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feat: naive migration from organization repo bumpversion skip
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‎.coveragerc‎

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[run]
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branch = true
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parallel = true
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relative_files = true
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source =
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src
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[report]
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show_missing = true
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precision = 4

‎.github/workflows/main.yaml‎

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name: Publish
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permissions:
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contents: write
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id-token: write
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on:
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push:
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branches:
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- main
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jobs:
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publish:
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name: Publish
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if: ${{ ! contains(toJSON(github.event.commits.*.message), '[skip ci]') }}
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repo
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Setup python
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uses: actions/setup-python@v5
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with:
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python-version: "3.9"
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- name: Install semver
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run: python -m pip install semver
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- name: Authenticate to Google Cloud
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uses: google-github-actions/auth@v1
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with:
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workload_identity_provider: projects/1045208284552/locations/global/workloadIdentityPools/vantai-github-actions-pool/providers/vantai-github-actions-provider
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service_account: default-gha@vantai-analysis.iam.gserviceaccount.com
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- name: Setup gcloud
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uses: google-github-actions/setup-gcloud@v1
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- name: Configure docker
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run: gcloud auth configure-docker us-east1-docker.pkg.dev
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- name: Get version bump
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id: get-tag
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run: echo "bump=$(python flows/docker.py bump)" >> $GITHUB_OUTPUT
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- name: Pull, build, tag, bump base image
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if: steps.get-tag.outputs.bump != ''
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run: python flows/docker.py pull --build --promote
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- name: Build image
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if: steps.get-tag.outputs.bump != ''
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run: python flows/docker.py build
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- name: Run tests against new image and save images
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if: steps.get-tag.outputs.bump != ''
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run: python flows/docker.py test --push
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- name: Save git tag
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if: steps.get-tag.outputs.bump != ''
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run: git push origin ${{ steps.get-tag.outputs.bump }}

‎.github/workflows/pr.yaml‎

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name: CI Workflow
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permissions:
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contents: write
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id-token: write
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pull-requests: write
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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on:
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pull_request:
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jobs:
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test:
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name: Code quality checks
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repo
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uses: actions/checkout@v4
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- name: Setup python
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uses: actions/setup-python@v5
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with:
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python-version: "3.9"
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- name: Install tox
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run: pip install tox
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- name: Run quality checks
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run: tox -e py39-lint,py39-type
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- name: Directory Cache
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uses: actions/cache@v4
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with:
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path: .tox
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key: tox-${{ runner.os }}-3.9-${{ hashFiles('tox.ini') }}
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restore-keys: |
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tox-${{ runner.os }}-3.9-
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build:
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name: Build and test docker image
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repo
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uses: actions/checkout@v4
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with:
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ref: ${{ github.event.pull_request.head.sha }}
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fetch-depth: 0
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- name: Authenticate to Google Cloud
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uses: google-github-actions/auth@v1
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with:
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workload_identity_provider: projects/1045208284552/locations/global/workloadIdentityPools/vantai-github-actions-pool/providers/vantai-github-actions-provider
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service_account: default-gha@vantai-analysis.iam.gserviceaccount.com
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- name: Setup gcloud
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uses: google-github-actions/setup-gcloud@v1
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- name: Configure docker
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run: gcloud auth configure-docker us-east1-docker.pkg.dev
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- name: Get changed files
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id: changed-files
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uses: tj-actions/changed-files@v39
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with:
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files: dockerfiles/base/*
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- name: Pull base image and build
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if: steps.changed-files.outputs.any_changed == 'true'
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run: python flows/docker.py pull --build
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- name: Pull base image
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if: steps.changed-files.outputs.any_changed != 'true'
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run: python flows/docker.py pull
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- name: Build image
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run: python flows/docker.py build --push
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- name: Run test image
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run: python flows/docker.py test
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- name: Copy coverage
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run: cp reports/.coverage .
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- name: Post coverage comment
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uses: py-cov-action/python-coverage-comment-action@v3
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continue-on-error: true
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with:
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GITHUB_TOKEN: ${{ github.token }}

‎.gitignore‎

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reports/
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tox_conda*
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# extra folder
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Dataset
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Dataset_backup
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data_local
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openstructure
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my_log.txt
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examples/cluster_try1.ipynb
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examples/pli_cluster_split_challenge/benchmark.ipynb
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examples/pli_cluster_split_challenge/split_challenge_leaderboard.pdf
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*.feather
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*.pickle
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wandb
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src/plinder-data/plinder/data/pipeline/tmp
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src/plinder-eval/plinder/eval/split_qc/
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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cover/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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.pybuilder/
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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# For a library or package, you might want to ignore these files since the code is
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# intended to run in multiple environments; otherwise, check them in:
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# .python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# poetry
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# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
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# This is especially recommended for binary packages to ensure reproducibility, and is more
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# commonly ignored for libraries.
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# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
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#poetry.lock
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# pdm
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# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
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#pdm.lock
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# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
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# in version control.
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# https://pdm.fming.dev/#use-with-ide
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.pdm.toml
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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.metaflow/
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# PyCharm
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# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
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# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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# and can be added to the global gitignore or merged into this file. For a more nuclear
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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#.idea/
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.vscode
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.DS_Store
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*/.DS_Store
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*/*/DS_Store
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src/plinder-data/plinder/data/artifacts
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#src/plinder-core
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*.bak*
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*.1.*
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tests/xx
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artifacts

‎.pre-commit-config.yaml‎

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# See https://pre-commit.com for more information
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# See https://pre-commit.com/hooks.html for more hooks
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exclude: |
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(?x)^(
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docs/.*png|
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tests/test_data/.*|
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private/.*ipynb
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)$
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v3.2.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-yaml
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- id: check-added-large-files
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- repo: local
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hooks:
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- id: ruff-format
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name: ruff-format
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entry: bash -c 'ruff format --force-exclude --preview src'
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language: system
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types: [python]
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- id: ruff-linter
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name: ruff-linter
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entry: bash -c 'ruff check --fix src/plinder-core'
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language: system
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types: [python]

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