BLD: Add Cython Coverage option

.github/workflows/unit-tests.yml

@@ -238,7 +238,7 @@ jobs:
         run: |
           /opt/python/cp311-cp311/bin/python -m venv ~/virtualenvs/pandas-dev
           . ~/virtualenvs/pandas-dev/bin/activate
-          python -m pip install --no-cache-dir -U pip wheel setuptools meson[ninja]==1.0.1 meson-python==0.13.1
+          python -m pip install --no-cache-dir -U pip wheel setuptools meson[ninja]==1.1.1 meson-python==0.13.1
           python -m pip install --no-cache-dir versioneer[toml] cython numpy python-dateutil pytz pytest>=7.3.2 pytest-xdist>=2.2.0 pytest-asyncio>=0.17 hypothesis>=6.46.1
           python -m pip install --no-cache-dir --no-build-isolation -e .
           python -m pip list --no-cache-dir
@@ -276,7 +276,7 @@ jobs:
         run: |
           /opt/python/cp311-cp311/bin/python -m venv ~/virtualenvs/pandas-dev
           . ~/virtualenvs/pandas-dev/bin/activate
-          python -m pip install --no-cache-dir -U pip wheel setuptools meson-python==0.13.1 meson[ninja]==1.0.1
+          python -m pip install --no-cache-dir -U pip wheel setuptools meson-python==0.13.1 meson[ninja]==1.1.1
           python -m pip install --no-cache-dir versioneer[toml] cython numpy python-dateutil pytz pytest>=7.3.2 pytest-xdist>=2.2.0 pytest-asyncio>=0.17 hypothesis>=6.46.1
           python -m pip install --no-cache-dir --no-build-isolation -e .
           python -m pip list --no-cache-dir
@@ -348,7 +348,7 @@ jobs:
       - name: Install dependencies
         run: |
           python --version
-          python -m pip install --upgrade pip setuptools wheel meson[ninja]==1.0.1 meson-python==0.13.1
+          python -m pip install --upgrade pip setuptools wheel meson[ninja]==1.1.1 meson-python==0.13.1
           python -m pip install --pre --extra-index-url https://pypi.anaconda.org/scientific-python-nightly-wheels/simple numpy
           python -m pip install versioneer[toml]
           python -m pip install python-dateutil pytz tzdata cython hypothesis>=6.46.1 pytest>=7.3.2 pytest-xdist>=2.2.0 pytest-cov pytest-asyncio>=0.17

ci/deps/actions-310.yaml

@@ -7,7 +7,7 @@ dependencies:
   # build dependencies
   - versioneer[toml]
   - cython>=3.0.0
-  - meson[ninja]=1.0.1
+  - meson[ninja]=1.1.1
   - meson-python=0.13.1
 
   # test dependencies

ci/deps/actions-311-downstream_compat.yaml

@@ -8,7 +8,7 @@ dependencies:
   # build dependencies
   - versioneer[toml]
   - cython>=3.0.0
-  - meson[ninja]=1.0.1
+  - meson[ninja]=1.1.1
   - meson-python=0.13.1
 
   # test dependencies

ci/deps/actions-311-numpydev.yaml

@@ -6,7 +6,7 @@ dependencies:
 
   # build dependencies
   - versioneer[toml]
-  - meson[ninja]=1.0.1
+  - meson[ninja]=1.1.1
   - meson-python=0.13.1
 
   # test dependencies

ci/deps/actions-311-pyarrownightly.yaml

@@ -6,7 +6,7 @@ dependencies:
 
   # build dependencies
   - versioneer[toml]
-  - meson[ninja]=1.0.1
+  - meson[ninja]=1.1.1
   - cython>=3.0.0
   - meson-python=0.13.1
 

ci/deps/actions-311.yaml

@@ -7,7 +7,7 @@ dependencies:
   # build dependencies
   - versioneer[toml]
   - cython>=3.0.0
-  - meson[ninja]=1.0.1
+  - meson[ninja]=1.1.1
   - meson-python=0.13.1
 
   # test dependencies

ci/deps/actions-39-minimum_versions.yaml

@@ -9,7 +9,7 @@ dependencies:
   # build dependencies
   - versioneer[toml]
   - cython>=3.0.0
-  - meson[ninja]=1.0.1
+  - meson[ninja]=1.1.1
   - meson-python=0.13.1
 
   # test dependencies

ci/deps/actions-39.yaml

@@ -7,7 +7,7 @@ dependencies:
   # build dependencies
   - versioneer[toml]
   - cython>=3.0.0
-  - meson[ninja]=1.0.1
+  - meson[ninja]=1.1.1
   - meson-python=0.13.1
 
   # test dependencies

ci/deps/actions-pypy-39.yaml

@@ -10,7 +10,7 @@ dependencies:
   # build dependencies
   - versioneer[toml]
   - cython>=3.0.0
-  - meson[ninja]=1.0.1
+  - meson[ninja]=1.1.1
   - meson-python=0.13.1
 
   # test dependencies

ci/deps/circle-310-arm64.yaml

@@ -7,7 +7,7 @@ dependencies:
   # build dependencies
   - versioneer[toml]
   - cython>=3.0.0
-  - meson[ninja]=1.0.1
+  - meson[ninja]=1.1.1
   - meson-python=0.13.1
 
   # test dependencies

environment.yml

@@ -9,7 +9,7 @@ dependencies:
   # build dependencies
   - versioneer[toml]
   - cython=3.0.0
-  - meson[ninja]=1.0.1
+  - meson[ninja]=1.1.1
   - meson-python=0.13.1
 
   # test dependencies

meson.build

@@ -4,7 +4,7 @@ project(
     'c', 'cpp', 'cython',
     version: run_command(['python', 'generate_version.py', '--print'], check: true).stdout().strip(),
     license: 'BSD-3',
-    meson_version: '>=1.0.1',
+    meson_version: '>=1.1',
     default_options: [
         # TODO: investigate, does meson try to compile against debug Python
         # when buildtype = debug, this seems to be causing problems on CI
@@ -33,6 +33,7 @@ add_project_arguments('-DNPY_NO_DEPRECATED_API=0', language : 'cpp')
 add_project_arguments('-DNPY_TARGET_VERSION=NPY_1_21_API_VERSION', language : 'c')
 add_project_arguments('-DNPY_TARGET_VERSION=NPY_1_21_API_VERSION', language : 'cpp')
 
+cython_coverage = get_option('CYTHON_COVERAGE')
 
 if fs.exists('_version_meson.py')
     py.install_sources('_version_meson.py', pure: false, subdir: 'pandas')

meson.options

@@ -0,0 +1 @@
+option('CYTHON_COVERAGE', type: 'boolean', value: false)

pandas/_libs/meson.build

@@ -56,8 +56,6 @@ _intervaltree_helper = custom_target('intervaltree_helper_pxi',
 )
 _khash_primitive_helper_dep = declare_dependency(sources: _khash_primitive_helper)
 
-subdir('tslibs')
-
 libs_sources = {
     # Dict of extension name -> dict of {sources, include_dirs, and deps}
     # numpy include dir is implicitly included
@@ -100,12 +98,24 @@ libs_sources = {
     'writers': {'sources': ['writers.pyx']}
 }
 
+cython_args = ['--include-dir', meson.current_build_dir(), '-X always_allow_keywords=true']
+if cython_coverage
+    cython_args += ['-X linetrace=true']
+    # Linetrace is not enough to ensure coverage is turned on
+    add_project_arguments('-DCYTHON_TRACE=1', language : 'c')
+    add_project_arguments('-DCYTHON_TRACE=1', language : 'cpp')
+
+    add_project_arguments('-DCYTHON_TRACE_NOGIL=1', language : 'c')
+    add_project_arguments('-DCYTHON_TRACE_NOGIL=1', language : 'cpp')
+endif
+
+subdir('tslibs')
 
 foreach ext_name, ext_dict : libs_sources
     py.extension_module(
         ext_name,
         ext_dict.get('sources'),
-        cython_args: ['--include-dir', meson.current_build_dir(), '-X always_allow_keywords=true'],
+        cython_args: cython_args,
         include_directories: [inc_np, inc_pd],
         dependencies: ext_dict.get('deps', ''),
         subdir: 'pandas/_libs',

pandas/_libs/tslibs/meson.build

@@ -23,7 +23,8 @@ foreach ext_name, ext_dict : tslibs_sources
     py.extension_module(
         ext_name,
         ext_dict.get('sources'),
-        cython_args: ['--include-dir', meson.current_build_dir(), '-X always_allow_keywords=true'],
+        #cython_args: ['--include-dir', meson.current_build_dir(), '-X always_allow_keywords=true'],
+        cython_args: cython_args,
         include_directories: [inc_np, inc_pd],
         dependencies: ext_dict.get('deps', ''),
         subdir: 'pandas/_libs/tslibs',

pandas/_libs/window/meson.build

@@ -1,7 +1,7 @@
 py.extension_module(
     'aggregations',
     ['aggregations.pyx'],
-    cython_args: ['-X always_allow_keywords=true'],
+    cython_args: cython_args, #['-X always_allow_keywords=true'],
     include_directories: [inc_np, inc_pd],
     dependencies: [py_dep],
     subdir: 'pandas/_libs/window',
@@ -12,7 +12,7 @@ py.extension_module(
 py.extension_module(
     'indexers',
     ['indexers.pyx'],
-    cython_args: ['-X always_allow_keywords=true'],
+    cython_args: cython_args, #['-X always_allow_keywords=true'],
     include_directories: [inc_np, inc_pd],
     dependencies: [py_dep],
     subdir: 'pandas/_libs/window',

pyproject.toml

@@ -3,7 +3,7 @@
 # See https://github.com/scipy/scipy/pull/12940 for the AIX issue.
 requires = [
     "meson-python==0.13.1",
-    "meson==1.0.1",
+    "meson==1.1.1",
     "wheel",
     "Cython>=3.0.0",  # Note: sync with setup.py, environment.yml and asv.conf.json
     # Note: numpy 1.25 has a backwards compatible C API by default

requirements-dev.txt

@@ -4,7 +4,7 @@
 pip
 versioneer[toml]
 cython==3.0.0
-meson[ninja]==1.0.1
+meson[ninja]==1.1.1
 meson-python==0.13.1
 pytest>=7.3.2
 pytest-cov