Closes #1509: Research Coverage Tools for Testing

.coveragerc

@@ -0,0 +1,142 @@
+[run]
+omit =
+    arkouda/_version.py
+    arkouda/accessor.py 
+    arkouda/alignment.py
+    arkouda/apply.py
+    arkouda/array_api/_dtypes.py
+    arkouda/array_api/array_object.py
+    arkouda/array_api/creation_functions.py
+    arkouda/array_api/data_type_functions.py
+    arkouda/array_api/elementwise_functions.py
+    arkouda/array_api/indexing_functions.py
+    arkouda/array_api/linalg.py
+    arkouda/array_api/manipulation_functions.py
+    arkouda/array_api/searching_functions.py
+    arkouda/array_api/sorting_functions.py
+    arkouda/array_api/statistical_functions.py
+    arkouda/array_api/utility_functions.py
+    arkouda/client.py
+    arkouda/client_dtypes.py
+    arkouda/comm_diagnostics.py
+    arkouda/infoclass.py
+    arkouda/logger.py
+    arkouda/message.py
+    arkouda/numpy/_typing/_typing.py
+    arkouda/numpy/_bigint.py 
+    arkouda/numpy/alignment.py
+    arkouda/numpy/char.py
+    arkouda/numpy/dtypes.py
+    arkouda/numpy/err.py
+    arkouda/numpy/manipulation_functions.py
+    arkouda/numpy/numeric.py
+    arkouda/numpy/pdarrayclass.py
+    arkouda/numpy/pdarraycreation.py
+    arkouda/numpy/pdarraymanipulation.py
+    arkouda/numpy/pdarraysetops.py
+    arkouda/numpy/random/generator.py
+    arkouda/numpy/random/legacy.py
+    arkouda/numpy/segarray.py
+    arkouda/numpy/sorting.py
+    arkouda/numpy/strings.py
+    arkouda/numpy/timeclass.py
+    arkouda/numpy/util.py
+    arkouda/numpy/utils.py
+    arkouda/pandas/categorical.py
+    arkouda/pandas/dataframe.py
+    arkouda/pandas/extension/_arkouda_array.py
+    arkouda/pandas/extension/_arkouda_categorical_array.py
+    arkouda/pandas/extension/_arkouda_extension_array.py
+    arkouda/pandas/extension/_arkouda_string_array.py
+    arkouda/pandas/extension/_dtypes.py
+    arkouda/pandas/extension/_index_accessor.py
+    arkouda/pandas/extension/_dataframe_accessor.py
+    arkouda/pandas/groupbyclass.py
+    arkouda/pandas/index.py
+    arkouda/pandas/io.py
+    arkouda/pandas/io_util.py
+    arkouda/pandas/join.py
+    arkouda/pandas/match.py
+    arkouda/pandas/matcher.py
+    arkouda/pandas/row.py
+    arkouda/pandas/series.py
+    arkouda/plotting.py
+    arkouda/scipy/_stats_py.py
+    arkouda/scipy/sparrayclass.py
+    arkouda/scipy/sparsematrix.py
+    arkouda/scipy/special/_math.py
+    arkouda/security.py
+    arkouda/testing/_asserters.py
+    arkouda/testing/_equivalence_asserters.py
+    server_util/test/server_test_util.py
+    tests/apply_test.py
+    tests/array_api/array_creation.py
+    tests/array_api/array_manipulation.py
+    tests/array_api/constants.py
+    tests/array_api/data_type_functions.py
+    tests/array_api/elementwise_functions.py
+    tests/array_api/indexing.py
+    tests/array_api/linalg.py
+    tests/array_api/searching_functions.py
+    tests/array_api/set_functions.py
+    tests/array_api/sorting.py
+    tests/array_api/stats_functions.py
+    tests/array_api/typing_test.py
+    tests/array_api/utility_functions.py
+    tests/check.py
+    tests/checkpoint_test.py
+    tests/client_dtypes_test.py
+    tests/client_test.py
+    tests/coargsort_test.py
+    tests/comm_diagnostics_test.py
+    tests/conftest.py
+    tests/extrema_test.py
+    tests/history_test.py
+    tests/indexing_test.py
+    tests/infoclass_test.py
+    tests/logger_test.py
+    tests/message_test.py
+    tests/numpy/alignment_test.py
+    tests/numpy/bigint_test.py
+    tests/numpy/char_test.py
+    tests/numpy/datetime_test.py
+    tests/numpy/dtypes_test.py
+    tests/numpy/err_test.py
+    tests/numpy/manipulation_functions_test.py
+    tests/numpy/numeric_test.py
+    tests/numpy/pdarray_creation_test.py
+    tests/numpy/pdarrayclass_test.py
+    tests/numpy/pdarraymanipulation_tests.py
+    tests/numpy/random_test.py
+    tests/numpy/segarray_test.py
+    tests/numpy/setops_test.py
+    tests/numpy/sort_test.py
+    tests/numpy/string_test.py
+    tests/numpy/util_test.py
+    tests/operator_test.py
+    tests/pandas/categorical_test.py
+    tests/pandas/dataframe_test.py
+    tests/pandas/extension/arkouda_array_extension.py
+    tests/pandas/extension/arkouda_categorical_extension.py
+    tests/pandas/extension/arkouda_extension.py
+    tests/pandas/extension/arkouda_strings_extension.py
+    tests/pandas/extension/dtypes_extension.py
+    tests/pandas/extension/index_accessor.py
+    tests/pandas/extension/dataframe_accessor.py
+    tests/pandas/groupby_test.py
+    tests/pandas/index_test.py
+    tests/pandas/io_test.py
+    tests/pandas/io_util_test.py
+    tests/pandas/join_test.py
+    tests/pandas/parquet_edge_test.py
+    tests/pandas/row_test.py
+    tests/pandas/series_test.py
+    tests/regex_test.py
+    tests/scipy/scipy_test.py
+    tests/scipy/sparse_test.py
+    tests/security_test.py
+    tests/test_no_ak_connect_doctest.py
+    tests/testing/asserters_test.py
+    tests/testing/equivalence_asserters_test.py
+    tests/version_test.py
+

.github/workflows/CI.yml

@@ -472,6 +472,90 @@ jobs:
       run: |
         make test-python size=100
 
+
+  arkouda_multi-dim_test_coverage:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        chpl-version: ['2.6.0']
+      max-parallel: 3
+    container:
+      image: ghcr.io/bears-r-us/ubuntu-with-arkouda-deps-chpl-${{ matrix.chpl-version }}:latest
+      credentials:
+        username: ${{ github.actor }}
+        password: ${{ secrets.github_token }}
+    steps:
+    - name: Show memory available
+      run: |
+        echo "Memory info:"
+        free -h
+        echo "CPU info:"
+        nproc
+    - name: Checkout Repository
+      uses: actions/checkout@v4
+    - name: Set Python version to 3.13
+      run: |
+        update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.13 1
+    - name: Check Chapel version
+      run: |
+        chpl --version
+    - name: Install dependencies
+      uses: nick-fields/retry@v2
+      with:
+        timeout_seconds: 1200  # or use timeout_minutes
+        max_attempts: 2
+        retry_wait_seconds: 60
+        retry_on: error
+        command: |
+          apt-get update && apt-get install -y time
+          python3 -m ensurepip --default-pip
+          echo "\$(eval \$(call add-path,/usr/lib/x86_64-linux-gnu/hdf5/serial/))" >> Makefile.paths
+          echo "\$(eval \$(call add-path,$DEP_INSTALL_DIR/arrow-install/))" >> Makefile.paths
+          echo "\$(eval \$(call add-path,$DEP_INSTALL_DIR/libiconv-install/))" >> Makefile.paths
+    - name: Use MultiDim Configs
+      run: |
+        cp .configs/registration-config-multi-dim.json registration-config.json
+        bash scripts/trim_server_modules.sh
+    - name: Build arkouda_server
+      shell: bash
+      run: |
+        set -euxo pipefail
+        /usr/bin/time -v make
+        echo "$PWD" >> "$GITHUB_PATH"
+        echo "$PWD"
+    - name: Install Arkouda
+      run: |
+        python3 -m pip install .[dev]
+    - name: Run tests with coverage (fail if below threshold)
+      run: |
+        make coverage size=10
+    - name: Sanity check coverage.xml
+      if: always()
+      run: |
+        pwd
+        ls -l
+        [ -f coverage.xml ] && echo "coverage.xml present" || (echo "coverage.xml MISSING"; exit 1)
+        head -n 20 coverage.xml || true
+    - name: Upload coverage artifacts
+      if: always()
+      uses: actions/upload-artifact@v4
+      with:
+        name: coverage-artifacts
+        path: |
+          coverage.xml
+          .coverage
+          .pytest/report.html
+        if-no-files-found: warn
+    - name: Upload to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}   # not needed for public repos
+        files: coverage.xml
+        flags: ${{ matrix.python-version }}
+        fail_ci_if_error: true
+
+
+
   arkouda_tests_linux:
     runs-on: ubuntu-latest
     env:

arkouda-env-dev.yml

@@ -58,3 +58,5 @@ dependencies:
     - docstr-coverage
     - numba
     - pytest-html
+    - pytest-cov
+    - coverage[toml]

arkouda/numpy/random/generator.py

@@ -65,7 +65,7 @@ def __str__(self):
         _str += "(PCG64)"
         return _str
 
-    def __del__(self):
+    def __del__(self):  # pragma: no cover
         try:
             if self.handle and not self.handle.closed:
                 self.handle.close()

arkouda/scipy/sparrayclass.py

@@ -83,7 +83,7 @@ def __init__(
         if max_bits:
             self.max_bits = max_bits
 
-    def __del__(self):
+    def __del__(self):  # pragma: no cover
         from arkouda.client import generic_msg
 
         try:

make/Dev.mk

@@ -20,3 +20,9 @@ docstr-coverage:
 chplcheck:
 	#   Check chapel linter, ignoring files in .chplcheckignore:
 	find src -type f -name '*.chpl'   | grep -v -f .chplcheckignore   | xargs chplcheck --setting LineLength.Max=105 --add-rules src/scripts/chplcheck_ak_prefix.py --disable-rule CamelCaseFunctions  
+
+
+COV_MIN ?= 100
+.PHONY: coverage
+coverage:
+	python3 -m pytest -c pytest.ini  --cov --cov-report=term-missing --cov-report=xml:coverage.xml --cov-fail-under=$(COV_MIN) --size=$(size) $(ARKOUDA_PYTEST_OPTIONS) --skip_doctest="True"

pyproject.toml

@@ -62,6 +62,8 @@ dev = [
   "pre-commit",
   "pydoclint[flake8]==0.6.10",
   "numba",
+  "pytest-cov",
+  "coverage[toml]",
 ]