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Merge branch 'main' into GA_feedback_implementation
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.github/CODEOWNERS

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/communities/biodiversity/ @scorreard
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/communities/earth/ @Marie59
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/communities/imaging/ @nagoue
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/communities/workflow4metabolomics @lecorguille @hechth @melpetera
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/communities/microgalaxy/ @bebatut
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/communities/spoc/ @MarisaJL @pavanvidem
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.github/workflows/deploy_jekyll.yml

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- name: Checkout
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uses: actions/checkout@v7
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- name: Setup Ruby
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uses: ruby/setup-ruby@v1.314.0
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uses: ruby/setup-ruby@v1.319.0
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with:
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ruby-version: '3.3'
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bundler-cache: true

.github/workflows/fetch_filter_resources.yaml

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steps:
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- name: Checkout main
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uses: actions/checkout@v7
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- uses: actions/setup-python@v6
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- uses: actions/setup-python@v7
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with:
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python-version: '3.11'
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- name: Install requirement
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sudo apt-get install jq
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- name: Fetch list of all available servers
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run: |
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python sources/bin/get_public_galaxy_servers.py -o sources/data/available_public_servers.csv
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python sources/bin/get_public_galaxy_servers.py -o sources/data/available_public_servers.csv -c sources/data/custom_servers.csv
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- name: Archive available servers
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uses: actions/upload-artifact@v7
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with:
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steps:
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- name: Checkout main
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uses: actions/checkout@v7
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- uses: actions/setup-python@v6
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- uses: actions/setup-python@v7
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with:
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python-version: '3.11'
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- name: Install requirement
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steps:
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- name: Checkout main
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uses: actions/checkout@v7
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- uses: actions/setup-python@v6
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- uses: actions/setup-python@v7
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with:
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python-version: '3.11'
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- name: Install requirement
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steps:
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- name: Checkout main
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uses: actions/checkout@v7
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- uses: actions/setup-python@v6
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- uses: actions/setup-python@v7
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with:
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python-version: '3.11'
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- name: Install requirement
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# steps:
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# - name: Checkout main
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# uses: actions/checkout@v7
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# - uses: actions/setup-python@v6
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# - uses: actions/setup-python@v7
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# with:
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# python-version: '3.11'
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# - name: Install requirement
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with:
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# We pass the "PAT" secret to the checkout action; if no PAT secret is available to the workflow runner (eg. Dependabot) we fall back to the default "GITHUB_TOKEN".
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token: ${{ secrets.PAT || secrets.GH_ACTIONS_PAT }}
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- uses: actions/setup-python@v6
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- uses: actions/setup-python@v7
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with:
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python-version: '3.11'
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- name: Install requirement

.github/workflows/filter_communities.yaml

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id: prepare
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run: |
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# produce a JSON array string, e.g. from a file or script
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echo '["assembly","biodiversity","earth","genome","imaging","machine-learning","metabolomics","microgalaxy","proteomics","spoc"]' > communities.json
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echo '["assembly","biodiversity","earth","genome","imaging","machine-learning","workflow4metabolomics","microgalaxy","proteomics","spoc"]' > communities.json
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communities=$(cat communities.json)
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echo "communities=$communities" >> $GITHUB_OUTPUT
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steps:
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- name: Checkout main
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uses: actions/checkout@v7
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- uses: actions/setup-python@v6
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- uses: actions/setup-python@v7
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with:
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python-version: '3.11'
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- name: Install requirement

.github/workflows/labs_post_comments.yml

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ref: main
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- name: Set up Python
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uses: actions/setup-python@v6
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uses: actions/setup-python@v7
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python-version: '3.12'
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.github/workflows/labs_test.yml

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fetch-depth: 0 # ensure full history for merge-base diff
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- name: Set up Python
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uses: actions/setup-python@v6
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uses: actions/setup-python@v7
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.github/workflows/lint_and_unittest.yaml

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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v7
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- uses: actions/setup-python@v6
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- uses: actions/setup-python@v7
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with:
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python-version: '3.11'
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- name: Install tox
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- uses: actions/checkout@v7
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- uses: actions/setup-python@v6
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- uses: actions/setup-python@v7
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python-version: ${{ matrix.python-version }}
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.github/workflows/lint_jekyll.yaml

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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v7
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- uses: ruby/setup-ruby@v1.314.0
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- uses: ruby/setup-ruby@v1.319.0
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bundler-cache: true

.github/workflows/monthly-release.yml

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setup:
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if: github.repository_owner == 'galaxyproject'
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runs-on: ubuntu-latest
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environment: create-release
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# This is only needed for the final step of gh release creation.
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# That should be separated into a separate dependent job at some point.
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run: |
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git tag -l
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- uses: actions/setup-python@v7
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with:
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python-version: '3.11'
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- name: Generate Release Notes
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run: |
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# Find the previous tag to compute the date range
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PREV_TAG=$(git tag -l --sort=-version:refname | head -1)
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if [ -z "$PREV_TAG" ]; then
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# No previous tag: look back 30 days
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SINCE=$(date -d '30 days ago' --iso-8601=seconds)
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else
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SINCE=$(git log -1 --format=%aI "$PREV_TAG")
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fi
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{
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# Release header with archive link
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echo "## Galaxy Codex Monthly Release"
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echo ""
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echo "Monthly release of Galaxy Codex is now [available on GitHub](https://github.com/galaxyproject/galaxy_codex/releases/tag/${RELEASE_TAG})."
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echo ""
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# Resource stats from script
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python3 sources/bin/collect_release_stats.py --ref "$PREV_TAG" | tail -n +3
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echo ""
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# Git activity summary
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echo "### Activity Summary"
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echo ""
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COMMITS=$(git log --since="$SINCE" --oneline --no-merges | wc -l)
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echo "- **${COMMITS} commits** merged"
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echo ""
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# Merged PRs: only "Merge pull request #" commits
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echo "### Pull Requests Merged"
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echo ""
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git log --since="$SINCE" --merges --oneline --grep="Merge pull request" | while IFS= read -r line; do
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MSG=$(echo "$line" | sed 's/^.*Merge pull request //')
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echo "- ${MSG}"
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done
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echo ""
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# Per-community file changes
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echo "### Community File Changes"
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echo ""
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for community_dir in communities/*/; do
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community=$(basename "$community_dir")
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[ "$community" = "all" ] && continue
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[ "$community" = "README.md" ] && continue
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CHANGED=$(git log --since="$SINCE" --name-only --pretty=format: -- "$community_dir" | grep -c . || true)
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if [ "$CHANGED" -gt 0 ]; then
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echo "- **${community}**: ${CHANGED} files updated"
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fi
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done
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echo ""
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echo "---"
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echo "*Browse the full catalog: https://galaxyproject.github.io/galaxy_codex/*"
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} > /tmp/last-month-on.md
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echo "Generated release notes:"
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cat /tmp/last-month-on.md
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- name: Create Release
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id: create_release
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env:
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GH_TOKEN: ${{ secrets.GH_TOKEN }}
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GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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RELEASE_TAG: ${{ env.release_tag }}
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RELEASE_TITLE: ${{ env.release_title }}
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run: |
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# Create the release
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gh release create "$RELEASE_TAG" --title "Release $RELEASE_TITLE" --notes-file /tmp/last-month-on.md --target main --latest
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gh release create "$RELEASE_TAG" --title "Release $RELEASE_TITLE" --notes-file /tmp/last-month-on.md --target main --latest

.github/workflows/run_tests.yaml

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- name: Checkout
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- uses: actions/setup-python@v6
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- uses: actions/setup-python@v7
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- name: Install requirements
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- name: Checkout
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uses: actions/checkout@v7
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- uses: actions/setup-python@v6
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- uses: actions/setup-python@v7
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- name: Install requirements
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- name: Checkout
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uses: actions/checkout@v7
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- uses: actions/setup-python@v7
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- name: Install requirements
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# steps:
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# - name: Checkout
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# uses: actions/checkout@v7
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# - uses: actions/setup-python@v6
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# - uses: actions/setup-python@v7
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# with:
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# python-version: ${{ matrix.python-version }}
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# - name: Install requirements

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