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CHANGELOG

v1.6.1 (2024-08-01)

Fix

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

v1.6.0 (2024-07-18)

Feature

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

v1.5.1 (2024-07-16)

Fix

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

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)

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)

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)

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)

v1.2.1 (2024-02-06)

Unknown

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

v1.2.0 (2024-02-06)

Chore

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

  • 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: 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)

  • fix: make the linter happy (6cc52f6)

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)

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

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)

v1.1.2 (2023-09-12)

Fix

v1.1.1 (2023-09-12)

Fix

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

  • fix: Version in pyproject.toml (dd2d9a2)

v1.1.0 (2023-09-12)

Feature

  • feat: Set up python-semantic-release (4019f18)

v1.0.2 (2023-09-12)

Unknown

  • Bump version (e7c404d)

  • Unit tests updated for latest API changes (#20) (2a32d1d)

  • Fix for new "Entity" object names in tests (cdcf484)

  • Add req/response to server error exception message (00f2ff6)

v1.0.1 (2023-08-29)

Unknown

  • Bump version (0ba8b2f)

  • Fix for empty paged results (aba2c01)

  • Add page utility function (accad89)

  • Fix taxa tests for fathomnet provider (dfe44fe)

v1.0.0 (2023-08-03)

Unknown

v0.7.0 (2023-08-03)

Unknown

  • Bump version (23286d7)

  • Use v3 checkout/setup-python actions (f590e28)

  • Add changes missed in last commit (0a10130)

  • Support for fathomnet-rest-api v1.5.0 Several fixes to pageable endpoints Require Python 3.7 -> 3.8.1 Add test suite for user endpoints Slight tweaks to GH action linting (8db72d3)

  • Cleanup imports (19dd45f)

  • Added MBARI MB Benthic model (e7d7938)

  • Add poetry.lock to .gitignore (886a726)

  • Refactor fathomnet.models -> fathomnet.dto (ce4ad97)

  • Minor fixes (7206e14)

  • More coco manipulation and reorganizing (582290e)

  • Add coco download section to tutorial notebook (40369e3)

v0.6.0 (2023-02-07)

Unknown

  • Merge branch 'develop' (4a7bc1e)

  • Add Python 3.10 to CI (01d48da)

  • Flake8 nits (8477666)

  • Merge branch 'develop' (a25582e)

  • Add test for audit endpoints (5e9f4b9)

  • Merge branch 'develop' (1e5e69b)

  • Support boundingboxes audit endpoints (46a47ea)

  • Removed forced debug print statement (3ae2f69)

v0.5.2 (2022-04-07)

Unknown

  • Merge branch 'develop' into main (1f71f63)

  • Fix missing functions in fathomnet-generate (31477ab)

  • Merge branch 'develop' (1dc6689)

  • Bump version (ccccb89)

  • Merge branch 'develop' (2ff153b)

  • Added region endpoint per REST API 1.1.1 (d5cdf1a)

  • Cleaned up fathomnet_generate formatting (2aad07b)

v0.5.1 (2022-03-31)

Unknown

  • Merge branch 'develop' into main (abceeea)

  • Fix fathomnet-generate bug in Python 3.7 (df8e25a)

v0.5.0 (2022-03-31)

Unknown

  • Merge branch 'develop' into main (e2dc5fd)

  • Bump version, require newer coco-lib (566587e)

  • Merge branch 'develop' into main (7ff1d32)

  • Updated README (dbfb2b2)

  • Removed unused cell (0bce7b3)

  • Changed day two order. Removed calls to Google Drive (56ae925)

  • Update CoLab link to main

Changed CoLab link in README to open main instead of dev branch notebook. (9c57174)

  • Workshop-ready version of tutorial notebook (0ca5c81)

  • Updated tutorial.ipynb (2b93d26)

  • Colab badge for tutorial notebook (e3880b5)

  • add tutorial notebook (60dfa5f)

v0.4.2 (2022-03-09)

Unknown

  • Bump version (507b0b1)

  • Merge pull request #7 from fathomnet/download

Download function in fathomnet-generate (173a9ee)

  • Merge remote-tracking branch 'origin/download' into download (01cc97d)

  • Context manager for image download

More responsible file management for copyfilebobj

Co-authored-by: Kevin Barnard <[email protected]> (7cbab3b)

  • Delete print statement

Remove debugging print of args in main

Co-authored-by: Kevin Barnard <[email protected]> (25bc618)

  • Add progressbar2 to deps (b6d914c)

  • Added parser argument and if-loop to run download in main (5111f7c)

  • Updated download image function to download from list (a07a622)

  • Add download function to generate (5195b82)

  • updated filename to image uuid in generate coco (bb71d64)

v0.4.1 (2022-02-09)

Unknown

v0.4.0 (2022-02-09)

Unknown

  • Tags API (f48d468)

  • Bump copyright year (5e126d8)

  • CImageSetUploadDTO -> BImageSetUploadDTO (d8b072a)

  • CDarwinCore -> BDarwinCore (0fd8689)

  • BBoundingBoxDTO -> BoundingBoxDTO (3c864c6)

  • Removed Python 3.6 from automated tests (ba34e25)

v0.3.0 (2022-02-08)

Unknown

  • Bump version (3c6437a)

  • Bumped required Python version to ^3.7 (0af9132)

  • Allow search unconstrained by concept (#2) (c278ba5)

  • Review changes from #4 (106f268)

  • Added parser arg for concepts from text file (#4)

  • added parser options for concept list as text file

  • spelling error

  • arg naming error

  • arg naming error again

Co-authored-by: ecor <[email protected]> (5c1e799)

v0.2.1 (2021-11-30)

Unknown

  • Fixed ISO8601 encoding and count on empty (b271f42)

v0.2.0 (2021-11-29)

Unknown

  • fathomnet-generate tool release (63e368d)

  • Added extra links and classifiers (0bff623)

  • Changed build to poetry (87be7ff)

  • New flags, count mechanism (e2d4e62)

  • Added example fathomnet-generate script (ab5445c)

v0.1.0 (2021-10-19)

Unknown

  • Prep for release 0.1.0 (133f54e)

  • Added missing lxml dep (54fbc51)

  • Added AImageDTO -> Pascal VOC transform (e67b165)

  • Improved docs (7fbedf7)

  • New test UUIDs due to data reload (d2b4f6d)

v0.0.2 (2021-09-29)

Unknown

  • Fix for PyPI (9c60937)

  • Added starter text to README.md (a62a58c)

  • Fix badge link (517ff68)

  • Removed api-ci action, updated README badge (4ed01bb)

  • Renamed api-ci to tests (dd291af)

  • readthedocs config patch (75fef58)

  • readthedocs setup, badge (23e61d1)

  • Basic Sphinx autodocs (61b4eee)

  • Added CI badge to README (ead322e)

  • Added .gitignore (03b07e4)

  • Rename job build -> lint-and-test (72e8e58)

  • Remove missing Python 3.10 test, rename job (1e9f6e8)

  • Fix github action for CI (6024c21)

  • Ported tests, set up github CI action (8f6e06d)

  • Added missing docstrings (33ae5a3)

  • Added init.py for fathomnet package (f0519f4)

  • Migrated API and setuptools config (1a28c25)

  • Initial commit (b8a7fd5)