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‎.github/PULL_REQUEST_TEMPLATE.md‎

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## What does this PR do?
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<!--
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Please include a summary of the change and which issue is fixed.
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Please also include relevant motivation and context.
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List any dependencies that are required for this change.
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List all the breaking changes introduced by this pull request.
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-->
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Fixes #\<issue_number>
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## Before submitting
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- [ ] Did you make sure **title is self-explanatory** and **the description concisely explains the PR**?
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- [ ] Did you make sure your **PR does only one thing**, instead of bundling different changes together?
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- [ ] Did you list all the **breaking changes** introduced by this pull request?
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- [ ] Did you **run pre-commit hooks** with `pre-commit run -a` command?
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## Did you have fun?
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Make sure you had fun coding 🙃

‎.github/codecov.yml‎

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coverage:
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status:
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# measures overall project coverage
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project:
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default:
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threshold: 100% # how much decrease in coverage is needed to not consider success
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# measures PR or single commit coverage
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patch:
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default:
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threshold: 100% # how much decrease in coverage is needed to not consider success
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# project: off
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# patch: off

‎.github/dependabot.yml‎

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# To get started with Dependabot version updates, you'll need to specify which
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# package ecosystems to update and where the package manifests are located.
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# Please see the documentation for all configuration options:
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# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
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version: 2
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updates:
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- package-ecosystem: "pip" # See documentation for possible values
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directory: "/" # Location of package manifests
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schedule:
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interval: "daily"
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ignore:
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- dependency-name: "pytorch-lightning"
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update-types: ["version-update:semver-patch"]
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- dependency-name: "torchmetrics"
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update-types: ["version-update:semver-patch"]

‎.github/documentation.yaml‎

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name: documentation
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on: [push, pull_request, workflow_dispatch]
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permissions:
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contents: write
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jobs:
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docs:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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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: Setup miniconda
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uses: conda-incubator/setup-miniconda@v3
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with:
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miniforge-variant: Mambaforge
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python-version: ${{ matrix.python-version }}
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auto-update-conda: true
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use-mamba: true
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auto-activate-base: false
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activate-environment: "MULTICOM_ligand-Documentation"
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environment-file: docs/.docs.environment.yaml
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- name: Install dependencies
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run: |
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$CONDA/envs/MULTICOM_ligand-Documentation/bin/pip install -e .
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- name: Sphinx build
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run: |
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rm -rf docs/build/ && $CONDA/envs/MULTICOM_ligand-Documentation/bin/sphinx-build docs/source/ docs/build/
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- name: Deploy to GitHub Pages
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uses: peaceiris/actions-gh-pages@v4
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if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
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with:
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publish_branch: gh-pages
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: docs/build/
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force_orphan: true

‎.github/release-drafter.yml‎

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name-template: "v$RESOLVED_VERSION"
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tag-template: "v$RESOLVED_VERSION"
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categories:
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- title: "🚀 Features"
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labels:
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- "feature"
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- "enhancement"
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- title: "🐛 Bug Fixes"
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labels:
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- "fix"
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- "bugfix"
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- "bug"
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- title: "🧹 Maintenance"
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labels:
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- "maintenance"
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- "dependencies"
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- "refactoring"
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- "cosmetic"
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- "chore"
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- title: "📝️ Documentation"
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labels:
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- "documentation"
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- "docs"
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change-template: "- $TITLE @$AUTHOR (#$NUMBER)"
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change-title-escapes: '\<*_&' # You can add # and @ to disable mentions
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version-resolver:
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major:
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labels:
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- "major"
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minor:
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labels:
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- "minor"
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patch:
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labels:
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- "patch"
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default: patch
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template: |
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## Changes
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$CHANGES

‎.github/workflows/changelog-enforcer.yaml‎

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name: Changelog Enforcer
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on: # yamllint disable-line rule:truthy
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pull_request:
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types: [opened, synchronize, reopened, ready_for_review, labeled, unlabeled]
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jobs:
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changelog:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: dangoslen/changelog-enforcer@v3
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with:
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skipLabels: "skip-changelog"

‎.github/workflows/code-quality-main.yaml‎

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# Same as `code-quality-pr.yaml` but triggered on commit to main branch
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# and runs on all files (instead of only the changed ones)
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name: Code Quality Main
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on:
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push:
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branches: [main]
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jobs:
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code-quality:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.10"
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- name: Run pre-commits
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uses: pre-commit/[email protected]

‎.github/workflows/code-quality-pr.yaml‎

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# This workflow finds which files were changed, prints them,
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# and runs `pre-commit` on those files.
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# Inspired by the sktime library:
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# https://github.com/alan-turing-institute/sktime/blob/main/.github/workflows/test.yml
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name: Code Quality PR
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on:
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pull_request:
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branches: [main, "release/*", "dev"]
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jobs:
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code-quality:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.10"
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- name: Find modified files
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id: file_changes
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uses: trilom/[email protected]
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with:
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output: " "
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- name: List modified files
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run: echo '${{ steps.file_changes.outputs.files}}'
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- name: Run pre-commits
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uses: pre-commit/[email protected]
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with:
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extra_args: --files ${{ steps.file_changes.outputs.files}}

‎.github/workflows/documentation.yaml‎

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name: documentation
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on: [push, pull_request, workflow_dispatch]
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permissions:
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contents: write
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jobs:
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docs:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: "3.10"
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- name: Setup miniconda
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uses: conda-incubator/setup-miniconda@v3
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with:
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miniforge-variant: Mambaforge
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python-version: ${{ matrix.python-version }}
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auto-update-conda: true
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use-mamba: true
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auto-activate-base: false
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activate-environment: "MULTICOM_ligand-Documentation"
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environment-file: docs/.docs.environment.yaml
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- name: Install dependencies
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run: |
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$CONDA/envs/MULTICOM_ligand-Documentation/bin/pip install -e .
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- name: Sphinx build
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run: |
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rm -rf docs/build/ && $CONDA/envs/MULTICOM_ligand-Documentation/bin/sphinx-build docs/source/ docs/build/
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- name: Deploy to GitHub Pages
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uses: peaceiris/actions-gh-pages@v4
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if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
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with:
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publish_branch: gh-pages
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: docs/build/
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force_orphan: true

‎.github/workflows/publish.yaml‎

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# This workflow will upload a Python Package using Twine when a release is created
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# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
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# This workflow uses actions that are not certified by GitHub.
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# They are provided by a third-party and are governed by
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# separate terms of service, privacy policy, and support
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# documentation.
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name: Upload Python Package
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on:
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release:
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types: [published]
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jobs:
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deploy:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python 3.10
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uses: actions/setup-python@v5
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with:
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python-version: "3.10"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install build
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- name: Build package
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run: python -m build
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- name: Publish package
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uses: pypa/[email protected]
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with:
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user: __token__
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password: ${{ secrets.PYPI_API_TOKEN }}

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