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stewarthe6stewarthe6
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Merge branch '1.8.0' into feat_scaled_rdkit_mordred
2 parents 1086a93 + 96bc75a commit 6cd5746

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‎.github/workflows/lint.yml‎

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python-version: ["3.9"]
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steps:
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- name: Update apt cache
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run: |
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sudo apt-get update || sudo apt-get update --fix-missing
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- name: System Dependencies
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run: |
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sudo apt install -y build-essential \

‎.github/workflows/pytest.yml‎

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steps:
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- name: System Dependencies
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run: |
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sudo apt-get update
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sudo apt install -y build-essential \
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libcairo2-dev \
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pkg-config \
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- name: pytest
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run: |
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# python3.9 -m pytest --capture=sys --capture=fd --cov=atomsci/ -vv atomsci/ddm/test/unit
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python3.9 -m pytest --capture=sys --capture=fd --cov=atomsci/ -vv atomsci/modac/test/unit
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cd atomsci/ddm/test/unit && python3.9 -m pytest -n 2 --capture=sys --capture=fd --cov=atomsci -vv
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cd atomsci/modac/test/unit && python3.9 -m pytest --capture=sys --capture=fd --cov=atomsci/ -vv
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cd ../../../../atomsci/ddm/test/unit && python3.9 -m pytest -m "not moe_required" -n 2 --capture=sys --capture=fd --cov=atomsci -vv
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env:
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ENV: test
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- name: Upload coverage reports to Codecov
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uses: codecov/codecov-action@v4
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env:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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- name: Debug - Find all coverage files
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run: |
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echo "=== Current directory ==="
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pwd
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echo ""
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echo "=== Contents of current directory ==="
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ls -la
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echo ""
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echo "=== Searching for ALL .coverage files recursively ==="
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find . -name ".coverage*" -type f 2>/dev/null || echo "No .coverage files found"
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echo ""
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echo "=== Contents of test directory ==="
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ls -la atomsci/ddm/test/integrative/ || echo "Directory not found"
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echo ""
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echo "=== Checking if coverage was even run ==="
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which coverage
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coverage --version || echo "Coverage not installed"
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- name: Save coverage
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uses: actions/upload-artifact@v4
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with:
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name: coverage-pytest-unit
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path: |
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atomsci/ddm/test/unit/.coverage*
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atomsci/modac/test/unit/.coverage*
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include-hidden-files: true
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if-no-files-found: error
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pytest-integrative-1:
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runs-on: ubuntu-24.04
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strategy:
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steps:
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- name: System Dependencies
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run: |
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sudo apt-get update
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sudo apt install -y build-essential \
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libcairo2-dev \
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pkg-config \
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env:
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ENV: test
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- name: Upload coverage reports to Codecov
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uses: codecov/codecov-action@v4
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env:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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- name: Debug - Find all coverage files
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run: |
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echo "=== Current directory ==="
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pwd
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echo ""
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echo "=== Contents of current directory ==="
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ls -la
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echo ""
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echo "=== Searching for ALL .coverage files recursively ==="
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find . -name ".coverage*" -type f 2>/dev/null || echo "No .coverage files found"
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echo ""
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echo "=== Contents of test directory ==="
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ls -la atomsci/ddm/test/integrative/ || echo "Directory not found"
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echo ""
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echo "=== Checking if coverage was even run ==="
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which coverage
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coverage --version || echo "Coverage not installed"
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- name: Save coverage
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uses: actions/upload-artifact@v4
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with:
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name: coverage-pytest-integrative-1
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path: atomsci/ddm/test/integrative/**/.coverage*
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include-hidden-files: true
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if-no-files-found: error
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pytest-integrative-2:
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runs-on: ubuntu-24.04
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strategy:
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steps:
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- name: System Dependencies
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run: |
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sudo apt-get update
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sudo apt install -y build-essential \
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libcairo2-dev \
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pkg-config \
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- name: pytest
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run: |
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# TODO: Run this test with pytest for paralell testing
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# python3.9 -m pytest -n 2 --capture=sys --capture=fd --cov=atomsci -vv atomsci/ddm/test/integrative
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cd atomsci/ddm/test/integrative && ./integrative_batch_chunk_tests 1
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echo 'done'
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env:
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ENV: test
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- name: Upload coverage reports to Codecov
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uses: codecov/codecov-action@v4
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env:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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- name: Debug - Find all coverage files
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run: |
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echo "=== Current directory ==="
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pwd
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echo ""
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echo "=== Contents of current directory ==="
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ls -la
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echo ""
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echo "=== Searching for ALL .coverage files recursively ==="
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find . -name ".coverage*" -type f 2>/dev/null || echo "No .coverage files found"
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echo ""
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echo "=== Contents of test directory ==="
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ls -la atomsci/ddm/test/integrative/ || echo "Directory not found"
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echo ""
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echo "=== Checking if coverage was even run ==="
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which coverage
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coverage --version || echo "Coverage not installed"
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- name: Save coverage
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uses: actions/upload-artifact@v4
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with:
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name: coverage-pytest-integrative-2
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path: atomsci/ddm/test/integrative/**/.coverage*
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include-hidden-files: true
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if-no-files-found: error
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pytest-integrative-3:
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runs-on: ubuntu-24.04
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strategy:
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steps:
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- name: System Dependencies
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run: |
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sudo apt-get update
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sudo apt install -y build-essential \
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libcairo2-dev \
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pkg-config \
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env:
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ENV: test
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- name: Upload coverage reports to Codecov
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uses: codecov/codecov-action@v4
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env:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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- name: Debug - Find all coverage files
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run: |
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echo "=== Current directory ==="
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pwd
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echo ""
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echo "=== Contents of current directory ==="
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ls -la
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echo ""
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echo "=== Searching for ALL .coverage files recursively ==="
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find . -name ".coverage*" -type f 2>/dev/null || echo "No .coverage files found"
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echo ""
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echo "=== Contents of test directory ==="
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ls -la atomsci/ddm/test/integrative/ || echo "Directory not found"
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echo ""
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echo "=== Checking if coverage was even run ==="
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which coverage
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coverage --version || echo "Coverage not installed"
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- name: Save coverage
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uses: actions/upload-artifact@v4
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with:
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name: coverage-pytest-integrative-3
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path: atomsci/ddm/test/integrative/**/.coverage*
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include-hidden-files: true
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if-no-files-found: error
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pytest-integrative-4:
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runs-on: ubuntu-24.04
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strategy:
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- name: System Dependencies
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run: |
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sudo apt-get update
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sudo apt install -y build-essential \
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libcairo2-dev \
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pkg-config \
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env:
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ENV: test
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- name: Upload coverage reports to Codecov
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- name: Debug - Find all coverage files
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run: |
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echo "=== Current directory ==="
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pwd
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echo ""
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echo "=== Contents of current directory ==="
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ls -la
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echo ""
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echo "=== Searching for ALL .coverage files recursively ==="
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find . -name ".coverage*" -type f 2>/dev/null || echo "No .coverage files found"
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echo ""
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echo "=== Contents of test directory ==="
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ls -la atomsci/ddm/test/integrative/ || echo "Directory not found"
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echo ""
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echo "=== Checking if coverage was even run ==="
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which coverage
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coverage --version || echo "Coverage not installed"
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- name: Save coverage
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uses: actions/upload-artifact@v4
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with:
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name: coverage-pytest-integrative-4
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path: atomsci/ddm/test/integrative/**/.coverage*
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include-hidden-files: true
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if-no-files-found: error
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coverage-merge:
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runs-on: ubuntu-24.04
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needs: [pytest-unit, pytest-integrative-1, pytest-integrative-2, pytest-integrative-3, pytest-integrative-4]
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: "3.9"
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- name: Install coverage
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run: pip install coverage
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- name: Download all coverage artifacts
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uses: actions/download-artifact@v5
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with:
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path: coverage-reports
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- name: Merge coverage reports
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run: |
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# List directory structure for debugging
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ls -la
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ls -la coverage-reports/ || echo "coverage-reports directory not found"
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# Find and combine all coverage files
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find coverage-reports -name ".coverage*" -type f
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# Combine all coverage files
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coverage combine $(find coverage-reports -name ".coverage*" -type f -print)
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# Generate XML report for codecov
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coverage xml
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- name: Upload merged coverage to Codecov
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uses: codecov/codecov-action@v4
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with:
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files: ./coverage.xml
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flags: unittests
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name: codecov-umbrella
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env:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

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