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Merge pull request #4 from kenblu24/ornl-urls
SuperNeuroMAT 3.1.0
2 parents 60474e4 + cc20772 commit 4dc522a

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‎.github/ISSUE_TEMPLATE/bug_report.md‎

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---
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name: Bug report
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about: Create a report to help us improve
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title: "[Bug]: "
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labels: bug
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assignees: kenblu24
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---
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**Describe the bug**
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A clear and concise description of what the bug is.
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**To Reproduce**
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Steps to reproduce the behavior:
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**Expected behavior**
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A clear and concise description of what you expected to happen.
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**Screenshots**
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If applicable, add screenshots to help explain your problem.
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**Environment & Version Info (please complete the following information):**
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- OS (i.e. Windows 10 x64, MacOS, Linux Distro...):
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- Python Version :
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- SuperNeuroMAT Version :
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**Additional context**
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Add any other context about the problem here.

‎.github/ISSUE_TEMPLATE/feature_request.md‎

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---
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name: Feature request
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about: Suggest an idea for this project
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title: "<Suggestion> "
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labels: enhancement
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assignees: ''
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---
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**Is your feature request related to a problem? Please describe.**
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A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
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**Describe the solution you'd like**
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A clear and concise description of what you want to happen.
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**Describe alternatives you've considered**
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A clear and concise description of any alternative solutions or features you've considered.
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**Additional context**
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Add any other context or screenshots about the feature request here.

‎.github/workflows/draft-release.yml‎

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name: "Create Draft Release w/ Docs"
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# deploy the documentation to GitHub Pages via an artifact
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# does not create a branch or any commits
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# define triggers
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on:
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push:
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branches:
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- release-test
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tags:
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- "v*"
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# pull_request:
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# branches:
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# - main
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jobs:
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# build the documentation
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build-docs:
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runs-on: ubuntu-latest
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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v4
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- name: Install uv
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uses: astral-sh/setup-uv@v5
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# - name: Setup Graphviz
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# uses: ts-graphviz/setup-graphviz@v2
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- name: Set up Python # use uv to install Python
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run: uv python install
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- name: Install superneuromat
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run: |
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uv venv venv
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. venv/bin/activate
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echo PATH=$PATH >> $GITHUB_ENV
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uv pip install .[docs]
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echo $PATH
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# note: need to modify GITHUB_ENV path for the new venv to be used
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# as each run step is a new shell
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- name: List src directory for debugging
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run: |
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ls -R src
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echo $PATH
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- name: Verify installation
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run: |
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uv pip show superneuromat
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- name: Build HTML
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run: |
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cd docs
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./single html
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- name: Add to archive
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run: |
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zip -r superneuromat-${{ github.ref_name }}-docs.zip docs/superneuromat-docs/build
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- name: Upload artifacts
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uses: actions/upload-artifact@v4
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id: docs-release
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with:
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name: superneuromat-docs
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path: superneuromat-${{ github.ref_name }}-docs.zip
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- name: Upload pages artifacts
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uses: actions/upload-pages-artifact@v3
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id: docs-pages
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with:
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name: github-pages
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path: docs/superneuromat-docs/build/html/
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# - name: Deploy
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# uses: peaceiris/actions-gh-pages@v3
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# if: github.ref == 'refs/heads/main'
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# with:
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# github_token: ${{ secrets.GITHUB_TOKEN }}
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# publish_dir: docs/build/html
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# Deploy job
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draft-release:
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# Add a dependency to the build job
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needs: build-docs
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if: github.ref_type == 'tag'
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# Specify runner + deployment step
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runs-on: ubuntu-latest
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permissions:
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contents: write
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discussions: write
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steps:
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- name: Download artifacts
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uses: actions/download-artifact@v4
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with:
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name: superneuromat-docs
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- name: show files
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run: ls -lAR
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- name: Create Draft Release and attach artifacts
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id: release
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uses: softprops/action-gh-release@v2
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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with:
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draft: true
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files: |
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superneuromat-${{ github.ref_name }}-docs.zip
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generate_release_notes: true
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fail_on_unmatched_files: true
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# Deploy job
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deploy-pages:
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# Add a dependency to the build job
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needs: build-docs
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# only deploy pages if not a test tag
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if: ${{! contains(github.ref_name, 'test')}}
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# Grant GITHUB_TOKEN the permissions required to make a Pages deployment
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permissions:
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pages: write # to deploy to Pages
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id-token: write # to verify the deployment originates from an appropriate source
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# Deploy to the github-pages environment
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environment:
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name: github-pages
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url: ${{ steps.docs-pages.outputs.page_url }}
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# Specify runner + deployment step
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runs-on: ubuntu-latest
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steps:
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- name: Deploy to GitHub Pages
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id: docs-pages
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uses: actions/deploy-pages@v4

‎.github/workflows/pages-build.yaml‎

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name: "Sphinx: Build HTML"
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# deploy the documentation to GitHub Pages via an artifact
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# does not create a branch or any commits
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# define triggers
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on:
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push:
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branches:
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- main
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- actions-test
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pull_request:
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branches:
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- main
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jobs:
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# build the documentation
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build:
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runs-on: ubuntu-latest
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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v4
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- name: Install uv
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uses: astral-sh/setup-uv@v5
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# - name: Setup Graphviz
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# uses: ts-graphviz/setup-graphviz@v2
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- name: Set up Python # use uv to install Python
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run: uv python install
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- name: Install superneuromat
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run: |
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uv venv venv
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. venv/bin/activate
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echo PATH=$PATH >> $GITHUB_ENV
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uv pip install .[docs]
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echo $PATH
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# note: need to modify GITHUB_ENV path for the new venv to be used
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# as each run step is a new shell
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- name: List src directory for debugging
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run: |
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ls -R src
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echo $PATH
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- name: Verify installation
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run: |
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uv pip show superneuromat
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- name: Build HTML
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run: |
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cd docs
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./single html
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- name: Upload artifacts
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uses: actions/upload-pages-artifact@v3
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id: deployment
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with:
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name: github-pages
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path: docs/superneuromat-docs/build/html/
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# - name: Deploy
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# uses: peaceiris/actions-gh-pages@v3
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# if: github.ref == 'refs/heads/main'
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# with:
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# github_token: ${{ secrets.GITHUB_TOKEN }}
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# publish_dir: docs/build/html
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# Deploy job
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deploy:
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# Add a dependency to the build job
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needs: build
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if: github.ref == 'refs/heads/main'
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# Grant GITHUB_TOKEN the permissions required to make a Pages deployment
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permissions:
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pages: write # to deploy to Pages
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id-token: write # to verify the deployment originates from an appropriate source
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# Deploy to the github-pages environment
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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# Specify runner + deployment step
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runs-on: ubuntu-latest
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steps:
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@v4

‎.github/workflows/pypi-release.yml‎

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# This workflow will upload a Python Package to PyPI when a release is created
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# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#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: Build & Upload Python Package
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on:
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release:
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types: [published]
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permissions:
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contents: read
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jobs:
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release-build:
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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.x"
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- name: Build release distributions
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run: |
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python -m pip install build
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python -m build
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- name: Upload distributions
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uses: actions/upload-artifact@v4
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with:
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name: release-dists
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path: dist/
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pypi-publish:
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runs-on: ubuntu-latest
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needs:
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- release-build
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permissions:
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# IMPORTANT: this permission is mandatory for trusted publishing
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id-token: write
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# Dedicated environments with protections for publishing are strongly recommended.
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# For more information, see: https://docs.github.com/en/actions/deployment/targeting-different-environments/using-environments-for-deployment#deployment-protection-rules
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environment:
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name: pypi
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# OPTIONAL: uncomment and update to include your PyPI project URL in the deployment status:
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# url: https://pypi.org/p/YOURPROJECT
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#
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# ALTERNATIVE: if your GitHub Release name is the PyPI project version string
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# ALTERNATIVE: exactly, uncomment the following line instead:
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# url: https://pypi.org/project/YOURPROJECT/${{ github.event.release.name }}
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steps:
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- name: Retrieve release distributions
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uses: actions/download-artifact@v4
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with:
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name: release-dists
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path: dist/
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- name: Publish release distributions to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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packages-dir: dist/

‎.github/workflows/test.yaml‎

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name: "Tox Tests (partial)"
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# run tests via tox
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# define triggers
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on:
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push:
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branches:
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- main
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- actions-test
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# tags:
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# - "v*"
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pull_request:
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branches:
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- main
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jobs:
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test:
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name: test with ${{ matrix.env }} on ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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env: # see entries in [tool.tox.gh.python] in pyproject.toml
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- "3.13"
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- "3.9"
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os:
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- ubuntu-latest
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- macos-latest
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- windows-latest
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steps:
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- uses: actions/checkout@v4
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- name: Install the latest version of uv
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uses: astral-sh/setup-uv@v5
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- name: Install tox
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run: uv tool install --python-preference only-managed --python 3.13 tox --with tox-uv --with tox-gh
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- name: Install Python
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if: matrix.env != '3.13'
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run: uv python install --python-preference only-managed ${{ matrix.env }}
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- name: Setup test suite
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run: tox run -vv --notest --skip-missing-interpreters false
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env:
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TOX_GH_MAJOR_MINOR: ${{ matrix.env }}
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- name: Run test suite
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run: tox run --skip-pkg-install
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env:
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TOX_GH_MAJOR_MINOR: ${{ matrix.env }}

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