Circuitscape - v5.15.0

Circuitscape v5.15.0

Diff since v5.14.0

Merged pull requests:

• Bump codecov/codecov-action from 4 to 5 (#426) (@dependabot[bot])
• Update to AlgebraicMultigrid 1.x (#430) (@ViralBShah)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] 8 months ago

Circuitscape - v5.14.0

Circuitscape v5.14.0

Diff since v5.13.3

Merged pull requests:

• Bump julia-actions/setup-julia from 1 to 2 (#413) (@dependabot[bot])
• CHOLMOD can now solve matrices with float32 values (Julia 1.11) (#418) (@ViralBShah)
• Update ci.yml (#420) (@ViralBShah)
• Support flags: use_unit_currents and use_direct_grounds (#421) (@ranjanan)
• Fix accumulator bug in network pairwise parallel mode (#422) (@ranjanan)
• Update Project.toml (#425) (@ViralBShah)

Closed issues:

• Loading Circuitscape in R (via Julia) (#381)
• Use Pkg extensions for CircuitscapeMKLPardiso (#389)
• type GraphProblem has no field cum_node_curr when parallelize=True (#398)
• Circuitscape not running in container (#401)
• Is there a QGIS version of the Circuitscape Tool in ArcGIS? (#402)
• different outputs from Circuitscape Python and Julia in advanced mode (#414)
• UndefRefError: access to undefined reference (#417)
• Included pairs file throw no method isless() (#423)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] about 1 year ago

Circuitscape - v5.13.3

Circuitscape v5.13.3

Diff since v5.13.2

Merged pull requests:

• Increase error tolerance for advanced mode (#410) (@vlandau)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] almost 2 years ago

Circuitscape - v5.13.2

Circuitscape v5.13.2

Diff since v5.13.1

Merged pull requests:

• Bump actions/checkout from 3 to 4 (#395) (@dependabot[bot])
• CompatHelper: bump compat for AlgebraicMultigrid to 0.6, (keep existing compat) (#396) (@github-actions[bot])
• Bump actions/cache from 3 to 4 (#404) (@dependabot[bot])
• increase solve error tolerance from 1e-6 to 1e-4 (#407) (@vlandau)
• Bump codecov/codecov-action from 3 to 4 (#409) (@dependabot[bot])

Closed issues:

• pkg test failed (#364)
• Precompilation warning for a missing type (#403)
• Increase tolerance of assert check for solve accuracy, or add option to allow failure. (#406)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] almost 2 years ago

Circuitscape - v5.13.1

Circuitscape v5.13.1

Diff since v5.13.0

Closed issues:

• "KeyError: key ([#],[#]) not found" (#260)
• Julia states my habitat file is empty (#366)
• Circuitscape stop working in advanced and one-to-all mode (#382)

Merged pull requests:

• CompatHelper: add new compat entry for DelimitedFiles at version 1, (keep existing compat) (#391) (@github-actions[bot])
• CompatHelper: bump compat for GZip to 0.6, (keep existing compat) (#392) (@github-actions[bot])
• In advanced mode, write current maps if any of the current map flags are true (#393) (@ranjanan)
• Release 5.13.1 (#394) (@ranjanan)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] over 2 years ago

Circuitscape - v5.13.0

Circuitscape v5.13.0

Diff since v5.12.3

Merged pull requests:

• Update Julia version compat to 1.9 (#384) (@ranjanan)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] over 2 years ago

Circuitscape - v5.12.3

Circuitscape v5.12.3

Diff since v5.12.2

Merged pull requests:

• Fix indexing while reading source and ground files (#378) (@ranjanan)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] almost 3 years ago

Circuitscape - v5.12.2

Circuitscape v5.12.2

Diff since v5.12.1

Closed issues:

• .out file not correct (#159)
• ERROR: DimensionMismatch (#199)
• Include pairs not implemented in the polygon focal point case (#278)
• ncol warning (#285)
• Included pairs file ignored (#341)
• Short circuit regions not recognized (#353)
• Assertion error: linear solve did not converge in single precision (#362)
• Nothing happens after first round of calculations in all-to-one mode (#367)
• AssertionError: norm(G * v .- curr) / norm(curr) - multiple failures (#370)

Merged pull requests:

• add include pairs logic when polygons in point files (#374) (@ranjanan)
• write correct solver in output file (#375) (@ranjanan)
• network: check if nodes start from zero (#376) (@ranjanan)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] almost 3 years ago

Circuitscape - v5.12.1

Circuitscape v5.12.1

Diff since v5.12.0

Closed issues:

• Error happens in Julia. "At least one focal node location falls outside of habitat map" (#360)
• Invalid index Error, but model runs fine on GUI (#368)
• Advanced run not completing (see also #131) (#369)

Merged pull requests:

• While making current maps, check for both (node1,node2) and (node2,node1) (#372) (@ranjanan)
• Speedup a common advanced mode calc (#373) (@ranjanan)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] almost 3 years ago

Circuitscape - v5.12.0

Circuitscape v5.12.0

Diff since v5.11.2

Closed issues:

• ERROR: LoadError: InitError: could not load library "libproj.so" libcurl.so: version `CURL_4' not found (#352)
• Error issue question (#356)

Merged pull requests:

• CompatHelper: bump compat for ArchGDAL to 0.9, (keep existing compat) (#361) (@github-actions[bot])
• Move Pardiso solver to lib (#371) (@ranjanan)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] about 3 years ago

Circuitscape - v5.11.2

Circuitscape v5.11.2

Diff since v5.11.1

Closed issues:

• ERROR: ArgumentError: column indices J[k] must satisfy 1 <= J[k] <= n (#333)
• ArgumentError: dense matrix construction failed for unknown reasons (#334)

Merged pull requests:

• fix sparse mat constrcution (#357) (@ranjanan)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] over 3 years ago

Circuitscape - v5.11.1

Circuitscape v5.11.1

Diff since v5.11.0

Closed issues:

• AssertionError: norm(G * v .- curr, Inf) / norm(v, Inf) < 1.0e-5 (#345)
• Core Mapper not reading .xlsx file (#347)
• ERROR: SuiteSparse.CHOLMOD.CHOLMODException("") (#351)

Merged pull requests:

• Make assertion check consistent with iterativesolvers.jl (#348) (@ranjanan)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] almost 4 years ago

Circuitscape - v5.11.0

Circuitscape v5.11.0

Diff since v5.10.2

Merged pull requests:

• CompatHelper: bump compat for AlgebraicMultigrid to 0.5, (keep existing compat) (#343) (@github-actions[bot])
• Bump deps versions. Disable Pardiso tests (#346) (@ViralBShah)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] almost 4 years ago

Circuitscape - v5.10.2

Circuitscape v5.10.2

Diff since v5.10.1

Closed issues:

• Ground files need to take in txt files (advanced mode) (#338)

Merged pull requests:

• Some txt file reading logic for advanced mode (#339) (@ranjanan)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] about 4 years ago

Circuitscape - v5.10.1

Circuitscape v5.10.1

Diff since v5.10.0

Closed issues:

• Install Error due to GDAL: libgdal-28.dll module could not be found (#329)
• CS tries to solve thousands of pairs (#332)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] about 4 years ago

Circuitscape - v5.10.0

Circuitscape v5.10.0

Diff since v5.9.1

Closed issues:

• Issue branch_current output in network mode (#282)
• memory error (#292)
• ERROR: MethodError: no method matching connected_components(::SimpleWeightedGraphs.SimpleWeightedGraph{Int64,Float64}) (#325)
• Empty output file (#327)
• Current file not written? Circuitscape runs, but has no output (#328)

Merged pull requests:

• Fix some cumulative current map logic (#330) (@ranjanan)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] about 4 years ago

Circuitscape - v5.9.1

Circuitscape v5.9.1

Diff since v5.9.0

Merged pull requests:

• Add internal function to use in Omniscape (#326) (@vlandau)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] about 4 years ago

Circuitscape - v5.9.0

Circuitscape v5.9.0

Diff since v5.8.4

Closed issues:

• Create cumulative branch and node currents in network mode (#119)
• ERROR: ArgumentError: column indices J[k] must satisfy 1<= J[k] <= n (#281)
• Error with networks consisting of multiple components (#283)
• Circuitscape 5 is not writing cumulative branch and node current files for network mode (#303)
• ERROR: SuiteSparse.CHOLMOD.CHOLMODException("") (#316)
• Test failed on Debian : no method matching connected_components(::SimpleWeightedGraphs.SimpleWeightedGraph{Int64, Float64}) (#321)

Merged pull requests:

• Currents and cumulative currents in network mode (#318) (@ranjanan)
• Move to Graphs from LightGraphs (#319) (@ranjanan)
• Network advanced - connected components (#320) (@ranjanan)
• CompatHelper: add new compat entry for SimpleWeightedGraphs at version 1, (keep existing compat) (#322) (@github-actions[bot])
• CompatHelper: add new compat entry for Graphs at version 1, (keep existing compat) (#323) (@github-actions[bot])
• Add info about 0 vs 1 based indexing, throw error if not 0 or 1 (#324) (@ranjanan)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] about 4 years ago

Circuitscape - v5.8.4

Circuitscape v5.8.4

Diff since v5.8.3

Closed issues:

• Compress grids has no effect (#168)
• Blank screen on GUI after running main executable (#192)
• Convert circuitscape manual to Julia Documenter format (#242)
• Get CI to pass (#245)
• Pemission denied and paralell processes number (#284)
• Docs point to non-existent "examples" folder for examples (#286)
• Cumulative current map all NODATA in circuitscape.jl, but show currents in circuitscape GUI (#289)
• CHOLMOD solver error (#300)
• AssertErrors for several users -- norm(G * v - curr) < 1e-6 check failing (#305)
• MethodError: no method matching Circuitscape.RasterData(::Matrix{Float64}, ::Matrix{Int64}, ::Matrix{Float64}, ::Matrix{Float64}, ::Tuple{Vector{Int64}, Vector{Int64}, Vector{Int64}}, ::Matrix{Float64}, ::Nothing, ::Circuitscape.RasterMeta) (#306)
• What wrong by "output/mgNetworkVerify1.out" (#307)
• Circuitscape 5.0.0 with INIBuilder: habitat_map_is_resistance = resistance incorrectly treats habitat map as conductance. (#312)
• GDALError (CE_Failure, code 1): write failed, disk full? (#314)
• resistance_3columns file (#315)

Merged pull requests:

• Add better error message when include pairs file is incorrect (#310) (@ranjanan)
• builder passed incorrect value to habitat_map_is_resistances, (#313) (@vlandau)
• remove references to examples directory from docs (#317) (@vlandau)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] about 4 years ago

Circuitscape - v5.8.3

Circuitscape v5.8.3

Diff since v5.8.2

Closed issues:

• Pkg.test("Circuitscape") fail in double precision, raster pairwise and advanced (Ubuntu) (#302)

Merged pull requests:

• Ask for > 5 digits of precision when solving linear system (#309) (@ranjanan)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] over 4 years ago

Circuitscape - v5.8.2

Circuitscape v5.8.2

Diff since v5.8.1

Closed issues:

• Make new release with AMG 0.4.0 (#276)
• AssertionError: norm(asolve * volt .- sources) < 1.0e-5 in "all-to-one" mode using the latest development version of Circuiscape. v5.7.1 (#288)

Merged pull requests:

• CompatHelper: bump compat for "ArchGDAL" to "0.7" (#301) (@github-actions[bot])
• Update Pardiso deps, julia deps (#304) (@ranjanan)
• Update issue templates (#308) (@ranjanan)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] over 4 years ago

Circuitscape - v5.8.1

Circuitscape v5.8.1

Diff since v5.8.0

Closed issues:

• Cholmod for advanced mode (#136)

Merged pull requests:

• Pass the suppress_messages arg to some functions new to 5.8.0 (#296) (@vlandau)
• Reduce error tolerance for matrix norms when using single precision (#297) (@vlandau)
• Revert "Reduce error tolerance for matrix norms when using single pre… (#298) (@ranjanan)
• Redo of assert tolerance after accidental revert of previous PR (#299) (@vlandau)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] over 4 years ago

Circuitscape - v5.8.0

Circuitscape v5.8.0

Diff since v5.7.1

Closed issues:

• disable logging during tests (#222)
• Fix or remove codecov badge (#250)
• effective resistance for one-to-all (#252)
• Denied access to folder (#261)
• Pkg.test("Circuitscape") fail on new installation (#266)
• trouble with variable source strengths (#268)
• "Error: syntax: invalid escape sequence" (#271)
• ValueError: could not broadcast input array fro, shape (3,1) into shape (3) (#272)
• ERROR: KeyError: key "Zlib_jll" not found (#274)
• Move CI/docs building to GitHub Actions (#275)
• BoundsError (#287)
• Tests fail with ArchGDAL 0.6.0 (#290)

Merged pull requests:

• Add option to use MKL Pardiso, reduce number of tests (#225) (@ranjanan)
• Use ArchGDAL.write() to persist rasters to disk. (#263) (@yeesian)
• Use do-blocks for managing rasters via ArchGDAL (#264) (@yeesian)
• Move documentation to Documenter (#265) (@ranjanan)
• Disable logging during tests (#267) (@ranjanan)
• Rework alltoone mode with and without var strengths (#270) (@ranjanan)
• CompatHelper: bump compat for "IterativeSolvers" to "0.9" (#279) (@github-actions[bot])
• CompatHelper: bump compat for "AlgebraicMultigrid" to "0.4" (#280) (@github-actions[bot])
• Fix ASCII header in some test files (#291) (@vlandau)
• tol -> reltol (#293) (@ranjanan)
• CompatHelper: add new compat entry for "AlgebraicMultigrid" at version "0.4" (#294) (@github-actions[bot])

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] over 4 years ago

Circuitscape - v5.7.1

Circuitscape v5.7.1

Diff since v5.7.0

Closed issues:

• InexactError: Int64 (#257)
• Add warning when there are non-integers in node file (#258)
• Error when using Circuitscape from R (#262)

Merged pull requests:

• add informative error throw if node file (point_file) contains non-integers (#259) (@vlandau)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] over 5 years ago

Circuitscape - v5.7.0

Circuitscape v5.7.0

Diff since v5.6.0

Closed issues:

• julia version and Circuitscape (#251)
• Installing master branch of Circuitscape fails (#254)

Merged pull requests:

• add option to suppress @info (#255) (@vlandau)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] over 5 years ago

Circuitscape - Zenodo release

Biosphere - Terrestrial Wildlife - Julia
Published by ranjanan over 5 years ago

Circuitscape - v5.6.0

Circuitscape v5.6.0

Diff since v5.5.5

Closed issues:

• New CHOLMOD memory errors (#150)
• Pkg.test("Circuitscape"): Single test failure - Raster Pairwise (#178)
• Make 64-bit indexing default. Was ERROR: LoadError: InexactError: trunc(Int32, 2147483653) (#200)
• ERROR: BoundsError: attempt to access 0-element Array{SharedArrays.SharedArray{Float64,2},1} at index [1] (#201)
• Failing tests in Raster one to all in Julia 1.4-dev (#202)
• JSExpr: Unsupported string expression, "$(e)"JSExpr: Unsupported string expression, "$(e)" 64-bit Windows installer (#208)
• Bounds error (#209)
• Error: zero resistance values are not currently supported for habitat maps. Use a shor circuit region file instead (#210)
• ERROR: LinearAlgebra.LAPACKException(2) (#211)
• Test failure on mac due to too many open shm segments (#212)
• Experiment with METIS ordering in cholesky (#213)
• Trouble executing script with specified library location (#214)
• Please reopen if the issue persists. (#215)
• No output with completed script (#216)
• Experiment with PARDISO solvers from MKL (#218)
• Add possibility to save as .tif with compression (#220)
• New GUI using Gtk? (#228)
• Circuitscape in Julia unable to process a 1.4 Billion pixel landscape (#232)
• GZip requirement 0.5.1 can't be met (#234)
• Maximum amount of pairs and batch processing (#235)
• InexactError while parsing nodata values (#239)
• More issues with opened files on Mac (#241)
• ArchGDAL version dependency error (#244)
• write_as_tif options only works if value is true, not True (#246)

Merged pull requests:

• Make 64 bit indexing default (#206) (@ranjanan)
• Fix a bug where max curr was not being initialized properly (#207) (@ranjanan)
• Install TagBot as a GitHub Action (#219) (@JuliaTagBot)
• Vl/travis - dependency stuff (#221) (@vlandau)
• Add a few closes for filehandles. (#223) (@ViralBShah)
• add tif/asc read and write support (#229) (@vlandau)
• Pkg.checkout not supported anymore (#237) (@VLucet)
• Fix InexactError in Read Raster (#240) (@vlandau)
• Modify default call to pmap when paralellizing (#243) (@VLucet)
• Check for write_as_tif to be in TRUELIST (#247) (@VLucet)

Biosphere - Terrestrial Wildlife - Julia
Published by github-actions[bot] over 5 years ago

Circuitscape - v5.5.5

v5.5.5 (2019-11-29)

Diff since v5.5.4

Closed issues:

• GZip broken for Windows in Julia 1.3, so Circuitscape (and Omniscape) also broken (#203)
• ERROR: Failed to read habitat map. There may be errors in your file. (#198)
• Error : UndefVarError : warn not defined (#193)
• Two Issues: Memory Error and Not working on my desktop (#191)
• Very Slow Processing (#190)
• Potential speedups (#174)

Merged pull requests:

• update GZip version in MANIFEST (#205) (vlandau)
• updated GZip dep (#204) (vlandau)
• Some bug squashing for INIBuilder (#195) (ranjanan)
• Add new UI (#194) (ranjanan)

Biosphere - Terrestrial Wildlife - Julia
Published by julia-tagbot[bot] about 6 years ago

Circuitscape - v5.5.4

v5.5.4 (2019-08-06)

Diff since v5.5.3

Closed issues:

• Documentation Clarification (#186)
• Questions from your “average user” (#179)
• how to cite circuitscape.jl? (#173)
• Warn() deprecated (#171)

Biosphere - Terrestrial Wildlife - Julia
Published by julia-tagbot[bot] over 6 years ago

Circuitscape - v5.5.3

Biosphere - Terrestrial Wildlife - Julia
Published by julia-tagbot[bot] over 6 years ago

Circuitscape -

Biosphere - Terrestrial Wildlife - Julia
Published by ranjanan over 6 years ago

Circuitscape -

Biosphere - Terrestrial Wildlife - Julia
Published by ranjanan over 6 years ago

Circuitscape -

• Parallelism in one to all and all to one modes
• Fix long standing include pairs bugs

Biosphere - Terrestrial Wildlife - Julia
Published by ranjanan almost 7 years ago

Circuitscape - Julia 1.0 compatible release

Biosphere - Terrestrial Wildlife - Julia
Published by ranjanan about 7 years ago

Circuitscape -

• Upgrades to Memento v0.7.0
• Stabilises the solver with some simple regularisation
• Fix a performance bug in advanced mode that stalls voltages being assigned to cells
• Fix a bug in shortcut mode while using the CHOLMOD solver which makes it do extra work
• Introduce a flag that lets you bump indexing to Int64

Biosphere - Terrestrial Wildlife - Julia
Published by ranjanan over 7 years ago

Circuitscape -

Bug fix for:

• not entering shortcut mode when we want cumulative maps and no other voltage or current maps

Biosphere - Terrestrial Wildlife - Julia
Published by ranjanan over 7 years ago

Circuitscape -

Includes the following fixes:

1. Parallel cumulative maps for raster mode (#123)
2. Batch mode for CHOLMOD (#126)

Biosphere - Terrestrial Wildlife - Julia
Published by ranjanan over 7 years ago

Circuitscape -

Fixes the following bugs:

• Improves logging for shortcut calculation mode (#109)
• Adds 1 as a way of specifying true (#112)
• Improves logging for when point files have polygons (#117)
• Fixes the 3 column resistance file bug (#120)
• Adds utils for reading and writing cum and max current maps (#115)

Biosphere - Terrestrial Wildlife - Julia
Published by ranjanan over 7 years ago

Circuitscape -

Biosphere - Terrestrial Wildlife - Julia
Published by ranjanan over 7 years ago

Circuitscape -

Biosphere - Terrestrial Wildlife - Julia
Published by ranjanan almost 8 years ago

Circuitscape -

Biosphere - Terrestrial Wildlife - Julia
Published by ranjanan about 8 years ago

Circuitscape -

Biosphere - Terrestrial Wildlife - Julia
Published by ranjanan over 8 years ago