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# top-most EditorConfig file | ||
root = true | ||
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# Unix-style newlines with a newline ending every file | ||
[*] | ||
end_of_line = lf | ||
insert_final_newline = true | ||
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[*.py] | ||
charset = utf-8 | ||
indent_style = space | ||
indent_size = 4 |
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name: CI for DGEB | ||
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on: | ||
push: | ||
branches: ["**"] | ||
pull_request: | ||
branches: ["**"] | ||
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permissions: | ||
id-token: write | ||
contents: read | ||
actions: write | ||
pull-requests: read | ||
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concurrency: | ||
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | ||
cancel-in-progress: true | ||
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jobs: | ||
ruff: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: actions/checkout@v3 | ||
- uses: actions/setup-python@v4 | ||
with: | ||
python-version: "3.11" | ||
- uses: yezz123/setup-uv@v4 | ||
with: | ||
uv-venv: ".geb_venv" | ||
- run: uv pip install ruff | ||
- run: ruff format . | ||
- run: ruff check . | ||
# TODO: pytest | ||
# TODO: pyright |
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# This workflow will | ||
# - Find the latest version tag based on the commit history | ||
# - Create a git tag for the new version | ||
# - Update the version number in pyproject.toml based on the commit history | ||
# - Upload the package to PyPI | ||
# - Create a release on GitHub | ||
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# This workflow required the following secrets to be set: | ||
# - a GitHub personal access token with the `repo` scope called `RELEASE` | ||
# - and that you setup trusted publishing using PyPI as described here: https://blog.pypi.org/posts/2023-04-20-introducing-trusted-publishers/ | ||
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name: Release | ||
on: | ||
push: | ||
branches: | ||
- main | ||
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jobs: | ||
release: | ||
runs-on: ubuntu-latest | ||
concurrency: release | ||
permissions: | ||
id-token: write # IMPORTANT: this permission is mandatory for trusted publishing using PyPI | ||
contents: write | ||
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steps: | ||
- uses: actions/checkout@v4 | ||
with: | ||
fetch-depth: 0 | ||
token: ${{ secrets.GH_TOKEN }} | ||
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- name: Python Semantic Release | ||
id: release | ||
uses: python-semantic-release/python-semantic-release@v9.8.3 | ||
with: | ||
github_token: ${{ secrets.GH_TOKEN }} | ||
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- name: Publish package distributions to PyPI | ||
uses: pypa/gh-action-pypi-publish@v1.9.0 | ||
if: steps.release.outputs.released == 'true' | ||
# This action supports PyPI's trusted publishing implementation, which allows authentication to PyPI without a manually | ||
# configured API token or username/password combination. To perform trusted publishing with this action, your project's | ||
# publisher must already be configured on PyPI. | ||
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- name: Publish package distributions to GitHub Releases | ||
uses: python-semantic-release/upload-to-gh-release@v9.8.3 | ||
if: steps.release.outputs.released == 'true' | ||
with: | ||
github_token: ${{ secrets.GITHUB_TOKEN }} | ||
tag: ${{ steps.release.outputs.tag }} |
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.venv/ | ||
__pycache__/ | ||
.vscode/ | ||
build/ | ||
dist/ | ||
*egg-info/ |
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# CHANGELOG | ||
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## v0.0.10 (2024-07-09) | ||
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### Fix | ||
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* fix: remove noop task ([`7d5b393`](https://github.com/TattaBio/DGEB/commit/7d5b3933f48e51fb4c71945f01af2cc5a7dba3ed)) | ||
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## v0.0.9 (2024-07-09) | ||
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### Fix | ||
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* fix: update cli script name ([`633e14d`](https://github.com/TattaBio/DGEB/commit/633e14db7e1eed0d9606ef1097e369e4f5e245f5)) | ||
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### Unknown | ||
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* 0.0.9 | ||
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Automatically generated by python-semantic-release [skip ci] ([`a8c1a96`](https://github.com/TattaBio/DGEB/commit/a8c1a96d18af589795bc9532fee8ad9764cd52ed)) | ||
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* Merge pull request #9 from TattaBio/andre | ||
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Update ModAC main metric ([`3c67e65`](https://github.com/TattaBio/DGEB/commit/3c67e6559d0e49d90ffe2858eb9e287abd1b6e6c)) | ||
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* ruff format ([`78461ac`](https://github.com/TattaBio/DGEB/commit/78461ac901b8617821ca15e543c0dd8e2dbf6e95)) | ||
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* update top_k=50 for modac ([`2c3dcd5`](https://github.com/TattaBio/DGEB/commit/2c3dcd5856b6679a80999b3c4b3512876ac0b58d)) | ||
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* remove revision ([`2d587da`](https://github.com/TattaBio/DGEB/commit/2d587daa79f32c49201b419892b7f95f3dc5eedb)) | ||
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* Merge pull request #8 from TattaBio/cli | ||
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Cli & cleanup ([`9698c8f`](https://github.com/TattaBio/DGEB/commit/9698c8f5ab0bab6c3c0a76d59dc29cfd964ebf15)) | ||
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* Exclude leaderboard files in anticipation of merging leaderboard PR ([`58bdcba`](https://github.com/TattaBio/DGEB/commit/58bdcba11af605bdef11cfecc087c9efb0e97b72)) | ||
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* Update README ([`d323905`](https://github.com/TattaBio/DGEB/commit/d3239059e29fb149f9c348b951bc4988d8b9f8dc)) | ||
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* cleanup ([`1f0fe16`](https://github.com/TattaBio/DGEB/commit/1f0fe16de6910200d88c918b08cbf26067313469)) | ||
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* Add cli to pyproject.toml ([`5404218`](https://github.com/TattaBio/DGEB/commit/54042181ef54c11db74ebb53c403b21a8114c02b)) | ||
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* Remove Dataset 'description' which does not exist on model. ([`46b0040`](https://github.com/TattaBio/DGEB/commit/46b0040a302384fa00791bbfdd6fae24645d6a6d)) | ||
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* Merge pull request #7 from TattaBio/add_dna_tasks | ||
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Add dna tasks ([`cfc5799`](https://github.com/TattaBio/DGEB/commit/cfc57995f9b1e584bb60e998f9cf68bea5ec39fa)) | ||
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* ruff ([`f9fa125`](https://github.com/TattaBio/DGEB/commit/f9fa12502df9837b5381da17b17198f3667c4911)) | ||
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* adding rpob datasets and updating ec revision ([`8f9cc3f`](https://github.com/TattaBio/DGEB/commit/8f9cc3f819beb70f51a5cc59f16c65bffceedbad)) | ||
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* Update README.md ([`d5d7c24`](https://github.com/TattaBio/DGEB/commit/d5d7c24215d347fc17d6016ac2a3eddfb3cf2a12)) | ||
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* Merge pull request #4 from TattaBio/andre | ||
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Add dataset revisions ([`95b6f11`](https://github.com/TattaBio/DGEB/commit/95b6f11ffee3dccc45ab119ac4f602066750f7ef)) | ||
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* add dataset revision numbers ([`7e069a2`](https://github.com/TattaBio/DGEB/commit/7e069a237de5391e7c6b7f09c108292ac10c25af)) | ||
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* Merge pull request #3 from TattaBio/andre | ||
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Update readme and task imports ([`ade30a8`](https://github.com/TattaBio/DGEB/commit/ade30a856deffe35ddf57d16705d030b6d0192c8)) | ||
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* rename dgeb ([`6b1c2ee`](https://github.com/TattaBio/DGEB/commit/6b1c2ee76798d89e487386116efe23c90d2d039c)) | ||
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* add intro ([`a2280dd`](https://github.com/TattaBio/DGEB/commit/a2280dd732984d58caed45b9a429038c0d81851a)) | ||
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* update readme and tasks ([`00e0a79`](https://github.com/TattaBio/DGEB/commit/00e0a791f070ca37e5b92770b3363ef066e2789f)) | ||
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* Merge pull request #2 from TattaBio/andre | ||
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rename dgeb imports ([`1894ba9`](https://github.com/TattaBio/DGEB/commit/1894ba9a92a8f369053ddb9d351ae48fd8e2d674)) | ||
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* rename dgeb imports ([`5f1f8b8`](https://github.com/TattaBio/DGEB/commit/5f1f8b850f271cd6785291e3feb2c2d4bf979f9c)) | ||
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## v0.0.8 (2024-07-01) | ||
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### Fix | ||
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* fix: don't run ci on release of new version ([`fa97104`](https://github.com/TattaBio/DGEB/commit/fa971049429975d06c8aca086e86b19d92383969)) | ||
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### Unknown | ||
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* 0.0.8 | ||
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Automatically generated by python-semantic-release [skip ci] ([`8dc15d3`](https://github.com/TattaBio/DGEB/commit/8dc15d34c6317087253950893974d16b9f75a17c)) | ||
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## v0.0.7 (2024-07-01) | ||
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### Fix | ||
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* fix: try again ([`e7d0ecd`](https://github.com/TattaBio/DGEB/commit/e7d0ecdcb63e909f9ab727f11fb3fd57414d2fa5)) | ||
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* fix: edit readme to see if job still works with restricted permissions ([`93cd728`](https://github.com/TattaBio/DGEB/commit/93cd728c8a632b9bed611c55dace2e2ffb103410)) | ||
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### Unknown | ||
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* 0.0.7 | ||
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Automatically generated by python-semantic-release ([`9808d4f`](https://github.com/TattaBio/DGEB/commit/9808d4f328a577c066affd34d408ad26eb6098d0)) | ||
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* Merge pull request #1 from TattaBio/edit-readme | ||
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fix: edit readme to see if job still works with restricted permissions ([`c45599c`](https://github.com/TattaBio/DGEB/commit/c45599cf9628155603245f906c09cf6483cffce8)) | ||
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## v0.0.6 (2024-07-01) | ||
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### Fix | ||
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* fix: nevermind that broke it ([`ec33a1c`](https://github.com/TattaBio/DGEB/commit/ec33a1c6539ac1fb2710869a2d436483a02236e0)) | ||
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* fix: see if I can remove this line ([`246d4e9`](https://github.com/TattaBio/DGEB/commit/246d4e9841a83d18217506d46f211f1341c63526)) | ||
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### Unknown | ||
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* 0.0.6 | ||
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Automatically generated by python-semantic-release ([`1b28df5`](https://github.com/TattaBio/DGEB/commit/1b28df559c95db0aea95111a5f27d01645d23786)) | ||
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## v0.0.5 (2024-07-01) | ||
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### Fix | ||
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* fix: try fixing release to handle protected branch ([`5cedad3`](https://github.com/TattaBio/DGEB/commit/5cedad3e9f34d249eda9257e3c21fc8443d000cf)) | ||
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* fix: another change... ([`c5ad3f0`](https://github.com/TattaBio/DGEB/commit/c5ad3f098d36e25afdf4fa9aae20967eb968568e)) | ||
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* fix: update pip install command in readme ([`ff90791`](https://github.com/TattaBio/DGEB/commit/ff90791398f9a9b907c308400f88811a8f8633dc)) | ||
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### Unknown | ||
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* 0.0.5 | ||
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Automatically generated by python-semantic-release ([`ec24ca3`](https://github.com/TattaBio/DGEB/commit/ec24ca343b49bee85c72907554772976f02eab1a)) | ||
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## v0.0.4 (2024-07-01) | ||
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### Fix | ||
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* fix: move gh token to env ([`95e292c`](https://github.com/TattaBio/DGEB/commit/95e292c46f7908659d46bc093ef4903609f1edc5)) | ||
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### Unknown | ||
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* 0.0.4 | ||
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Automatically generated by python-semantic-release ([`03f3004`](https://github.com/TattaBio/DGEB/commit/03f300476b0aeca2796b780139fce0be037ae636)) | ||
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## v0.0.3 (2024-07-01) | ||
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### Fix | ||
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* fix: remove persist credentials ([`2ae683e`](https://github.com/TattaBio/DGEB/commit/2ae683ed7a68b0559b81b1b7f5716636beef1415)) | ||
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* fix: try to fix release CI ([`1dfc938`](https://github.com/TattaBio/DGEB/commit/1dfc9383b2dab8bba444b09c6b85500dadee7203)) | ||
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### Unknown | ||
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* 0.0.3 | ||
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Automatically generated by python-semantic-release ([`7cbfc8d`](https://github.com/TattaBio/DGEB/commit/7cbfc8d0acef975d046ff485001ed289800d143f)) | ||
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## v0.0.2 (2024-07-01) | ||
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### Fix | ||
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* fix: new repository name ([`8fc1145`](https://github.com/TattaBio/DGEB/commit/8fc1145985eab8aa97562f697edab45a30b189ba)) | ||
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* fix: addl geb references ([`86a5af8`](https://github.com/TattaBio/DGEB/commit/86a5af8c24244ac8f2670801468e1a25b8e3e9df)) | ||
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### Unknown | ||
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* 0.0.2 | ||
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Automatically generated by python-semantic-release ([`1c7b19b`](https://github.com/TattaBio/DGEB/commit/1c7b19b50597e9dabe07fbf7cb7d3c589438917a)) | ||
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## v0.0.1 (2024-07-01) | ||
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### Fix | ||
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* fix: rename geb to dgeb ([`be712f8`](https://github.com/TattaBio/DGEB/commit/be712f8d19678801b9148ac8397f13afe826871b)) | ||
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### Unknown | ||
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* 0.0.1 | ||
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Automatically generated by python-semantic-release ([`1503e03`](https://github.com/TattaBio/DGEB/commit/1503e030bb1277e1a2dcad7b99c9ed3472243f5d)) | ||
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## v0.0.0 (2024-07-01) | ||
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### Unknown | ||
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* 0.0.0 | ||
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Automatically generated by python-semantic-release ([`4b791ee`](https://github.com/TattaBio/DGEB/commit/4b791ee07085647427afec31a1adf61977e6bd4c)) | ||
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* Initial commit ([`36fe62c`](https://github.com/TattaBio/DGEB/commit/36fe62c234331de97f2827a49bf62d5c35b92a1f)) |
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# Docker file for leaderboard | ||
FROM python:3.11-slim | ||
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WORKDIR /app | ||
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# install curl | ||
RUN apt-get update && apt-get install -y curl | ||
ADD https://astral.sh/uv/install.sh /install.sh | ||
RUN chmod +x /install.sh | ||
RUN /install.sh && rm /install.sh | ||
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# install deps | ||
COPY leaderboard/requirements.txt ./ | ||
RUN /root/.cargo/bin/uv pip install --system --no-cache -r requirements.txt | ||
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# copy src | ||
COPY dgeb dgeb | ||
COPY leaderboard/ leaderboard/ | ||
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# Run gradio when the container launches | ||
EXPOSE 7860 | ||
ENV GRADIO_SERVER_NAME="0.0.0.0" | ||
ENV GRADIO_TEMP_DIR="/app" | ||
WORKDIR /app/leaderboard | ||
CMD ["python", "app.py"] | ||
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