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eeholmeseeholmes
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Merge pull request #48 from nmfs-opensci/eeholmes-patch-2
Add action to create draft GitHub release from Dockerfile
2 parents 4f9ea95 + 2e7fd86 commit 7736041

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‎.github/actions/create-draft-release/action.yml‎

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name: Create draft release
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description: Create a draft GitHub Release using VERSION from Dockerfile (YYYY.MM.DD). Fails if VERSION is missing or malformed.
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inputs:
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tag_prefix:
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description: Optional prefix for the tag (e.g. v). Default is empty.
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required: false
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default: ""
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dockerfile_path:
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description: Path to Dockerfile to parse version from
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required: false
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default: Dockerfile
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target:
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description: Git ref/sha to tag (default: current commit SHA)
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required: false
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default: ""
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generate_notes:
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description: Whether to auto-generate release notes (true/false)
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required: false
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default: "true"
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runs:
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using: composite
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steps:
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- name: Extract and validate VERSION
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id: ver
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shell: bash
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run: |
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set -euo pipefail
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df="${{ inputs.dockerfile_path }}"
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if [ ! -f "$df" ]; then
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echo "::error::Dockerfile not found at: $df"
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exit 1
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fi
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if grep -q "LABEL org.opencontainers.image.version=" "$df"; then
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version=$(grep "LABEL org.opencontainers.image.version=" "$df" | head -1 | cut -d '=' -f2- | tr -d ' "')
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elif grep -q "LABEL VERSION=" "$df"; then
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version=$(grep "LABEL VERSION=" "$df" | head -1 | cut -d '=' -f2- | tr -d ' "')
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else
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echo "::error::No VERSION label found in $df"
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exit 1
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fi
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if ! echo "$version" | grep -Eq '^[0-9]{4}\.[0-9]{2}\.[0-9]{2}$'; then
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echo "::error::Invalid VERSION format: '$version' (expected YYYY.MM.DD)"
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exit 1
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fi
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tag="${{ inputs.tag_prefix }}${version}"
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echo "Resolved tag: $tag"
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echo "TAG=$tag" >> "$GITHUB_ENV"
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- name: Create draft release (fails if tag already exists)
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shell: bash
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env:
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GH_TOKEN: ${{ github.token }}
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run: |
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set -euo pipefail
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tag="${TAG}"
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title="Release ${tag}"
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target="${{ inputs.target }}"
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if [ -z "$target" ]; then
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target="${GITHUB_SHA}"
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fi
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if gh release view "$tag" >/dev/null 2>&1; then
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echo "::error::Release for tag '$tag' already exists."
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exit 1
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fi
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args=(release create "$tag" --draft --title "$title" --target "$target")
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if [ "${{ inputs.generate_notes }}" = "true" ]; then
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args+=(--generate-notes)
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fi
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gh "${args[@]}"
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echo "✓ Draft release created for tag $tag"

‎.github/actions/validate-packages/action.yml‎

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name: Validate packages in container
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description: Extract pinned Python/R package lists from a Docker image and run repo validation scripts, producing reproducibility/build.log.
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inputs:
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image:
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description: Full image reference including tag (e.g. ghcr.io/org/repo/image:sha)
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required: true
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repo_root_mount:
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description: Host repo mount path inside container (default: /repo)
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required: false
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default: /repo
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python_version:
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description: Python version for running validation scripts on the runner
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required: false
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default: "3.11"
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runs:
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using: composite
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steps:
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- name: Ensure reproducibility directory exists
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shell: bash
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run: |
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set -euo pipefail
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mkdir -p reproducibility
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- name: Extract base environment.yaml from container
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shell: bash
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run: |
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set -euo pipefail
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docker run --rm --entrypoint cat \
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"${{ inputs.image }}" \
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/srv/repo/environment.yml > base-environment.yaml
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echo "Base environment.yaml extracted to base-environment.yaml"
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head -20 base-environment.yaml || true
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- name: Extract Python packages with pinned versions
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shell: bash
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run: |
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set -euo pipefail
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docker run --rm "${{ inputs.image }}" \
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bash -lc 'conda list -n notebook --export' > reproducibility/packages-python-pinned.yaml
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echo "Python packages extracted to reproducibility/packages-python-pinned.yaml"
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head -20 reproducibility/packages-python-pinned.yaml || true
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- name: Set up Python for validation
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uses: actions/setup-python@v5
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with:
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python-version: ${{ inputs.python_version }}
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- name: Install Python dependencies
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shell: bash
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run: |
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set -euo pipefail
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python -m pip install --upgrade pip
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pip install pyyaml
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- name: Filter and validate Python packages
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shell: bash
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run: |
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set -euo pipefail
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python .github/scripts/filter_and_validate_packages.py
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echo "Validation complete. Check reproducibility/build.log for results."
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test -f reproducibility/build.log && cat reproducibility/build.log || true
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- name: Extract R packages with pinned versions
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shell: bash
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run: |
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set -euo pipefail
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docker run --rm \
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-v "$PWD:${{ inputs.repo_root_mount }}" \
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"${{ inputs.image }}" \
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Rscript "${{ inputs.repo_root_mount }}/.github/scripts/extract_pins_r.R" /usr/local/lib/R/site-library \
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> reproducibility/packages-r-pinned.R
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echo "R packages extracted to reproducibility/packages-r-pinned.R"
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head -30 reproducibility/packages-r-pinned.R || true
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- name: Validate R packages
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shell: bash
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run: |
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set -euo pipefail
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docker run --rm "${{ inputs.image }}" cat /rocker_scripts/install_geospatial.sh > /tmp/install_geospatial.sh
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docker run --rm "${{ inputs.image }}" cat /rocker_scripts/install_tidyverse.sh > /tmp/install_tidyverse.sh
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python .github/scripts/validate_r_packages.py
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echo "R package validation complete. Check reproducibility/build.log for results."
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test -f reproducibility/build.log && cat reproducibility/build.log || true
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- name: Compute validation status (writes to step summary)
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shell: bash
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run: |
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set -euo pipefail
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success_count=$(grep -c "STATUS: SUCCESS" reproducibility/build.log 2>/dev/null || true)
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if [ "$success_count" -eq 2 ]; then
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echo "✅ validation_status=success" | tee -a "$GITHUB_STEP_SUMMARY"
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else
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echo "⚠️ validation_status=failed" | tee -a "$GITHUB_STEP_SUMMARY"
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fi

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