Initial commit

.editorconfig

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+# top-most EditorConfig file
+root = true
+
+# Unix-style newlines with a newline ending every file
+[*]
+end_of_line = lf
+insert_final_newline = true
+
+[*.py]
+charset = utf-8
+indent_style = space
+indent_size = 4

.github/workflows/ci.yml

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+name: CI for DGEB
+
+on:
+  push:
+    branches: ["**"]
+  pull_request:
+    branches: ["**"]
+
+permissions:
+  id-token: write
+  contents: read
+  actions: write
+  pull-requests: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+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

.github/workflows/release.yml

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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
+
+# 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/
+
+name: Release
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    concurrency: release
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing using PyPI
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          token: ${{ secrets.GH_TOKEN }}
+
+      - name: Python Semantic Release
+        id: release
+        uses: python-semantic-release/python-semantic-release@v9.8.3
+        with:
+          github_token: ${{ secrets.GH_TOKEN }}
+
+      - 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.
+
+      - 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 }}

.gitignore

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+.venv/
+__pycache__/
+.vscode/
+build/
+dist/
+*egg-info/

CHANGELOG.md

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+# CHANGELOG
+
+## v0.0.10 (2024-07-09)
+
+### Fix
+
+* fix: remove noop task ([`7d5b393`](https://github.com/TattaBio/DGEB/commit/7d5b3933f48e51fb4c71945f01af2cc5a7dba3ed))
+
+## v0.0.9 (2024-07-09)
+
+### Fix
+
+* fix: update cli script name ([`633e14d`](https://github.com/TattaBio/DGEB/commit/633e14db7e1eed0d9606ef1097e369e4f5e245f5))
+
+### Unknown
+
+* 0.0.9
+
+Automatically generated by python-semantic-release [skip ci] ([`a8c1a96`](https://github.com/TattaBio/DGEB/commit/a8c1a96d18af589795bc9532fee8ad9764cd52ed))
+
+* Merge pull request #9 from TattaBio/andre
+
+Update ModAC main metric ([`3c67e65`](https://github.com/TattaBio/DGEB/commit/3c67e6559d0e49d90ffe2858eb9e287abd1b6e6c))
+
+* ruff format ([`78461ac`](https://github.com/TattaBio/DGEB/commit/78461ac901b8617821ca15e543c0dd8e2dbf6e95))
+
+* update top_k=50 for modac ([`2c3dcd5`](https://github.com/TattaBio/DGEB/commit/2c3dcd5856b6679a80999b3c4b3512876ac0b58d))
+
+* remove revision ([`2d587da`](https://github.com/TattaBio/DGEB/commit/2d587daa79f32c49201b419892b7f95f3dc5eedb))
+
+* Merge pull request #8 from TattaBio/cli
+
+Cli & cleanup ([`9698c8f`](https://github.com/TattaBio/DGEB/commit/9698c8f5ab0bab6c3c0a76d59dc29cfd964ebf15))
+
+* Exclude leaderboard files in anticipation of merging leaderboard PR ([`58bdcba`](https://github.com/TattaBio/DGEB/commit/58bdcba11af605bdef11cfecc087c9efb0e97b72))
+
+* Update README ([`d323905`](https://github.com/TattaBio/DGEB/commit/d3239059e29fb149f9c348b951bc4988d8b9f8dc))
+
+* cleanup ([`1f0fe16`](https://github.com/TattaBio/DGEB/commit/1f0fe16de6910200d88c918b08cbf26067313469))
+
+* Add cli to pyproject.toml ([`5404218`](https://github.com/TattaBio/DGEB/commit/54042181ef54c11db74ebb53c403b21a8114c02b))
+
+* Remove Dataset 'description' which does not exist on model. ([`46b0040`](https://github.com/TattaBio/DGEB/commit/46b0040a302384fa00791bbfdd6fae24645d6a6d))
+
+* Merge pull request #7 from TattaBio/add_dna_tasks
+
+Add dna tasks ([`cfc5799`](https://github.com/TattaBio/DGEB/commit/cfc57995f9b1e584bb60e998f9cf68bea5ec39fa))
+
+* ruff ([`f9fa125`](https://github.com/TattaBio/DGEB/commit/f9fa12502df9837b5381da17b17198f3667c4911))
+
+* adding rpob datasets and updating ec revision ([`8f9cc3f`](https://github.com/TattaBio/DGEB/commit/8f9cc3f819beb70f51a5cc59f16c65bffceedbad))
+
+* Update README.md ([`d5d7c24`](https://github.com/TattaBio/DGEB/commit/d5d7c24215d347fc17d6016ac2a3eddfb3cf2a12))
+
+* Merge pull request #4 from TattaBio/andre
+
+Add dataset revisions ([`95b6f11`](https://github.com/TattaBio/DGEB/commit/95b6f11ffee3dccc45ab119ac4f602066750f7ef))
+
+* add dataset revision numbers ([`7e069a2`](https://github.com/TattaBio/DGEB/commit/7e069a237de5391e7c6b7f09c108292ac10c25af))
+
+* Merge pull request #3 from TattaBio/andre
+
+Update readme and task imports ([`ade30a8`](https://github.com/TattaBio/DGEB/commit/ade30a856deffe35ddf57d16705d030b6d0192c8))
+
+* rename dgeb ([`6b1c2ee`](https://github.com/TattaBio/DGEB/commit/6b1c2ee76798d89e487386116efe23c90d2d039c))
+
+* add intro ([`a2280dd`](https://github.com/TattaBio/DGEB/commit/a2280dd732984d58caed45b9a429038c0d81851a))
+
+* update readme and tasks ([`00e0a79`](https://github.com/TattaBio/DGEB/commit/00e0a791f070ca37e5b92770b3363ef066e2789f))
+
+* Merge pull request #2 from TattaBio/andre
+
+rename dgeb imports ([`1894ba9`](https://github.com/TattaBio/DGEB/commit/1894ba9a92a8f369053ddb9d351ae48fd8e2d674))
+
+* rename dgeb imports ([`5f1f8b8`](https://github.com/TattaBio/DGEB/commit/5f1f8b850f271cd6785291e3feb2c2d4bf979f9c))
+
+## v0.0.8 (2024-07-01)
+
+### Fix
+
+* fix: don't run ci on release of new version ([`fa97104`](https://github.com/TattaBio/DGEB/commit/fa971049429975d06c8aca086e86b19d92383969))
+
+### Unknown
+
+* 0.0.8
+
+Automatically generated by python-semantic-release [skip ci] ([`8dc15d3`](https://github.com/TattaBio/DGEB/commit/8dc15d34c6317087253950893974d16b9f75a17c))
+
+## v0.0.7 (2024-07-01)
+
+### Fix
+
+* fix: try again ([`e7d0ecd`](https://github.com/TattaBio/DGEB/commit/e7d0ecdcb63e909f9ab727f11fb3fd57414d2fa5))
+
+* fix: edit readme to see if job still works with restricted permissions ([`93cd728`](https://github.com/TattaBio/DGEB/commit/93cd728c8a632b9bed611c55dace2e2ffb103410))
+
+### Unknown
+
+* 0.0.7
+
+Automatically generated by python-semantic-release ([`9808d4f`](https://github.com/TattaBio/DGEB/commit/9808d4f328a577c066affd34d408ad26eb6098d0))
+
+* Merge pull request #1 from TattaBio/edit-readme
+
+fix: edit readme to see if job still works with restricted permissions ([`c45599c`](https://github.com/TattaBio/DGEB/commit/c45599cf9628155603245f906c09cf6483cffce8))
+
+## v0.0.6 (2024-07-01)
+
+### Fix
+
+* fix: nevermind that broke it ([`ec33a1c`](https://github.com/TattaBio/DGEB/commit/ec33a1c6539ac1fb2710869a2d436483a02236e0))
+
+* fix: see if I can remove this line ([`246d4e9`](https://github.com/TattaBio/DGEB/commit/246d4e9841a83d18217506d46f211f1341c63526))
+
+### Unknown
+
+* 0.0.6
+
+Automatically generated by python-semantic-release ([`1b28df5`](https://github.com/TattaBio/DGEB/commit/1b28df559c95db0aea95111a5f27d01645d23786))
+
+## v0.0.5 (2024-07-01)
+
+### Fix
+
+* fix: try fixing release to handle protected branch ([`5cedad3`](https://github.com/TattaBio/DGEB/commit/5cedad3e9f34d249eda9257e3c21fc8443d000cf))
+
+* fix: another change... ([`c5ad3f0`](https://github.com/TattaBio/DGEB/commit/c5ad3f098d36e25afdf4fa9aae20967eb968568e))
+
+* fix: update pip install command in readme ([`ff90791`](https://github.com/TattaBio/DGEB/commit/ff90791398f9a9b907c308400f88811a8f8633dc))
+
+### Unknown
+
+* 0.0.5
+
+Automatically generated by python-semantic-release ([`ec24ca3`](https://github.com/TattaBio/DGEB/commit/ec24ca343b49bee85c72907554772976f02eab1a))
+
+## v0.0.4 (2024-07-01)
+
+### Fix
+
+* fix: move gh token to env ([`95e292c`](https://github.com/TattaBio/DGEB/commit/95e292c46f7908659d46bc093ef4903609f1edc5))
+
+### Unknown
+
+* 0.0.4
+
+Automatically generated by python-semantic-release ([`03f3004`](https://github.com/TattaBio/DGEB/commit/03f300476b0aeca2796b780139fce0be037ae636))
+
+## v0.0.3 (2024-07-01)
+
+### Fix
+
+* fix: remove persist credentials ([`2ae683e`](https://github.com/TattaBio/DGEB/commit/2ae683ed7a68b0559b81b1b7f5716636beef1415))
+
+* fix: try to fix release CI ([`1dfc938`](https://github.com/TattaBio/DGEB/commit/1dfc9383b2dab8bba444b09c6b85500dadee7203))
+
+### Unknown
+
+* 0.0.3
+
+Automatically generated by python-semantic-release ([`7cbfc8d`](https://github.com/TattaBio/DGEB/commit/7cbfc8d0acef975d046ff485001ed289800d143f))
+
+## v0.0.2 (2024-07-01)
+
+### Fix
+
+* fix: new repository name ([`8fc1145`](https://github.com/TattaBio/DGEB/commit/8fc1145985eab8aa97562f697edab45a30b189ba))
+
+* fix: addl geb references ([`86a5af8`](https://github.com/TattaBio/DGEB/commit/86a5af8c24244ac8f2670801468e1a25b8e3e9df))
+
+### Unknown
+
+* 0.0.2
+
+Automatically generated by python-semantic-release ([`1c7b19b`](https://github.com/TattaBio/DGEB/commit/1c7b19b50597e9dabe07fbf7cb7d3c589438917a))
+
+## v0.0.1 (2024-07-01)
+
+### Fix
+
+* fix: rename geb to dgeb ([`be712f8`](https://github.com/TattaBio/DGEB/commit/be712f8d19678801b9148ac8397f13afe826871b))
+
+### Unknown
+
+* 0.0.1
+
+Automatically generated by python-semantic-release ([`1503e03`](https://github.com/TattaBio/DGEB/commit/1503e030bb1277e1a2dcad7b99c9ed3472243f5d))
+
+## v0.0.0 (2024-07-01)
+
+### Unknown
+
+* 0.0.0
+
+Automatically generated by python-semantic-release ([`4b791ee`](https://github.com/TattaBio/DGEB/commit/4b791ee07085647427afec31a1adf61977e6bd4c))
+
+* Initial commit ([`36fe62c`](https://github.com/TattaBio/DGEB/commit/36fe62c234331de97f2827a49bf62d5c35b92a1f))

Dockerfile

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+# Docker file for leaderboard
+FROM python:3.11-slim
+
+WORKDIR /app
+
+# 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
+
+# install deps
+COPY leaderboard/requirements.txt ./
+RUN /root/.cargo/bin/uv pip install --system --no-cache -r requirements.txt
+
+# copy src
+COPY dgeb dgeb
+COPY leaderboard/ leaderboard/
+
+# 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"]
+
+