From 903eec5b1a8e10ec419b95fc729e9ebb28d0b76c Mon Sep 17 00:00:00 2001 From: semantic-release Date: Tue, 16 Jul 2024 18:58:40 +0000 Subject: [PATCH] 1.5.0 Automatically generated by python-semantic-release --- CHANGELOG.md | 111 ++++++++++++++++++++++++++----------------------- pyproject.toml | 2 +- 2 files changed, 61 insertions(+), 52 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9f3e9b7..87a1022 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,45 @@ # CHANGELOG +## v1.5.0 (2024-07-16) +### Chore + +* chore: apply pre-commit hook on all files ([`0190345`](https://github.com/fathomnet/fathomnet-py/commit/01903453d9e16c7716d91e7aacf165857c982dbf)) + +* chore: add Python 3.12 to CI pipeline targets ([`cf979cf`](https://github.com/fathomnet/fathomnet-py/commit/cf979cf18d5db307f6adea5d7b632045e1c6e353)) + +* chore: add formatting/linting pre-commit setup ([`ca07b19`](https://github.com/fathomnet/fathomnet-py/commit/ca07b193aa8562161fd02375641ea050d7d632d7)) + +### Documentation + +* docs: move tutorial notebook into examples dir ([`c4db176`](https://github.com/fathomnet/fathomnet-py/commit/c4db176c211235a1ce7479dacba237c68c0da6fc)) + +* 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`](https://github.com/fathomnet/fathomnet-py/commit/48afc496c0792d662709b2b9c28826afb78914b7)) + +* docs: fix broken readthedocs build #27 + +Install the current package (fathomnet-py) prior to building the Sphinx docs via RTD ([`3154b79`](https://github.com/fathomnet/fathomnet-py/commit/3154b790399aa7ce6def6c00b639679f6ac3bdb9)) + +### Feature + +* feat: add YOLO dataset generation to fathomnet-generate ([`1bacb1f`](https://github.com/fathomnet/fathomnet-py/commit/1bacb1fbbaf8802de23351fdaa9af7e8de6df73c)) + +### Fix + +* fix: make TEST_X_API_KEY use an environment variable of the same name ([`22508cf`](https://github.com/fathomnet/fathomnet-py/commit/22508cf16695621183c0a5f5fe76d14ffaf48bae)) + +### Unknown + +* Merge branch 'develop' ([`8202949`](https://github.com/fathomnet/fathomnet-py/commit/8202949e687c927fc18c0dc23097c7e52c6ab47b)) + +* Merge branch 'main' into develop ([`4a29a68`](https://github.com/fathomnet/fathomnet-py/commit/4a29a68528e1dbfe8e476a5dc3abf4da9604e243)) + +* add accepted flag to `worms.get_descendants_names` + +Add support for worms-server 0.5.2 ([`0dc9ed8`](https://github.com/fathomnet/fathomnet-py/commit/0dc9ed8d902adb6ddfc4fbf88ad0c4a188a62ec1)) ## v1.4.0 (2024-04-09) @@ -10,7 +49,6 @@ Add support for worms-server 0.5.2 ([`de0aec2`](https://github.com/fathomnet/fathomnet-py/commit/de0aec2e04915a922b7026189e7cfc0b55aabfd6)) - ## v1.3.0 (2024-02-29) ### Feature @@ -19,7 +57,6 @@ Add support for worms-server 0.5.2 ([`de0aec2`](https://github.com/fathomnet/fat 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`](https://github.com/fathomnet/fathomnet-py/commit/f1989bcfea8225d38749241709b9c98a9e47bae0)) - ## v1.2.2 (2024-02-21) ### Chore @@ -36,28 +73,18 @@ Add support for worms-server 0.5.1. This adds the `acceptedAphiaId` field to the Fixes #25 ([`5feeeb0`](https://github.com/fathomnet/fathomnet-py/commit/5feeeb0fa5fd95efd22fdc0e67e5dd69b9302408)) - ## v1.2.1 (2024-02-06) -### Chore - -* chore: use released ref for publish in CI/CD pipeline ([`d39c482`](https://github.com/fathomnet/fathomnet-py/commit/d39c4827ea612c6ea7e8b3eabfea4f08638c98e8)) - -### 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`](https://github.com/fathomnet/fathomnet-py/commit/f887a950cfe4741869b667410a1ceee9c92a11c9)) - ### Unknown * Merge branch 'main' into develop ([`86c574e`](https://github.com/fathomnet/fathomnet-py/commit/86c574e89fba7a858a9ca7abf1ff208c6829d8ae)) - ## v1.2.0 (2024-02-06) ### Chore +* chore: use released ref for publish in CI/CD pipeline ([`d39c482`](https://github.com/fathomnet/fathomnet-py/commit/d39c4827ea612c6ea7e8b3eabfea4f08638c98e8)) + * chore: merge CI/CD workflows ([`8e0d760`](https://github.com/fathomnet/fathomnet-py/commit/8e0d76006cec956cab009bf330a068f6e7a6adf4)) ### Documentation @@ -76,8 +103,11 @@ This is a temporary workaround for a bug in Micronaut that causes the fathomnet ### Fix -* fix: make the linter happy ([`6cc52f6`](https://github.com/fathomnet/fathomnet-py/commit/6cc52f6b6abbd1cbe1b14a435d82a9acb91e4f58)) +* 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`](https://github.com/fathomnet/fathomnet-py/commit/f887a950cfe4741869b667410a1ceee9c92a11c9)) +* fix: make the linter happy ([`6cc52f6`](https://github.com/fathomnet/fathomnet-py/commit/6cc52f6b6abbd1cbe1b14a435d82a9acb91e4f58)) ## v1.1.5 (2024-01-10) @@ -93,7 +123,6 @@ This is a temporary workaround for a bug in Micronaut that causes the fathomnet * fix: update activity find functions for new DTO ([`cdf5617`](https://github.com/fathomnet/fathomnet-py/commit/cdf56179cc802085ff1f8adbba2f717be550f08b)) - ## v1.1.4 (2024-01-09) ### Documentation @@ -108,7 +137,6 @@ This is a temporary workaround for a bug in Micronaut that causes the fathomnet * Merge branch 'develop' ([`14988d6`](https://github.com/fathomnet/fathomnet-py/commit/14988d63186d5c60e78c9e5039b1b2ca16d03dd0)) - ## v1.1.3 (2023-09-13) ### Documentation @@ -124,7 +152,6 @@ Closes #5 ([`1eadc8f`](https://github.com/fathomnet/fathomnet-py/commit/1eadc8ff 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`](https://github.com/fathomnet/fathomnet-py/commit/6b0b91110be90d7e41e7c2a8dab87cd29b331395)) - ## v1.1.2 (2023-09-12) ### Fix @@ -133,7 +160,6 @@ Add the fathomnet.util.debug_format_response to the ValueError exception * fix: Add CD ([`8979d75`](https://github.com/fathomnet/fathomnet-py/commit/8979d75b049d39c673feb0d78153d4e5a4de11c5)) - ## v1.1.1 (2023-09-12) ### Fix @@ -142,14 +168,12 @@ Add the fathomnet.util.debug_format_response to the ValueError exception * fix: Version in pyproject.toml ([`dd2d9a2`](https://github.com/fathomnet/fathomnet-py/commit/dd2d9a2d3e9a27610e17c119337e821fcea8bcbc)) - ## v1.1.0 (2023-09-12) ### Feature * feat: Set up python-semantic-release ([`4019f18`](https://github.com/fathomnet/fathomnet-py/commit/4019f1811cabc207f5972eb39b8a9a7720345f95)) - ## v1.0.2 (2023-09-12) ### Unknown @@ -162,7 +186,6 @@ Add the fathomnet.util.debug_format_response to the ValueError exception * Add req/response to server error exception message ([`00f2ff6`](https://github.com/fathomnet/fathomnet-py/commit/00f2ff64bd0b19cae74042287023d5802aee7165)) - ## v1.0.1 (2023-08-29) ### Unknown @@ -175,7 +198,6 @@ Add the fathomnet.util.debug_format_response to the ValueError exception * Fix taxa tests for fathomnet provider ([`dfe44fe`](https://github.com/fathomnet/fathomnet-py/commit/dfe44fe2771e6a4f962525d6f689ffa901487df2)) - ## v1.0.0 (2023-08-03) ### Unknown @@ -198,7 +220,6 @@ Add the fathomnet.util.debug_format_response to the ValueError exception * Bounding box comments ([`7aa63fd`](https://github.com/fathomnet/fathomnet-py/commit/7aa63fd5c68369b87bffb3a136fea1170973c78e)) - ## v0.7.0 (2023-08-03) ### Unknown @@ -229,7 +250,6 @@ Slight tweaks to GH action linting ([`8db72d3`](https://github.com/fathomnet/fat * Add coco download section to tutorial notebook ([`40369e3`](https://github.com/fathomnet/fathomnet-py/commit/40369e387144ac8ab90b61343eef0be47c2a6262)) - ## v0.6.0 (2023-02-07) ### Unknown @@ -250,7 +270,6 @@ Slight tweaks to GH action linting ([`8db72d3`](https://github.com/fathomnet/fat * Removed forced debug print statement ([`3ae2f69`](https://github.com/fathomnet/fathomnet-py/commit/3ae2f694c2a83688572254ca49a1954ee65fa420)) - ## v0.5.2 (2022-04-07) ### Unknown @@ -269,7 +288,6 @@ Slight tweaks to GH action linting ([`8db72d3`](https://github.com/fathomnet/fat * Cleaned up fathomnet_generate formatting ([`2aad07b`](https://github.com/fathomnet/fathomnet-py/commit/2aad07bdf4ae6499a094eb9f70c9dc2c9ea1d0df)) - ## v0.5.1 (2022-03-31) ### Unknown @@ -278,7 +296,6 @@ Slight tweaks to GH action linting ([`8db72d3`](https://github.com/fathomnet/fat * Fix fathomnet-generate bug in Python 3.7 ([`df8e25a`](https://github.com/fathomnet/fathomnet-py/commit/df8e25a5e3c77508191478d88a2fe735446124b6)) - ## v0.5.0 (2022-03-31) ### Unknown @@ -293,12 +310,12 @@ Slight tweaks to GH action linting ([`8db72d3`](https://github.com/fathomnet/fat * Removed unused cell ([`0bce7b3`](https://github.com/fathomnet/fathomnet-py/commit/0bce7b33f76cb5008a2429868647808e2ed55e95)) +* Changed day two order. Removed calls to Google Drive ([`56ae925`](https://github.com/fathomnet/fathomnet-py/commit/56ae925d8e19e321fa17c168a62bd6ff90de4233)) + * Update CoLab link to main Changed CoLab link in README to open main instead of dev branch notebook. ([`9c57174`](https://github.com/fathomnet/fathomnet-py/commit/9c571747bc6842a7d19f9e542585c9a001cd267e)) -* Changed day two order. Removed calls to Google Drive ([`56ae925`](https://github.com/fathomnet/fathomnet-py/commit/56ae925d8e19e321fa17c168a62bd6ff90de4233)) - * Workshop-ready version of tutorial notebook ([`0ca5c81`](https://github.com/fathomnet/fathomnet-py/commit/0ca5c81c04b1f652a3be645c4f9d7e5772c5de8f)) * Updated tutorial.ipynb ([`2b93d26`](https://github.com/fathomnet/fathomnet-py/commit/2b93d261c9da0969146af8542168489eafac2488)) @@ -307,7 +324,6 @@ Changed CoLab link in README to open main instead of dev branch notebook. ([`9c5 * add tutorial notebook ([`60dfa5f`](https://github.com/fathomnet/fathomnet-py/commit/60dfa5f54cb5af9854a84235d0675781ac38ce0b)) - ## v0.4.2 (2022-03-09) ### Unknown @@ -320,20 +336,20 @@ Download function in fathomnet-generate ([`173a9ee`](https://github.com/fathomne * Merge remote-tracking branch 'origin/download' into download ([`01cc97d`](https://github.com/fathomnet/fathomnet-py/commit/01cc97d7e1cc66b902c5b5ab3887f8112122ee03)) -* Add progressbar2 to deps ([`b6d914c`](https://github.com/fathomnet/fathomnet-py/commit/b6d914cc7266faa886408ed8f278d2da7eda2dde)) +* Context manager for image download -* Context manager for image download - More responsible file management for copyfilebobj Co-authored-by: Kevin Barnard <kbarnard@mbari.org> ([`7cbab3b`](https://github.com/fathomnet/fathomnet-py/commit/7cbab3bba252268eb44b269f65f95b0db903ce59)) -* Delete print statement - +* Delete print statement + Remove debugging print of args in main Co-authored-by: Kevin Barnard <kbarnard@mbari.org> ([`25bc618`](https://github.com/fathomnet/fathomnet-py/commit/25bc618cdaf55fabae07af3d6dc79dfd82484dca)) +* Add progressbar2 to deps ([`b6d914c`](https://github.com/fathomnet/fathomnet-py/commit/b6d914cc7266faa886408ed8f278d2da7eda2dde)) + * Added parser argument and if-loop to run download in main ([`5111f7c`](https://github.com/fathomnet/fathomnet-py/commit/5111f7cc704593d2354624a37c75d95403407c1b)) * Updated download image function to download from list ([`a07a622`](https://github.com/fathomnet/fathomnet-py/commit/a07a622bbc39b691c93831b7a9dac91ae03129ae)) @@ -342,7 +358,6 @@ Co-authored-by: Kevin Barnard <kbarnard@mbari.org> ([`25bc618`](https://gi * updated filename to image uuid in generate coco ([`bb71d64`](https://github.com/fathomnet/fathomnet-py/commit/bb71d6499cec0c81c8cda092b2a4fd864ba85bff)) - ## v0.4.1 (2022-02-09) ### Unknown @@ -351,7 +366,6 @@ Co-authored-by: Kevin Barnard <kbarnard@mbari.org> ([`25bc618`](https://gi * Tags API doc typo ([`aa33b81`](https://github.com/fathomnet/fathomnet-py/commit/aa33b81f0d71415275425c2f1d202c346fb0fd4a)) - ## v0.4.0 (2022-02-09) ### Unknown @@ -368,7 +382,6 @@ Co-authored-by: Kevin Barnard <kbarnard@mbari.org> ([`25bc618`](https://gi * Removed Python 3.6 from automated tests ([`ba34e25`](https://github.com/fathomnet/fathomnet-py/commit/ba34e25871234415848ab795c1c040c76daf8cfc)) - ## v0.3.0 (2022-02-08) ### Unknown @@ -383,16 +396,15 @@ Co-authored-by: Kevin Barnard <kbarnard@mbari.org> ([`25bc618`](https://gi * 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 <eorenstein@mbari.org> ([`5c1e799`](https://github.com/fathomnet/fathomnet-py/commit/5c1e7999859ed1afdc30fbcdb687910768c2e4e6)) +* added parser options for concept list as text file + +* spelling error +* arg naming error + +* arg naming error again + +Co-authored-by: ecor <eorenstein@mbari.org> ([`5c1e799`](https://github.com/fathomnet/fathomnet-py/commit/5c1e7999859ed1afdc30fbcdb687910768c2e4e6)) ## v0.2.1 (2021-11-30) @@ -400,7 +412,6 @@ Co-authored-by: ecor <eorenstein@mbari.org> ([`5c1e799`](https://github.co * Fixed ISO8601 encoding and count on empty ([`b271f42`](https://github.com/fathomnet/fathomnet-py/commit/b271f424c947276393ab1ac6c13240931a279340)) - ## v0.2.0 (2021-11-29) ### Unknown @@ -415,7 +426,6 @@ Co-authored-by: ecor <eorenstein@mbari.org> ([`5c1e799`](https://github.co * Added example fathomnet-generate script ([`ab5445c`](https://github.com/fathomnet/fathomnet-py/commit/ab5445c4062fd09aeaa4acd5331f5c20ca8582b7)) - ## v0.1.0 (2021-10-19) ### Unknown @@ -430,7 +440,6 @@ Co-authored-by: ecor <eorenstein@mbari.org> ([`5c1e799`](https://github.co * New test UUIDs due to data reload ([`d2b4f6d`](https://github.com/fathomnet/fathomnet-py/commit/d2b4f6d89d37aa84ee7dc195ba510d83eb74c961)) - ## v0.0.2 (2021-09-29) ### Unknown diff --git a/pyproject.toml b/pyproject.toml index c5490fd..55fccd3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "fathomnet" -version = "1.4.0" +version = "1.5.0" description = "fathomnet-py is a client-side API to help scientists, researchers, and developers interact with FathomNet data." license = "MIT" authors = ["Kevin Barnard "]