Speed up CI to complete within 15min (down from 25min) by switching off coverage except for the matrix entry that's uploaded

.github/workflows/ci.yaml

@@ -57,9 +57,6 @@ jobs:
     defaults:
       run:
         shell: bash -l {0}
-    env:
-      COVERAGE_FILE: ${{ github.workspace }}/.coverage@python=${{ matrix.python-version }},biopython=${{ matrix.biopython-version || 'latest' }}
-      COVERAGE_RCFILE: ${{ github.workspace }}/.coveragerc
     steps:
     - uses: actions/checkout@v4
 
@@ -73,7 +70,7 @@ jobs:
     - name: Install dependencies from Conda
       uses: mamba-org/setup-micromamba@v2
       with:
-        create-args: mafft raxml fasttree iqtree vcftools seqkit sqlite tsv-utils biopython=${{ matrix.biopython-version }} python=${{ matrix.python-version }}
+        create-args: mafft raxml fasttree iqtree vcftools seqkit sqlite tsv-utils biopython=${{ matrix.biopython-version }} python=${{ matrix.python-version }} numpy=1
         condarc: |
           channels:
             - conda-forge
@@ -85,19 +82,49 @@ jobs:
 
     # Replace the Conda Augur installation with the local version.
     - run: pip install .[dev]
+    - run: pip list
     - run: conda info
     - run: conda list
-    - run: pytest --cov=augur
-    - run: cram tests/
-      env:
-        AUGUR: coverage run -a ${{ github.workspace }}/bin/augur
-    # Only upload coverage for one job
-    - if: matrix.python-version == '3.11' && matrix.biopython-version == ''
+
+    # Set coverage environment variables only for the coverage job
+    - name: Set coverage environment variables
+      if: matrix.python-version == '3.11' && matrix.biopython-version == ''
+      run: |
+        echo "COVERAGE_FILE=${{ github.workspace }}/.coverage@python=${{ matrix.python-version }},biopython=${{ matrix.biopython-version || 'latest' }}" >> "$GITHUB_ENV"
+        echo "COVERAGE_RCFILE=${{ github.workspace }}/.coveragerc" >> "$GITHUB_ENV"
+        if python3 -c 'import sys; print(sys.version_info >= (3, 14))' | grep -q True; then
+            echo "Using sysmon for coverage to reduce overhead"
+            echo COVERAGE_CORE=sysmon >> "$GITHUB_ENV"
+        else
+            echo "Using default coverage collection method"
+        fi
+
+    - name: Run pytest
+      run: |
+        if [[ -n "${COVERAGE_FILE:-}" ]]; then
+          echo "Running pytest with coverage enabled"
+          pytest --cov=augur
+        else
+          echo "Running pytest without coverage"
+          pytest --no-cov
+        fi
+    - name: Run cram tests
+      run: |
+        if [[ -n "${COVERAGE_FILE:-}" ]]; then
+          echo "Running cram tests with coverage enabled"
+          export AUGUR="coverage run -a ${{ github.workspace }}/bin/augur"
+        else
+          echo "Running cram tests without coverage"
+          export AUGUR="${{ github.workspace }}/bin/augur"
+        fi
+        cram tests/
+    - name: Upload coverage
+      if: env.COVERAGE_FILE
       uses: actions/upload-artifact@v4
       with:
         name: coverage
         include-hidden-files: true
-        path: "${{ env.COVERAGE_FILE }}"
+        path: "${{ github.workspace }}/.coverage@python=${{ matrix.python-version }},biopython=${{ matrix.biopython-version || 'latest' }}"
 
   # Replicating pathogen-repo-ci workflow because we decided not to support
   # local versions of Augur in the centralized workflow

run_tests.sh

@@ -1,30 +1,50 @@
 #!/bin/sh
 
-# Default to running all tests.
+# Default to running all tests without coverage.
 partial_test=0
+run_coverage=0
+
+# Check if user explicitly requests coverage
+case "$@" in
+    *--cov*) run_coverage=1 ;;
+esac
 
 # If user requests a subset of tests for pytest, note this preference to avoid
 # running other tests.
 case "$@" in
     *-k*) partial_test=1 ;;
 esac
 
-if [ "$partial_test" = 1 ]; then
-    # skip test coverage when running a subset of the test suite
-    coverage_arg='--no-cov'
+if [ "$run_coverage" = 1 ]; then
+    # Remove --cov from args since pytest will handle coverage via --cov=augur
+    echo "Running tests with coverage enabled, remove --cov to disable"
+    filtered_args=$(echo "$*" | sed 's/--cov//g')
+    coverage_arg='--cov=augur'
+
+    # Set env variable COVERAGE_CORE to sysmon for coverage
+    # This reduces overhead of coverage collection
+    # But only if Python version >3.14
+    if python3 -c 'import sys; print(sys.version_info >= (3, 14))' | grep -q True; then
+        echo "Using sysmon for coverage to reduce overhead"
+        export COVERAGE_CORE=sysmon
+    else
+        echo "Using default coverage collection method"
+    fi
 else
-    coverage_arg=''
+    # Default to no coverage
+    echo "Running tests without coverage, use --cov to enable"
+    filtered_args="$*"
+    coverage_arg='--no-cov'
 fi
 
 echo "Running unit tests and doctests with pytest"
-python3 -m pytest $coverage_arg "$@"
+python3 -m pytest $coverage_arg $filtered_args
 
 # Only run functional tests if we are not running a subset of tests for pytest.
 if [ "$partial_test" = 0 ]; then
-    echo "Running functional tests with cram"
     cram tests/
 else
-    echo "Skipping functional tests when running a subset of unit tests"
+    echo "Skipping functional (cram) tests when running a subset of unit tests"
 fi
 
 exit $?