (#308)
  • [Viz/Analysis] Scenario outcomes (#311)
  • [Viz/Analysis] sensitivity analysis (bar/heatmap) (#312)
  • [Viz/Analysis] temporal sensitivity analysis (#313)
  • [Viz/Analysis] Regional Sensitivity Analysis (#314)
  • [Viz/Analysis] Outcome-based factor mapping (#315)
  • [Viz/Analysis] maps for/of site selection (#316)
  • [Viz/Analysis] Naive Bayes (#323)
  • Make run_site_selection() more user-friendly (#324)
  • Investigate alternative method for sampling mcda weights (#327)
  • Checking centrality is correctly calculated (#329)
  • Release v0.5.0 (#331)
  • MCDA crashes with mismatched array sizes for rankings and rankingsin (#333)
  • Create single ResultSet (#342)
  • MCDA method errors (#357)
  • Make n_sites a perturbable model factor (#360)
  • align_rankings! giving incorrect output rankings (#366)
  • Time series clustering (#368)
  • [Viz/Analysis] Clustering of scenarios to aid in MORDM (#369)
  • Separate model factors (#377)
  • Register v0.6.0 (#379)
  • Spatial clustering based on outcomes (#383)
  • [Viz/Analysis] Spatial plots of locations clustered by outcome (#384)
  • Register v0.7.0 (#388)
  • Remove coral cover conversion for ReefModEngine interface (#399)
  • Add Rule Induction (with SIRUS) (#404)
  • ADRIAmod uses excessive amounts of memory during runs (#405)
  • Errors when running scenarios in parallel when nworkers() > 1 (#413)
  • Change the way target_cluster function is works (#423)
  • Duplicate RCP issue when running scenarios generated using sample_site_selection() (#426)
  • Error: loc_trajectory and per_loc not qualifying dim (#427)
  • Error: non_null_sites (#428)
  • viz.outcome_map() gives duplicate x-axis values when plotting :guided factor (#440)
  • Register v0.8.0 (#447)
  • Update code style section in docs (#448)
  • Out of memory error when calculating PAWN sensitivity for 8192 scenarios (#450)
  • Target clusters with lower values of some metric (#451)
  • Show labels and units of measurement automatically for plots by default (#453)
  • Rule Extraction viz function is not included int viz extension (#454)
  • Relevant features/properties for rule induction (and scenario decision making) (#458)
  • Regional sensiyivity analysis gives duplicate values for categorical factors (#459)
  • Summarized vizualisation for time series clustering (#464)
  • Add example of Rule Induction usage to the Documentation (#473)
  • Update rule ADRIA.viz.rules_scatter to accept target_clusters vector instead of clusters (#474)
  • Conceptually align all coral cover calculations to be relative to k area (#480)
  • Make $k$ area in geospatial data consistent (#483)
  • Load initial coral cover data consistently across different Domain types (#484)
  • Scenario running methods to be refactored to expect only values relative to $k$ area (#487)
  • All metrics to be adjusted to expect $k$ area values (#488)
  • Duplicate x-axis values in outcome maps (Part 2) (#489)
  • Robust Decision Making (#493)
  • Properly handle plotting binary (target vs non-target) clusters (#494)
  • _time_labels gives duplicate labels in some cases (#495)
  • Register v0.9.0 (#498)
  • Adjust usage of k site area in location selection to align with coral cover being relative to k (#501)
  • Possible issue with settler_cover() when moving to k area based processes (#502)
  • Update deprecated writeheader=true at Domain.jl model_spec function (#503)
  • Create a function that uses Slices to compute some aggregation metric over given axis (#508)
  • Remove top_n from distance sorting as no longer needed (#509)
  • Fix bug when loading Domain due to DHWs containing missing values (#510)
  • [RFC] Change factors marked as "integer" types to "discrete" (#512)
  • Refactor tests so we have an available ResultSet instance (#513)
  • Incorporate cyclone mortality into ADRIAmod (#516)
  • Implement n_scenarios(rs) (#517)
  • Skip RCP entry from scenario specification by name rather than assuming position (#518)
  • Add method for selecting all parameters associated with a particular intervention (#520)
  • [Bug] Plotting subset of scenarios fail as not all scenario types may be included (#522)
  • Use more descriptive dimension/axis labels for ResultSet logs storage now that AxisKeys is in use (#524)
  • Make SRM apply to Reef clusters not whole of GBR (#525)
  • Generalise creation of MCDA decision matrices (#526)
  • Switch to YAXArrays (#528)
  • Develop cyclone mortality models based on R implementation (#529)
  • Filter coral species/site by branching_below_5, branching_above_5 and massive (#530)
  • Use cyclone mortality model and filter to implement cyclone mortality in ADRIAmod (#531)
  • Switch to WGLMakie for visualizations (#532)
  • Increase default worker timeout (#534)
  • Out of memory error for parallelised runs for whole of GBR domain (#535)
  • Error runing test/runtests.jl (#538)
  • Create plotting functions for sensitivity analysis convergence (#543)
  • Add documentation for Cyclone mortality (#544)
  • Add load_latest_results() (#548)
  • Cluster maps not working (#549)
  • Record/Log of DHW and wave stats in result sets are broken (#550)
  • Fix error in growth ODE test (#551)
  • Deployment location analysis methods/metrics leak into package namespace (#556)
  • Add MCDA weighting normalisation to scenario sampling post-processing (#559)
  • Delete/remove deprecated functions in prep for v1.0 release (#560)
  • Make all indices used in site selection aggregation functions symbols (#562)
  • Find and deprecate inconsistent methods (#564)
  • Separate weighting parameters for heat_stress and depth in the MCDA (#565)
  • Reorganize files/images for documentation (#567)
  • Error when tests run scenarios (#568)
  • Compute mean of truncated distribution using a Burman series (#572)
  • Remove unused version check (#580)
  • Move example scripts into the cookbook (#584)
  • Adjust sampling approach for flexibility (#586)
  • Changes in PR#552 breaks scenario visualizations (#587)
  • Tests raising error (#590)
  • Add function which returns list of MCDA methods which can be used in ADRIA (#591)
  • Use min-max normalisation for heat stress criteria (#592)
  • Update use of Makie (v0.20.0) to avoid deprecations (#600)
  • Loading RME datasets are broken due to cyclone data requirement (#609)
  • Fix "surprising" readjustment of the number of slices used to perform RSA/outcome mapping (#615)
  • Adjust distribute_seeded_corals to account for cases where the top 5 sites do not have enough space for seeded corals (#618)
  • Change log for dhws and waves to store mean and std for scenarios and sites/reefs (#619)
  • Add new 10 site test Domain to testing folder in ADRIA (#622)
  • Make decision matrices NamedDimsArrays (#624)
  • Register v0.10.0 (#626)
  • set_factor_bounds! setting value outside range for discrete variables (#630)
  • Priority sites criteria expecting different structure for strong_pred than what is implemented (#633)
  • Add connectivity matrix to ResultSet (#641)
  • Error precompiling ADRIA.jl (#645)
  • Support use of cluster identifier in spatial dataset (#655)
  • Fix bug in constrain_reef_cluster which assumes there will always be enough locations to satisfy the reef constraint (#656)
  • Add test domain for ReefModDomain type (#670)
  • Ignore constant factors when applying SIRUS (#672)
  • Add tests for standalone site selection using rank_locations (#680)
  • Larval spread via connectivity is not working as expected (#686)
  • Method Call error during testing from rsa function type. (#692)
  • Documentation image links are broken (#712)
  • viz.outcome_map not working when :guided is one of the factors of interest (#713)
  • Fix sampling of guided MCDA methods (#725)
  • Remove connectivity data from Domain types (#735)
  • Example given in #742 no longer works (#749)
  • Revisit use of temporary geojson (#768)
  • Order of scenarios plotted are inconsistent (#769)
  • Docstring example missing ending backticks (#781)
  • Delete stale branches (#783)
  • Improve loc_trajectory() function performance (#788)
  • Makie spatial plotting maps color vector to each polygon in a multipolygon, leaving white polygons for unmapped shapes (#792)
  • Geospatial dataset for the Test domain does not define a valid CRS (#800)
  • Register v0.11.0 (#816)
  • Delete defunct code after implementing changes to use CoralBlox.jl (#819)
  • ReefModDomain loading is not working (#825)
  • Dimension mismatch when logging DHW tolerances in debug mode (#826)
  • CoralBlox apparent incompatibility (#828)
  • Absolute cover calculations consider wrong area (#841)
  • mismatch of naming in Cscape results set (#849)
  • Investigate alternate chunking strategy for Zarr store (#851)
  • data saved as relative cover is actually absolute cover (#852)
  • Error when calculating total cover (#855)
  • Errors/issues in _get_result_paths() (C~scape interface) (#856)
  • Retrieve scenario IDs from CScapeResultsSet (#859)
  • DimensionalData compat 0.27 (#881)
  • GeoMakie compat 0.6 (#882)
  • DiskArrays pinned to 0.3.23 (#883)
  • StackOverflowError in tests failing on main branch (#890)
  • Rule extraction print_rules error attempting to access 1-element Vector{Float64} at index [2] (#900)
  • Seeding Intervention Habitable Area limit (#905)
  • NaNs in growth_constraints vector raising error at global_calib branch (#963)
  • Release v0.12.0 (#969)
  • Register v0.13.0 (#991)
  • Release v0.14.0 (#1012)
  • Release v0.14.1 (#1014)
  • Release v0.15.0 (#1015)
  • Release v0.15.1 (#1025)
  • JuliaFormatter workflow blocking well formatted files (#1029)

Biosphere - Conservation and Restoration - Julia
Published by github-actions[bot] 14 days ago

ADRIA.jl - ADRIAviz-v0.1.0

ADRIAviz ADRIAviz-v0.1.0

ADRIAviz v0.1.0 Initial Release

ADRIAviz is now a standalone subpackage within the ADRIA.jl mono-repo, replacing the
previous AvizExt package extension that lived inside the core ADRIA package. This
clean separation means the core package no longer pulls in any Makie or Plotly
dependencies.

Breaking Changes

Users must update their using statements:

Before (extension-trigger pattern):

using ADRIA, CairoMakie, GeoMakie, GraphMakie

After (subpackage pattern):

using ADRIA, ADRIAviz
ADRIAviz.activate()              # WGLMakie (default, interactive)
ADRIAviz.activate(CairoMakie)    # non-interactive / CI / scripts
ADRIAviz.activate(:plotly)       # Plotly backend

ADRIAviz.activate() loads the required backend dependencies automatically and raises an
actionable error listing the exact pkg> add command if any dependency is missing.

The experimental explore() interactive GUI dashboard has been removed. A proper
user-launchable dashboard is a longer-term goal and will be delivered as a dedicated
optional package.

New Features

Plotly backend (PlotlyBase extension)

A full Plotly rendering backend is now available alongside the existing Makie backend.
Load it with ADRIAviz.activate(:plotly).

Supported plot types:

  • scenarios() — scenario trajectories with confidence-interval bands
  • sensitivity() / rsa() / outcome_map() — sensitivity and RSA analysis
  • clustering() — scenario clustering
  • taxa_dynamics() — coral taxa dynamics over time
  • map(gdf) / map(rs, ...) — spatial choropleth and scatter-geo maps (no Mapbox token
    required; auto-zooms to reef extent)
  • connectivity() — connectivity network overlaid on spatial map
  • selection_criteria_map() — location selection criteria spatial view
  • data_envelopment(), environment plots (dhw, cyclones), rule_extraction() /
    rules_scatter()

Static export is available via ADRIAviz.savefig() when PlotlyKaleido is also
installed.

Spatial decorations (Makie backend)

The Makie spatial backend now renders NaturalEarth coastlines and decorations using shared
infrastructure (NaturalEarth.jl) that both backends can draw from.

Improvements

  • Visual consistency — shared color palette (PLOTLY_COLORS, ADRIA_LAYOUT_DEFAULTS)
    and label/unit helpers (outcome_label, _time_labels) used across both backends,
    reducing divergence between Makie and Plotly output.
  • Dynamic year axis — Plotly backend now infers the year axis from the data rather
    than assuming a fixed range.
  • TTFX / precompilation — PrecompileTools.jl workload added for _scenario_rcps /
    _scenario_clusters helpers; type annotations on discretize_outcomes and
    screen_scenarios reduce inference overhead on first use.
  • CI — dedicated ADRIAvizTests.yml workflow tests ADRIAviz in isolation with and
    without a Makie backend.
  • Figure consistency tests — new spatial_decorations.jl test suite validates
    rendered figure structure.

Dependency Notes

  • PlotlyBase and PlotlyKaleido are [weakdeps] — neither is loaded unless
    activate("plotly") is called.
  • Makie, GeoMakie, and GraphMakie remain [weakdeps] — only loaded via
    activate().
  • Requires Julia ≥ 1.11.

Merged pull requests:

  • CompatHelper: add new compat entry for CSV at version 0.10, (keep existing compat) (#2) (@github-actions[bot])
  • CompatHelper: add new compat entry for ModelingToolkit at version 8, (keep existing compat) (#3) (@github-actions[bot])
  • CompatHelper: add new compat entry for Compose at version 0.9, (keep existing compat) (#4) (@github-actions[bot])
  • CompatHelper: add new compat entry for BlackBoxOptim at version 0.6, (keep existing compat) (#5) (@github-actions[bot])
  • CompatHelper: add new compat entry for IJulia at version 1, (keep existing compat) (#6) (@github-actions[bot])
  • CompatHelper: add new compat entry for MATLAB at version 0.8, (keep existing compat) (#7) (@github-actions[bot])
  • CompatHelper: add new compat entry for ProfileView at version 1, (keep existing compat) (#8) (@github-actions[bot])
  • CompatHelper: add new compat entry for DataFrames at version 1, (keep existing compat) (#9) (@github-actions[bot])
  • CompatHelper: add new compat entry for Graphs at version 1, (keep existing compat) (#10) (@github-actions[bot])
  • CompatHelper: add new compat entry for StaticArrays at version 1, (keep existing compat) (#11) (@github-actions[bot])
  • CompatHelper: add new compat entry for ModelParameters at version 0.3, (keep existing compat) (#12) (@github-actions[bot])
  • CompatHelper: add new compat entry for Setfield at version 0.8, (keep existing compat) (#13) (@github-actions[bot])
  • CompatHelper: add new compat entry for WinRPM at version 1, (keep existing compat) (#14) (@github-actions[bot])
  • CompatHelper: add new compat entry for BenchmarkTools at version 1, (keep existing compat) (#15) (@github-actions[bot])
  • CompatHelper: add new compat entry for Plots at version 1, (keep existing compat) (#16) (@github-actions[bot])
  • CompatHelper: add new compat entry for DifferentialEquations at version 7, (keep existing compat) (#17) (@github-actions[bot])
  • CompatHelper: add new compat entry for OrdinaryDiffEq at version 6, (keep existing compat) (#18) (@github-actions[bot])
  • CompatHelper: add new compat entry for GraphPlot at version 0.5, (keep existing compat) (#19) (@github-actions[bot])
  • CompatHelper: add new compat entry for GeoDataFrames at version 0.2, (keep existing compat) (#20) (@github-actions[bot])
  • CompatHelper: add new compat entry for ProgressMeter at version 1, (keep existing compat) (#67) (@github-actions[bot])
  • CompatHelper: bump compat for Setfield to 1, (keep existing compat) (#72) (@github-actions[bot])
  • CompatHelper: add new compat entry for GR at version 0.64, (keep existing compat) (#73) (@github-actions[bot])
  • CompatHelper: add new compat entry for CpuId at version 0.3, (keep existing compat) (#74) (@github-actions[bot])
  • Site population cap (#76) (@ConnectedSystems)
  • Adding new total_cover function to RCI calculation (#80) (@Rosejoycrocker)
  • Changes to support site level metrics (#84) (@ConnectedSystems)
  • Changes to scaling for MCDA criteria (site capacity) (attempts to address #79) (#85) (@Rosejoycrocker)
  • Relative cover input to RCI be relative to the sites max coral cover? (#89) (@ConnectedSystems)
  • Scenario focused metrics (#93) (@ConnectedSystems)
  • More appropriate indication of cluster-wide outcomes (#97) (@ConnectedSystems)
  • Address TODO: Extract non-coral parameters to reduce memory use (#105) (@ConnectedSystems)
  • Ensure proportional adjustment of coral cover remain in bounds (#106) (@ConnectedSystems)
  • Expand docstring for proportional_adjustment() for clarity (#107) (@ConnectedSystems)
  • Address small Shelter Volume outcomes (#91) (#108) (@ConnectedSystems)
  • Unguided selection (#112) (@ConnectedSystems)
  • Sysimage builder (#115) (@ConnectedSystems)
  • Fix log scaling error in MCDA coral cover criteria (#117) (@Rosejoycrocker)
  • Detailed docstrings added + shading matrix function added (#118) (@Rosejoycrocker)
  • Environmental data layer component for ADRIA ecosystem model (#120) (@ConnectedSystems)
  • Fixes small issue introduced by compartmentalising SE and SH matrix creation (#122) (@Rosejoycrocker)
  • Adding function to generate csv summary result set (#125) (@Rosejoycrocker)
  • Fixes typos which were not picked up in previous PR (#126) (@Rosejoycrocker)
  • Include PowerBI post processing file in module (#131) (@ConnectedSystems)
  • Fixes for recruitment issue (#137) (@ConnectedSystems)
  • Fix site ranking log (#140) (@ConnectedSystems)
  • Correct simplified settler cover calculation (#141) (@ConnectedSystems)
  • Fixes undefined absolute_site_coral_cover (#142) (@Rosejoycrocker)
  • Remove tf from simulation constants (#143) (@ConnectedSystems)
  • Fixes missed tf definition (#144) (@Rosejoycrocker)
  • Distributes seeded corals at selected sites according to space available (#145) (@Rosejoycrocker)
  • Add timeframe datapackage property (#147) (@ConnectedSystems)
  • Adds function to distribute seeded corals at selected sites according to space available (addresses #146) (#148) (@Rosejoycrocker)
  • Update bleaching mortality model (#149) (@ConnectedSystems)
  • CompatHelper: bump compat for PkgVersion to 0.3, (keep existing compat) (#150) (@github-actions[bot])
  • Additional metrics for site rank analysis (#153) (@ConnectedSystems)
  • Applying depth offset to align with IPMF (#154) (@ConnectedSystems)
  • Add copy of model spec to ResultSet (#155) (@ConnectedSystems)
  • Add incoming and outgoing connectivity ranks and criteria (#156) (@ConnectedSystems)
  • Adds function to find top n sites in result set for each scenario (#159) (@Rosejoycrocker)
  • Adding coral cover area criteria in terms of absolute coral cover (#160) (@Rosejoycrocker)
  • Miscellaneous changes to clean up code (#161) (@ConnectedSystems)
  • Mix normalisation bug in MCDA (#162) (@Rosejoycrocker)
  • Support runs across multiple RCPs (#163) (@ConnectedSystems)
  • Scenario relative cover metric to return cluster wide values (#164) (@ConnectedSystems)
  • Fixes to ODE formulation and indexing (#165) (@Rosejoycrocker)
  • CompatHelper: add new compat entry for Distributions at version 0.25, (keep existing compat) (#166) (@github-actions[bot])
  • Changes to top_N_sites rank metric (#167) (@ConnectedSystems)
  • Support extraction of geometry data from inconsistent column names (#169) (@ConnectedSystems)
  • Robustness metrics (#172) (@ConnectedSystems)
  • Replace bleaching resistance with uncertain bleaching sensitivity (#174) (@ConnectedSystems)
  • Incorporation of zoning criteria in MCDA (#175) (@Rosejoycrocker)
  • Add sampling methods (#176) (@ConnectedSystems)
  • Spread site selection (#180) (@ConnectedSystems)
  • Add dhw summary statistics to ResultSet (#181) (@Rosejoycrocker)
  • Corrections to assignment of growth rates and tests for coral_spec() parameters (#183) (@Rosejoycrocker)
  • Coral model adjustments (#184) (@ConnectedSystems)
  • Switch to netCDF (#185) (@ConnectedSystems)
  • Correct connectivity alignment (#186) (@ConnectedSystems)
  • Update example domain with netCDF format datacubes (#187) (@ConnectedSystems)
  • Changes to support Multi-Objective Optimization (#188) (@ConnectedSystems)
  • Tentative support for Multi-Objective Robust Optimization (#189) (@ConnectedSystems)
  • Bug fix for ODE + change to definition of basal area (#190) (@Rosejoycrocker)
  • Consolidate site area calcs #170 (#191) (@ConnectedSystems)
  • Performance changes (#192) (@ConnectedSystems)
  • Reorganize data loading functions (#193) (@ConnectedSystems)
  • Adjust coral wave mortalities following recommendation by Ken (#195) (@Rosejoycrocker)
  • Adding within size class growth for size class 6 back in for ODE and adjusting within size class growth rates (#196) (@Rosejoycrocker)
  • Connectivity update (#197) (@ConnectedSystems)
  • Add distance sorting to MCDA (#198) (@Rosejoycrocker)
  • Update metrics (#199) (@ConnectedSystems)
  • Updated background mortality values (#201) (@ConnectedSystems)
  • Minor changes to get visualizations working for v0.4.2 (#202) (@ConnectedSystems)
  • v0.4.2 dev merge (#203) (@ConnectedSystems)
  • CompatHelper: add new compat entry for GeoInterface at version 1, (keep existing compat) (#206) (@github-actions[bot])
  • CompatHelper: add new compat entry for RelocatableFolders at version 1, (keep existing compat) (#207) (@github-actions[bot])
  • CompatHelper: add new compat entry for Surrogates at version 6, (keep existing compat) (#208) (@github-actions[bot])
  • CompatHelper: add new compat entry for FileIO at version 1, (keep existing compat) (#209) (@github-actions[bot])
  • CompatHelper: add new compat entry for DecisionTree at version 0.11, (keep existing compat) (#210) (@github-actions[bot])
  • CompatHelper: add new compat entry for Distances at version 0.10, (keep existing compat) (#211) (@github-actions[bot])
  • CompatHelper: add new compat entry for Combinatorics at version 1, (keep existing compat) (#212) (@github-actions[bot])
  • CompatHelper: add new compat entry for BlackBoxOptim at version 0.6, (keep existing compat) (#213) (@github-actions[bot])
  • CompatHelper: add new compat entry for SnoopPrecompile at version 1, (keep existing compat) (#214) (@github-actions[bot])
  • CompatHelper: add new compat entry for Bootstrap at version 2, (keep existing compat) (#215) (@github-actions[bot])
  • CompatHelper: add new compat entry for HypothesisTests at version 0.10, (keep existing compat) (#216) (@github-actions[bot])
  • CompatHelper: add new compat entry for GeoFormatTypes at version 0.4, (keep existing compat) (#217) (@github-actions[bot])
  • CompatHelper: add new compat entry for NCDatasets at version 0.12, (keep existing compat) (#218) (@github-actions[bot])
  • CompatHelper: add new compat entry for GLMakie at version 0.7, (keep existing compat) (#219) (@github-actions[bot])
  • CompatHelper: add new compat entry for GeoMakie at version 0.4, (keep existing compat) (#220) (@github-actions[bot])
  • Adjust rankings to match site reordering due to distance sorting (#224) (@Rosejoycrocker)
  • Add depth column to MCDA decision matrix to be used in seeding and shading decision matrices (#225) (@Rosejoycrocker)
  • Remove additional weighting that is no longer needed (#227) (@ConnectedSystems)
  • Re-order site data by unique site id column to align logged site ids (#228) (@ConnectedSystems)
  • CompatHelper: bump compat for GLMakie to 0.8, (keep existing compat) (#233) (@github-actions[bot])
  • v0.4.3 merge (#241) (@ConnectedSystems)
  • Initial documentation build (#244) (@ConnectedSystems)
  • Add support for Regional Sensitivity Analysis (RSA) (#258) (@ConnectedSystems)
  • Merge v0.4.4-dev (#259) (@ConnectedSystems)
  • Add temporal sensitivity analyses based on the PAWN method (#261) (@ConnectedSystems)
  • Metric restructure (#262) (@ConnectedSystems)
  • CompatHelper: bump compat for ArchGDAL to 0.10, (keep existing compat) (#263) (@github-actions[bot])
  • v0.4.4-dev.1 (#266) (@ConnectedSystems)
  • Add parameter name and description to model specification (#273) (@ConnectedSystems)
  • Adjust coral growth rate for size class 6 (#274) (@ConnectedSystems)
  • Remove references to Input Set (#275) (@ConnectedSystems)
  • Fix: calculate distance between sites (#276) (@ConnectedSystems)
  • Simplify display of model spec (#278) (@ConnectedSystems)
  • Parametric ResultSet (#279) (@ConnectedSystems)
  • Consolidate normalize (#280) (@ConnectedSystems)
  • Changes to site selection functions (#282) (@Rosejoycrocker)
  • Changes to address bug in site_selection example (addresses issue #285 ) (#286) (@Rosejoycrocker)
  • Consolidate Named array types to use NamedDims+AxisKeys (#287) (@ConnectedSystems)
  • Reduce allocations in load_domain() (#288) (@ConnectedSystems)
  • Add criteria parameter which indicates whether distance sorting is used. (#290) (@Rosejoycrocker)
  • Add function n_locations() to determine number of sites/reefs/clusters (#291) (@ConnectedSystems)
  • Miscellaneous cleanup (#293) (@ConnectedSystems)
  • Fix bug causing implausible juvenile indicator values (#294) (@ConnectedSystems)
  • Adjust samples when use of distance thresholds is turned off (#295) (@ConnectedSystems)
  • CompatHelper: add new compat entry for AxisKeys at version 0.2, (keep existing compat) (#297) (@github-actions[bot])
  • Additional safety checks for sampling (#298) (@ConnectedSystems)
  • Adds sampler which can sample only parameters needed for site selection (#299) (@Rosejoycrocker)
  • Adds function which calculates sites selection frequency for a set of provided samples (#301) (@Rosejoycrocker)
  • Fix error mapping continous samples to discrete values (#305) (@ConnectedSystems)
  • Adjust shelter volume to remove hardcoded index and leverage NamedDimsArray (#306) (@ConnectedSystems)
  • Fix initial slice potentially not including lowest value (#307) (@ConnectedSystems)
  • Clean up Project.toml + Precompile (#309) (@ConnectedSystems)
  • Correct issue with size of NamedDims array for storing ranks in run_site_selection() (#310) (@Rosejoycrocker)
  • Initial indicative visualization (#318) (@ConnectedSystems)
  • Fix function extension issues (#319) (@ConnectedSystems)
  • Better check for constancy in RSA (#320) (@ConnectedSystems)
  • Update exploration tool to latest ADRIA API (#321) (@ConnectedSystems)
  • Additional docs for Domain/ResultSets (#322) (@ConnectedSystems)
  • Add capability to fix factors in place (#325) (@ConnectedSystems)
  • Initial ReefMod interface and functionality (#326) (@ConnectedSystems)
  • Move n_adapt from Intervention component to Coral component (#332) (@ConnectedSystems)
  • Update use of functions due to new import approach (#334) (@ConnectedSystems)
  • Migrate from SnoopPrecompile to PrecompileTools (#335) (@timholy)
  • Add planning horizon factor (#336) (@ConnectedSystems)
  • Replace use of area attribute/field with call to function site_area() to ensure correct values (#337) (@ConnectedSystems)
  • Remove reference to defunct fields when making factors constant (#338) (@ConnectedSystems)
  • Fix error caused by mismatched locations (#339) (@ConnectedSystems)
  • Make use of planning horizon in sims (#340) (@ConnectedSystems)
  • Changes to support running ADRIA with external model (ReefMod Engine) data (#341) (@ConnectedSystems)
  • CompatHelper: add new compat entry for SimpleWeightedGraphs at version 1, (keep existing compat) (#343) (@github-actions[bot])
  • CompatHelper: add new compat entry for OrderedCollections at version 1, (keep existing compat) (#344) (@github-actions[bot])
  • CompatHelper: bump compat for StatsBase to 0.34, (keep existing compat) (#345) (@github-actions[bot])
  • Split ADRIA-mod domain definition (#346) (@ConnectedSystems)
  • Add GBR zones by priority (#347) (@ConnectedSystems)
  • Add option to use JMcDM functions in ADRIA site selection (#348) (@Rosejoycrocker)
  • Make Aviz into an extension package (#349) (@ConnectedSystems)
  • Exit with error if given path is not a directory (#350) (@ConnectedSystems)
  • CompatHelper: add new compat entry for Reexport at version 1, (keep existing compat) (#351) (@github-actions[bot])
  • CompatHelper: add new compat entry for ImageMagick at version 1, (keep existing compat) (#352) (@github-actions[bot])
  • Update bleaching mortality model to align with published paper (#354) (@ConnectedSystems)
  • Update scenario viz (#355) (@ConnectedSystems)
  • Add map visualization - displays k-area (#356) (@ConnectedSystems)
  • Address mismatched number of elements under certain conditions (#358) (@ConnectedSystems)
  • Remove Copras method due to erroring (#359) (@Rosejoycrocker)
  • Update documentation (#361) (@ConnectedSystems)
  • CompatHelper: add new compat entry for JMcDM at version 0.7, (keep existing compat) (#362) (@github-actions[bot])
  • CompatHelper: bump compat for HypothesisTests to 0.11, (keep existing compat) (#363) (@github-actions[bot])
  • Scenario discovery docs (#364) (@ConnectedSystems)
  • Fix: Metric errors when applied to a single simulation (#365) (@ConnectedSystems)
  • Address ranking errors in mcda outputs (#367) (@Rosejoycrocker)
  • Add temporal clustering (#370) (@Zapiano)
  • Fix incorrect type check (#371) (@Zapiano)
  • CompatHelper: add new compat entry for Clustering at version 0.15, (keep existing compat) (#372) (@github-actions[bot])
  • CompatHelper: bump compat for Zarr to 0.9, (keep existing compat) (#373) (@github-actions[bot])
  • Update time series clustering and add visualization functionality (#374) (@Zapiano)
  • Update docstrings for growth function (#375) (@ConnectedSystems)
  • Refactor run_scenarios to improve when running multiple rcps (#376) (@Zapiano)
  • Bump version number and add new author (#378) (@Zapiano)
  • Changes to number of species in ADRIA (#380) (@Rosejoycrocker)
  • Distribution-based bleaching mortality to capture natural adaptation and heritability (#381) (@ConnectedSystems)
  • Temporal clustering for spatial data (#382) (@Zapiano)
  • Remove duplicate function recruitment (#385) (@ConnectedSystems)
  • Reorganize package structure (#386) (@ConnectedSystems)
  • Consider near-term conditions with greater weight than far-future conditions (#387) (@ConnectedSystems)
  • Update release guide (#389) (@ConnectedSystems)
  • Changes to ode solver and time step for efficiency improvements (#390) (@Rosejoycrocker)
  • Add adaptive=false specification and remove tolerances (#391) (@Rosejoycrocker)
  • Scenario viz change (#393) (@ConnectedSystems)
  • CompatHelper: add new compat entry for JuliennedArrays at version 0.4, (keep existing compat) (#395) (@github-actions[bot])
  • CompatHelper: add new compat entry for FLoops at version 0.2, (keep existing compat) (#396) (@github-actions[bot])
  • Fix bug: Use wave condition for current timestep, not previous (#397) (@ConnectedSystems)
  • Update comment to reflect changes for wave condition usage (#398) (@ConnectedSystems)
  • Incorrect function being called (#400) (@ConnectedSystems)
  • Remove use of batch sizes when running parallel scenarios (#401) (@ConnectedSystems)
  • CompatHelper: bump compat for SparseArrayKit to 0.3, (keep existing compat) (#403) (@github-actions[bot])
  • Fix map display (default display when plotting Domain or ResultSet) (#407) (@ConnectedSystems)
  • Update ReefMod interface to match new species list (#408) (@Rosejoycrocker)
  • Fix excessive memory use (#405) (#409) (@ConnectedSystems)
  • Small miscellaneous changes for scenario visualizations (#412) (@ConnectedSystems)
  • Remove dependency on ImageMagick in favour of ImageIO (#414) (@ConnectedSystems)
  • Updated Reef Indices (#415) (@ConnectedSystems)
  • Fix workers crashing and leaking memory when running scenarios in parallel (#416) (@ConnectedSystems)
  • Adjustments to heritability based on feedback (#417) (@ConnectedSystems)
  • Update docstrings with missing detail (#418) (@ConnectedSystems)
  • Implement relevant struct to handle SIRUS rule extraction (#420) (@Zapiano)
  • Implement rule extracting function (#421) (@Zapiano)
  • Implement rule scatter plot function (#422) (@Zapiano)
  • Move and modify behaviour of target_cluster function (#424) (@Zapiano)
  • Fix unnecessarily squashed figure when plotting outcome map for 1 factor (#425) (@ConnectedSystems)
  • Documentation improvement (#429) (@Zapiano)
  • Fix scenario metrics with field :scenario instead of :scenarios (#430) (@Zapiano)
  • Adds a series of aggregation functions for location selection ranks (#431) (@Rosejoycrocker)
  • Fix error when running samples generated from sample_site_selection() (#432) (@Rosejoycrocker)
  • Fix time_series_clustering for variable series with k > 0 (#433) (@Zapiano)
  • Add functions for repeated tasks when performing location selection (#434) (@Rosejoycrocker)
  • Address very slow extraction of relative cover values (#435) (@ConnectedSystems)
  • Update prototype exploration UI to work with recent changes (#436) (@ConnectedSystems)
  • Incorporate settler DHW tolerances (#437) (@ConnectedSystems)
  • Fix loc_trajectory and per_loc function (#438) (@Zapiano)
  • Fix clustering map visualisation (#439) (@Zapiano)
  • Add Blue Style Guide badge to README (#441) (@Zapiano)
  • Fix duplicate x-axis values bug in viz.outcome_map() (#442) (@Rosejoycrocker)
  • Update SIRUS StableRules type (#443) (@Zapiano)
  • Fix print_rules adding & when there are two clauses (#444) (@Zapiano)
  • More updates to documentation (#446) (@ConnectedSystems)
  • Functions to plot spatial distributions of site selection frequencies (#449) (@Rosejoycrocker)
  • Miscellaneous changes to improve type infererability and precompilation times (#455) (@ConnectedSystems)
  • Changes to improve performance of PAWN sensitivity analysis (#457) (@ConnectedSystems)
  • Fix print_rules condition (#460) (@Zapiano)
  • Update ADRIA logo (#461) (@Zapiano)
  • Adjust PAWN function to support 1D matrix for convenience (#462) (@ConnectedSystems)
  • Add function to find robust scenarios across several metrics (#463) (@Zapiano)
  • Update Reef Tourism Index regression coefficient (temporary solution) (#466) (@ConnectedSystems)
  • Add new cluster_rules method that accepts BitVector or Vector{Bool} (#467) (@Zapiano)
  • Include rule_extraction.jl in viz.jl (#468) (@Zapiano)
  • Precompilation reduction (#469) (@ConnectedSystems)
  • Add option to show GBRMPA management zones (#470) (@ConnectedSystems)
  • Update sensitivity module to follow Blue style (#471) (@ConnectedSystems)
  • Update Doc mentioning blue style guide (#472) (@Zapiano)
  • Update viz.rules_scatter to accept targeted clusters (#475) (@Zapiano)
  • Deprecate run_scenarios(scens, dom, ...) (#476) (@ConnectedSystems)
  • Add Documentation Sensitivity section for Rule Induction algorithm (#477) (@Zapiano)
  • Rename time_series_clustering and ts_cluster (#478) (@Zapiano)
  • Remove locations with no space from consideration for interventions (#479) (@ConnectedSystems)
  • Adjust run_model() to only require values relative to $k$ area (#481) (@ConnectedSystems)
  • Update viz.clustered_scenarios to allow confidence interval plot (#482) (@Zapiano)
  • Consistent treatment of k area on data load (#485) (@ConnectedSystems)
  • Transform ICC from relative to absolute area to relative to k area (#486) (@ConnectedSystems)
  • Add function to alter sampling bounds on parameters to specified value. (#490) (@Rosejoycrocker)
  • Fix bug in how sensitivity.outcome_map() treats categorical variables. (#491) (@Rosejoycrocker)
  • Fix _time_labels missing last label (#496) (@Zapiano)
  • Update version number to 0.9.0 (#497) (@Rosejoycrocker)
  • Add .JuliaFormatter.toml to .gitignore (#499) (@Zapiano)
  • Refactor viz.scenario (#500) (@Zapiano)
  • CompatHelper: bump compat for SciMLBase to 2, (keep existing compat) (#504) (@github-actions[bot])
  • Add :summary option to viz.scenarios (#505) (@Zapiano)
  • Update CSV.write writeheader parameter to header (#506) (@Zapiano)
  • Fix bug causing Domain loading with RCP to error (#511) (@Rosejoycrocker)
  • Remove top_n parameter from usage (#514) (@Rosejoycrocker)
  • CompatHelper: bump compat for MLJ to 0.20, (keep existing compat) (#515) (@github-actions[bot])
  • Add support series and map binary clusters plots (#521) (@Zapiano)
  • Fix scenarios subsetting now working (#523) (@Zapiano)
  • Add interface function to query number of scenarios in result set (#527) (@ConnectedSystems)
  • Rename rs_input with scenarios (#533) (@Zapiano)
  • CompatHelper: bump compat for NCDatasets to 0.13, (keep existing compat) (#536) (@github-actions[bot])
  • Add summarize and turn per_loc and loc_trajectory into alias (#537) (@Zapiano)
  • Broadcast _check_discrete inside update_params (#539) (@Zapiano)
  • Extract call to run scenarios inside tests to external function (#540) (@Zapiano)
  • Add missing scenario analysis function definitions to analysis module (#541) (@ConnectedSystems)
  • Resolve Out-of-Memory issues when working with larger spatial areas (#542) (@ConnectedSystems)
  • Update analysis docs with recent scenarios and clusters developments (#545) (@Zapiano)
  • Fix failing test cases due to recent changes (#546) (@ConnectedSystems)
  • Changes to mcda functions to reflect coral cover being in terms of k area (#547) (@Rosejoycrocker)
  • Add ability to perform convergence analysis (#552) (@Rosejoycrocker)
  • CompatHelper: add new compat entry for TOML at version 1, (keep existing compat) (#553) (@github-actions[bot])
  • CompatHelper: add new compat entry for Statistics at version 1, (keep existing compat) (#554) (@github-actions[bot])
  • Coral cover consistently represented as relative to coral habitable area (#555) (@ConnectedSystems)
  • Avoid assuming where the RCP column is when adjusting scenario spec (#558) (@ConnectedSystems)
  • Fix integer dims reference in location_selection_frequency() (#563) (@Rosejoycrocker)
  • Fix bug due to missing default_bounds in EnvironmentalLayer and Coral model components (#569) (@Rosejoycrocker)
  • Visualizations to be agnostic to Makie backend (#570) (@ConnectedSystems)
  • Add functions used for location selection to separate decision module (#571) (@Rosejoycrocker)
  • Add separate weighting parameter for depth criteria (#573) (@Rosejoycrocker)
  • Add conversion to scientific notation (#574) (@Zapiano)
  • Fix plot map (#575) (@Zapiano)
  • Prevent test_rs() from creating tmp dir inside test/data (#576) (@Zapiano)
  • Apply blue styleguide to some files (#579) (@Zapiano)
  • Update use of progress meter to resolve deprecation warning (#581) (@ConnectedSystems)
  • Normalize sampled MCDA weights (#582) (@Rosejoycrocker)
  • Replace package NCDatasets by NetCDF (#583) (@Zapiano)
  • Implement cyclone mortality scenarios (#585) (@Zapiano)
  • CompatHelper: add new compat entry for NetCDF at version 0.11, (keep existing compat) (#588) (@github-actions[bot])
  • Fix viz.scenarios bug introduced in changes to scenario_confint! usage (#589) (@Rosejoycrocker)
  • Change approach to listing supported MCDA methods (#593) (@ConnectedSystems)
  • Remove defunct function for post processing results into power-BI friendly csv file (#594) (@Rosejoycrocker)
  • Use min-max normalisation for heat stress (#595) (@Rosejoycrocker)
  • Use min-max normalisation for heat stress (#596) (@Rosejoycrocker)
  • Handle cases where connectivity directories may be empty (#597) (@ConnectedSystems)
  • Deactivated interventions should be considered separately (#598) (@ConnectedSystems)
  • Remove list of ignored JMcDM methods (#599) (@ConnectedSystems)
  • Fix treatment of categorical factors in regional sensitivity analysis (#601) (@Rosejoycrocker)
  • Separate shading and fogging timing parameters (#602) (@Rosejoycrocker)
  • CompatHelper: bump compat for Interpolations to 0.15, (keep existing compat) (#604) (@github-actions[bot])
  • CompatHelper: add new compat entry for YAXArrays at version 0.5, (keep existing compat) (#605) (@github-actions[bot])
  • CompatHelper: add new compat entry for DimensionalData at version 0.25, (keep existing compat) (#606) (@github-actions[bot])
  • Fix proportional_adjustment vector conversion computational error (#607) (@Zapiano)
  • Add tests for figure creation (#608) (@ConnectedSystems)
  • Fix bug where cover instead of leftover space was being used in stand alone site selection (#610) (@Rosejoycrocker)
  • Add more detail regarding sequence of events (#611) (@ConnectedSystems)
  • Adjust language in architectural overview to match recent changes (#612) (@ConnectedSystems)
  • Support RSA with large sample sizes (#614) (@ConnectedSystems)
  • Attach dummy wave and cyclone data (#616) (@ConnectedSystems)
  • CompatHelper: bump compat for SIRUS to 2, (keep existing compat) (#617) (@github-actions[bot])
  • Changes to dhw and wave logs to store scenario and site means and stds (#623) (@Rosejoycrocker)
  • Fix bug introduced by SIRUS v2.0.1 (#625) (@Zapiano)
  • Add a new ten site example domain for testing (#628) (@Rosejoycrocker)
  • Fix mcda method bugs (#629) (@Rosejoycrocker)
  • Fix set_factor_bounds! out of bounds for discrete factors (#631) (@Zapiano)
  • Consolidate methods that transform factor values into sampling.jl (#632) (@ConnectedSystems)
  • Replaces distance sorting with restrictions on the number of selected locations in the same reef (#635) (@Rosejoycrocker)
  • Update factor types and their use (#636) (@ConnectedSystems)
  • Update factor definitions to use custom constructor (#637) (@ConnectedSystems)
  • Update sampling methods for newly defined factor definitions (#638) (@ConnectedSystems)
  • Update interactions with Param types across ADRIA more generally (#639) (@ConnectedSystems)
  • Address MCDA error for single locations (#640) (@ConnectedSystems)
  • Add connectivity data to result set storage (#643) (@Rosejoycrocker)
  • Changes to make ADRIA precompilable under Julia v1.10 (#646) (@ConnectedSystems)
  • Update use of Makie/GeoMakie to address deprecation errors (#647) (@ConnectedSystems)
  • Fix larval connectivity bug (#648) (@ConnectedSystems)
  • Remove examples dir issue #584 (#651) (@DanTanAtAims)
  • Speed up calculation of truncated normal mean and cdf (#652) (@DanTanAtAims)
  • Update tests for new sampling method/factor definitions (#653) (@ConnectedSystems)
  • Update factor type documentation (#654) (@ConnectedSystems)
  • Add a default size for scenario plots (#657) (@ConnectedSystems)
  • CompatHelper: add new compat entry for StatsFuns at version 1, (keep existing compat) (#658) (@github-actions[bot])
  • CompatHelper: add new compat entry for SpecialFunctions at version 2, (keep existing compat) (#659) (@github-actions[bot])
  • Fix bleaching mortality (#660) (@ConnectedSystems)
  • Clean up settler cover function to reduce confusion (#662) (@ConnectedSystems)
  • Only load up relevant RME SSP datasets (#663) (@ConnectedSystems)
  • Reset deployed-coral-risk-tol range (#664) (@ConnectedSystems)
  • Clean up scenario running methods (#665) (@ConnectedSystems)
  • Return 0 in cases where lb > ub (#666) (@ConnectedSystems)
  • Clean up use of TP matrices to align with conceptualisation of connectivity (#667) (@ConnectedSystems)
  • Adjustment to simulated events to address numerical errors (#668) (@ConnectedSystems)
  • Support updated domain structure (#669) (@ConnectedSystems)
  • Fix erroneous handling of location IDs (#671) (@ConnectedSystems)
  • Fix error in domain loading when cluster_id is already in string format (#673) (@Rosejoycrocker)
  • Add test domain for ReefModDomain type (#675) (@Rosejoycrocker)
  • Additional setup instructions for code style and formatting (#676) (@ConnectedSystems)
  • Implementation of new MCDA types (#678) (@ConnectedSystems)
  • Fix readjustment of number of slices bug in RSA (#679) (@Rosejoycrocker)
  • Fix cyclone sorting (#683) (@Zapiano)
  • removed deprecate functions and function calls (#684) (@DanTanAtAims)
  • restructured documentation image directories (#685) (@DanTanAtAims)
  • Truncated normal changes (#687) (@DanTanAtAims)
  • Allow user to set whatever bounds they wish (#688) (@ConnectedSystems)
  • Yax loaddomain (#689) (@Zapiano)
  • Switch to YAXArrays when runnin scenarios (#690) (@Zapiano)
  • Adjustments to allow loading newest Domain datasets (#691) (@ConnectedSystems)
  • Update rank metrics to use YAXArrays (#693) (@ConnectedSystems)
  • Update viz.clustering to expect AbstractMatrix (#694) (@ConnectedSystems)
  • Migrate from NamedDimsArrays to YAXArrays (#695) (@Zapiano)
  • Remove factors input from rsa() and use scenario dataframe column names instead (#696) (@Rosejoycrocker)
  • updated data loading test for migration to YAXArrays (#697) (@DanTanAtAims)
  • Further updates to scenario runs with MCDA (#698) (@ConnectedSystems)
  • Update support for standalone MCDA use (#699) (@ConnectedSystems)
  • Yax test update (#700) (@DanTanAtAims)
  • added nameddimsarray2yaxarray (#701) (@DanTanAtAims)
  • Fix error in bin size for sensitivity.outcome_map (#702) (@Rosejoycrocker)
  • Yax viz (#703) (@DanTanAtAims)
  • Yax cube tests (#704) (@DanTanAtAims)
  • Remove MKL from build process (#705) (@ConnectedSystems)
  • Reef mod matlab domain (#706) (@DanTanAtAims)
  • Yax analysis (#707) (@DanTanAtAims)
  • Migrate metrics.jl to YAXArrays (#709) (@Zapiano)
  • Yax sensitivity (#710) (@DanTanAtAims)
  • Remove GC workaround (#711) (@ConnectedSystems)
  • CompatHelper: bump compat for DimensionalData to 0.26, (keep existing compat) (#714) (@github-actions[bot])
  • Yax migration miscellaneous (#715) (@Zapiano)
  • Keep metadata in results (#716) (@ConnectedSystems)
  • Finalize update of standalone MCDA methods (#717) (@ConnectedSystems)
  • Update all tests and remove NamedDims and AxisKeys from ADRIA.jl (#718) (@Zapiano)
  • Validating MCDA methods and initial clean/update of tests (#719) (@ConnectedSystems)
  • Provide a succinct overview of MCDA (#720) (@ConnectedSystems)
  • Add support to cyclone mortality to ReefModDomain (#722) (@Zapiano)
  • Fix locations selection in ReefMod datapackage cyclone mortality loading (#723) (@Zapiano)
  • Save right intervention label at ResultSet ranks YAXArray (#724) (@Zapiano)
  • Add counterfactual minus guided/unguided diff at location level (#726) (@Zapiano)
  • Hacky support for later RME reef id list (#731) (@ConnectedSystems)
  • Add support for specifying locations (#732) (@ConnectedSystems)
  • improve load_domain docs (#733) (@arlowhite)
  • Only rank locations with available area > 0 (#734) (@ConnectedSystems)
  • Support more vector types for maps (#736) (@ConnectedSystems)
  • Clean up connectivity and centrality methods (#737) (@ConnectedSystems)
  • Additional rank methods to determine number of locations intervened on per timestep (#738) (@ConnectedSystems)
  • Collection of miscellaneous changes (#740) (@ConnectedSystems)
  • Fix bug, min. locations to select > available locations (#741) (@ConnectedSystems)
  • Connectivity viz (#742) (@DanTanAtAims)
  • CompatHelper: bump compat for DimensionalData to 0.27, (keep existing compat) (#744) (@github-actions[bot])
  • RME Result Interface (#745) (@DanTanAtAims)
  • Working example of CUDA-fied settler_cover() (#747) (@ConnectedSystems)
  • Repeat mention that the VS Code extension is being setup (#748) (@ConnectedSystems)
  • Improved support for spatial maps (#750) (@ConnectedSystems)
  • use provided centrality measures instead of defaults (#751) (@DanTanAtAims)
  • Convenience plotting method for connectivity/centralities (#752) (@ConnectedSystems)
  • Misc cleanup (coral dynamics) (#753) (@ConnectedSystems)
  • Changes to make use of expected multi-dimensional data structure (#754) (@ConnectedSystems)
  • remove hardcoded coral spec from metrics and data store (#755) (@DanTanAtAims)
  • fix initial cover block constructor (#757) (@DanTanAtAims)
  • Support plotting DHW and cyclone (mortality) scenarios (#758) (@ConnectedSystems)
  • Support deactivating environmental disturbances (#759) (@ConnectedSystems)
  • Multidimensional cover (#761) (@DanTanAtAims)
  • add range to for loop (#762) (@DanTanAtAims)
  • Visualization for taxonomy cover. (#763) (@DanTanAtAims)
  • CompatHelper: add new compat entry for Makie in [weakdeps] at version 0.21, (keep existing compat) (#764) (@github-actions[bot])
  • CompatHelper: bump compat for NetCDF to 0.12, (keep existing compat) (#765) (@github-actions[bot])
  • CompatHelper: add new compat entry for GraphMakie in [weakdeps] at version 0.5, (keep existing compat) (#766) (@github-actions[bot])
  • CompatHelper: add new compat entry for GeoMakie in [weakdeps] at version 0.6, (keep existing compat) (#767) (@github-actions[bot])
  • Change assisted adaptation to a Discrete Uniform value (#770) (@ConnectedSystems)
  • Use underlying data instead of YAXArray type (#771) (@ConnectedSystems)
  • Increase compression level for ResultSet (#772) (@ConnectedSystems)
  • Fix erroneous function call in docstrings (#773) (@ConnectedSystems)
  • Add methods to extract deployment location info (#774) (@ConnectedSystems)
  • Clean up defunct dependencies (#776) (@ConnectedSystems)
  • Fix visualization type error (#777) (@DanTanAtAims)
  • Fix mismatched function name in docstring (#778) (@ConnectedSystems)
  • constrain growth by available area (#779) (@DanTanAtAims)
  • Fix site_level dosctring (#782) (@Zapiano)
  • remove breakpoint in code (#784) (@DanTanAtAims)
  • Assortment of improvements to SIRUS and Time Series Clustering (#786) (@Zapiano)
  • Add default option to _sort_keys (#787) (@Zapiano)
  • Julia format GH workflow, format all files (#790) (@arlowhite)
  • julia-actions recommended dependabot.yml (#791) (@arlowhite)
  • Coerce to MultiPolygon instead of Polygon (#793) (@ConnectedSystems)
  • Bump julia-actions/cache from 1 to 2 (#795) (@dependabot[bot])
  • Bump julia-actions/setup-julia from 1 to 2 (#796) (@dependabot[bot])
  • Bump actions/checkout from 2 to 4 (#797) (@dependabot[bot])
  • Minor updates to geospatial functions/handling (#798) (@ConnectedSystems)
  • use apply_mortality not apply_survival (#799) (@DanTanAtAims)
  • Address tests failing due to type mismatch (scenario confint) (#801) (@ConnectedSystems)
  • Fix depth min/offset being sampled for counterfactual scenarios (#802) (@ConnectedSystems)
  • Use CoralBlox linear_extension_scale_factor (#805) (@Zapiano)
  • Implement linear extension scale factor (#806) (@Zapiano)
  • Fix add run_model method that do not require functional_groups (#807) (@Zapiano)
  • build: prototype CD integration with Provena to update model (#808) (@PeterBaker0)
  • Fix broken tests (#809) (@Zapiano)
  • update fecundity min area variable name for clarity (#810) (@eco-ben)
  • fix permutation of initial cover dimensions (#811) (@DanTanAtAims)
  • Breaks new initial_cover.nc file into size classes assuming a LogNormal distribution (#812) (@Zapiano)
  • Fix miscellaneous of broken tests (#813) (@Zapiano)
  • Fix sampling test (#814) (@Zapiano)
  • Increase release version (#815) (@DanTanAtAims)
  • Apply changes to ADRIA to make it compatible with CoralBlox model (#817) (@Zapiano)
  • CompatHelper: add new compat entry for CoralBlox at version 1, (keep existing compat) (#821) (@github-actions[bot])
  • Fix docs builder, add .git-blame-ignore-revs and document (#823) (@arlowhite)
  • fix helper dimension size error (#824) (@DanTanAtAims)
  • Add reshape to fix dimension mismatch when logging dhw tolerances (#827) (@Rosejoycrocker)
  • updates docs github action to use Julia 1.10.* (#829) (@arlowhite)
  • Remove Manifest from gitignore (#830) (@Zapiano)
  • Rename metrics :sites dimension with :locations (#831) (@Zapiano)
  • Fix docs errors (#832) (@arlowhite)
  • Fix cover loading and size class lower bound (#833) (@DanTanAtAims)
  • convert recruitment from relative area to area before use (#834) (@DanTanAtAims)
  • lowercase png extensions to fix Documenter (#837) (@arlowhite)
  • Cscape interface improvements (#838) (@ConnectedSystems)
  • feat: migrating and updating docker functionality + publish pipeline (#839) (@PeterBaker0)
  • fix: stale links in docker docs (#843) (@PeterBaker0)
  • Overly constrained argument types causing tests to fail (#844) (@ConnectedSystems)
  • feat: restore unit testing and add julia caching (#845) (@PeterBaker0)
  • fix reefmod domain load initial cover (#846) (@DanTanAtAims)
  • Add metadata to metrics YAXArrays (#847) (@Zapiano)
  • Update interface to use correct gpkg (#850) (@DanTanAtAims)
  • correct calculation of relative cover (#853) (@DanTanAtAims)
  • Speed up CScape Result Interface (#854) (@DanTanAtAims)
  • rename dimension from sites to locations (#857) (@DanTanAtAims)
  • throw more informative error message (#858) (@DanTanAtAims)
  • add scenario id to scenario dataframe (#860) (@DanTanAtAims)
  • Improve summarize performance by using mapslices (#862) (@Zapiano)
  • Viz metadata (#863) (@Zapiano)
  • Pin NetCDF.jl and Zarr.jl in order to pin DiskArrays.jl (#864) (@Zapiano)
  • Bump actions/checkout from 3 to 4 (#865) (@dependabot[bot])
  • Bump docker/login-action from 2 to 3 (#866) (@dependabot[bot])
  • Bump docker/build-push-action from 4 to 6 (#867) (@dependabot[bot])
  • Bump docker/metadata-action from 4 to 5 (#868) (@dependabot[bot])
  • Fix rule extraction to handle constant factors (#870) (@Zapiano)
  • Improvements to model performance by reducing allocations (#871) (@ConnectedSystems)
  • Julia 1.11 Manifest and Pkg update (#876) (@arlowhite)
  • Minor change for performance (#877) (@ConnectedSystems)
  • Apply CompatHelper suggestions, free NetCDF,Zarr; add & pin DiskArrays (#878) (@arlowhite)
  • LERC_jll 3 to 4, downgrade DimensionalData to 0.27.9, Julia Pkg update (#879) (@arlowhite)
  • Update code and dependencies to GeoMakie v0.7.x (#884) (@ConnectedSystems)
  • Cyclone mortalities assigned to wrong group (#888) (@DanTanAtAims)
  • DiskArrays 0.4.5, Pkg update (#889) (@arlowhite)
  • Fix StackOverflow error when plotting maps (#891) (@ConnectedSystems)
  • Add spatial visualisations for decision matrices (#893) (@Rosejoycrocker)
  • Add DEA functions and plotting to ADRIA.analysis (#896) (@Rosejoycrocker)
  • Remove duplicate rules (#899) (@Zapiano)
  • Bump codecov/codecov-action from 4 to 5 (#901) (@dependabot[bot])
  • Fix DHW scenario viz again (#903) (@ConnectedSystems)
  • Incorporate recruitment to growth constraints and cap seeding to habitable area (#906) (@DanTanAtAims)
  • Add extraction of feature set to support analyses and assessment (#907) (@ConnectedSystems)
  • Add additional convenience functions and update docstrings (#908) (@ConnectedSystems)
  • Remove defunct method seed_corals! (#909) (@ConnectedSystems)
  • Switch to logging number of coral deployed (#910) (@ConnectedSystems)
  • Add method to display all DHW scenarios for the currently set RCP/SSP (#914) (@ConnectedSystems)
  • Minor tweaks to taxa visualization (#915) (@ConnectedSystems)
  • Updated factor bounds setting method (#917) (@ConnectedSystems)
  • Minor fix on docs (#920) (@vitorhirata)
  • Pin DiskArrays to 0.4.9 (#922) (@vitorhirata)
  • Fix tests of viz/spatial and metrics/spatial (#923) (@vitorhirata)
  • Pin DiskArrays to 0.4.9 in docs Manifest and v1.11 Manifest (#924) (@vitorhirata)
  • Custom categorical distribution (#927) (@DanTanAtAims)
  • Small change to parameter description to avoid confusion (#928) (@ConnectedSystems)
  • Replace and deprecate remaining use of site_k_area (#929) (@ConnectedSystems)
  • CompatHelper: bump compat for Makie in [weakdeps] to 0.22, (keep existing compat) (#930) (@github-actions[bot])
  • CompatHelper: bump compat for DimensionalData to 0.29, (keep existing compat) (#931) (@github-actions[bot])
  • CompatHelper: bump compat for YAXArrays to 0.6, (keep existing compat) (#932) (@github-actions[bot])
  • Avoid reshape for performance (#933) (@ConnectedSystems)
  • Considering spatial dispersal of intervention locations (#934) (@ConnectedSystems)
  • Add cyclone mortality to documentation (#936) (@Zapiano)
  • Correct RCP identifier in result directory (#937) (@ConnectedSystems)
  • Remove synopsis from documentation (#938) (@Zapiano)
  • Update docs to configure Julia Formatter extension (#939) (@ConnectedSystems)
  • Fix docs build (#945) (@Zapiano)
  • CompatHelper: bump compat for JMcDM to 0.8, (keep existing compat) (#946) (@github-actions[bot])
  • Fix rounding problem, leading to coral overgrowth, when cover plus recruits fill an entire reef (#947) (@Zapiano)
  • Bump julia-actions/julia-format from 3 to 4 (#948) (@dependabot[bot])
  • Speed up timeseries clustering (#949) (@Zapiano)
  • add bin edges used in calibration to ADRIA (#950) (@DanTanAtAims)
  • Fix multiple tests (#951) (@Zapiano)
  • Changes to enable recent RME domain loading (#952) (@Zapiano)
  • CompatHelper: bump compat for Interpolations to 0.16, (keep existing compat) (#953) (@github-actions[bot])
  • Speedup bleaching (#954) (@Zapiano)
  • Add plot for single scenario stratified by size class and functional group (#955) (@Zapiano)
  • CompatHelper: bump compat for Makie in [weakdeps] to 0.23, (keep existing compat) (#956) (@github-actions[bot])
  • Update Manifest (#957) (@Zapiano)
  • CompatHelper: bump compat for Makie in [weakdeps] to 0.24, (keep existing compat) (#958) (@github-actions[bot])
  • Update calibrated factors (#960) (@Zapiano)
  • docs: minor clarification to Makie backend selection (#961) (@PeterBaker0)
  • CompatHelper: bump compat for GraphMakie in [weakdeps] to 0.6, (keep existing compat) (#964) (@github-actions[bot])
  • Fix tests prior to merging global-calib to main (#965) (@Zapiano)
  • CompatHelper: bump compat for DataStructures to 0.19, (keep existing compat) (#966) (@github-actions[bot])
  • Calibration and SA changes (#967) (@Zapiano)
  • Bump project version prior to new release (#968) (@Zapiano)
  • Fix conn data load location selection when force_single_reef is true (#970) (@Zapiano)
  • Update compatible datapackage version to 0.8.0 (#972) (@Zapiano)
  • Deactivate criteria factors when running deactivate_interventions (#973) (@Zapiano)
  • Fix _init_cover_weights dicstring (#974) (@Zapiano)
  • Specify timeframe when loading RME dhw_scens (#975) (@Zapiano)
  • Bump actions/checkout from 4 to 5 (#976) (@dependabot[bot])
  • Doc guided sampling (#977) (@Zapiano)
  • Support independent scenarios viz legend rendering (#978) (@Zapiano)
  • CompatHelper: bump compat for YAXArrays to 0.7, (keep existing compat) (#979) (@github-actions[bot])
  • CompatHelper: bump compat for MLJ to 0.21, (keep existing compat) (#981) (@github-actions[bot])
  • Refactor Reef Index Metrics (#982) (@DanTanAtAims)
  • Export bin_edges (#983) (@Zapiano)
  • CompatHelper: bump compat for JSON to 1, (keep existing compat) (#984) (@github-actions[bot])
  • Update calibrated parameter base values (#985) (@Zapiano)
  • CompatHelper: bump compat for JSON to 1, (keep existing compat) (#986) (@github-actions[bot])
  • Fix factor update bug (#988) (@ConnectedSystems)
  • Update key dependencies and bump version (#989) (@ConnectedSystems)
  • Bump project version prior to new release (#990) (@Zapiano)
  • fix: Correct growth constraint calculation in scenario.jl (#992) (@DanTanAtAims)
  • CompatHelper: bump compat for MLJ to 0.22, (keep existing compat) (#993) (@github-actions[bot])
  • CompatHelper: bump compat for SIRUS to 3, (keep existing compat) (#994) (@github-actions[bot])
  • Refactor out recruitment constraint from timestep loop (#996) (@Zapiano)
  • Remove MAT dependency (#997) (@ConnectedSystems)
  • Update GeoDataFrame handling (#998) (@ConnectedSystems)
  • Remove broadcasting to avoid intermediate allocations (#999) (@ConnectedSystems)
  • Remove intermediate array (#1000) (@ConnectedSystems)
  • fix: fix input type declaration for _render_legend (#1001) (@DanTanAtAims)
  • Initial cleanup in prep for restructure (#1002) (@ConnectedSystems)
  • Support arbitrary number of time series clusters (#1003) (@ConnectedSystems)
  • Reorganizing code structure (#1004) (@ConnectedSystems)
  • Bump actions/checkout from 5 to 6 (#1005) (@dependabot[bot])
  • Adjusted scenario sampling and default parameters (#1006) (@ConnectedSystems)
  • Refactor Spatial Data Loading and Update Input Data Handling (#1007) (@DanTanAtAims)
  • Speedups (#1008) (@DanTanAtAims)
  • Fix incorrect use of single reef idx (#1009) (@DanTanAtAims)
  • fix: Fix categorical bug where bounds are passed instead of categories (#1010) (@DanTanAtAims)
  • Improves scenario assessment workflow (#1011) (@ConnectedSystems)
  • Pin YAXArray dependency (#1013) (@ConnectedSystems)
  • Implements decision strategies (#1019) (@ConnectedSystems)
  • Mention use of shared depot paths (#1020) (@ConnectedSystems)
  • Fix single reef load and sampling (#1023) (@Zapiano)
  • Bump project version prior to new release (#1024) (@Zapiano)
  • Restrict minimum compatible Julia version to 1.11 (#1026) (@Zapiano)
  • Improve fecundity (#1027) (@Zapiano)
  • Add Allee effect (#1031) (@Zapiano)
  • Fix: All axis values were being stripped when creating new DataCube (#1033) (@ConnectedSystems)
  • Fix LTMP Taxa Cover and Metric Metadata (#1034) (@DanTanAtAims)
  • reformat with JuliaFormatter V1 (#1035) (@arlowhite)
  • Fix wrong use of reactive strategy index (#1036) (@Zapiano)
  • Fix sampling tests (and others) (#1037) (@Zapiano)
  • Update documentation project (#1038) (@Zapiano)
  • Update Julia version used in github doc build to 1.11 (#1039) (@Zapiano)
  • Extend seeding intervention to all functional groups (#1040) (@Zapiano)
  • Rename ENV variable TEST to ADRIA_TEST (#1041) (@Zapiano)
  • Remove ODE related code (and clean up) (#1042) (@Zapiano)
  • Fix fog and seed location fixing (#1043) (@Zapiano)
  • Fix fog strategy builder (#1047) (@Zapiano)
  • Limit environmental data loading to timeframe in datapackage.json (#1048) (@DanTanAtAims)
  • Use newest version of ADRIAIndicators (#1049) (@DanTanAtAims)
  • Enforce location ids in environmental data. (#1050) (@DanTanAtAims)
  • Implement moving corals intervention (#1052) (@Zapiano)
  • Allow target locations for MCB (#1053) (@Zapiano)
  • Use seeding device density to distribute seeded corals (#1056) (@Zapiano)
  • Assisted adaptation relative to recent past (#1057) (@Zapiano)
  • Update Breeder's equation usage (#1058) (@Zapiano)
  • Add min_iv_locs param specific for moving corals (#1059) (@Zapiano)
  • Add moving corals stats to feature set (#1060) (@Zapiano)
  • Add Marine Cloud Brightening with Multi-dimensional DHW NetCDFs (#1062) (@DanTanAtAims)
  • Bump codecov/codecov-action from 5 to 6 (#1063) (@dependabot[bot])
  • Bump docker/login-action from 3 to 4 (#1064) (@dependabot[bot])
  • Bump julia-actions/cache from 2 to 3 (#1065) (@dependabot[bot])

Closed issues:

  • Core functionality to be ported from ADRIA (MATLAB) (#1)
  • Pretty display for ResultSet (#68)
  • Include site area data in result set (#69)
  • Precompilation step to include dummy runs (#70)
  • Example and test data packages (#71)
  • Investigate optimizations to improve precompilation times (#75)
  • Add total coral cover metric (#77)
  • Adjust RCI to use new total coral cover (#78)
  • Investigate alternative site selection weightings for coral cover (#79)
  • Separate coral_cover() metric into individual functions (#81)
  • Switch default behaviour of ADRIA.jl to store aggregated results? (#82)
  • Use NamedDims and NamedArrays (#83)
  • Adapt siteselection() to use dMCDA to avoid code repetition (#86)
  • Shelter Volume: investigate very small values (#91)
  • Juvenile metric: investigate small values (#92)
  • Auto-adjust site offset/depth bounds on loading Domain (#94)
  • Add an additional model component for environmental layers (#95)
  • Coral evenness: Metric returns NaNs (#96)
  • Replace duplicate proportional growth constraint with single function (#99)
  • Make relative_cover() relative to site max coral cover area (k) instead of total site area (#109)
  • ADRIA specific sampling functions (#119)
  • Update result set to derive spatial data from stored geopackage (#124)
  • Distribute seeded corals acording to available space, not k (#128)
  • Exporting to PowerBI format very slow (#132)
  • Double check recruitment calculation? (#133)
  • Add scenario index to csv created by result_post_processing.jl and filter counterfactual according to dhw scenario (#136)
  • Bleaching mortality may be over-estimated (#138)
  • DHW dataset may over-represent extreme DHW trajectories (#139)
  • Refactor seeding step into its own function with tests (#146)
  • Use measure of dhw time distribution for MCDA heat stress criteria (#151)
  • Check scaling of coral real estate criteria in MCDA function and add measure of space for coral to be seeded. (#152)
  • Make shading of seeded sites user controllable (#157)
  • Metric function to extract the top N performing sites (#158)
  • Process area data on file read (#170)
  • Add support for NetCDF data files (#173)
  • Adjust MCDA functions to be more generic (#177)
  • Deprecate support for .mat files (#182)
  • Update site_selection() function in Domain.jl and use within ADRIA model site selection process to reduce replication (#194)
  • Standardize to NamedDimsArray + AxisKeys (#200)
  • Standardize relative cover metric to report values relative to k area (#204)
  • Adjust scenario input IDs for clarity (#205)
  • Use NamedDims+AxisKeys instead of matrix for MCDA decision matrices (#221)
  • Site ranks are never updated after distance sorting (#223)
  • Update the bleaching response to formally account for depth, surface shading and water quality. (#226)
  • Move natural adaptation parameter to be part of the Coral component (#229)
  • Add human-readable name to Parameter types (#230)
  • List management zones in order of preference for targeted deployment (#231)
  • Change triangular distributions to specify peak in absolute terms (#234)
  • Use Haversine instead of Euclidean distance (#236)
  • Use mean distance threshold and change in aggregate criteria value threshold instead of site by site distance threshold and top_n in distance sorting (#237)
  • Adjust definition or sampling of dist_thresh so that the value representing 'don't use distance sorting' is as likely as values representing using distance sorting (#238)
  • Investigate bounds used for coral_cover_tol (#239)
  • Set up documentation system and website (#240)
  • Consider using JMcDM (#242)
  • Register package (#245)
  • Change reference to Input Set to Domain to align with interface functions (#246)
  • Address possible double switching of RCPs (#248)
  • Make plotting functions more generic to support rapid workflows (#249)
  • Better separation of Aviz sub-system (#250)
  • Make MCDA functions generic (#252)
  • Move example scripts into documentation (#253)
  • pareto analysis (#256)
  • Regional Sensitivity Analysis (#257)
  • Temporal Sensitivity Analysis (#260)
  • Favicon for Documentation site (#265)
  • Use LTMP observations (#267)
  • Update growth rates for size class 6 (#268)
  • TagBot trigger issue (#269)
  • [Discussion] Natural adaptation (#270)
  • Release v0.4.5 (#272)
  • Separate fogging from shading (#277)
  • Possible bug in site_selection (#284)
  • Bug in site selection example (#285)
  • Scenario juvenile metric returning implausible values (?) and values > 1 (#292)
  • Create function which returns just the set of criteria values needed for MCDA (#296)
  • Re-enable tests/CI when Julia v1.9 is released (#300)
  • Connectivity data cubes (#302)
  • First conversion of model specification to DataFrame is excruciatingly slow (#303)
  • map_to_discrete() erroring due to type mismatch (#304)
  • run_site_selection() errors out (#308)
  • [Viz/Analysis] Scenario outcomes (#311)
  • [Viz/Analysis] sensitivity analysis (bar/heatmap) (#312)
  • [Viz/Analysis] temporal sensitivity analysis (#313)
  • [Viz/Analysis] Regional Sensitivity Analysis (#314)
  • [Viz/Analysis] Outcome-based factor mapping (#315)
  • [Viz/Analysis] maps for/of site selection (#316)
  • [Viz/Analysis] Naive Bayes (#323)
  • Make run_site_selection() more user-friendly (#324)
  • Investigate alternative method for sampling mcda weights (#327)
  • Checking centrality is correctly calculated (#329)
  • Release v0.5.0 (#331)
  • MCDA crashes with mismatched array sizes for rankings and rankingsin (#333)
  • Create single ResultSet (#342)
  • MCDA method errors (#357)
  • Make n_sites a perturbable model factor (#360)
  • align_rankings! giving incorrect output rankings (#366)
  • Time series clustering (#368)
  • [Viz/Analysis] Clustering of scenarios to aid in MORDM (#369)
  • Separate model factors (#377)
  • Register v0.6.0 (#379)
  • Spatial clustering based on outcomes (#383)
  • [Viz/Analysis] Spatial plots of locations clustered by outcome (#384)
  • Register v0.7.0 (#388)
  • Remove coral cover conversion for ReefModEngine interface (#399)
  • Add Rule Induction (with SIRUS) (#404)
  • ADRIAmod uses excessive amounts of memory during runs (#405)
  • Errors when running scenarios in parallel when nworkers() > 1 (#413)
  • Change the way target_cluster function is works (#423)
  • Duplicate RCP issue when running scenarios generated using sample_site_selection() (#426)
  • Error: loc_trajectory and per_loc not qualifying dim (#427)
  • Error: non_null_sites (#428)
  • viz.outcome_map() gives duplicate x-axis values when plotting :guided factor (#440)
  • Register v0.8.0 (#447)
  • Update code style section in docs (#448)
  • Out of memory error when calculating PAWN sensitivity for 8192 scenarios (#450)
  • Target clusters with lower values of some metric (#451)
  • Show labels and units of measurement automatically for plots by default (#453)
  • Rule Extraction viz function is not included int viz extension (#454)
  • Relevant features/properties for rule induction (and scenario decision making) (#458)
  • Regional sensiyivity analysis gives duplicate values for categorical factors (#459)
  • Summarized vizualisation for time series clustering (#464)
  • Add example of Rule Induction usage to the Documentation (#473)
  • Update rule ADRIA.viz.rules_scatter to accept target_clusters vector instead of clusters (#474)
  • Conceptually align all coral cover calculations to be relative to k area (#480)
  • Make $k$ area in geospatial data consistent (#483)
  • Load initial coral cover data consistently across different Domain types (#484)
  • Scenario running methods to be refactored to expect only values relative to $k$ area (#487)
  • All metrics to be adjusted to expect $k$ area values (#488)
  • Duplicate x-axis values in outcome maps (Part 2) (#489)
  • Robust Decision Making (#493)
  • Properly handle plotting binary (target vs non-target) clusters (#494)
  • _time_labels gives duplicate labels in some cases (#495)
  • Register v0.9.0 (#498)
  • Adjust usage of k site area in location selection to align with coral cover being relative to k (#501)
  • Possible issue with settler_cover() when moving to k area based processes (#502)
  • Update deprecated writeheader=true at Domain.jl model_spec function (#503)
  • Create a function that uses Slices to compute some aggregation metric over given axis (#508)
  • Remove top_n from distance sorting as no longer needed (#509)
  • Fix bug when loading Domain due to DHWs containing missing values (#510)
  • [RFC] Change factors marked as "integer" types to "discrete" (#512)
  • Refactor tests so we have an available ResultSet instance (#513)
  • Incorporate cyclone mortality into ADRIAmod (#516)
  • Implement n_scenarios(rs) (#517)
  • Skip RCP entry from scenario specification by name rather than assuming position (#518)
  • Add method for selecting all parameters associated with a particular intervention (#520)
  • [Bug] Plotting subset of scenarios fail as not all scenario types may be included (#522)
  • Use more descriptive dimension/axis labels for ResultSet logs storage now that AxisKeys is in use (#524)
  • Make SRM apply to Reef clusters not whole of GBR (#525)
  • Generalise creation of MCDA decision matrices (#526)
  • Switch to YAXArrays (#528)
  • Develop cyclone mortality models based on R implementation (#529)
  • Filter coral species/site by branching_below_5, branching_above_5 and massive (#530)
  • Use cyclone mortality model and filter to implement cyclone mortality in ADRIAmod (#531)
  • Switch to WGLMakie for visualizations (#532)
  • Increase default worker timeout (#534)
  • Out of memory error for parallelised runs for whole of GBR domain (#535)
  • Error runing test/runtests.jl (#538)
  • Create plotting functions for sensitivity analysis convergence (#543)
  • Add documentation for Cyclone mortality (#544)
  • Add load_latest_results() (#548)
  • Cluster maps not working (#549)
  • Record/Log of DHW and wave stats in result sets are broken (#550)
  • Fix error in growth ODE test (#551)
  • Deployment location analysis methods/metrics leak into package namespace (#556)
  • Add MCDA weighting normalisation to scenario sampling post-processing (#559)
  • Delete/remove deprecated functions in prep for v1.0 release (#560)
  • Make all indices used in site selection aggregation functions symbols (#562)
  • Find and deprecate inconsistent methods (#564)
  • Separate weighting parameters for heat_stress and depth in the MCDA (#565)
  • Reorganize files/images for documentation (#567)
  • Error when tests run scenarios (#568)
  • Compute mean of truncated distribution using a Burman series (#572)
  • Remove unused version check (#580)
  • Move example scripts into the cookbook (#584)
  • Adjust sampling approach for flexibility (#586)
  • Changes in PR#552 breaks scenario visualizations (#587)
  • Tests raising error (#590)
  • Add function which returns list of MCDA methods which can be used in ADRIA (#591)
  • Use min-max normalisation for heat stress criteria (#592)
  • Update use of Makie (v0.20.0) to avoid deprecations (#600)
  • Loading RME datasets are broken due to cyclone data requirement (#609)
  • Fix "surprising" readjustment of the number of slices used to perform RSA/outcome mapping (#615)
  • Adjust distribute_seeded_corals to account for cases where the top 5 sites do not have enough space for seeded corals (#618)
  • Change log for dhws and waves to store mean and std for scenarios and sites/reefs (#619)
  • Add new 10 site test Domain to testing folder in ADRIA (#622)
  • Make decision matrices NamedDimsArrays (#624)
  • Register v0.10.0 (#626)
  • set_factor_bounds! setting value outside range for discrete variables (#630)
  • Priority sites criteria expecting different structure for strong_pred than what is implemented (#633)
  • Add connectivity matrix to ResultSet (#641)
  • Error precompiling ADRIA.jl (#645)
  • Support use of cluster identifier in spatial dataset (#655)
  • Fix bug in constrain_reef_cluster which assumes there will always be enough locations to satisfy the reef constraint (#656)
  • Add test domain for ReefModDomain type (#670)
  • Ignore constant factors when applying SIRUS (#672)
  • Add tests for standalone site selection using rank_locations (#680)
  • Larval spread via connectivity is not working as expected (#686)
  • Method Call error during testing from rsa function type. (#692)
  • Documentation image links are broken (#712)
  • viz.outcome_map not working when :guided is one of the factors of interest (#713)
  • Fix sampling of guided MCDA methods (#725)
  • Remove connectivity data from Domain types (#735)
  • Example given in #742 no longer works (#749)
  • Revisit use of temporary geojson (#768)
  • Order of scenarios plotted are inconsistent (#769)
  • Docstring example missing ending backticks (#781)
  • Delete stale branches (#783)
  • Improve loc_trajectory() function performance (#788)
  • Makie spatial plotting maps color vector to each polygon in a multipolygon, leaving white polygons for unmapped shapes (#792)
  • Geospatial dataset for the Test domain does not define a valid CRS (#800)
  • Register v0.11.0 (#816)
  • Delete defunct code after implementing changes to use CoralBlox.jl (#819)
  • ReefModDomain loading is not working (#825)
  • Dimension mismatch when logging DHW tolerances in debug mode (#826)
  • CoralBlox apparent incompatibility (#828)
  • Absolute cover calculations consider wrong area (#841)
  • mismatch of naming in Cscape results set (#849)
  • Investigate alternate chunking strategy for Zarr store (#851)
  • data saved as relative cover is actually absolute cover (#852)
  • Error when calculating total cover (#855)
  • Errors/issues in _get_result_paths() (C~scape interface) (#856)
  • Retrieve scenario IDs from CScapeResultsSet (#859)
  • DimensionalData compat 0.27 (#881)
  • GeoMakie compat 0.6 (#882)
  • DiskArrays pinned to 0.3.23 (#883)
  • StackOverflowError in tests failing on main branch (#890)
  • Rule extraction print_rules error attempting to access 1-element Vector{Float64} at index [2] (#900)
  • Seeding Intervention Habitable Area limit (#905)
  • NaNs in growth_constraints vector raising error at global_calib branch (#963)
  • Release v0.12.0 (#969)
  • Register v0.13.0 (#991)
  • Release v0.14.0 (#1012)
  • Release v0.14.1 (#1014)
  • Release v0.15.0 (#1015)
  • Release v0.15.1 (#1025)
  • JuliaFormatter workflow blocking well formatted files (#1029)

Biosphere - Conservation and Restoration - Julia
Published by github-actions[bot] 14 days ago

ADRIA.jl - ADRIA-v0.17.0

ADRIA ADRIA-v0.17.0

What's Changed

Breaking changes

ADRIA has been separated into subpackages:

  • ADRIA: Provides core simulation and assessment infrastructure
  • ADRIAanalysis: Provides the decision analysis and assessment functionality
  • ADRIAviz: Provides the visualization capability

See the documentation for an overview.

Full Changelog: https://github.com/open-AIMS/ADRIA.jl/compare/v0.16.0...v0.17.0

Merged pull requests:

  • CompatHelper: add new compat entry for CSV at version 0.10, (keep existing compat) (#2) (@github-actions[bot])
  • CompatHelper: add new compat entry for ModelingToolkit at version 8, (keep existing compat) (#3) (@github-actions[bot])
  • CompatHelper: add new compat entry for Compose at version 0.9, (keep existing compat) (#4) (@github-actions[bot])
  • CompatHelper: add new compat entry for BlackBoxOptim at version 0.6, (keep existing compat) (#5) (@github-actions[bot])
  • CompatHelper: add new compat entry for IJulia at version 1, (keep existing compat) (#6) (@github-actions[bot])
  • CompatHelper: add new compat entry for MATLAB at version 0.8, (keep existing compat) (#7) (@github-actions[bot])
  • CompatHelper: add new compat entry for ProfileView at version 1, (keep existing compat) (#8) (@github-actions[bot])
  • CompatHelper: add new compat entry for DataFrames at version 1, (keep existing compat) (#9) (@github-actions[bot])
  • CompatHelper: add new compat entry for Graphs at version 1, (keep existing compat) (#10) (@github-actions[bot])
  • CompatHelper: add new compat entry for StaticArrays at version 1, (keep existing compat) (#11) (@github-actions[bot])
  • CompatHelper: add new compat entry for ModelParameters at version 0.3, (keep existing compat) (#12) (@github-actions[bot])
  • CompatHelper: add new compat entry for Setfield at version 0.8, (keep existing compat) (#13) (@github-actions[bot])
  • CompatHelper: add new compat entry for WinRPM at version 1, (keep existing compat) (#14) (@github-actions[bot])
  • CompatHelper: add new compat entry for BenchmarkTools at version 1, (keep existing compat) (#15) (@github-actions[bot])
  • CompatHelper: add new compat entry for Plots at version 1, (keep existing compat) (#16) (@github-actions[bot])
  • CompatHelper: add new compat entry for DifferentialEquations at version 7, (keep existing compat) (#17) (@github-actions[bot])
  • CompatHelper: add new compat entry for OrdinaryDiffEq at version 6, (keep existing compat) (#18) (@github-actions[bot])
  • CompatHelper: add new compat entry for GraphPlot at version 0.5, (keep existing compat) (#19) (@github-actions[bot])
  • CompatHelper: add new compat entry for GeoDataFrames at version 0.2, (keep existing compat) (#20) (@github-actions[bot])
  • CompatHelper: add new compat entry for ProgressMeter at version 1, (keep existing compat) (#67) (@github-actions[bot])
  • CompatHelper: bump compat for Setfield to 1, (keep existing compat) (#72) (@github-actions[bot])
  • CompatHelper: add new compat entry for GR at version 0.64, (keep existing compat) (#73) (@github-actions[bot])
  • CompatHelper: add new compat entry for CpuId at version 0.3, (keep existing compat) (#74) (@github-actions[bot])
  • Site population cap (#76) (@ConnectedSystems)
  • Adding new total_cover function to RCI calculation (#80) (@Rosejoycrocker)
  • Changes to support site level metrics (#84) (@ConnectedSystems)
  • Changes to scaling for MCDA criteria (site capacity) (attempts to address #79) (#85) (@Rosejoycrocker)
  • Relative cover input to RCI be relative to the sites max coral cover? (#89) (@ConnectedSystems)
  • Scenario focused metrics (#93) (@ConnectedSystems)
  • More appropriate indication of cluster-wide outcomes (#97) (@ConnectedSystems)
  • Address TODO: Extract non-coral parameters to reduce memory use (#105) (@ConnectedSystems)
  • Ensure proportional adjustment of coral cover remain in bounds (#106) (@ConnectedSystems)
  • Expand docstring for proportional_adjustment() for clarity (#107) (@ConnectedSystems)
  • Address small Shelter Volume outcomes (#91) (#108) (@ConnectedSystems)
  • Unguided selection (#112) (@ConnectedSystems)
  • Sysimage builder (#115) (@ConnectedSystems)
  • Fix log scaling error in MCDA coral cover criteria (#117) (@Rosejoycrocker)
  • Detailed docstrings added + shading matrix function added (#118) (@Rosejoycrocker)
  • Environmental data layer component for ADRIA ecosystem model (#120) (@ConnectedSystems)
  • Fixes small issue introduced by compartmentalising SE and SH matrix creation (#122) (@Rosejoycrocker)
  • Adding function to generate csv summary result set (#125) (@Rosejoycrocker)
  • Fixes typos which were not picked up in previous PR (#126) (@Rosejoycrocker)
  • Include PowerBI post processing file in module (#131) (@ConnectedSystems)
  • Fixes for recruitment issue (#137) (@ConnectedSystems)
  • Fix site ranking log (#140) (@ConnectedSystems)
  • Correct simplified settler cover calculation (#141) (@ConnectedSystems)
  • Fixes undefined absolute_site_coral_cover (#142) (@Rosejoycrocker)
  • Remove tf from simulation constants (#143) (@ConnectedSystems)
  • Fixes missed tf definition (#144) (@Rosejoycrocker)
  • Distributes seeded corals at selected sites according to space available (#145) (@Rosejoycrocker)
  • Add timeframe datapackage property (#147) (@ConnectedSystems)
  • Adds function to distribute seeded corals at selected sites according to space available (addresses #146) (#148) (@Rosejoycrocker)
  • Update bleaching mortality model (#149) (@ConnectedSystems)
  • CompatHelper: bump compat for PkgVersion to 0.3, (keep existing compat) (#150) (@github-actions[bot])
  • Additional metrics for site rank analysis (#153) (@ConnectedSystems)
  • Applying depth offset to align with IPMF (#154) (@ConnectedSystems)
  • Add copy of model spec to ResultSet (#155) (@ConnectedSystems)
  • Add incoming and outgoing connectivity ranks and criteria (#156) (@ConnectedSystems)
  • Adds function to find top n sites in result set for each scenario (#159) (@Rosejoycrocker)
  • Adding coral cover area criteria in terms of absolute coral cover (#160) (@Rosejoycrocker)
  • Miscellaneous changes to clean up code (#161) (@ConnectedSystems)
  • Mix normalisation bug in MCDA (#162) (@Rosejoycrocker)
  • Support runs across multiple RCPs (#163) (@ConnectedSystems)
  • Scenario relative cover metric to return cluster wide values (#164) (@ConnectedSystems)
  • Fixes to ODE formulation and indexing (#165) (@Rosejoycrocker)
  • CompatHelper: add new compat entry for Distributions at version 0.25, (keep existing compat) (#166) (@github-actions[bot])
  • Changes to top_N_sites rank metric (#167) (@ConnectedSystems)
  • Support extraction of geometry data from inconsistent column names (#169) (@ConnectedSystems)
  • Robustness metrics (#172) (@ConnectedSystems)
  • Replace bleaching resistance with uncertain bleaching sensitivity (#174) (@ConnectedSystems)
  • Incorporation of zoning criteria in MCDA (#175) (@Rosejoycrocker)
  • Add sampling methods (#176) (@ConnectedSystems)
  • Spread site selection (#180) (@ConnectedSystems)
  • Add dhw summary statistics to ResultSet (#181) (@Rosejoycrocker)
  • Corrections to assignment of growth rates and tests for coral_spec() parameters (#183) (@Rosejoycrocker)
  • Coral model adjustments (#184) (@ConnectedSystems)
  • Switch to netCDF (#185) (@ConnectedSystems)
  • Correct connectivity alignment (#186) (@ConnectedSystems)
  • Update example domain with netCDF format datacubes (#187) (@ConnectedSystems)
  • Changes to support Multi-Objective Optimization (#188) (@ConnectedSystems)
  • Tentative support for Multi-Objective Robust Optimization (#189) (@ConnectedSystems)
  • Bug fix for ODE + change to definition of basal area (#190) (@Rosejoycrocker)
  • Consolidate site area calcs #170 (#191) (@ConnectedSystems)
  • Performance changes (#192) (@ConnectedSystems)
  • Reorganize data loading functions (#193) (@ConnectedSystems)
  • Adjust coral wave mortalities following recommendation by Ken (#195) (@Rosejoycrocker)
  • Adding within size class growth for size class 6 back in for ODE and adjusting within size class growth rates (#196) (@Rosejoycrocker)
  • Connectivity update (#197) (@ConnectedSystems)
  • Add distance sorting to MCDA (#198) (@Rosejoycrocker)
  • Update metrics (#199) (@ConnectedSystems)
  • Updated background mortality values (#201) (@ConnectedSystems)
  • Minor changes to get visualizations working for v0.4.2 (#202) (@ConnectedSystems)
  • v0.4.2 dev merge (#203) (@ConnectedSystems)
  • CompatHelper: add new compat entry for GeoInterface at version 1, (keep existing compat) (#206) (@github-actions[bot])
  • CompatHelper: add new compat entry for RelocatableFolders at version 1, (keep existing compat) (#207) (@github-actions[bot])
  • CompatHelper: add new compat entry for Surrogates at version 6, (keep existing compat) (#208) (@github-actions[bot])
  • CompatHelper: add new compat entry for FileIO at version 1, (keep existing compat) (#209) (@github-actions[bot])
  • CompatHelper: add new compat entry for DecisionTree at version 0.11, (keep existing compat) (#210) (@github-actions[bot])
  • CompatHelper: add new compat entry for Distances at version 0.10, (keep existing compat) (#211) (@github-actions[bot])
  • CompatHelper: add new compat entry for Combinatorics at version 1, (keep existing compat) (#212) (@github-actions[bot])
  • CompatHelper: add new compat entry for BlackBoxOptim at version 0.6, (keep existing compat) (#213) (@github-actions[bot])
  • CompatHelper: add new compat entry for SnoopPrecompile at version 1, (keep existing compat) (#214) (@github-actions[bot])
  • CompatHelper: add new compat entry for Bootstrap at version 2, (keep existing compat) (#215) (@github-actions[bot])
  • CompatHelper: add new compat entry for HypothesisTests at version 0.10, (keep existing compat) (#216) (@github-actions[bot])
  • CompatHelper: add new compat entry for GeoFormatTypes at version 0.4, (keep existing compat) (#217) (@github-actions[bot])
  • CompatHelper: add new compat entry for NCDatasets at version 0.12, (keep existing compat) (#218) (@github-actions[bot])
  • CompatHelper: add new compat entry for GLMakie at version 0.7, (keep existing compat) (#219) (@github-actions[bot])
  • CompatHelper: add new compat entry for GeoMakie at version 0.4, (keep existing compat) (#220) (@github-actions[bot])
  • Adjust rankings to match site reordering due to distance sorting (#224) (@Rosejoycrocker)
  • Add depth column to MCDA decision matrix to be used in seeding and shading decision matrices (#225) (@Rosejoycrocker)
  • Remove additional weighting that is no longer needed (#227) (@ConnectedSystems)
  • Re-order site data by unique site id column to align logged site ids (#228) (@ConnectedSystems)
  • CompatHelper: bump compat for GLMakie to 0.8, (keep existing compat) (#233) (@github-actions[bot])
  • v0.4.3 merge (#241) (@ConnectedSystems)
  • Initial documentation build (#244) (@ConnectedSystems)
  • Add support for Regional Sensitivity Analysis (RSA) (#258) (@ConnectedSystems)
  • Merge v0.4.4-dev (#259) (@ConnectedSystems)
  • Add temporal sensitivity analyses based on the PAWN method (#261) (@ConnectedSystems)
  • Metric restructure (#262) (@ConnectedSystems)
  • CompatHelper: bump compat for ArchGDAL to 0.10, (keep existing compat) (#263) (@github-actions[bot])
  • v0.4.4-dev.1 (#266) (@ConnectedSystems)
  • Add parameter name and description to model specification (#273) (@ConnectedSystems)
  • Adjust coral growth rate for size class 6 (#274) (@ConnectedSystems)
  • Remove references to Input Set (#275) (@ConnectedSystems)
  • Fix: calculate distance between sites (#276) (@ConnectedSystems)
  • Simplify display of model spec (#278) (@ConnectedSystems)
  • Parametric ResultSet (#279) (@ConnectedSystems)
  • Consolidate normalize (#280) (@ConnectedSystems)
  • Changes to site selection functions (#282) (@Rosejoycrocker)
  • Changes to address bug in site_selection example (addresses issue #285 ) (#286) (@Rosejoycrocker)
  • Consolidate Named array types to use NamedDims+AxisKeys (#287) (@ConnectedSystems)
  • Reduce allocations in load_domain() (#288) (@ConnectedSystems)
  • Add criteria parameter which indicates whether distance sorting is used. (#290) (@Rosejoycrocker)
  • Add function n_locations() to determine number of sites/reefs/clusters (#291) (@ConnectedSystems)
  • Miscellaneous cleanup (#293) (@ConnectedSystems)
  • Fix bug causing implausible juvenile indicator values (#294) (@ConnectedSystems)
  • Adjust samples when use of distance thresholds is turned off (#295) (@ConnectedSystems)
  • CompatHelper: add new compat entry for AxisKeys at version 0.2, (keep existing compat) (#297) (@github-actions[bot])
  • Additional safety checks for sampling (#298) (@ConnectedSystems)
  • Adds sampler which can sample only parameters needed for site selection (#299) (@Rosejoycrocker)
  • Adds function which calculates sites selection frequency for a set of provided samples (#301) (@Rosejoycrocker)
  • Fix error mapping continous samples to discrete values (#305) (@ConnectedSystems)
  • Adjust shelter volume to remove hardcoded index and leverage NamedDimsArray (#306) (@ConnectedSystems)
  • Fix initial slice potentially not including lowest value (#307) (@ConnectedSystems)
  • Clean up Project.toml + Precompile (#309) (@ConnectedSystems)
  • Correct issue with size of NamedDims array for storing ranks in run_site_selection() (#310) (@Rosejoycrocker)
  • Initial indicative visualization (#318) (@ConnectedSystems)
  • Fix function extension issues (#319) (@ConnectedSystems)
  • Better check for constancy in RSA (#320) (@ConnectedSystems)
  • Update exploration tool to latest ADRIA API (#321) (@ConnectedSystems)
  • Additional docs for Domain/ResultSets (#322) (@ConnectedSystems)
  • Add capability to fix factors in place (#325) (@ConnectedSystems)
  • Initial ReefMod interface and functionality (#326) (@ConnectedSystems)
  • Move n_adapt from Intervention component to Coral component (#332) (@ConnectedSystems)
  • Update use of functions due to new import approach (#334) (@ConnectedSystems)
  • Migrate from SnoopPrecompile to PrecompileTools (#335) (@timholy)
  • Add planning horizon factor (#336) (@ConnectedSystems)
  • Replace use of area attribute/field with call to function site_area() to ensure correct values (#337) (@ConnectedSystems)
  • Remove reference to defunct fields when making factors constant (#338) (@ConnectedSystems)
  • Fix error caused by mismatched locations (#339) (@ConnectedSystems)
  • Make use of planning horizon in sims (#340) (@ConnectedSystems)
  • Changes to support running ADRIA with external model (ReefMod Engine) data (#341) (@ConnectedSystems)
  • CompatHelper: add new compat entry for SimpleWeightedGraphs at version 1, (keep existing compat) (#343) (@github-actions[bot])
  • CompatHelper: add new compat entry for OrderedCollections at version 1, (keep existing compat) (#344) (@github-actions[bot])
  • CompatHelper: bump compat for StatsBase to 0.34, (keep existing compat) (#345) (@github-actions[bot])
  • Split ADRIA-mod domain definition (#346) (@ConnectedSystems)
  • Add GBR zones by priority (#347) (@ConnectedSystems)
  • Add option to use JMcDM functions in ADRIA site selection (#348) (@Rosejoycrocker)
  • Make Aviz into an extension package (#349) (@ConnectedSystems)
  • Exit with error if given path is not a directory (#350) (@ConnectedSystems)
  • CompatHelper: add new compat entry for Reexport at version 1, (keep existing compat) (#351) (@github-actions[bot])
  • CompatHelper: add new compat entry for ImageMagick at version 1, (keep existing compat) (#352) (@github-actions[bot])
  • Update bleaching mortality model to align with published paper (#354) (@ConnectedSystems)
  • Update scenario viz (#355) (@ConnectedSystems)
  • Add map visualization - displays k-area (#356) (@ConnectedSystems)
  • Address mismatched number of elements under certain conditions (#358) (@ConnectedSystems)
  • Remove Copras method due to erroring (#359) (@Rosejoycrocker)
  • Update documentation (#361) (@ConnectedSystems)
  • CompatHelper: add new compat entry for JMcDM at version 0.7, (keep existing compat) (#362) (@github-actions[bot])
  • CompatHelper: bump compat for HypothesisTests to 0.11, (keep existing compat) (#363) (@github-actions[bot])
  • Scenario discovery docs (#364) (@ConnectedSystems)
  • Fix: Metric errors when applied to a single simulation (#365) (@ConnectedSystems)
  • Address ranking errors in mcda outputs (#367) (@Rosejoycrocker)
  • Add temporal clustering (#370) (@Zapiano)
  • Fix incorrect type check (#371) (@Zapiano)
  • CompatHelper: add new compat entry for Clustering at version 0.15, (keep existing compat) (#372) (@github-actions[bot])
  • CompatHelper: bump compat for Zarr to 0.9, (keep existing compat) (#373) (@github-actions[bot])
  • Update time series clustering and add visualization functionality (#374) (@Zapiano)
  • Update docstrings for growth function (#375) (@ConnectedSystems)
  • Refactor run_scenarios to improve when running multiple rcps (#376) (@Zapiano)
  • Bump version number and add new author (#378) (@Zapiano)
  • Changes to number of species in ADRIA (#380) (@Rosejoycrocker)
  • Distribution-based bleaching mortality to capture natural adaptation and heritability (#381) (@ConnectedSystems)
  • Temporal clustering for spatial data (#382) (@Zapiano)
  • Remove duplicate function recruitment (#385) (@ConnectedSystems)
  • Reorganize package structure (#386) (@ConnectedSystems)
  • Consider near-term conditions with greater weight than far-future conditions (#387) (@ConnectedSystems)
  • Update release guide (#389) (@ConnectedSystems)
  • Changes to ode solver and time step for efficiency improvements (#390) (@Rosejoycrocker)
  • Add adaptive=false specification and remove tolerances (#391) (@Rosejoycrocker)
  • Scenario viz change (#393) (@ConnectedSystems)
  • CompatHelper: add new compat entry for JuliennedArrays at version 0.4, (keep existing compat) (#395) (@github-actions[bot])
  • CompatHelper: add new compat entry for FLoops at version 0.2, (keep existing compat) (#396) (@github-actions[bot])
  • Fix bug: Use wave condition for current timestep, not previous (#397) (@ConnectedSystems)
  • Update comment to reflect changes for wave condition usage (#398) (@ConnectedSystems)
  • Incorrect function being called (#400) (@ConnectedSystems)
  • Remove use of batch sizes when running parallel scenarios (#401) (@ConnectedSystems)
  • CompatHelper: bump compat for SparseArrayKit to 0.3, (keep existing compat) (#403) (@github-actions[bot])
  • Fix map display (default display when plotting Domain or ResultSet) (#407) (@ConnectedSystems)
  • Update ReefMod interface to match new species list (#408) (@Rosejoycrocker)
  • Fix excessive memory use (#405) (#409) (@ConnectedSystems)
  • Small miscellaneous changes for scenario visualizations (#412) (@ConnectedSystems)
  • Remove dependency on ImageMagick in favour of ImageIO (#414) (@ConnectedSystems)
  • Updated Reef Indices (#415) (@ConnectedSystems)
  • Fix workers crashing and leaking memory when running scenarios in parallel (#416) (@ConnectedSystems)
  • Adjustments to heritability based on feedback (#417) (@ConnectedSystems)
  • Update docstrings with missing detail (#418) (@ConnectedSystems)
  • Implement relevant struct to handle SIRUS rule extraction (#420) (@Zapiano)
  • Implement rule extracting function (#421) (@Zapiano)
  • Implement rule scatter plot function (#422) (@Zapiano)
  • Move and modify behaviour of target_cluster function (#424) (@Zapiano)
  • Fix unnecessarily squashed figure when plotting outcome map for 1 factor (#425) (@ConnectedSystems)
  • Documentation improvement (#429) (@Zapiano)
  • Fix scenario metrics with field :scenario instead of :scenarios (#430) (@Zapiano)
  • Adds a series of aggregation functions for location selection ranks (#431) (@Rosejoycrocker)
  • Fix error when running samples generated from sample_site_selection() (#432) (@Rosejoycrocker)
  • Fix time_series_clustering for variable series with k > 0 (#433) (@Zapiano)
  • Add functions for repeated tasks when performing location selection (#434) (@Rosejoycrocker)
  • Address very slow extraction of relative cover values (#435) (@ConnectedSystems)
  • Update prototype exploration UI to work with recent changes (#436) (@ConnectedSystems)
  • Incorporate settler DHW tolerances (#437) (@ConnectedSystems)
  • Fix loc_trajectory and per_loc function (#438) (@Zapiano)
  • Fix clustering map visualisation (#439) (@Zapiano)
  • Add Blue Style Guide badge to README (#441) (@Zapiano)
  • Fix duplicate x-axis values bug in viz.outcome_map() (#442) (@Rosejoycrocker)
  • Update SIRUS StableRules type (#443) (@Zapiano)
  • Fix print_rules adding & when there are two clauses (#444) (@Zapiano)
  • More updates to documentation (#446) (@ConnectedSystems)
  • Functions to plot spatial distributions of site selection frequencies (#449) (@Rosejoycrocker)
  • Miscellaneous changes to improve type infererability and precompilation times (#455) (@ConnectedSystems)
  • Changes to improve performance of PAWN sensitivity analysis (#457) (@ConnectedSystems)
  • Fix print_rules condition (#460) (@Zapiano)
  • Update ADRIA logo (#461) (@Zapiano)
  • Adjust PAWN function to support 1D matrix for convenience (#462) (@ConnectedSystems)
  • Add function to find robust scenarios across several metrics (#463) (@Zapiano)
  • Update Reef Tourism Index regression coefficient (temporary solution) (#466) (@ConnectedSystems)
  • Add new cluster_rules method that accepts BitVector or Vector{Bool} (#467) (@Zapiano)
  • Include rule_extraction.jl in viz.jl (#468) (@Zapiano)
  • Precompilation reduction (#469) (@ConnectedSystems)
  • Add option to show GBRMPA management zones (#470) (@ConnectedSystems)
  • Update sensitivity module to follow Blue style (#471) (@ConnectedSystems)
  • Update Doc mentioning blue style guide (#472) (@Zapiano)
  • Update viz.rules_scatter to accept targeted clusters (#475) (@Zapiano)
  • Deprecate run_scenarios(scens, dom, ...) (#476) (@ConnectedSystems)
  • Add Documentation Sensitivity section for Rule Induction algorithm (#477) (@Zapiano)
  • Rename time_series_clustering and ts_cluster (#478) (@Zapiano)
  • Remove locations with no space from consideration for interventions (#479) (@ConnectedSystems)
  • Adjust run_model() to only require values relative to $k$ area (#481) (@ConnectedSystems)
  • Update viz.clustered_scenarios to allow confidence interval plot (#482) (@Zapiano)
  • Consistent treatment of k area on data load (#485) (@ConnectedSystems)
  • Transform ICC from relative to absolute area to relative to k area (#486) (@ConnectedSystems)
  • Add function to alter sampling bounds on parameters to specified value. (#490) (@Rosejoycrocker)
  • Fix bug in how sensitivity.outcome_map() treats categorical variables. (#491) (@Rosejoycrocker)
  • Fix _time_labels missing last label (#496) (@Zapiano)
  • Update version number to 0.9.0 (#497) (@Rosejoycrocker)
  • Add .JuliaFormatter.toml to .gitignore (#499) (@Zapiano)
  • Refactor viz.scenario (#500) (@Zapiano)
  • CompatHelper: bump compat for SciMLBase to 2, (keep existing compat) (#504) (@github-actions[bot])
  • Add :summary option to viz.scenarios (#505) (@Zapiano)
  • Update CSV.write writeheader parameter to header (#506) (@Zapiano)
  • Fix bug causing Domain loading with RCP to error (#511) (@Rosejoycrocker)
  • Remove top_n parameter from usage (#514) (@Rosejoycrocker)
  • CompatHelper: bump compat for MLJ to 0.20, (keep existing compat) (#515) (@github-actions[bot])
  • Add support series and map binary clusters plots (#521) (@Zapiano)
  • Fix scenarios subsetting now working (#523) (@Zapiano)
  • Add interface function to query number of scenarios in result set (#527) (@ConnectedSystems)
  • Rename rs_input with scenarios (#533) (@Zapiano)
  • CompatHelper: bump compat for NCDatasets to 0.13, (keep existing compat) (#536) (@github-actions[bot])
  • Add summarize and turn per_loc and loc_trajectory into alias (#537) (@Zapiano)
  • Broadcast _check_discrete inside update_params (#539) (@Zapiano)
  • Extract call to run scenarios inside tests to external function (#540) (@Zapiano)
  • Add missing scenario analysis function definitions to analysis module (#541) (@ConnectedSystems)
  • Resolve Out-of-Memory issues when working with larger spatial areas (#542) (@ConnectedSystems)
  • Update analysis docs with recent scenarios and clusters developments (#545) (@Zapiano)
  • Fix failing test cases due to recent changes (#546) (@ConnectedSystems)
  • Changes to mcda functions to reflect coral cover being in terms of k area (#547) (@Rosejoycrocker)
  • Add ability to perform convergence analysis (#552) (@Rosejoycrocker)
  • CompatHelper: add new compat entry for TOML at version 1, (keep existing compat) (#553) (@github-actions[bot])
  • CompatHelper: add new compat entry for Statistics at version 1, (keep existing compat) (#554) (@github-actions[bot])
  • Coral cover consistently represented as relative to coral habitable area (#555) (@ConnectedSystems)
  • Avoid assuming where the RCP column is when adjusting scenario spec (#558) (@ConnectedSystems)
  • Fix integer dims reference in location_selection_frequency() (#563) (@Rosejoycrocker)
  • Fix bug due to missing default_bounds in EnvironmentalLayer and Coral model components (#569) (@Rosejoycrocker)
  • Visualizations to be agnostic to Makie backend (#570) (@ConnectedSystems)
  • Add functions used for location selection to separate decision module (#571) (@Rosejoycrocker)
  • Add separate weighting parameter for depth criteria (#573) (@Rosejoycrocker)
  • Add conversion to scientific notation (#574) (@Zapiano)
  • Fix plot map (#575) (@Zapiano)
  • Prevent test_rs() from creating tmp dir inside test/data (#576) (@Zapiano)
  • Apply blue styleguide to some files (#579) (@Zapiano)
  • Update use of progress meter to resolve deprecation warning (#581) (@ConnectedSystems)
  • Normalize sampled MCDA weights (#582) (@Rosejoycrocker)
  • Replace package NCDatasets by NetCDF (#583) (@Zapiano)
  • Implement cyclone mortality scenarios (#585) (@Zapiano)
  • CompatHelper: add new compat entry for NetCDF at version 0.11, (keep existing compat) (#588) (@github-actions[bot])
  • Fix viz.scenarios bug introduced in changes to scenario_confint! usage (#589) (@Rosejoycrocker)
  • Change approach to listing supported MCDA methods (#593) (@ConnectedSystems)
  • Remove defunct function for post processing results into power-BI friendly csv file (#594) (@Rosejoycrocker)
  • Use min-max normalisation for heat stress (#595) (@Rosejoycrocker)
  • Use min-max normalisation for heat stress (#596) (@Rosejoycrocker)
  • Handle cases where connectivity directories may be empty (#597) (@ConnectedSystems)
  • Deactivated interventions should be considered separately (#598) (@ConnectedSystems)
  • Remove list of ignored JMcDM methods (#599) (@ConnectedSystems)
  • Fix treatment of categorical factors in regional sensitivity analysis (#601) (@Rosejoycrocker)
  • Separate shading and fogging timing parameters (#602) (@Rosejoycrocker)
  • CompatHelper: bump compat for Interpolations to 0.15, (keep existing compat) (#604) (@github-actions[bot])
  • CompatHelper: add new compat entry for YAXArrays at version 0.5, (keep existing compat) (#605) (@github-actions[bot])
  • CompatHelper: add new compat entry for DimensionalData at version 0.25, (keep existing compat) (#606) (@github-actions[bot])
  • Fix proportional_adjustment vector conversion computational error (#607) (@Zapiano)
  • Add tests for figure creation (#608) (@ConnectedSystems)
  • Fix bug where cover instead of leftover space was being used in stand alone site selection (#610) (@Rosejoycrocker)
  • Add more detail regarding sequence of events (#611) (@ConnectedSystems)
  • Adjust language in architectural overview to match recent changes (#612) (@ConnectedSystems)
  • Support RSA with large sample sizes (#614) (@ConnectedSystems)
  • Attach dummy wave and cyclone data (#616) (@ConnectedSystems)
  • CompatHelper: bump compat for SIRUS to 2, (keep existing compat) (#617) (@github-actions[bot])
  • Changes to dhw and wave logs to store scenario and site means and stds (#623) (@Rosejoycrocker)
  • Fix bug introduced by SIRUS v2.0.1 (#625) (@Zapiano)
  • Add a new ten site example domain for testing (#628) (@Rosejoycrocker)
  • Fix mcda method bugs (#629) (@Rosejoycrocker)
  • Fix set_factor_bounds! out of bounds for discrete factors (#631) (@Zapiano)
  • Consolidate methods that transform factor values into sampling.jl (#632) (@ConnectedSystems)
  • Replaces distance sorting with restrictions on the number of selected locations in the same reef (#635) (@Rosejoycrocker)
  • Update factor types and their use (#636) (@ConnectedSystems)
  • Update factor definitions to use custom constructor (#637) (@ConnectedSystems)
  • Update sampling methods for newly defined factor definitions (#638) (@ConnectedSystems)
  • Update interactions with Param types across ADRIA more generally (#639) (@ConnectedSystems)
  • Address MCDA error for single locations (#640) (@ConnectedSystems)
  • Add connectivity data to result set storage (#643) (@Rosejoycrocker)
  • Changes to make ADRIA precompilable under Julia v1.10 (#646) (@ConnectedSystems)
  • Update use of Makie/GeoMakie to address deprecation errors (#647) (@ConnectedSystems)
  • Fix larval connectivity bug (#648) (@ConnectedSystems)
  • Remove examples dir issue #584 (#651) (@DanTanAtAims)
  • Speed up calculation of truncated normal mean and cdf (#652) (@DanTanAtAims)
  • Update tests for new sampling method/factor definitions (#653) (@ConnectedSystems)
  • Update factor type documentation (#654) (@ConnectedSystems)
  • Add a default size for scenario plots (#657) (@ConnectedSystems)
  • CompatHelper: add new compat entry for StatsFuns at version 1, (keep existing compat) (#658) (@github-actions[bot])
  • CompatHelper: add new compat entry for SpecialFunctions at version 2, (keep existing compat) (#659) (@github-actions[bot])
  • Fix bleaching mortality (#660) (@ConnectedSystems)
  • Clean up settler cover function to reduce confusion (#662) (@ConnectedSystems)
  • Only load up relevant RME SSP datasets (#663) (@ConnectedSystems)
  • Reset deployed-coral-risk-tol range (#664) (@ConnectedSystems)
  • Clean up scenario running methods (#665) (@ConnectedSystems)
  • Return 0 in cases where lb > ub (#666) (@ConnectedSystems)
  • Clean up use of TP matrices to align with conceptualisation of connectivity (#667) (@ConnectedSystems)
  • Adjustment to simulated events to address numerical errors (#668) (@ConnectedSystems)
  • Support updated domain structure (#669) (@ConnectedSystems)
  • Fix erroneous handling of location IDs (#671) (@ConnectedSystems)
  • Fix error in domain loading when cluster_id is already in string format (#673) (@Rosejoycrocker)
  • Add test domain for ReefModDomain type (#675) (@Rosejoycrocker)
  • Additional setup instructions for code style and formatting (#676) (@ConnectedSystems)
  • Implementation of new MCDA types (#678) (@ConnectedSystems)
  • Fix readjustment of number of slices bug in RSA (#679) (@Rosejoycrocker)
  • Fix cyclone sorting (#683) (@Zapiano)
  • removed deprecate functions and function calls (#684) (@DanTanAtAims)
  • restructured documentation image directories (#685) (@DanTanAtAims)
  • Truncated normal changes (#687) (@DanTanAtAims)
  • Allow user to set whatever bounds they wish (#688) (@ConnectedSystems)
  • Yax loaddomain (#689) (@Zapiano)
  • Switch to YAXArrays when runnin scenarios (#690) (@Zapiano)
  • Adjustments to allow loading newest Domain datasets (#691) (@ConnectedSystems)
  • Update rank metrics to use YAXArrays (#693) (@ConnectedSystems)
  • Update viz.clustering to expect AbstractMatrix (#694) (@ConnectedSystems)
  • Migrate from NamedDimsArrays to YAXArrays (#695) (@Zapiano)
  • Remove factors input from rsa() and use scenario dataframe column names instead (#696) (@Rosejoycrocker)
  • updated data loading test for migration to YAXArrays (#697) (@DanTanAtAims)
  • Further updates to scenario runs with MCDA (#698) (@ConnectedSystems)
  • Update support for standalone MCDA use (#699) (@ConnectedSystems)
  • Yax test update (#700) (@DanTanAtAims)
  • added nameddimsarray2yaxarray (#701) (@DanTanAtAims)
  • Fix error in bin size for sensitivity.outcome_map (#702) (@Rosejoycrocker)
  • Yax viz (#703) (@DanTanAtAims)
  • Yax cube tests (#704) (@DanTanAtAims)
  • Remove MKL from build process (#705) (@ConnectedSystems)
  • Reef mod matlab domain (#706) (@DanTanAtAims)
  • Yax analysis (#707) (@DanTanAtAims)
  • Migrate metrics.jl to YAXArrays (#709) (@Zapiano)
  • Yax sensitivity (#710) (@DanTanAtAims)
  • Remove GC workaround (#711) (@ConnectedSystems)
  • CompatHelper: bump compat for DimensionalData to 0.26, (keep existing compat) (#714) (@github-actions[bot])
  • Yax migration miscellaneous (#715) (@Zapiano)
  • Keep metadata in results (#716) (@ConnectedSystems)
  • Finalize update of standalone MCDA methods (#717) (@ConnectedSystems)
  • Update all tests and remove NamedDims and AxisKeys from ADRIA.jl (#718) (@Zapiano)
  • Validating MCDA methods and initial clean/update of tests (#719) (@ConnectedSystems)
  • Provide a succinct overview of MCDA (#720) (@ConnectedSystems)
  • Add support to cyclone mortality to ReefModDomain (#722) (@Zapiano)
  • Fix locations selection in ReefMod datapackage cyclone mortality loading (#723) (@Zapiano)
  • Save right intervention label at ResultSet ranks YAXArray (#724) (@Zapiano)
  • Add counterfactual minus guided/unguided diff at location level (#726) (@Zapiano)
  • Hacky support for later RME reef id list (#731) (@ConnectedSystems)
  • Add support for specifying locations (#732) (@ConnectedSystems)
  • improve load_domain docs (#733) (@arlowhite)
  • Only rank locations with available area > 0 (#734) (@ConnectedSystems)
  • Support more vector types for maps (#736) (@ConnectedSystems)
  • Clean up connectivity and centrality methods (#737) (@ConnectedSystems)
  • Additional rank methods to determine number of locations intervened on per timestep (#738) (@ConnectedSystems)
  • Collection of miscellaneous changes (#740) (@ConnectedSystems)
  • Fix bug, min. locations to select > available locations (#741) (@ConnectedSystems)
  • Connectivity viz (#742) (@DanTanAtAims)
  • CompatHelper: bump compat for DimensionalData to 0.27, (keep existing compat) (#744) (@github-actions[bot])
  • RME Result Interface (#745) (@DanTanAtAims)
  • Working example of CUDA-fied settler_cover() (#747) (@ConnectedSystems)
  • Repeat mention that the VS Code extension is being setup (#748) (@ConnectedSystems)
  • Improved support for spatial maps (#750) (@ConnectedSystems)
  • use provided centrality measures instead of defaults (#751) (@DanTanAtAims)
  • Convenience plotting method for connectivity/centralities (#752) (@ConnectedSystems)
  • Misc cleanup (coral dynamics) (#753) (@ConnectedSystems)
  • Changes to make use of expected multi-dimensional data structure (#754) (@ConnectedSystems)
  • remove hardcoded coral spec from metrics and data store (#755) (@DanTanAtAims)
  • fix initial cover block constructor (#757) (@DanTanAtAims)
  • Support plotting DHW and cyclone (mortality) scenarios (#758) (@ConnectedSystems)
  • Support deactivating environmental disturbances (#759) (@ConnectedSystems)
  • Multidimensional cover (#761) (@DanTanAtAims)
  • add range to for loop (#762) (@DanTanAtAims)
  • Visualization for taxonomy cover. (#763) (@DanTanAtAims)
  • CompatHelper: add new compat entry for Makie in [weakdeps] at version 0.21, (keep existing compat) (#764) (@github-actions[bot])
  • CompatHelper: bump compat for NetCDF to 0.12, (keep existing compat) (#765) (@github-actions[bot])
  • CompatHelper: add new compat entry for GraphMakie in [weakdeps] at version 0.5, (keep existing compat) (#766) (@github-actions[bot])
  • CompatHelper: add new compat entry for GeoMakie in [weakdeps] at version 0.6, (keep existing compat) (#767) (@github-actions[bot])
  • Change assisted adaptation to a Discrete Uniform value (#770) (@ConnectedSystems)
  • Use underlying data instead of YAXArray type (#771) (@ConnectedSystems)
  • Increase compression level for ResultSet (#772) (@ConnectedSystems)
  • Fix erroneous function call in docstrings (#773) (@ConnectedSystems)
  • Add methods to extract deployment location info (#774) (@ConnectedSystems)
  • Clean up defunct dependencies (#776) (@ConnectedSystems)
  • Fix visualization type error (#777) (@DanTanAtAims)
  • Fix mismatched function name in docstring (#778) (@ConnectedSystems)
  • constrain growth by available area (#779) (@DanTanAtAims)
  • Fix site_level dosctring (#782) (@Zapiano)
  • remove breakpoint in code (#784) (@DanTanAtAims)
  • Assortment of improvements to SIRUS and Time Series Clustering (#786) (@Zapiano)
  • Add default option to _sort_keys (#787) (@Zapiano)
  • Julia format GH workflow, format all files (#790) (@arlowhite)
  • julia-actions recommended dependabot.yml (#791) (@arlowhite)
  • Coerce to MultiPolygon instead of Polygon (#793) (@ConnectedSystems)
  • Bump julia-actions/cache from 1 to 2 (#795) (@dependabot[bot])
  • Bump julia-actions/setup-julia from 1 to 2 (#796) (@dependabot[bot])
  • Bump actions/checkout from 2 to 4 (#797) (@dependabot[bot])
  • Minor updates to geospatial functions/handling (#798) (@ConnectedSystems)
  • use apply_mortality not apply_survival (#799) (@DanTanAtAims)
  • Address tests failing due to type mismatch (scenario confint) (#801) (@ConnectedSystems)
  • Fix depth min/offset being sampled for counterfactual scenarios (#802) (@ConnectedSystems)
  • Use CoralBlox linear_extension_scale_factor (#805) (@Zapiano)
  • Implement linear extension scale factor (#806) (@Zapiano)
  • Fix add run_model method that do not require functional_groups (#807) (@Zapiano)
  • build: prototype CD integration with Provena to update model (#808) (@PeterBaker0)
  • Fix broken tests (#809) (@Zapiano)
  • update fecundity min area variable name for clarity (#810) (@eco-ben)
  • fix permutation of initial cover dimensions (#811) (@DanTanAtAims)
  • Breaks new initial_cover.nc file into size classes assuming a LogNormal distribution (#812) (@Zapiano)
  • Fix miscellaneous of broken tests (#813) (@Zapiano)
  • Fix sampling test (#814) (@Zapiano)
  • Increase release version (#815) (@DanTanAtAims)
  • Apply changes to ADRIA to make it compatible with CoralBlox model (#817) (@Zapiano)
  • CompatHelper: add new compat entry for CoralBlox at version 1, (keep existing compat) (#821) (@github-actions[bot])
  • Fix docs builder, add .git-blame-ignore-revs and document (#823) (@arlowhite)
  • fix helper dimension size error (#824) (@DanTanAtAims)
  • Add reshape to fix dimension mismatch when logging dhw tolerances (#827) (@Rosejoycrocker)
  • updates docs github action to use Julia 1.10.* (#829) (@arlowhite)
  • Remove Manifest from gitignore (#830) (@Zapiano)
  • Rename metrics :sites dimension with :locations (#831) (@Zapiano)
  • Fix docs errors (#832) (@arlowhite)
  • Fix cover loading and size class lower bound (#833) (@DanTanAtAims)
  • convert recruitment from relative area to area before use (#834) (@DanTanAtAims)
  • lowercase png extensions to fix Documenter (#837) (@arlowhite)
  • Cscape interface improvements (#838) (@ConnectedSystems)
  • feat: migrating and updating docker functionality + publish pipeline (#839) (@PeterBaker0)
  • fix: stale links in docker docs (#843) (@PeterBaker0)
  • Overly constrained argument types causing tests to fail (#844) (@ConnectedSystems)
  • feat: restore unit testing and add julia caching (#845) (@PeterBaker0)
  • fix reefmod domain load initial cover (#846) (@DanTanAtAims)
  • Add metadata to metrics YAXArrays (#847) (@Zapiano)
  • Update interface to use correct gpkg (#850) (@DanTanAtAims)
  • correct calculation of relative cover (#853) (@DanTanAtAims)
  • Speed up CScape Result Interface (#854) (@DanTanAtAims)
  • rename dimension from sites to locations (#857) (@DanTanAtAims)
  • throw more informative error message (#858) (@DanTanAtAims)
  • add scenario id to scenario dataframe (#860) (@DanTanAtAims)
  • Improve summarize performance by using mapslices (#862) (@Zapiano)
  • Viz metadata (#863) (@Zapiano)
  • Pin NetCDF.jl and Zarr.jl in order to pin DiskArrays.jl (#864) (@Zapiano)
  • Bump actions/checkout from 3 to 4 (#865) (@dependabot[bot])
  • Bump docker/login-action from 2 to 3 (#866) (@dependabot[bot])
  • Bump docker/build-push-action from 4 to 6 (#867) (@dependabot[bot])
  • Bump docker/metadata-action from 4 to 5 (#868) (@dependabot[bot])
  • Fix rule extraction to handle constant factors (#870) (@Zapiano)
  • Improvements to model performance by reducing allocations (#871) (@ConnectedSystems)
  • Julia 1.11 Manifest and Pkg update (#876) (@arlowhite)
  • Minor change for performance (#877) (@ConnectedSystems)
  • Apply CompatHelper suggestions, free NetCDF,Zarr; add & pin DiskArrays (#878) (@arlowhite)
  • LERC_jll 3 to 4, downgrade DimensionalData to 0.27.9, Julia Pkg update (#879) (@arlowhite)
  • Update code and dependencies to GeoMakie v0.7.x (#884) (@ConnectedSystems)
  • Cyclone mortalities assigned to wrong group (#888) (@DanTanAtAims)
  • DiskArrays 0.4.5, Pkg update (#889) (@arlowhite)
  • Fix StackOverflow error when plotting maps (#891) (@ConnectedSystems)
  • Add spatial visualisations for decision matrices (#893) (@Rosejoycrocker)
  • Add DEA functions and plotting to ADRIA.analysis (#896) (@Rosejoycrocker)
  • Remove duplicate rules (#899) (@Zapiano)
  • Bump codecov/codecov-action from 4 to 5 (#901) (@dependabot[bot])
  • Fix DHW scenario viz again (#903) (@ConnectedSystems)
  • Incorporate recruitment to growth constraints and cap seeding to habitable area (#906) (@DanTanAtAims)
  • Add extraction of feature set to support analyses and assessment (#907) (@ConnectedSystems)
  • Add additional convenience functions and update docstrings (#908) (@ConnectedSystems)
  • Remove defunct method seed_corals! (#909) (@ConnectedSystems)
  • Switch to logging number of coral deployed (#910) (@ConnectedSystems)
  • Add method to display all DHW scenarios for the currently set RCP/SSP (#914) (@ConnectedSystems)
  • Minor tweaks to taxa visualization (#915) (@ConnectedSystems)
  • Updated factor bounds setting method (#917) (@ConnectedSystems)
  • Minor fix on docs (#920) (@vitorhirata)
  • Pin DiskArrays to 0.4.9 (#922) (@vitorhirata)
  • Fix tests of viz/spatial and metrics/spatial (#923) (@vitorhirata)
  • Pin DiskArrays to 0.4.9 in docs Manifest and v1.11 Manifest (#924) (@vitorhirata)
  • Custom categorical distribution (#927) (@DanTanAtAims)
  • Small change to parameter description to avoid confusion (#928) (@ConnectedSystems)
  • Replace and deprecate remaining use of site_k_area (#929) (@ConnectedSystems)
  • CompatHelper: bump compat for Makie in [weakdeps] to 0.22, (keep existing compat) (#930) (@github-actions[bot])
  • CompatHelper: bump compat for DimensionalData to 0.29, (keep existing compat) (#931) (@github-actions[bot])
  • CompatHelper: bump compat for YAXArrays to 0.6, (keep existing compat) (#932) (@github-actions[bot])
  • Avoid reshape for performance (#933) (@ConnectedSystems)
  • Considering spatial dispersal of intervention locations (#934) (@ConnectedSystems)
  • Add cyclone mortality to documentation (#936) (@Zapiano)
  • Correct RCP identifier in result directory (#937) (@ConnectedSystems)
  • Remove synopsis from documentation (#938) (@Zapiano)
  • Update docs to configure Julia Formatter extension (#939) (@ConnectedSystems)
  • Fix docs build (#945) (@Zapiano)
  • CompatHelper: bump compat for JMcDM to 0.8, (keep existing compat) (#946) (@github-actions[bot])
  • Fix rounding problem, leading to coral overgrowth, when cover plus recruits fill an entire reef (#947) (@Zapiano)
  • Bump julia-actions/julia-format from 3 to 4 (#948) (@dependabot[bot])
  • Speed up timeseries clustering (#949) (@Zapiano)
  • add bin edges used in calibration to ADRIA (#950) (@DanTanAtAims)
  • Fix multiple tests (#951) (@Zapiano)
  • Changes to enable recent RME domain loading (#952) (@Zapiano)
  • CompatHelper: bump compat for Interpolations to 0.16, (keep existing compat) (#953) (@github-actions[bot])
  • Speedup bleaching (#954) (@Zapiano)
  • Add plot for single scenario stratified by size class and functional group (#955) (@Zapiano)
  • CompatHelper: bump compat for Makie in [weakdeps] to 0.23, (keep existing compat) (#956) (@github-actions[bot])
  • Update Manifest (#957) (@Zapiano)
  • CompatHelper: bump compat for Makie in [weakdeps] to 0.24, (keep existing compat) (#958) (@github-actions[bot])
  • Update calibrated factors (#960) (@Zapiano)
  • docs: minor clarification to Makie backend selection (#961) (@PeterBaker0)
  • CompatHelper: bump compat for GraphMakie in [weakdeps] to 0.6, (keep existing compat) (#964) (@github-actions[bot])
  • Fix tests prior to merging global-calib to main (#965) (@Zapiano)
  • CompatHelper: bump compat for DataStructures to 0.19, (keep existing compat) (#966) (@github-actions[bot])
  • Calibration and SA changes (#967) (@Zapiano)
  • Bump project version prior to new release (#968) (@Zapiano)
  • Fix conn data load location selection when force_single_reef is true (#970) (@Zapiano)
  • Update compatible datapackage version to 0.8.0 (#972) (@Zapiano)
  • Deactivate criteria factors when running deactivate_interventions (#973) (@Zapiano)
  • Fix _init_cover_weights dicstring (#974) (@Zapiano)
  • Specify timeframe when loading RME dhw_scens (#975) (@Zapiano)
  • Bump actions/checkout from 4 to 5 (#976) (@dependabot[bot])
  • Doc guided sampling (#977) (@Zapiano)
  • Support independent scenarios viz legend rendering (#978) (@Zapiano)
  • CompatHelper: bump compat for YAXArrays to 0.7, (keep existing compat) (#979) (@github-actions[bot])
  • CompatHelper: bump compat for MLJ to 0.21, (keep existing compat) (#981) (@github-actions[bot])
  • Refactor Reef Index Metrics (#982) (@DanTanAtAims)
  • Export bin_edges (#983) (@Zapiano)
  • CompatHelper: bump compat for JSON to 1, (keep existing compat) (#984) (@github-actions[bot])
  • Update calibrated parameter base values (#985) (@Zapiano)
  • CompatHelper: bump compat for JSON to 1, (keep existing compat) (#986) (@github-actions[bot])
  • Fix factor update bug (#988) (@ConnectedSystems)
  • Update key dependencies and bump version (#989) (@ConnectedSystems)
  • Bump project version prior to new release (#990) (@Zapiano)
  • fix: Correct growth constraint calculation in scenario.jl (#992) (@DanTanAtAims)
  • CompatHelper: bump compat for MLJ to 0.22, (keep existing compat) (#993) (@github-actions[bot])
  • CompatHelper: bump compat for SIRUS to 3, (keep existing compat) (#994) (@github-actions[bot])
  • Refactor out recruitment constraint from timestep loop (#996) (@Zapiano)
  • Remove MAT dependency (#997) (@ConnectedSystems)
  • Update GeoDataFrame handling (#998) (@ConnectedSystems)
  • Remove broadcasting to avoid intermediate allocations (#999) (@ConnectedSystems)
  • Remove intermediate array (#1000) (@ConnectedSystems)
  • fix: fix input type declaration for _render_legend (#1001) (@DanTanAtAims)
  • Initial cleanup in prep for restructure (#1002) (@ConnectedSystems)
  • Support arbitrary number of time series clusters (#1003) (@ConnectedSystems)
  • Reorganizing code structure (#1004) (@ConnectedSystems)
  • Bump actions/checkout from 5 to 6 (#1005) (@dependabot[bot])
  • Adjusted scenario sampling and default parameters (#1006) (@ConnectedSystems)
  • Refactor Spatial Data Loading and Update Input Data Handling (#1007) (@DanTanAtAims)
  • Speedups (#1008) (@DanTanAtAims)
  • Fix incorrect use of single reef idx (#1009) (@DanTanAtAims)
  • fix: Fix categorical bug where bounds are passed instead of categories (#1010) (@DanTanAtAims)
  • Improves scenario assessment workflow (#1011) (@ConnectedSystems)
  • Pin YAXArray dependency (#1013) (@ConnectedSystems)
  • Implements decision strategies (#1019) (@ConnectedSystems)
  • Mention use of shared depot paths (#1020) (@ConnectedSystems)
  • Fix single reef load and sampling (#1023) (@Zapiano)
  • Bump project version prior to new release (#1024) (@Zapiano)
  • Restrict minimum compatible Julia version to 1.11 (#1026) (@Zapiano)
  • Improve fecundity (#1027) (@Zapiano)
  • Add Allee effect (#1031) (@Zapiano)
  • Fix: All axis values were being stripped when creating new DataCube (#1033) (@ConnectedSystems)
  • Fix LTMP Taxa Cover and Metric Metadata (#1034) (@DanTanAtAims)
  • reformat with JuliaFormatter V1 (#1035) (@arlowhite)
  • Fix wrong use of reactive strategy index (#1036) (@Zapiano)
  • Fix sampling tests (and others) (#1037) (@Zapiano)
  • Update documentation project (#1038) (@Zapiano)
  • Update Julia version used in github doc build to 1.11 (#1039) (@Zapiano)
  • Extend seeding intervention to all functional groups (#1040) (@Zapiano)
  • Rename ENV variable TEST to ADRIA_TEST (#1041) (@Zapiano)
  • Remove ODE related code (and clean up) (#1042) (@Zapiano)
  • Fix fog and seed location fixing (#1043) (@Zapiano)
  • Fix fog strategy builder (#1047) (@Zapiano)
  • Limit environmental data loading to timeframe in datapackage.json (#1048) (@DanTanAtAims)
  • Use newest version of ADRIAIndicators (#1049) (@DanTanAtAims)
  • Enforce location ids in environmental data. (#1050) (@DanTanAtAims)
  • Implement moving corals intervention (#1052) (@Zapiano)
  • Allow target locations for MCB (#1053) (@Zapiano)
  • Use seeding device density to distribute seeded corals (#1056) (@Zapiano)
  • Assisted adaptation relative to recent past (#1057) (@Zapiano)
  • Update Breeder's equation usage (#1058) (@Zapiano)
  • Add min_iv_locs param specific for moving corals (#1059) (@Zapiano)
  • Add moving corals stats to feature set (#1060) (@Zapiano)
  • Add Marine Cloud Brightening with Multi-dimensional DHW NetCDFs (#1062) (@DanTanAtAims)
  • Bump codecov/codecov-action from 5 to 6 (#1063) (@dependabot[bot])
  • Bump docker/login-action from 3 to 4 (#1064) (@dependabot[bot])
  • Bump julia-actions/cache from 2 to 3 (#1065) (@dependabot[bot])

Closed issues:

  • Core functionality to be ported from ADRIA (MATLAB) (#1)
  • Pretty display for ResultSet (#68)
  • Include site area data in result set (#69)
  • Precompilation step to include dummy runs (#70)
  • Example and test data packages (#71)
  • Investigate optimizations to improve precompilation times (#75)
  • Add total coral cover metric (#77)
  • Adjust RCI to use new total coral cover (#78)
  • Investigate alternative site selection weightings for coral cover (#79)
  • Separate coral_cover() metric into individual functions (#81)
  • Switch default behaviour of ADRIA.jl to store aggregated results? (#82)
  • Use NamedDims and NamedArrays (#83)
  • Adapt siteselection() to use dMCDA to avoid code repetition (#86)
  • Shelter Volume: investigate very small values (#91)
  • Juvenile metric: investigate small values (#92)
  • Auto-adjust site offset/depth bounds on loading Domain (#94)
  • Add an additional model component for environmental layers (#95)
  • Coral evenness: Metric returns NaNs (#96)
  • Replace duplicate proportional growth constraint with single function (#99)
  • Make relative_cover() relative to site max coral cover area (k) instead of total site area (#109)
  • ADRIA specific sampling functions (#119)
  • Update result set to derive spatial data from stored geopackage (#124)
  • Distribute seeded corals acording to available space, not k (#128)
  • Exporting to PowerBI format very slow (#132)
  • Double check recruitment calculation? (#133)
  • Add scenario index to csv created by result_post_processing.jl and filter counterfactual according to dhw scenario (#136)
  • Bleaching mortality may be over-estimated (#138)
  • DHW dataset may over-represent extreme DHW trajectories (#139)
  • Refactor seeding step into its own function with tests (#146)
  • Use measure of dhw time distribution for MCDA heat stress criteria (#151)
  • Check scaling of coral real estate criteria in MCDA function and add measure of space for coral to be seeded. (#152)
  • Make shading of seeded sites user controllable (#157)
  • Metric function to extract the top N performing sites (#158)
  • Process area data on file read (#170)
  • Add support for NetCDF data files (#173)
  • Adjust MCDA functions to be more generic (#177)
  • Deprecate support for .mat files (#182)
  • Update site_selection() function in Domain.jl and use within ADRIA model site selection process to reduce replication (#194)
  • Standardize to NamedDimsArray + AxisKeys (#200)
  • Standardize relative cover metric to report values relative to k area (#204)
  • Adjust scenario input IDs for clarity (#205)
  • Use NamedDims+AxisKeys instead of matrix for MCDA decision matrices (#221)
  • Site ranks are never updated after distance sorting (#223)
  • Update the bleaching response to formally account for depth, surface shading and water quality. (#226)
  • Move natural adaptation parameter to be part of the Coral component (#229)
  • Add human-readable name to Parameter types (#230)
  • List management zones in order of preference for targeted deployment (#231)
  • Change triangular distributions to specify peak in absolute terms (#234)
  • Use Haversine instead of Euclidean distance (#236)
  • Use mean distance threshold and change in aggregate criteria value threshold instead of site by site distance threshold and top_n in distance sorting (#237)
  • Adjust definition or sampling of dist_thresh so that the value representing 'don't use distance sorting' is as likely as values representing using distance sorting (#238)
  • Investigate bounds used for coral_cover_tol (#239)
  • Set up documentation system and website (#240)
  • Consider using JMcDM (#242)
  • Register package (#245)
  • Change reference to Input Set to Domain to align with interface functions (#246)
  • Address possible double switching of RCPs (#248)
  • Make plotting functions more generic to support rapid workflows (#249)
  • Better separation of Aviz sub-system (#250)
  • Make MCDA functions generic (#252)
  • Move example scripts into documentation (#253)
  • pareto analysis (#256)
  • Regional Sensitivity Analysis (#257)
  • Temporal Sensitivity Analysis (#260)
  • Favicon for Documentation site (#265)
  • Use LTMP observations (#267)
  • Update growth rates for size class 6 (#268)
  • TagBot trigger issue (#269)
  • [Discussion] Natural adaptation (#270)
  • Release v0.4.5 (#272)
  • Separate fogging from shading (#277)
  • Possible bug in site_selection (#284)
  • Bug in site selection example (#285)
  • Scenario juvenile metric returning implausible values (?) and values > 1 (#292)
  • Create function which returns just the set of criteria values needed for MCDA (#296)
  • Re-enable tests/CI when Julia v1.9 is released (#300)
  • Connectivity data cubes (#302)
  • First conversion of model specification to DataFrame is excruciatingly slow (#303)
  • map_to_discrete() erroring due to type mismatch (#304)
  • run_site_selection() errors out (#308)
  • [Viz/Analysis] Scenario outcomes (#311)
  • [Viz/Analysis] sensitivity analysis (bar/heatmap) (#312)
  • [Viz/Analysis] temporal sensitivity analysis (#313)
  • [Viz/Analysis] Regional Sensitivity Analysis (#314)
  • [Viz/Analysis] Outcome-based factor mapping (#315)
  • [Viz/Analysis] maps for/of site selection (#316)
  • [Viz/Analysis] Naive Bayes (#323)
  • Make run_site_selection() more user-friendly (#324)
  • Investigate alternative method for sampling mcda weights (#327)
  • Checking centrality is correctly calculated (#329)
  • Release v0.5.0 (#331)
  • MCDA crashes with mismatched array sizes for rankings and rankingsin (#333)
  • Create single ResultSet (#342)
  • MCDA method errors (#357)
  • Make n_sites a perturbable model factor (#360)
  • align_rankings! giving incorrect output rankings (#366)
  • Time series clustering (#368)
  • [Viz/Analysis] Clustering of scenarios to aid in MORDM (#369)
  • Separate model factors (#377)
  • Register v0.6.0 (#379)
  • Spatial clustering based on outcomes (#383)
  • [Viz/Analysis] Spatial plots of locations clustered by outcome (#384)
  • Register v0.7.0 (#388)
  • Remove coral cover conversion for ReefModEngine interface (#399)
  • Add Rule Induction (with SIRUS) (#404)
  • ADRIAmod uses excessive amounts of memory during runs (#405)
  • Errors when running scenarios in parallel when nworkers() > 1 (#413)
  • Change the way target_cluster function is works (#423)
  • Duplicate RCP issue when running scenarios generated using sample_site_selection() (#426)
  • Error: loc_trajectory and per_loc not qualifying dim (#427)
  • Error: non_null_sites (#428)
  • viz.outcome_map() gives duplicate x-axis values when plotting :guided factor (#440)
  • Register v0.8.0 (#447)
  • Update code style section in docs (#448)
  • Out of memory error when calculating PAWN sensitivity for 8192 scenarios (#450)
  • Target clusters with lower values of some metric (#451)
  • Show labels and units of measurement automatically for plots by default (#453)
  • Rule Extraction viz function is not included int viz extension (#454)
  • Relevant features/properties for rule induction (and scenario decision making) (#458)
  • Regional sensiyivity analysis gives duplicate values for categorical factors (#459)
  • Summarized vizualisation for time series clustering (#464)
  • Add example of Rule Induction usage to the Documentation (#473)
  • Update rule ADRIA.viz.rules_scatter to accept target_clusters vector instead of clusters (#474)
  • Conceptually align all coral cover calculations to be relative to k area (#480)
  • Make $k$ area in geospatial data consistent (#483)
  • Load initial coral cover data consistently across different Domain types (#484)
  • Scenario running methods to be refactored to expect only values relative to $k$ area (#487)
  • All metrics to be adjusted to expect $k$ area values (#488)
  • Duplicate x-axis values in outcome maps (Part 2) (#489)
  • Robust Decision Making (#493)
  • Properly handle plotting binary (target vs non-target) clusters (#494)
  • _time_labels gives duplicate labels in some cases (#495)
  • Register v0.9.0 (#498)
  • Adjust usage of k site area in location selection to align with coral cover being relative to k (#501)
  • Possible issue with settler_cover() when moving to k area based processes (#502)
  • Update deprecated writeheader=true at Domain.jl model_spec function (#503)
  • Create a function that uses Slices to compute some aggregation metric over given axis (#508)
  • Remove top_n from distance sorting as no longer needed (#509)
  • Fix bug when loading Domain due to DHWs containing missing values (#510)
  • [RFC] Change factors marked as "integer" types to "discrete" (#512)
  • Refactor tests so we have an available ResultSet instance (#513)
  • Incorporate cyclone mortality into ADRIAmod (#516)
  • Implement n_scenarios(rs) (#517)
  • Skip RCP entry from scenario specification by name rather than assuming position (#518)
  • Add method for selecting all parameters associated with a particular intervention (#520)
  • [Bug] Plotting subset of scenarios fail as not all scenario types may be included (#522)
  • Use more descriptive dimension/axis labels for ResultSet logs storage now that AxisKeys is in use (#524)
  • Make SRM apply to Reef clusters not whole of GBR (#525)
  • Generalise creation of MCDA decision matrices (#526)
  • Switch to YAXArrays (#528)
  • Develop cyclone mortality models based on R implementation (#529)
  • Filter coral species/site by branching_below_5, branching_above_5 and massive (#530)
  • Use cyclone mortality model and filter to implement cyclone mortality in ADRIAmod (#531)
  • Switch to WGLMakie for visualizations (#532)
  • Increase default worker timeout (#534)
  • Out of memory error for parallelised runs for whole of GBR domain (#535)
  • Error runing test/runtests.jl (#538)
  • Create plotting functions for sensitivity analysis convergence (#543)
  • Add documentation for Cyclone mortality (#544)
  • Add load_latest_results() (#548)
  • Cluster maps not working (#549)
  • Record/Log of DHW and wave stats in result sets are broken (#550)
  • Fix error in growth ODE test (#551)
  • Deployment location analysis methods/metrics leak into package namespace (#556)
  • Add MCDA weighting normalisation to scenario sampling post-processing (#559)
  • Delete/remove deprecated functions in prep for v1.0 release (#560)
  • Make all indices used in site selection aggregation functions symbols (#562)
  • Find and deprecate inconsistent methods (#564)
  • Separate weighting parameters for heat_stress and depth in the MCDA (#565)
  • Reorganize files/images for documentation (#567)
  • Error when tests run scenarios (#568)
  • Compute mean of truncated distribution using a Burman series (#572)
  • Remove unused version check (#580)
  • Move example scripts into the cookbook (#584)
  • Adjust sampling approach for flexibility (#586)
  • Changes in PR#552 breaks scenario visualizations (#587)
  • Tests raising error (#590)
  • Add function which returns list of MCDA methods which can be used in ADRIA (#591)
  • Use min-max normalisation for heat stress criteria (#592)
  • Update use of Makie (v0.20.0) to avoid deprecations (#600)
  • Loading RME datasets are broken due to cyclone data requirement (#609)
  • Fix "surprising" readjustment of the number of slices used to perform RSA/outcome mapping (#615)
  • Adjust distribute_seeded_corals to account for cases where the top 5 sites do not have enough space for seeded corals (#618)
  • Change log for dhws and waves to store mean and std for scenarios and sites/reefs (#619)
  • Add new 10 site test Domain to testing folder in ADRIA (#622)
  • Make decision matrices NamedDimsArrays (#624)
  • Register v0.10.0 (#626)
  • set_factor_bounds! setting value outside range for discrete variables (#630)
  • Priority sites criteria expecting different structure for strong_pred than what is implemented (#633)
  • Add connectivity matrix to ResultSet (#641)
  • Error precompiling ADRIA.jl (#645)
  • Support use of cluster identifier in spatial dataset (#655)
  • Fix bug in constrain_reef_cluster which assumes there will always be enough locations to satisfy the reef constraint (#656)
  • Add test domain for ReefModDomain type (#670)
  • Ignore constant factors when applying SIRUS (#672)
  • Add tests for standalone site selection using rank_locations (#680)
  • Larval spread via connectivity is not working as expected (#686)
  • Method Call error during testing from rsa function type. (#692)
  • Documentation image links are broken (#712)
  • viz.outcome_map not working when :guided is one of the factors of interest (#713)
  • Fix sampling of guided MCDA methods (#725)
  • Remove connectivity data from Domain types (#735)
  • Example given in #742 no longer works (#749)
  • Revisit use of temporary geojson (#768)
  • Order of scenarios plotted are inconsistent (#769)
  • Docstring example missing ending backticks (#781)
  • Delete stale branches (#783)
  • Improve loc_trajectory() function performance (#788)
  • Makie spatial plotting maps color vector to each polygon in a multipolygon, leaving white polygons for unmapped shapes (#792)
  • Geospatial dataset for the Test domain does not define a valid CRS (#800)
  • Register v0.11.0 (#816)
  • Delete defunct code after implementing changes to use CoralBlox.jl (#819)
  • ReefModDomain loading is not working (#825)
  • Dimension mismatch when logging DHW tolerances in debug mode (#826)
  • CoralBlox apparent incompatibility (#828)
  • Absolute cover calculations consider wrong area (#841)
  • mismatch of naming in Cscape results set (#849)
  • Investigate alternate chunking strategy for Zarr store (#851)
  • data saved as relative cover is actually absolute cover (#852)
  • Error when calculating total cover (#855)
  • Errors/issues in _get_result_paths() (C~scape interface) (#856)
  • Retrieve scenario IDs from CScapeResultsSet (#859)
  • DimensionalData compat 0.27 (#881)
  • GeoMakie compat 0.6 (#882)
  • DiskArrays pinned to 0.3.23 (#883)
  • StackOverflowError in tests failing on main branch (#890)
  • Rule extraction print_rules error attempting to access 1-element Vector{Float64} at index [2] (#900)
  • Seeding Intervention Habitable Area limit (#905)
  • NaNs in growth_constraints vector raising error at global_calib branch (#963)
  • Release v0.12.0 (#969)
  • Register v0.13.0 (#991)
  • Release v0.14.0 (#1012)
  • Release v0.14.1 (#1014)
  • Release v0.15.0 (#1015)
  • Release v0.15.1 (#1025)
  • JuliaFormatter workflow blocking well formatted files (#1029)

Biosphere - Conservation and Restoration - Julia
Published by github-actions[bot] 14 days ago

openfoodnetwork - v5.7.1 Palak Paneer

What's Changed

User-facing changes 👀

API changes ⚠️

Technical changes 🛠️

Dependencies 📦

Full Changelog: https://github.com/openfoodfoundation/openfoodnetwork/compare/v5.7.0...v5.7.1

Consumption - Agriculture and Nutrition - Ruby
Published by chahmedejaz 14 days ago

MetNet - v4.1.24

Atmosphere - Meteorological Observation and Forecast - Python
Published by github-actions[bot] 15 days ago

acoupi - v0.5.2

What's Changed

Full Changelog: https://github.com/acoupi/acoupi/compare/v0.5.1...v0.5.2

Biosphere - Bioacoustics and Acoustic Data Analysis - Python
Published by mbsantiago 15 days ago

PlantCV - PlantCV v4.11.2

What's Changed

Full Changelog: https://github.com/danforthcenter/plantcv/compare/v4.11.1...v4.11.2

Biosphere - Plants and Vegetation - Python
Published by nfahlgren 15 days ago

Deadtrees.earth - v2026.06.29

What's Changed

Other Changes

Full Changelog: https://github.com/Deadwood-ai/deadtrees/compare/v2026.06.26.3...v2026.06.29

Biosphere - Forest Remote Sensing - TypeScript
Published by github-actions[bot] 15 days ago

ToOp - v0.8.0

Features

Fixes

Misc

Full Changelog: https://github.com/eliagroup/ToOp/compare/v0.7.1...v0.8.0

Energy Systems - Grid Analysis and Planning - Python
Published by spetznick-elia 15 days ago

Monitorfish - v1.115.0

What's Changed

🎉 Fonctionnalités

🐛 Corrections

Full Changelog: https://github.com/MTES-MCT/monitorfish/compare/v1.114.0...v1.115.0

Biosphere - Marine Life and Fishery - HTML
Published by louptheron 15 days ago

Ecoscope - v2.16.1

What's Changed

Other Changes

Full Changelog: https://github.com/wildlife-dynamics/ecoscope/compare/v2.16.0...v2.16.1

Biosphere - Conservation and Restoration - Python
Published by github-actions[bot] 15 days ago

timflow - Release v0.4.0

Highlights

  • Compute heads and velocities on unstructured grids of x,y points with ml.head_array() and ml.velocity_array()
  • Actually compute heads and velocities (see previous point) in parallel now using multiprocessing instead of multithreading
  • New well.capturezone() and ml.plots.plot_capture_zone() methods
  • Support custom layer names in cross-section plots
  • Better and more consistent input checks in Model classes
  • Better support for Model class (note: breaking change in argument order of c and z to match other model class definitions)
  • Better unit dictionary support (use timflow parameter names as keys) and consistently applied for all Model types now (cross sections and Maq/3D)
  • Removed write methods to save timflow models as a python script (old code that has been untested for a long time and will eventually be replaced by something new).
  • Improve some docs things (citations, update code in notebooks, etc).

What's Changed

Full Changelog: https://github.com/timflow-org/timflow/compare/v0.3.0...v0.4.0

Hydrosphere - Freshwater and Hydrology - Python
Published by dbrakenhoff 15 days ago

CoralNet-Toolbox - v1.0.0

What's Changed

Full Changelog: https://github.com/Jordan-Pierce/CoralNet-Toolbox/compare/v0.0.105...v1.0.0

Biosphere - Marine Life and Fishery - Python
Published by Jordan-Pierce 15 days ago

mizer - mizer 3.1.0

Version 3.1.0 builds on 3.0.0 with an experimental second-order accurate
numerical scheme in size, additional higher-order time-stepping options, and a
range of smaller improvements and bug fixes. Unless you opt in to the
experimental scheme, results are unchanged from 3.0.0.

For an overview see the release announcement on the mizer blog.

Experimental second-order in w accuracy

mizer gains an optional, experimental second-order accurate finite-volume scheme
in the size variable w. It is controlled by a new second_order_w slot and is
switched off by default, so all default results are unchanged (the first-order
path is byte-identical to previous mizer). Enabling it shifts size-integrated
diagnostics and the resource spectrum by O(Δw) (more on coarse grids), so
calibrated models may need recalibrating. See ?second_order_w and the
"Numerical Details" vignette.

  • The second_order_w slot is a named list with a character entry flux
    ("upwind", "van_leer" or "centred") selecting the advective
    reconstruction, and a logical entry bin_average selecting the bin-averaged
    rate quadratures. A fully second-order scheme needs both. Use the new
    second_order_w() / second_order_w<-() accessors to get and set them. The
    setter accepts a single logical, which sets both entries — flux = "van_leer"
    (a TVD reconstruction that keeps abundances non-negative) and
    bin_average = TRUE — or a named vector for individual control, e.g.
    second_order_w(params) <- c(flux = "centred") for the unlimited flux that is
    genuinely second order even at extrema. Setting it re-runs setParams() to
    rebuild the precomputed arrays. The default flux = "upwind",
    bin_average = FALSE is the original first-order upwind scheme. Old objects
    are upgraded automatically.

  • newMultispeciesParams(), newTraitParams(), newCommunityParams() and
    newSingleSpeciesParams() gain a second_order_w argument (default FALSE,
    accepting the same values as the setter) that builds the new model with the
    scheme already selected. Under bin_average the resource and abundance power
    laws are constructed bin-averaged from the start; the construction-time
    steady-state solve always uses the robust upwind flux, and the chosen flux is
    activated only for the returned model. (#379)

  • When bin_average is TRUE, every point-sampled power law and quadrature that
    feeds the finite-volume update is replaced by its exact bin average over each
    size bin (the bin straddling w_pp_cutoff receiving the partial average), so
    the sinks, sources and capacities are consistent with the bin-integrated
    encounter convolution (#374):

    • the external mortality \eqn{z_{ext} w^d} (setExtMort()) and external
      diffusion \eqn{D_{ext} w^{n+1}} (setExtDiffusion());
    • the auto-calculated resource intrinsic growth \eqn{r_p w^{n-1}} and carrying
      capacity \eqn{\kappa w^{-\lambda}} (setResource(); user-supplied full
      vectors are left untouched), together with the matching initial resource
      abundance \eqn{\kappa w^{-\lambda}} used both for the initial spectrum and
      for the temporary prey spectra behind the default gamma/f0 and consumer
      abundances;
    • the predation kernels, which are now predator- and prey-bin averaged (via
      trapezoid folds), so getEncounter(), getPredRate(), getPredMort(),
      getResourceMort() and getDiffusion() become second order with no change
      to the rate functions and no extra runtime cost. The predation-diffusion
      integral uses a dedicated Fourier kernel held in the new ft_pred_kernel_d
      slot, which carries the extra power of prey size (\eqn{w_p^2 dw_p}, the
      \eqn{\beta^{3s}} Jacobian) that the diffusion integrand needs; in the
      first-order scheme it equals ft_pred_kernel_e, so existing models are
      byte-identical. (#384)
    • the gear selectivity (calc_selectivity()), so a knife-edge gear gets the
      exact fraction of the straddling bin above the knife edge and fishing
      mortality is second order;
    • the per-capita reproductive investment \eqn{\psi(w) E_r(w)} in mizerRDI()
      (the full investment averaged together, not psi alone), making
      density-independent reproduction second order.

  • The advective growth flux uses the chosen flux reconstruction ("van_leer"
    or "centred") for a second-order transport step. Combined with the
    bin-averaged diffusion from getDiffusion(), the full growth-transport step is
    second order. The diffusion coefficient is consumed from getDiffusion()
    directly rather than being re-averaged by the transport routine.

  • Size-integrated and size-resolved diagnostics are placed and weighted
    consistently with the finite-volume scheme when bin_average is TRUE:

    • the summary integrals getBiomass(), getSSB(), getYield(),
      getYieldGear(), getDiet() and getTrophicLevel() use the trapezoidal
      bin-average of the size weight (getN() is already exact);
    • the size-resolved bin-average diagnostics — the mortalities getPredMort(),
      getFMort(), getMort(), getExtMort() and the reproductive investment
      getERepro() — are reported at the geometric bin centre
      \eqn{\sqrt{w_j w_{j+1}}}, the location where a bin average actually lives,
      while point-valued quantities (encounter, growth) stay on the grid nodes.
      The ArraySpeciesBySize / ArrayTimeBySpeciesBySize classes carry a
      representation tag ("point" / "average") recording this. (#382)
    • the spectrum plots plotSpectra(), plotlySpectra(),
      plotSpectraRelative() and animateSpectra() evaluate both the w^power
      weight and the marker location at the geometric bin centre
      \eqn{w^* = w \sqrt{\beta}}, placing each marker as a point on the continuous
      N w^power curve instead of misplacing it at the bin edge (the error grows
      with power, worst for the common power = 2 Sheldon plot). (#383)

Higher-order time-stepping

  • project() gains a new time-stepping option method = "tr_bdf2". This is an
    L-stable, second-order TR-BDF2 scheme that retains the second-order accuracy of
    method = "predictor_corrector" while damping the oscillations the
    Crank-Nicolson corrector can show at large time steps. Like the other methods
    it only requires tridiagonal solves. See the "Numerical Details" vignette.

  • Under the second-order methods ("predictor_corrector" and "tr_bdf2") the
    resource is now advanced with midpoint resource mortality rather than the
    start-of-step value, and the other components (set via setComponent()) now
    also receive a corrector step with the midpoint rates. So the resource and the
    other components are integrated to the same second-order accuracy in time as
    the consumer spectra. The "euler" method and the steady states are unchanged.

Other improvements

  • Extension packages can now upgrade their own data in saved model objects
    independently of the mizer version. The @extensions slot can record, for
    each extension, the version of the extension package that the object conforms
    to (write entries with the new recordExtension()). needs_upgrading() flags
    an object when an extension's recorded version is missing or older than the
    installed package version, and validParams() then calls the extension's own
    upgrade() method (an S3 method on utils::upgrade(), registered with
    @exportS3Method utils::upgrade). The core mizer upgrade is now itself the
    upgrade.MizerParams() / upgrade.MizerSim() method. See the "Upgrading
    objects across versions of your extension" section of
    vignette("creating-extension-packages").

  • getDiet() gains a MizerSim method and plotDiet() for a MizerSim now
    accepts a time_range argument, computing the diet from the simulated
    abundances at the requested times rather than always using the initial
    abundances. As for the other MizerSim plotting functions, time_range
    defaults to the final saved time step. When a range spanning several saved
    time steps is given, the consumption rates are averaged over the range and
    then normalised to proportions (rather than averaging the per-step
    proportions, which are normalised independently). (#357)

  • New getFluxGradient() function returns the flux divergence
    \eqn{(J_{j+1} - J_j)/\Delta w_j} that appears as the transport term in the
    discretised size-spectrum equation. The bin-boundary fluxes are obtained from
    getFlux(), so the advective-flux scheme stored in the flux entry of the
    second_order_w slot is used, with the largest size class closed by the
    boundary condition \eqn{N_{K+1} = 0}. Like getFlux(), it has both
    MizerParams and MizerSim methods, returning an ArraySpeciesBySize or
    ArrayTimeBySpeciesBySize object respectively.

  • getDiffusion() now works with a custom predation kernel that depends on
    predator and prey size separately rather than only on their ratio. As for
    getEncounter(), when such a kernel has been set (with
    setPredKernel(params, pred_kernel = ...)) the diffusion integral is
    evaluated by direct summation over the full predation kernel instead of via
    the FFT method, which assumes a ratio-only kernel. (#373)

  • getTrophicLevel() and getTrophicLevelBySpecies() now assign the resource a
    size-dependent trophic level
    \eqn{T_R(w) = \max(1, 1 + \log(w / w_R) / \log(\beta_R))} instead of treating
    it as trophic level 0. The new w_R (average primary-producer size) and
    beta_R (average resource predator/prey mass ratio) arguments control this.

  • Resource functions now return classed objects that support the same
    convenient print(), summary(), plot() and as.data.frame() methods as
    the consumer rate functions. getResourceMort(), initialNResource(),
    finalNResource(), resource_rate(), resource_capacity() and
    resource_level() return an ArrayResourceBySize object, and NResource()
    returns an ArrayTimeByResourceBySize object, so you can now do e.g.
    plot(getResourceMort(NS_params)) or plot(NResource(NS_sim)).

  • summary() of a MizerSim object now reports the fishing effort that was
    actually used during the simulation rather than the model's initial_effort.
    Gears whose effort varied over time show the mean effort, flagged with a note
    giving the min-max range.

  • Added a new vignette explaining the calculation of default parameter values
    (#189).

Breaking changes

  • The maximum-size species parameters have been clarified (#325). The von
    Bertalanffy asymptotic size w_inf is now the required maximum-size parameter
    and is used as the default for w_repro_max (previously w_max) and w_mat.
    w_max is now purely a computational boundary (the size grid and plot range)
    and defaults to 1.5 * w_inf. w_repro_max is documented as the size at which
    a typical mature individual invests all its energy into reproduction, not as a
    hard ceiling on size. The default value of the external mortality parameter
    z0 is now calculated from w_inf rather than w_max, so the purely
    computational boundary w_max no longer influences any model parameter. For
    backwards compatibility, if w_inf is not supplied it is taken from
    w_repro_max or w_max, so existing models and scripts are unaffected;
    however, new models built from the defaults may differ from 3.0.0.

Bug fixes

  • Fixed a bug in project() where the abundances of other components (set via
    setComponent()) were advanced only once per saved time step instead of once
    per dt time step. Their dynamics are now integrated with the same time step
    as the consumer and resource spectra, so results no longer depend on t_save.

  • getGrowthCurves() no longer emits a cryptic
    collapsing to unique 'x' values warning when a species' w_max lies exactly
    on a grid point. (#413)

  • getRDI(), getRDD() and getFlux() on a MizerSim object now correctly use
    the simulated time-varying effort instead of the initial effort. (#370)

  • plotCDF() / plotlyCDF() now plot each cumulative value on its bin's
    upper edge w_k + dw_k, following the inclusive cumulative-sum convention
    (the sum through bin k is the integral up to that bin's upper edge). This
    corrects a long-standing one-bin location offset and applies in both the
    default and the second-order schemes; under second-order bin-averaging the CDF
    is then second-order accurate in its placement as well as its increments.
    (#383)

  • plotYield() now uses sim2 = NULL instead of missing(sim2) to detect the
    optional second simulation argument, so it works correctly with do.call().
    This is backward-compatible.

  • distanceMaxRelRDI() now returns Inf instead of NaN when a previous RDI
    is zero, so projectToSteady() no longer mistakes a NaN distance for
    convergence.

Biosphere - Marine Life and Fishery - R
Published by gustavdelius 16 days ago

PowerCalc - Development build

Moving development build from master.

Energy Systems - Building Energy Monitoring - Python
Published by github-actions[bot] 17 days ago

b3gbi - Release v0.9.2

b3gbi 0.9.2 - Minor update:

  • Fixed add_ci() crash for completeness and relative_occupancy: Corrected the exclusion list (noci_list) in add_ci() to replace "coverage" with "completeness" and add "relative_occupancy". This ensures these unsupported indicators warn and return cleanly instead of throwing a fatal error.
  • Improved uncertainty calculation documentation: Fully documented the uncertainty calculations (or reasons for exclusion) for all indicators outside the scope of add_ci(), including observed species richness, richness density, sample completeness, relative occupancy, cumulative richness, turnover, and taxonomic distinctness.

Biosphere - Biodiversity Data Access and Management - R
Published by shawndove 17 days ago

PowerCalc - v1.21.2 🌈

Changes

  • #4223 Retry on average measurements @phoenixxx-1
  • #4227 Cleanup measure testsuite by introducing common fixtures @bramstroker

💡 Power profiles

  • #4188 Add hue centura spot @phoenixxx-1
  • #4202 Add hue lustre e14 @phoenixxx-1
  • #4231 Fix APC BE650G1 profile to discover per-device with sane defaults @brianegge
  • #4234 Add VeSync Core 200S & Core 300S air purifier profiles @SH1FT-W

🚀 Features

  • #4221 Add convergence option to effect measurements for more stable measurements @bramstroker
  • #4224 Implement internal forced naming for only_self_usage profiles @bramstroker
  • #4226 Cleanup profile library naming overrides @bramstroker
  • #4237 Fix security issues in github actions and use zizmor for scanning @bramstroker

🐛 Bug Fixes

  • #4220 Fix translation placeholder error @bramstroker
  • #4229 Fix global config persistence issues @bramstroker
  • #4235 Fix sonarqube issues @bramstroker
  • #4236 Cleanup github actions workflows and fix security issue @bramstroker

Supporters powering this project ⚡ 👇

🏆 5 coffees
pinkfin
@fakre
CloCkWeRX
and other legends

🥈 3 coffees
Lara Wiz
@marek.riebmann
Stephan Ristow
and other legends

🥉 2 coffees
@danielectronik
Sandro
Dale P

⭐ 1 coffee
Mauro T.
Rigo
Jan
and other legends

Support the project at https://buymeacoffee.com/bramski

Energy Systems - Building Energy Monitoring - Python
Published by github-actions[bot] 17 days ago

goat - v2.4.43 Bugfix Release

This release is a maintenance update addressing various issues identified since the 2.4.42 release. It does not introduce any new major features, but focuses solely on improving stability and reliability.

Full Changelog: https://github.com/plan4better/goat/compare/v2.4.42...v2.4.43

Consumption - Mobility and Transportation - TypeScript
Published by majkshkurti 18 days ago

Deadtrees.earth - v2026.06.26.3

What's Changed

Other Changes

Full Changelog: https://github.com/Deadwood-ai/deadtrees/compare/v2026.06.26.2...v2026.06.26.3

Biosphere - Forest Remote Sensing - TypeScript
Published by github-actions[bot] 18 days ago

Deadtrees.earth - v2026.06.26.2

What's Changed

Other Changes

Full Changelog: https://github.com/Deadwood-ai/deadtrees/compare/v2026.06.26.1...v2026.06.26.2

Biosphere - Forest Remote Sensing - TypeScript
Published by github-actions[bot] 18 days ago

Deadtrees.earth - v2026.06.26.1

What's Changed

Other Changes

Full Changelog: https://github.com/Deadwood-ai/deadtrees/compare/v2026.06.26...v2026.06.26.1

Biosphere - Forest Remote Sensing - TypeScript
Published by github-actions[bot] 18 days ago

BoaviztAPI - v2.3.0

Features

  • feat(gpu): add support for specific GPUs in API by @jonperron in #525

Fixes

  • fix(gpu): scale embedded impact by units and include GPU power in server use phase by @abrissard in #528
  • fix(openapi): fix description being not displayed after latest FastAPI update by @jonperron in #536

Chores

  • chore(security): update FastAPI and Starlette to latest version by @jonperron in #532
  • chore(deps): bump aiohttp from 3.13.5 to 3.14.0 by @dependabot[bot] in #526
  • chore(deps): bump shell-quote from 1.8.3 to 1.8.4 by @dependabot[bot] in #529
  • chore(deps): bump pydantic-settings from 2.14.1 to 2.14.2 by @dependabot[bot] in #533
  • chore(dev): add a devcontainer to quickly set up a development environment by @demeringo in #534
  • chore(update): bump to version 2.3.0 by @jonperron in #535

New Contributors

  • @abrissard made their first contribution in #528

Full Changelog: v2.2.0...v2.3.0

Consumption - Computation and Communication - Python
Published by jonperron 18 days ago

Deadtrees.earth - v2026.06.26

What's Changed

Other Changes

Full Changelog: https://github.com/Deadwood-ai/deadtrees/compare/v2026.06.25.8...v2026.06.26

Biosphere - Forest Remote Sensing - TypeScript
Published by github-actions[bot] 18 days ago

XRO - v1.0.2

Includes the code to calculate the XRO indices, along with notebooks for loading CDS ORAS5 data and performing real-time forecasts.

Full Changelog: https://github.com/senclimate/XRO/commits/v1.0.2

Climate Change - Earth and Climate Modeling - Jupyter Notebook
Published by senclimate 18 days ago

GridPath - GridPath v2026.5.0

What's Changed

Full Changelog: https://github.com/blue-marble/gridpath/compare/v2026.4.0...v2026.5.0

Energy Systems - Energy System Modeling Frameworks - Python
Published by anamileva 18 days ago

PortalData - 6.86.0

v6.86.0

Biosphere - Biodiversity Data Access and Management - R
Published by github-actions[bot] 19 days ago

Deadtrees.earth - v2026.06.25.8

What's Changed

Other Changes

Full Changelog: https://github.com/Deadwood-ai/deadtrees/compare/v2026.06.25.7...v2026.06.25.8

Biosphere - Forest Remote Sensing - TypeScript
Published by github-actions[bot] 19 days ago

PlantCV - PlantCV v4.11.1

What's Changed

Full Changelog: https://github.com/danforthcenter/plantcv/compare/v4.11...v4.11.1

Biosphere - Plants and Vegetation - Python
Published by nfahlgren 19 days ago

ha-evcc - Enable/Disable repeating vehicle charging plans #2 - #10 (+patch)

Repeating vehicle charging plans [+patch]

Evcc offer the configuration of repeating charging plans per vehicle since begin of this year. This feature never made it into this integration so far (I would like to say for good reasons). This morning I thought it would be at least nice to allow automations to enable/disable existing repeating plans. This have been added in this release.

Without going into the details - this feature is different implementation wise - specially the handling by the evcc-API (you need to post always the full JSON of all plans, even if you just want to modify one attribute). Anyway, after the update you have by default three additional switch entities shown in the vehicle devices. If you need more, you must enable the additional switched via the HA GUI.

Another thing, that is very special about these new switches are the actual setting (time, SOC, or days of week). They are not instantly visible. The plan data is accessible via the attributes (via the context menu 'details', reachable via the 3-dot's). In templates you can use {{state_attr("entity_id", "attribute")} to get a specific value.

IMHO most important is to be aware that the number of a repeating plan will/can change! As example, when you have plan#2 starting at 8:00, a plan#3 starting at 16:00 and a plan#4 starting at 18:00. When you now delete (in the evcc GUI) the plan#3, then previous plan#4 will become plan#3 - so in HA the time-attribute of the switch for the repeating plan#3 will change from 16:00 to 18:00!

Thanks @mkshb for the fix/patch - I am just a python noob!

My latest HA-Integration... (some sort of advertisement)

If you have some investments in ETF's (in €) and you want to see the development of different ISIN in near real time (of course only during trading hours), then I would kindly ask you to try my latest HA integration: ha-justetf-live and provide some feedback - The integration have it's focus on daily/monthly changes. TIA

Please consider supporting me

Thanks to those who have already supported me in the past weeks or month that is highly appreciated! To the other users: I am putting quite an amount of energy and passion into this integration. Perhaps you could give yourself a little push (if you can afford it) and become a sponsor.

GithubSponsor Wero Wise Revolut PayPal BuyMeCoffee Github Stars

If you haven't starred this integration in Github yet - please do so - TIA

Consumption - Mobility and Transportation - Python
Published by marq24 19 days ago

GISWATER - v4.14.5

🔽 Read the summarized changelog here 🔽

Fixed

  • Fix get_major_version function on tools_qgis to return the correct major version.

Full Changelog: https://github.com/Giswater/giswater_qgis_plugin/compare/v4.14.4...v4.14.5

📃 Check the official documentation here: ⛓️‍💥 Giswater Documentation

Natural Resources - Water Supply and Quality - PLpgSQL
Published by danimarinBG 19 days ago

Deadtrees.earth - v2026.06.25.7

What's Changed

Other Changes

Full Changelog: https://github.com/Deadwood-ai/deadtrees/compare/v2026.06.25.6...v2026.06.25.7

Biosphere - Forest Remote Sensing - TypeScript
Published by github-actions[bot] 19 days ago

Deadtrees.earth - v2026.06.25.6

What's Changed

Other Changes

Full Changelog: https://github.com/Deadwood-ai/deadtrees/compare/v2026.06.25.5...v2026.06.25.6

Biosphere - Forest Remote Sensing - TypeScript
Published by github-actions[bot] 19 days ago

Deadtrees.earth - v2026.06.25.5

What's Changed

Other Changes

Full Changelog: https://github.com/Deadwood-ai/deadtrees/compare/v2026.06.25.4...v2026.06.25.5

Biosphere - Forest Remote Sensing - TypeScript
Published by github-actions[bot] 19 days ago

Deadtrees.earth - v2026.06.25.4

What's Changed

Other Changes

Full Changelog: https://github.com/Deadwood-ai/deadtrees/compare/v2026.06.25.3...v2026.06.25.4

Biosphere - Forest Remote Sensing - TypeScript
Published by github-actions[bot] 19 days ago

Deadtrees.earth - v2026.06.25.3

What's Changed

Other Changes

Full Changelog: https://github.com/Deadwood-ai/deadtrees/compare/v2026.06.25.2...v2026.06.25.3

Biosphere - Forest Remote Sensing - TypeScript
Published by github-actions[bot] 19 days ago

Deadtrees.earth - v2026.06.25.2

What's Changed

Other Changes

Full Changelog: https://github.com/Deadwood-ai/deadtrees/compare/v2026.06.25.1...v2026.06.25.2

Biosphere - Forest Remote Sensing - TypeScript
Published by github-actions[bot] 19 days ago

Deadtrees.earth - v2026.06.25.1

What's Changed

Other Changes

Full Changelog: https://github.com/Deadwood-ai/deadtrees/compare/v2026.06.25...v2026.06.25.1

Biosphere - Forest Remote Sensing - TypeScript
Published by github-actions[bot] 19 days ago

Deadtrees.earth - v2026.06.25

What's Changed

Other Changes

Full Changelog: https://github.com/Deadwood-ai/deadtrees/compare/v2026.06.24.5...v2026.06.25

Biosphere - Forest Remote Sensing - TypeScript
Published by github-actions[bot] 19 days ago

Hydrocron - 1.9.0rc7

Full Changelog: https://github.com/podaac/hydrocron/compare/1.9.0rc6...1.9.0rc7

Hydrosphere - Ocean and Hydrology Data Access - Python
Published by github-actions[bot] 19 days ago

goat - v2.4.42 Bugfix Release

This release is a maintenance update addressing various issues identified since the 2.4.41 release. It does not introduce any new major features, but focuses solely on improving stability and reliability.

Full Changelog: https://github.com/plan4better/goat/compare/v2.4.41...v2.4.42

Consumption - Mobility and Transportation - TypeScript
Published by majkshkurti 19 days ago

PowerIO - v0.3.3

  • MCP server: unified the advertised tool surface to semantic verbs:
    convert, save, summary, parse, normalize, matrix, and display.
    The tools route transmission cases, distribution cases, PyPSA CSV folders, and
    gridfm datasets by format. Distribution parse returns canonical bmopf-json
    as its serial transport; transmission parse returns powerio-json.
    summary now has one canonical JSON schema across MCP and the CLI's new
    powerio summary command. Gridfm is a format behind parse/save, not its
    own MCP tool. PowerWorld .pwd display files parse through display, leaving
    room for a future open display format without renaming the tool. Older case,
    matrix, and PyPSA helper names stay as direct Python compatibility callables
    for one release, but they are no longer advertised as MCP tools.
  • Python API: restored the undocumented powerio.Case = Network alias for one
    release, but left it out of __all__ and docs; remove it in 0.4.0. The
    experimental distribution surface now uses powerio.dist.DistNetwork as
    the primary name to match the native DistNetwork hub type, while the
    exported powerio.dist.DistCase = DistNetwork alias stays for one release.
    powerio.dist is gated on the draft BMOPF schema (PIO_DIST_ABI_VERSION = 1)
    and not yet under the stability guarantee.
  • No C ABI change: PIO_ABI_VERSION stays 4 and PIO_DIST_ABI_VERSION stays 1,
    and the matrix builders are unchanged. The native extension's internal pyclass
    names changed (PyCase → PyNetwork, _DistCase → _DistNetwork) so repr()
    now renders the public Network(...) / DistNetwork(...) form directly; a
    rebuilt wheel is required.

What's Changed

Full Changelog: https://github.com/eigenergy/powerio/compare/v0.3.2...v0.3.3

Energy Systems - Energy Data Accessibility and Integration - Rust
Published by github-actions[bot] 19 days ago

Deadtrees.earth - v2026.06.24.5

What's Changed

Other Changes

Full Changelog: https://github.com/Deadwood-ai/deadtrees/compare/v2026.06.24.4...v2026.06.24.5

Biosphere - Forest Remote Sensing - TypeScript
Published by github-actions[bot] 19 days ago

Deadtrees.earth - v2026.06.24.4

What's Changed

Other Changes

Full Changelog: https://github.com/Deadwood-ai/deadtrees/compare/v2026.06.24.3...v2026.06.24.4

Biosphere - Forest Remote Sensing - TypeScript
Published by github-actions[bot] 19 days ago

Deadtrees.earth - v2026.06.24.3

What's Changed

Other Changes

Full Changelog: https://github.com/Deadwood-ai/deadtrees/compare/v2026.06.24.2...v2026.06.24.3

Biosphere - Forest Remote Sensing - TypeScript
Published by github-actions[bot] 19 days ago

pycontrails - v0.63.3

Fixes

  • Fix release workflow that prevented v0.63.2 wheels from being uploaded to PyPI.

Breaking changes

  • No longer build wheels for macOS x86_64. (macOS arm64 wheels will continue to be built and supported.)

Internals

  • Move cibuildwheel configs from the .github/workflows/release.yaml workflow to the pyproject.toml for easier local testing.
  • Remove mypy check for python 3.11 in the test workflow (numpy 2.5 only supports python 3.12 and above).
  • Remove the pytest.mark.unreliable marker in favor of skipping tests that make network calls with pytest.mark.skipif(OFFLINE). Set the PYCONTRAILS_OFFLINE environment variable to force these tests to be skipped regardless of network availability. This variable is now set in the release workflow to skip all tests that make network calls.
  • Remove the IN_GITHUB_ACTIONS flag from the LEO tests, which was redundant with the PYCONTRAILS_SKIP_LEO_TESTS environment variable.

Climate Change - Earth and Climate Modeling - Python
Published by zebengberg 19 days ago

Volca - v0.8.1

What's Changed

Full Changelog: https://github.com/ccomb/volca/compare/v0.8.0...v0.8.1

Industrial Ecology - Life Cycle Assessment - Haskell
Published by github-actions[bot] 19 days ago

Deadtrees.earth - v2026.06.24.2

What's Changed

Other Changes

Full Changelog: https://github.com/Deadwood-ai/deadtrees/compare/v2026.06.24.1...v2026.06.24.2

Biosphere - Forest Remote Sensing - TypeScript
Published by github-actions[bot] 19 days ago

ha-evcc - Enable/Disable repeating vehicle charging plans #2 - #10

Repeating vehicle charging plans

Evcc offer the configuration of repeating charging plans per vehicle since begin of this year. This feature never made it into this integration so far (I would like to say for good reasons). This morning I thought it would be at least nice to allow automations to enable/disable existing repeating plans. This have been added in this release.

Without going into the details - this feature is different implementation wise - specially the handling by the evcc-API (you need to post always the full JSON of all plans, even if you just want to modify one attribute). Anyway, after the update you have by default three additional switch entities shown in the vehicle devices. If you need more, you must enable the additional switched via the HA GUI.

Another thing, that is very special about these new switches are the actual setting (time, SOC, or days of week). They are not instantly visible. The plan data is accessible via the attributes (via the context menu 'details', reachable via the 3-dot's). In templates you can use {{state_attr("entity_id", "attribute")} to get a specific value.

IMHO most important is to be aware that the number of a repeating plan will/can change! As example, when you have plan#2 starting at 8:00, a plan#3 starting at 16:00 and a plan#4 starting at 18:00. When you now delete (in the evcc GUI) the plan#3, then previous plan#4 will become plan#3 - so in HA the time-attribute of the switch for the repeating plan#3 will change from 16:00 to 18:00!

My latest HA-Integration... (some sort of advertisement)

If you have some investments in ETF's (in €) and you want to see the development of different ISIN in near real time (of course only during trading hours), then I would kindly ask you to try my latest HA integration: ha-justetf-live and provide some feedback - The integration have it's focus on daily/monthly changes. TIA

Please consider supporting me

Thanks to those who have already supported me in the past weeks or month that is highly appreciated! To the other users: I am putting quite an amount of energy and passion into this integration. Perhaps you could give yourself a little push (if you can afford it) and become a sponsor.

GithubSponsor Wero Wise Revolut PayPal BuyMeCoffee Github Stars

If you haven't starred this integration in Github yet - please do so - TIA

Consumption - Mobility and Transportation - Python
Published by marq24 19 days ago

LISF - LISF master (pre-release) image

This AppImage is compatible with:

  • Linux: x86_64 machines (as reported by uname -s -m)
  • GLIBC: 2.22 or newer (as reported by ldd --version)
  • MPI: MPICH, Intel MPI, or Cray MPI

After downloading the AppImage, run:

chmod 755 ./LISF-x86_64.AppImage

To get started with the AppImage, run:

./LISF-x86_64.AppImage -h

Note:

This AppImage requires FUSE to run. If you get an error, then try:

mkdir LISF-x86_64
cd LISF-x86_64
../LISF-x86_64.AppImage --appimage-extract
cd ..
./LISF-x86_64/squashfs-root/AppRun -h

Hydrosphere - Freshwater and Hydrology - Fortran
Published by github-actions[bot] 19 days ago

Deadtrees.earth - v2026.06.24.1

What's Changed

Other Changes

Full Changelog: https://github.com/Deadwood-ai/deadtrees/compare/v2026.06.24...v2026.06.24.1

Biosphere - Forest Remote Sensing - TypeScript
Published by github-actions[bot] 19 days ago

goat - v2.4.41 Bugfix Release

This release is a maintenance update addressing various issues identified since the 2.4.40 release. It does not introduce any new major features, but focuses solely on improving stability and reliability.

What's Changed

Full Changelog: https://github.com/plan4better/goat/compare/v2.4.39...v2.4.41

Consumption - Mobility and Transportation - TypeScript
Published by majkshkurti 20 days ago

Deadtrees.earth - v2026.06.24

What's Changed

Other Changes

Full Changelog: https://github.com/Deadwood-ai/deadtrees/compare/v2026.06.23.1...v2026.06.24

Biosphere - Forest Remote Sensing - TypeScript
Published by github-actions[bot] 20 days ago

Monitorfish - v1.114.0

Cette version est tagguée en v1.113.0 (écrase la version précédente)

What's Changed

🎉 Fonctionnalités

Full Changelog: https://github.com/MTES-MCT/monitorfish/compare/v1.113.0...v1.114.0

Biosphere - Marine Life and Fishery - HTML
Published by louptheron 20 days ago