tests: Gunittest coverage slipcover 01

.coveragerc

@@ -5,7 +5,7 @@ concurrency = multiprocessing,thread
 parallel = True
 data_file = ${INITIAL_PWD-.}/.coverage
 omit =
-    ${INITIAL_PWD-.}/testreport
+    **/testreport/*
     ${INITIAL_PWD-.}/.github/*
     ${INITIAL_PWD-.}/bin.*/*
     ${INITIAL_PWD-.}/dist.*/*

.github/workflows/macos.yml

@@ -89,6 +89,17 @@ jobs:
         if: ${{ !cancelled() }}
         shell: micromamba-shell {0}
         run: source ./.github/workflows/print_versions.sh
+      - name: Place a usercustomize.py file enabling subprocess code coverage
+        shell: bash -el {0}
+        run: |
+          mkdir -p $(python -m site --user-site)
+          printf "import coverage\ncoverage.process_startup()" \
+            > "$(python -m site --user-site)/usercustomize.py"
+      - name: Set COVERAGE_PROCESS_START env variable
+        shell: bash -el {0}
+        run: |
+          echo "COVERAGE_PROCESS_START=${PWD}/.coveragerc" >> $GITHUB_ENV
+          echo "COVERAGE_RCFILE=${PWD}/.coveragerc" >> $GITHUB_ENV
 
       - name: Run pytest with multiple workers in parallel
         shell: micromamba-shell {0}
@@ -135,15 +146,65 @@ jobs:
 
       - name: Run gunittest tests
         shell: micromamba-shell {0}
-        run: .github/workflows/test_thorough.sh --config .github/workflows/macos_gunittest.cfg
+        run: |
+          export INITIAL_GISBASE="$(grass --config path)"
+          export INITIAL_PWD="${PWD}"
+          grass --tmp-project XY --exec \
+              g.download.location url=${{ env.SAMPLE_DATA_URL }} path=$HOME
+          grass --tmp-project XY --exec \
+              ${PYTHON}  -m grass.gunittest.main \
+              --grassdata $HOME --location nc_spm_full_v2alpha2 --location-type nc \
+              --min-success 100 --config .github/workflows/macos_gunittest.cfg
         env:
           SAMPLE_DATA_URL: "file://${{ github.workspace }}/sample-data/\
             nc_spm_full_v2alpha2.tar.gz"
-
+          PYTHON: coverage run
+      - name: Fix non-standard installed script paths in coverage data
+        shell: bash -el {0}
+        run: |
+          export PYTHONPATH=`grass --config python_path`:$PYTHONPATH
+          # export LD_LIBRARY_PATH=$(grass --config path)/lib:$LD_LIBRARY_PATH
+          export INITIAL_GISBASE="$(grass --config path)"
+          export INITIAL_PWD="${PWD}"
+          coverage combine
+          python utils/coverage_mapper.py
+          coverage combine
+      - name: Show python coverage report summary
+        shell: bash -el {0}
+        run: |
+          export PYTHONPATH=`grass --config python_path`:$PYTHONPATH
+          # export LD_LIBRARY_PATH=$(grass --config path)/lib:$LD_LIBRARY_PATH
+          export INITIAL_GISBASE="$(grass --config path)"
+          export INITIAL_PWD="${PWD}"
+          coverage report
+          coverage json
+      - name: Generate HTML coverage report
+        shell: bash -el {0}
+        run: |
+          export PYTHONPATH=`grass --config python_path`:$PYTHONPATH
+          # export LD_LIBRARY_PATH=$(grass --config path)/lib:$LD_LIBRARY_PATH
+          export INITIAL_GISBASE="$(grass --config path)"
+          export INITIAL_PWD="${PWD}"
+          coverage html
       - name: Make HTML test report available
         if: ${{ !cancelled() }}
         uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2
         with:
-          name: testreport-macOS
+          name: testreport-${{ runner.os }}
           path: testreport
           retention-days: 3
+      - name: Make python-only code coverage test report available
+        if: ${{ !cancelled() }}
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2
+        with:
+          name: >-
+            python-codecoverage-report-${{ 'macos-14' }}
+          path: coverage_html_report
+          retention-days: 1
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@18283e04ce6e62d37312384ff67231eb8fd56d24 # v5.4.3
+        with:
+          verbose: true
+          flags: gunittest-${{ 'macos-14' }}
+          name: gunittest-${{ 'macos-14' }}
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/test_thorough.sh

@@ -5,10 +5,16 @@ set -e
 
 SAMPLE_DATA_URL=${SAMPLE_DATA_URL:-"https://grass.osgeo.org/sampledata/north_carolina/nc_spm_full_v2alpha2.tar.gz"}
 
+if [[ -z "${PYTHON}" ]]; then
+  PYTHON="python3"
+else
+  PYTHON="${PYTHON}"
+fi
+
 grass --tmp-project XY --exec \
     g.download.project url=$SAMPLE_DATA_URL path=$HOME
 
 grass --tmp-project XY --exec \
-    python3 -m grass.gunittest.main \
+    ${PYTHON} -m grass.gunittest.main \
     --grassdata $HOME --location nc_spm_full_v2alpha2 --location-type nc \
     --min-success 100 $@

.github/workflows/ubuntu.yml

@@ -44,6 +44,7 @@
           # newlines with spaces, and strip newline at end.
           # See https://yaml-multiline.info/
           - temporal
+          - db
           - >-
             db display doc docker general gui
             imagery lib misc ps python raster raster3d scripts
@@ -76,21 +77,41 @@
           echo "${delete[@]}"
           for target in "${delete[@]}"; do
             for i in "${!array[@]}"; do
-              if [[ ${array[i]} = $target ]]; then
+              if [[ ${array[i]} = "$target" ]]; then
                 unset 'array[i]'
               fi
             done
           done
           unset new_array
           for i in "${!array[@]}"; do
-              new_array+=( "${array[i]}" )
+            new_array+=( "${array[i]}" )
           done
           echo "Excluded folders:"
           echo "${new_array[@]}"
           printf -v extra_exclude './%s/* ' "${new_array[@]}"
           echo "Exclusion string to add to gunittest config"
           echo "${extra_exclude}"
           echo "extra-exclude=${extra_exclude}" >> "${GITHUB_OUTPUT}"
+          echo "Inclusion string for tags"
+          printf -v extra_include_tag ' %s' "${delete[@]}"
+          extra_include_tag="${extra_include_tag:1}" # trim extra first space
+          extra_include_tag=${extra_include_tag// /-} # replace spaces by hyphens
+          echo "${extra_include_tag}"
+          echo "extra-include-tag=${extra_include_tag}" >> "${GITHUB_OUTPUT}"
+          echo "Truncated string for codecov upload"
+          max_flag_len=45
+          max_flag_prefix_len=33 # gunittest-ubuntu-22.04_without_x-
+          max_flag_suffix_len=$((max_flag_len - max_flag_prefix_len))
+          extra_include_tag_len=${#extra_include_tag} # string's length
+          extra_include_tag_len_len=${#extra_include_tag_len} # length of string's length
+          if [[ "${extra_include_tag_len}" -gt "${max_flag_suffix_len}" ]]; then
+            # Extra include too long
+            extra_include_tag_trunc="${extra_include_tag:0:$max_flag_suffix_len-1-$extra_include_tag_len_len}.${extra_include_tag_len}"
+          else
+            extra_include_tag_trunc="${extra_include_tag}"
+          fi
+          echo "${extra_include_tag_trunc}"
+          echo "extra-include-tag-trunc=${extra_include_tag_trunc}" >> "${GITHUB_OUTPUT}"
         env:
           DELETE_ARRAY: ${{ matrix.extra-include }}
 
@@ -107,6 +128,9 @@
           sudo apt-get install -y wget git gawk findutils
           xargs -a <(awk '! /^ *(#|$)/' ".github/workflows/apt.txt") -r -- \
               sudo apt-get install -y --no-install-recommends --no-install-suggests
+      - name: Install python coverage tools
+        run: pip install coverage slipcover
+      - run: python -m slipcover --help
 
       - name: Create installation directory
         run: |
@@ -139,13 +163,35 @@
         run: |
           echo "$HOME/install/bin" >> $GITHUB_PATH
 
+      - name: Replace scripts with symbolic links to have files with .py extensions
+        if: ${{ false }}
+        run: |
+          cd "$(grass --config path)"
+          cp -R scripts/ scrips_orig/
+          # Output first lines of files
+          head $(grass --config path)/scripts/* -n1 -q
+          # Rename files to have .py extension
+          ls | xargs -I fileName mv fileName fileName.py
+          # Copy with symbolic link
+          for old in scripts/*.py
+            do new=`echo $old | sed -e's/.py//'`
+            cp --symbolic-link "$old" "$new"
+          done
+          ls -la
+
       - name: Print installed versions
-        if: always()
+        if: ${{ !cancelled() }}
         run: .github/workflows/print_versions.sh
 
       - name: Test executing of the grass command
         run: .github/workflows/test_simple.sh
 
+      # - name: Place a usercustomize.py file enabling subprocess code coverage
+      #   run: |
+      #     mkdir -p $(python -m site --user-site)
+      #     printf "import coverage\ncoverage.process_startup()" \
+      #      > "$(python -m site --user-site)/usercustomize.py"
+
       - name: Cache GRASS Sample Dataset
         id: cached-data
         uses: actions/cache@5a3ec84eff668545956fd18022155c47e93e2684 # v4.2.3
@@ -163,19 +209,88 @@
           SAMPLE_DATA: "https://grass.osgeo.org/sampledata/north_carolina/\
             nc_spm_full_v2alpha2.tar.gz"
 
+      # - name: Set COVERAGE_PROCESS_START env variable
+      #   run: |
+      #     echo "COVERAGE_PROCESS_START=${PWD}/.coveragerc" >> $GITHUB_ENV
+      #     echo "COVERAGE_RCFILE=${PWD}/.coveragerc" >> $GITHUB_ENV
+
       - name: Run tests
-        run: .github/workflows/test_thorough.sh --config .gunittest.extra.cfg
+        run: |
+          export INITIAL_GISBASE="$(grass --config path)"
+          export INITIAL_PWD="${PWD}"
+          #export PYTHON="${PYTHON} --source ${INITIAL_PWD}/ --source ${INITIAL_GISBASE}/"
+          #export PYTHON="${PYTHON} --source ${INITIAL_GISBASE}/scripts"
+          echo "$PYTHON"
+          export PYTHON="${PYTHON} --source .,${INITIAL_PWD}/,${INITIAL_GISBASE}/,${INITIAL_GISBASE}/scripts"
+          echo "$PYTHON"
+          .github/workflows/test_thorough.sh --config .gunittest.extra.cfg
         env:
+          PYTHON: >-
+            python -m slipcover
+            --json
+            --out ${{ github.workspace }}/slipcover.json
+          #--source ${{ github.workspace }}
           SAMPLE_DATA_URL: "file://${{ github.workspace }}/sample-data/\
             nc_spm_full_v2alpha2.tar.gz"
+      - run: cat slipcover.json
+      - run: jq . slipcover.json
+      - name: Convert slipcover's output to coverage.py data file
+        run: python utils/slipcover_to_coverage.py slipcover.json .coverage.slipcover
+      - run: ls -la
+      - name: Fix non-standard installed script paths in coverage data
+        run: |
+          export PYTHONPATH=`grass --config python_path`:$PYTHONPATH
+          export LD_LIBRARY_PATH=$(grass --config path)/lib:$LD_LIBRARY_PATH
+          export INITIAL_GISBASE="$(grass --config path)"
+          export INITIAL_PWD="${PWD}"
+          coverage combine
+          python utils/coverage_mapper.py
+          coverage combine
+
+      - name: Show python coverage report summary
+        run: |
+          export PYTHONPATH=`grass --config python_path`:$PYTHONPATH
+          export LD_LIBRARY_PATH=$(grass --config path)/lib:$LD_LIBRARY_PATH
+          export INITIAL_GISBASE="$(grass --config path)"
+          export INITIAL_PWD="${PWD}"
+          coverage report
+        continue-on-error: true
+      - name: Generate HTML coverage report
+        run: |
+          export PYTHONPATH=`grass --config python_path`:$PYTHONPATH
+          export LD_LIBRARY_PATH=$(grass --config path)/lib:$LD_LIBRARY_PATH
+          export INITIAL_GISBASE="$(grass --config path)"
+          export INITIAL_PWD="${PWD}"
+          coverage html
+        continue-on-error: true
 
       - name: Make HTML test report available
-        if: ${{ always() }}
+        if: ${{ !cancelled() }}
         uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2
         with:
-          name: testreport-${{ matrix.os }}-${{ matrix.config }}-${{ matrix.extra-include }}
+          name: >-
+            testreport-${{ matrix.os }}-${{ matrix.config }}-${{
+            '' }}${{ steps.get-exclude.outputs.extra-include-tag }}
           path: testreport
           retention-days: 3
+      - name: Make python-only code coverage test report available
+        if: ${{ !cancelled() }}
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2
+        with:
+          name: >-
+            python-codecoverage-report-${{ matrix.os }}-${{ matrix.config }}-${{
+            '' }}${{ steps.get-exclude.outputs.extra-include-tag }}
+          path: coverage_html_report
+          retention-days: 1
+
+      - name: Upload coverage reports to Codecov
+        if: ${{ !cancelled() }}
+        uses: codecov/codecov-action@18283e04ce6e62d37312384ff67231eb8fd56d24 # v5.4.3
+        with:
+          verbose: true
+          flags: gunittest-${{ matrix.config }}-${{ steps.get-exclude.outputs.extra-include-tag-trunc }}
+          name: gunittest-${{ matrix.config }}-${{ steps.get-exclude.outputs.extra-include-tag-trunc }}
+          token: ${{ secrets.CODECOV_TOKEN }}
 
   build-and-test-success:
     name: Build & Test Result

macos/files/conda-requirements-dev-arm64.txt

@@ -3,6 +3,7 @@ cairo
 clangxx_osx-arm64
 clang_osx-arm64
 cmake
+coverage
 expat
 fftw
 flex

utils/slipcover_to_coverage.py

@@ -0,0 +1,28 @@
+from coverage import CoverageData
+import json
+from pathlib import Path
+import sys
+
+
+def convert_slipcover_json_to_coverage(input_path, output_path):
+    with Path(input_path).open("r") as input_fp:
+        input_json = json.load(input_fp)
+    data_file = CoverageData(output_path)
+    data_file.read()
+
+    line_data = {
+        str(Path().joinpath(file).resolve()): data["executed_lines"]
+        for file, data in input_json["files"].items()
+    }
+    data_file.add_lines(line_data)
+    data_file.write()
+
+
+def main():
+    infile = sys.argv[1]
+    outfile = sys.argv[2]
+    convert_slipcover_json_to_coverage(infile, outfile)
+
+
+if __name__ == "__main__":
+    main()