fathomnet-py - v1.8.1

v1.8.1 (2025-04-08)

This release is published under the MIT License.

Bug Fixes

• fathomnet-generate: Use new DTO BaseModel syntax for model copy and JSON dump (8611d68)

Chores

• Add CITATION.cff (d4cc5a5)

Testing

• Temporarily disable tests for broken endpoints (efdbede)

---

Detailed Changes: v1.8.0...v1.8.1

Biosphere - Marine Life and Fishery - Python
Published by github-actions[bot] 24 days ago

fathomnet-py - v1.8.0

v1.8.0 (2025-03-03)

This release is published under the MIT License.

Bug Fixes

• Fix typing for Python 3.8, 3.9 (bb29e5f)

Chores

• Correct syntax for setting PATH in CI/CD workflow (a694975)

Features

• Migrate from fathomnet.org to database.fathomnet.org; rye -> uv; dataclasses_json -> pydantic (fc86d07)

---

Detailed Changes: v1.7.1...v1.8.0

Biosphere - Marine Life and Fishery - Python
Published by github-actions[bot] about 2 months ago

fathomnet-py - v1.7.1

v1.7.1 (2024-11-11)

Bug Fixes

• Remove debug print statements from find_by_display_name function, worms test (092d807)

Chores

• Update CI/CD workflow to set PATH for Rye installation (6959642)

Biosphere - Marine Life and Fishery - Python
Published by github-actions[bot] 6 months ago

fathomnet-py - v1.7.0

v1.7.0 (2024-11-04)

Chores

• chore: add docs rye script for building docs (66e97f5)

• chore: swap Poetry for Rye build system (e698cd6)

Code Style

• style: apply ruff linting & formatting (1bdc3d8)

Documentation

• docs: slight tweaks to README.md (0895d5c)

• docs: fix badge display in README.md (7c6dd4b)

• docs: update README.md with badges (2fe5256)

• docs: add CONTRIBUTING.md (befbcf0)

Features

• feat: add function to retrieve owner institution codes by image UUID (773290a)

Biosphere - Marine Life and Fishery - Python
Published by github-actions[bot] 6 months ago

fathomnet-py - v1.6.1

v1.6.1 (2024-08-01)

Fix

• fix: fix bbox conversion to Pascal VOC to use 1-based pixel index (440afb0)

Biosphere - Marine Life and Fishery - Python
Published by github-actions[bot] 9 months ago

fathomnet-py - v1.6.0

v1.6.0 (2024-07-18)

Feature

• feat: allow a start page number in fathomnet.util.page (62ca914)

Biosphere - Marine Life and Fishery - Python
Published by github-actions[bot] 10 months ago

fathomnet-py - v1.5.1

v1.5.1 (2024-07-16)

Fix

• fix: fix typo in -f option for fathomnet-generate (c304ce1)

Biosphere - Marine Life and Fishery - Python
Published by github-actions[bot] 10 months ago

fathomnet-py - v1.5.0

v1.5.0 (2024-07-16)

Chore

• chore: apply pre-commit hook on all files (0190345)

• chore: add Python 3.12 to CI pipeline targets (cf979cf)

• chore: add formatting/linting pre-commit setup (ca07b19)

Documentation

• docs: move tutorial notebook into examples dir (c4db176)

• docs: switch order of imports/pip install in tutorial notebook

switched order of imports to avoid ipyleaflet error with fathomnet install and added explanation on running outside of colab. (#28) (48afc49)

• docs: fix broken readthedocs build #27

Install the current package (fathomnet-py) prior to building the Sphinx docs via RTD (3154b79)

Feature

• feat: add YOLO dataset generation to fathomnet-generate (1bacb1f)

Fix

• fix: make TEST_X_API_KEY use an environment variable of the same name (22508cf)

Unknown

• Merge branch 'develop' (8202949)

• Merge branch 'main' into develop (4a29a68)

• add accepted flag to worms.get_descendants_names

Add support for worms-server 0.5.2 (0dc9ed8)

Biosphere - Marine Life and Fishery - Python
Published by github-actions[bot] 10 months ago

fathomnet-py - v1.4.0

v1.4.0 (2024-04-09)

Feature

• feat: add accepted flag to worms.get_descendants_names

Add support for worms-server 0.5.2 (de0aec2)

Biosphere - Marine Life and Fishery - Python
Published by github-actions[bot] about 1 year ago

fathomnet-py - v1.3.0

v1.3.0 (2024-02-29)

Feature

• feat: support worms-server 0.5.1

Add support for worms-server 0.5.1. This adds the acceptedAphiaId field to the WormsNode DTOs as well as a new endpoint for getting a WormsNames DTO by Aphia ID. (f1989bc)

Biosphere - Marine Life and Fishery - Python
Published by github-actions[bot] about 1 year ago

fathomnet-py - v1.2.2

v1.2.2 (2024-02-21)

Chore

• chore: add missing v for ref spec (3212b13)

Documentation

• docs: add worms API module documentation (11c0112)

Fix

• fix: correct typo in WormsNode.aphiaId

Fixes #25 (5feeeb0)

Biosphere - Marine Life and Fishery - Python
Published by github-actions[bot] about 1 year ago

fathomnet-py - v1.2.1

v1.2.1 (2024-02-06)

Chore

• chore: use released ref for publish in CI/CD pipeline (d39c482)

Fix

• fix: use worms API directly for fathomnet taxa provider

This is a temporary workaround for a bug in Micronaut that causes the fathomnet taxa provider to fail for large trees (e.g., Scleractinia). (f887a95)

Unknown

• Merge branch 'main' into develop (86c574e)

Biosphere - Marine Life and Fishery - Python
Published by github-actions[bot] about 1 year ago

fathomnet-py - v1.2.0

v1.2.0 (2024-02-06)

Chore

• chore: merge CI/CD workflows (8e0d760)

Documentation

• docs: add Sphinx RTD theme build requirement (fccd808)

• docs: update copyright year to 2024 (1650bc5)

• docs: add sphinx-rtd-theme as a dev dependency (9be9dee)

• docs: update Python version and build configuration for readthedocs (ef96d8d)

Feature

• feat: add functions to call fast WoRMS API directly (21942b8)

Fix

• fix: make the linter happy (6cc52f6)

Biosphere - Marine Life and Fishery - Python
Published by github-actions[bot] about 1 year ago

fathomnet-py - v1.1.5

v1.1.5 (2024-01-10)

Fix

• fix: quote display/org names in users find functions (591e67a)

• fix: quote provider name and concept in taxa find functions, remove print from test (dde9eb5)

• fix: quote observer name in boundingboxes.audit_by_observer (b94c87e)

• fix: quote boundingboxes.audit_by_concepts URL fragment, add test case (5ea7b45)

• fix: update activity find functions for new DTO (cdf5617)

Biosphere - Marine Life and Fishery - Python
Published by github-actions[bot] over 1 year ago

fathomnet-py - v1.1.4

v1.1.4 (2024-01-09)

Documentation

• docs: fix broken tests badge (dbfbea8)

Fix

• fix: quote concept in images.find_by_concept, add test (33aa430)

Unknown

• Merge branch 'develop' (14988d6)

Biosphere - Marine Life and Fishery - Python
Published by github-actions[bot] over 1 year ago

fathomnet-py - v1.1.3

v1.1.3 (2023-09-13)

Documentation

• docs: Add script documentation

Closes #5 (1eadc8f)

Fix

• fix(api): Improve client error exception

Add the fathomnet.util.debug_format_response to the ValueError exception
raised when a status code < 500 and != 401 / 403 is returned. Fixes #16 (6b0b911)

Biosphere - Marine Life and Fishery - Python
Published by github-actions[bot] over 1 year ago

fathomnet-py - v1.1.2

v1.1.2 (2023-09-12)

Fix

• fix: Add condition to CD workflow (df3432d)

• fix: Add CD (8979d75)

Biosphere - Marine Life and Fishery - Python
Published by github-actions[bot] over 1 year ago

fathomnet-py - v1.1.1

v1.1.1 (2023-09-12)

Fix

• fix: Remove publish step from CI (for now) (3ba596b)

• fix: Version in pyproject.toml (dd2d9a2)

Biosphere - Marine Life and Fishery - Python
Published by kevinsbarnard over 1 year ago

fathomnet-py - v1.0.0

The FathomNet Python API is out of beta! This release includes all API support for the FathomNet v1.0 release.

Biosphere - Marine Life and Fishery - Python
Published by kevinsbarnard over 1 year ago