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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,45 @@ | ||
| # CHANGELOG | ||
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| ## v1.5.0 (2024-07-16) | ||
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| ### Chore | ||
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| * chore: apply pre-commit hook on all files ([`0190345`](https://github.com/fathomnet/fathomnet-py/commit/01903453d9e16c7716d91e7aacf165857c982dbf)) | ||
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| * chore: add Python 3.12 to CI pipeline targets ([`cf979cf`](https://github.com/fathomnet/fathomnet-py/commit/cf979cf18d5db307f6adea5d7b632045e1c6e353)) | ||
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| * chore: add formatting/linting pre-commit setup ([`ca07b19`](https://github.com/fathomnet/fathomnet-py/commit/ca07b193aa8562161fd02375641ea050d7d632d7)) | ||
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| ### Documentation | ||
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| * docs: move tutorial notebook into examples dir ([`c4db176`](https://github.com/fathomnet/fathomnet-py/commit/c4db176c211235a1ce7479dacba237c68c0da6fc)) | ||
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| * docs: switch order of imports/pip install in tutorial notebook | ||
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| 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)) | ||
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| * docs: fix broken readthedocs build #27 | ||
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| Install the current package (fathomnet-py) prior to building the Sphinx docs via RTD ([`3154b79`](https://github.com/fathomnet/fathomnet-py/commit/3154b790399aa7ce6def6c00b639679f6ac3bdb9)) | ||
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| ### Feature | ||
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| * feat: add YOLO dataset generation to fathomnet-generate ([`1bacb1f`](https://github.com/fathomnet/fathomnet-py/commit/1bacb1fbbaf8802de23351fdaa9af7e8de6df73c)) | ||
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| ### Fix | ||
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| * fix: make TEST_X_API_KEY use an environment variable of the same name ([`22508cf`](https://github.com/fathomnet/fathomnet-py/commit/22508cf16695621183c0a5f5fe76d14ffaf48bae)) | ||
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| ### Unknown | ||
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| * Merge branch 'develop' ([`8202949`](https://github.com/fathomnet/fathomnet-py/commit/8202949e687c927fc18c0dc23097c7e52c6ab47b)) | ||
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| * Merge branch 'main' into develop ([`4a29a68`](https://github.com/fathomnet/fathomnet-py/commit/4a29a68528e1dbfe8e476a5dc3abf4da9604e243)) | ||
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| * add accepted flag to `worms.get_descendants_names` | ||
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| Add support for worms-server 0.5.2 ([`0dc9ed8`](https://github.com/fathomnet/fathomnet-py/commit/0dc9ed8d902adb6ddfc4fbf88ad0c4a188a62ec1)) | ||
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| ## v1.4.0 (2024-04-09) | ||
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@@ -10,7 +49,6 @@ | |
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| Add support for worms-server 0.5.2 ([`de0aec2`](https://github.com/fathomnet/fathomnet-py/commit/de0aec2e04915a922b7026189e7cfc0b55aabfd6)) | ||
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| ## v1.3.0 (2024-02-29) | ||
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| ### Feature | ||
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@@ -19,7 +57,6 @@ Add support for worms-server 0.5.2 ([`de0aec2`](https://github.com/fathomnet/fat | |
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| 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)) | ||
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| ## v1.2.2 (2024-02-21) | ||
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| ### Chore | ||
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@@ -36,28 +73,18 @@ Add support for worms-server 0.5.1. This adds the `acceptedAphiaId` field to the | |
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| Fixes #25 ([`5feeeb0`](https://github.com/fathomnet/fathomnet-py/commit/5feeeb0fa5fd95efd22fdc0e67e5dd69b9302408)) | ||
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| ## v1.2.1 (2024-02-06) | ||
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| ### Chore | ||
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| * chore: use released ref for publish in CI/CD pipeline ([`d39c482`](https://github.com/fathomnet/fathomnet-py/commit/d39c4827ea612c6ea7e8b3eabfea4f08638c98e8)) | ||
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| ### Fix | ||
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| * fix: use worms API directly for fathomnet taxa provider | ||
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| 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)) | ||
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| ### Unknown | ||
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| * Merge branch 'main' into develop ([`86c574e`](https://github.com/fathomnet/fathomnet-py/commit/86c574e89fba7a858a9ca7abf1ff208c6829d8ae)) | ||
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| ## v1.2.0 (2024-02-06) | ||
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| ### Chore | ||
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| * chore: use released ref for publish in CI/CD pipeline ([`d39c482`](https://github.com/fathomnet/fathomnet-py/commit/d39c4827ea612c6ea7e8b3eabfea4f08638c98e8)) | ||
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| * chore: merge CI/CD workflows ([`8e0d760`](https://github.com/fathomnet/fathomnet-py/commit/8e0d76006cec956cab009bf330a068f6e7a6adf4)) | ||
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| ### Documentation | ||
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@@ -76,8 +103,11 @@ This is a temporary workaround for a bug in Micronaut that causes the fathomnet | |
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| ### Fix | ||
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| * fix: make the linter happy ([`6cc52f6`](https://github.com/fathomnet/fathomnet-py/commit/6cc52f6b6abbd1cbe1b14a435d82a9acb91e4f58)) | ||
| * fix: use worms API directly for fathomnet taxa provider | ||
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| 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)) | ||
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| * fix: make the linter happy ([`6cc52f6`](https://github.com/fathomnet/fathomnet-py/commit/6cc52f6b6abbd1cbe1b14a435d82a9acb91e4f58)) | ||
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| ## v1.1.5 (2024-01-10) | ||
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@@ -93,7 +123,6 @@ This is a temporary workaround for a bug in Micronaut that causes the fathomnet | |
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| * fix: update activity find functions for new DTO ([`cdf5617`](https://github.com/fathomnet/fathomnet-py/commit/cdf56179cc802085ff1f8adbba2f717be550f08b)) | ||
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| ## v1.1.4 (2024-01-09) | ||
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| ### Documentation | ||
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@@ -108,7 +137,6 @@ This is a temporary workaround for a bug in Micronaut that causes the fathomnet | |
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| * Merge branch 'develop' ([`14988d6`](https://github.com/fathomnet/fathomnet-py/commit/14988d63186d5c60e78c9e5039b1b2ca16d03dd0)) | ||
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| ## v1.1.3 (2023-09-13) | ||
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| ### Documentation | ||
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@@ -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)) | ||
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| ## v1.1.2 (2023-09-12) | ||
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| ### Fix | ||
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@@ -133,7 +160,6 @@ Add the fathomnet.util.debug_format_response to the ValueError exception | |
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| * fix: Add CD ([`8979d75`](https://github.com/fathomnet/fathomnet-py/commit/8979d75b049d39c673feb0d78153d4e5a4de11c5)) | ||
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| ## v1.1.1 (2023-09-12) | ||
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| ### Fix | ||
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@@ -142,14 +168,12 @@ Add the fathomnet.util.debug_format_response to the ValueError exception | |
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| * fix: Version in pyproject.toml ([`dd2d9a2`](https://github.com/fathomnet/fathomnet-py/commit/dd2d9a2d3e9a27610e17c119337e821fcea8bcbc)) | ||
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| ## v1.1.0 (2023-09-12) | ||
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| ### Feature | ||
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| * feat: Set up python-semantic-release ([`4019f18`](https://github.com/fathomnet/fathomnet-py/commit/4019f1811cabc207f5972eb39b8a9a7720345f95)) | ||
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| ## v1.0.2 (2023-09-12) | ||
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| ### Unknown | ||
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@@ -162,7 +186,6 @@ Add the fathomnet.util.debug_format_response to the ValueError exception | |
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| * Add req/response to server error exception message ([`00f2ff6`](https://github.com/fathomnet/fathomnet-py/commit/00f2ff64bd0b19cae74042287023d5802aee7165)) | ||
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| ## v1.0.1 (2023-08-29) | ||
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| ### Unknown | ||
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@@ -175,7 +198,6 @@ Add the fathomnet.util.debug_format_response to the ValueError exception | |
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| * Fix taxa tests for fathomnet provider ([`dfe44fe`](https://github.com/fathomnet/fathomnet-py/commit/dfe44fe2771e6a4f962525d6f689ffa901487df2)) | ||
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| ## v1.0.0 (2023-08-03) | ||
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| ### Unknown | ||
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@@ -198,7 +220,6 @@ Add the fathomnet.util.debug_format_response to the ValueError exception | |
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| * Bounding box comments ([`7aa63fd`](https://github.com/fathomnet/fathomnet-py/commit/7aa63fd5c68369b87bffb3a136fea1170973c78e)) | ||
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| ## v0.7.0 (2023-08-03) | ||
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| ### Unknown | ||
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@@ -229,7 +250,6 @@ Slight tweaks to GH action linting ([`8db72d3`](https://github.com/fathomnet/fat | |
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| * Add coco download section to tutorial notebook ([`40369e3`](https://github.com/fathomnet/fathomnet-py/commit/40369e387144ac8ab90b61343eef0be47c2a6262)) | ||
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| ## v0.6.0 (2023-02-07) | ||
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| ### Unknown | ||
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@@ -250,7 +270,6 @@ Slight tweaks to GH action linting ([`8db72d3`](https://github.com/fathomnet/fat | |
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| * Removed forced debug print statement ([`3ae2f69`](https://github.com/fathomnet/fathomnet-py/commit/3ae2f694c2a83688572254ca49a1954ee65fa420)) | ||
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| ## v0.5.2 (2022-04-07) | ||
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| ### Unknown | ||
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@@ -269,7 +288,6 @@ Slight tweaks to GH action linting ([`8db72d3`](https://github.com/fathomnet/fat | |
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| * Cleaned up fathomnet_generate formatting ([`2aad07b`](https://github.com/fathomnet/fathomnet-py/commit/2aad07bdf4ae6499a094eb9f70c9dc2c9ea1d0df)) | ||
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| ## v0.5.1 (2022-03-31) | ||
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| ### Unknown | ||
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@@ -278,7 +296,6 @@ Slight tweaks to GH action linting ([`8db72d3`](https://github.com/fathomnet/fat | |
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| * Fix fathomnet-generate bug in Python 3.7 ([`df8e25a`](https://github.com/fathomnet/fathomnet-py/commit/df8e25a5e3c77508191478d88a2fe735446124b6)) | ||
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| ## v0.5.0 (2022-03-31) | ||
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| ### Unknown | ||
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@@ -293,12 +310,12 @@ Slight tweaks to GH action linting ([`8db72d3`](https://github.com/fathomnet/fat | |
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| * Removed unused cell ([`0bce7b3`](https://github.com/fathomnet/fathomnet-py/commit/0bce7b33f76cb5008a2429868647808e2ed55e95)) | ||
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| * Changed day two order. Removed calls to Google Drive ([`56ae925`](https://github.com/fathomnet/fathomnet-py/commit/56ae925d8e19e321fa17c168a62bd6ff90de4233)) | ||
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| * Update CoLab link to main | ||
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| Changed CoLab link in README to open main instead of dev branch notebook. ([`9c57174`](https://github.com/fathomnet/fathomnet-py/commit/9c571747bc6842a7d19f9e542585c9a001cd267e)) | ||
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| * Changed day two order. Removed calls to Google Drive ([`56ae925`](https://github.com/fathomnet/fathomnet-py/commit/56ae925d8e19e321fa17c168a62bd6ff90de4233)) | ||
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| * Workshop-ready version of tutorial notebook ([`0ca5c81`](https://github.com/fathomnet/fathomnet-py/commit/0ca5c81c04b1f652a3be645c4f9d7e5772c5de8f)) | ||
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| * Updated tutorial.ipynb ([`2b93d26`](https://github.com/fathomnet/fathomnet-py/commit/2b93d261c9da0969146af8542168489eafac2488)) | ||
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@@ -307,7 +324,6 @@ Changed CoLab link in README to open main instead of dev branch notebook. ([`9c5 | |
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| * add tutorial notebook ([`60dfa5f`](https://github.com/fathomnet/fathomnet-py/commit/60dfa5f54cb5af9854a84235d0675781ac38ce0b)) | ||
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| ## v0.4.2 (2022-03-09) | ||
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| ### Unknown | ||
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@@ -320,20 +336,20 @@ Download function in fathomnet-generate ([`173a9ee`](https://github.com/fathomne | |
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| * Merge remote-tracking branch 'origin/download' into download ([`01cc97d`](https://github.com/fathomnet/fathomnet-py/commit/01cc97d7e1cc66b902c5b5ab3887f8112122ee03)) | ||
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| * Add progressbar2 to deps ([`b6d914c`](https://github.com/fathomnet/fathomnet-py/commit/b6d914cc7266faa886408ed8f278d2da7eda2dde)) | ||
| * Context manager for image download | ||
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| * Context manager for image download | ||
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| More responsible file management for copyfilebobj | ||
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| Co-authored-by: Kevin Barnard <[email protected]> ([`7cbab3b`](https://github.com/fathomnet/fathomnet-py/commit/7cbab3bba252268eb44b269f65f95b0db903ce59)) | ||
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| * Delete print statement | ||
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| * Delete print statement | ||
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| Remove debugging print of args in main | ||
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| Co-authored-by: Kevin Barnard <[email protected]> ([`25bc618`](https://github.com/fathomnet/fathomnet-py/commit/25bc618cdaf55fabae07af3d6dc79dfd82484dca)) | ||
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| * Add progressbar2 to deps ([`b6d914c`](https://github.com/fathomnet/fathomnet-py/commit/b6d914cc7266faa886408ed8f278d2da7eda2dde)) | ||
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| * Added parser argument and if-loop to run download in main ([`5111f7c`](https://github.com/fathomnet/fathomnet-py/commit/5111f7cc704593d2354624a37c75d95403407c1b)) | ||
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| * Updated download image function to download from list ([`a07a622`](https://github.com/fathomnet/fathomnet-py/commit/a07a622bbc39b691c93831b7a9dac91ae03129ae)) | ||
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@@ -342,7 +358,6 @@ Co-authored-by: Kevin Barnard <[email protected]> ([`25bc618`](https://gi | |
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| * updated filename to image uuid in generate coco ([`bb71d64`](https://github.com/fathomnet/fathomnet-py/commit/bb71d6499cec0c81c8cda092b2a4fd864ba85bff)) | ||
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| ## v0.4.1 (2022-02-09) | ||
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| ### Unknown | ||
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@@ -351,7 +366,6 @@ Co-authored-by: Kevin Barnard <[email protected]> ([`25bc618`](https://gi | |
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| * Tags API doc typo ([`aa33b81`](https://github.com/fathomnet/fathomnet-py/commit/aa33b81f0d71415275425c2f1d202c346fb0fd4a)) | ||
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| ## v0.4.0 (2022-02-09) | ||
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| ### Unknown | ||
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@@ -368,7 +382,6 @@ Co-authored-by: Kevin Barnard <[email protected]> ([`25bc618`](https://gi | |
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| * Removed Python 3.6 from automated tests ([`ba34e25`](https://github.com/fathomnet/fathomnet-py/commit/ba34e25871234415848ab795c1c040c76daf8cfc)) | ||
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| ## v0.3.0 (2022-02-08) | ||
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| ### Unknown | ||
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@@ -383,24 +396,22 @@ Co-authored-by: Kevin Barnard <[email protected]> ([`25bc618`](https://gi | |
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| * Added parser arg for concepts from text file (#4) | ||
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| * added parser options for concept list as text file | ||
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| * spelling error | ||
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| * arg naming error | ||
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| * arg naming error again | ||
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| Co-authored-by: ecor <[email protected]> ([`5c1e799`](https://github.com/fathomnet/fathomnet-py/commit/5c1e7999859ed1afdc30fbcdb687910768c2e4e6)) | ||
| * added parser options for concept list as text file | ||
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| * spelling error | ||
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| * arg naming error | ||
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| * arg naming error again | ||
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| Co-authored-by: ecor <[email protected]> ([`5c1e799`](https://github.com/fathomnet/fathomnet-py/commit/5c1e7999859ed1afdc30fbcdb687910768c2e4e6)) | ||
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| ## v0.2.1 (2021-11-30) | ||
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| ### Unknown | ||
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| * Fixed ISO8601 encoding and count on empty ([`b271f42`](https://github.com/fathomnet/fathomnet-py/commit/b271f424c947276393ab1ac6c13240931a279340)) | ||
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| ## v0.2.0 (2021-11-29) | ||
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| ### Unknown | ||
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@@ -415,7 +426,6 @@ Co-authored-by: ecor <[email protected]> ([`5c1e799`](https://github.co | |
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| * Added example fathomnet-generate script ([`ab5445c`](https://github.com/fathomnet/fathomnet-py/commit/ab5445c4062fd09aeaa4acd5331f5c20ca8582b7)) | ||
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| ## v0.1.0 (2021-10-19) | ||
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| ### Unknown | ||
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@@ -430,7 +440,6 @@ Co-authored-by: ecor <[email protected]> ([`5c1e799`](https://github.co | |
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| * New test UUIDs due to data reload ([`d2b4f6d`](https://github.com/fathomnet/fathomnet-py/commit/d2b4f6d89d37aa84ee7dc195ba510d83eb74c961)) | ||
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| ## v0.0.2 (2021-09-29) | ||
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| ### Unknown | ||
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This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 <[email protected]>"] | ||
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