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BLD: Add Cython Coverage option #54453

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f90433b
BLD: Add Cython Coverage option
lithomas1 Aug 7, 2023
7f1b4c3
bump more
lithomas1 Aug 8, 2023
ead496f
fix segfault by declaring gil correctly
lithomas1 Aug 9, 2023
2a11d7d
Merge branch 'main' into cy-coverage
lithomas1 Dec 6, 2023
7db484a
Merge branch 'main' into cy-coverage
lithomas1 Dec 20, 2023
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6 changes: 3 additions & 3 deletions .github/workflows/unit-tests.yml
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
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2 changes: 1 addition & 1 deletion ci/deps/actions-310.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion ci/deps/actions-311-downstream_compat.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion ci/deps/actions-311-numpydev.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion ci/deps/actions-311-pyarrownightly.yaml
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Expand Up @@ -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

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2 changes: 1 addition & 1 deletion ci/deps/actions-311.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion ci/deps/actions-39-minimum_versions.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion ci/deps/actions-39.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion ci/deps/actions-pypy-39.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion ci/deps/circle-310-arm64.yaml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion environment.yml
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Expand Up @@ -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
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3 changes: 2 additions & 1 deletion meson.build
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Expand Up @@ -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
Expand Down Expand Up @@ -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')
Expand Down
1 change: 1 addition & 0 deletions meson.options
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@@ -0,0 +1 @@
option('CYTHON_COVERAGE', type: 'boolean', value: false)
16 changes: 13 additions & 3 deletions pandas/_libs/meson.build
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Expand Up @@ -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
Expand Down Expand Up @@ -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',
Expand Down
6 changes: 3 additions & 3 deletions pandas/_libs/parsers.pyx
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Expand Up @@ -254,8 +254,8 @@ cdef extern from "pandas/parser/pd_parser.h":

int del_rd_source(void *src)

void* buffer_rd_bytes(void *source, size_t nbytes,
size_t *bytes_read, int *status, const char *encoding_errors)
void* buffer_rd_bytes(void *source, size_t nbytes, size_t *bytes_read,
int *status, const char *encoding_errors) nogil

void uint_state_init(uint_state *self)
int uint64_conflict(uint_state *self)
Expand Down Expand Up @@ -325,7 +325,7 @@ cdef double round_trip_wrapper(const char *p, char **q, char decimal,

cdef void* buffer_rd_bytes_wrapper(void *source, size_t nbytes,
size_t *bytes_read, int *status,
const char *encoding_errors) noexcept:
const char *encoding_errors) noexcept nogil:
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Needed to mark this as nogil or we would segfault since the tracing code would try to use GIL requiring code (and this function would be called in a nogil block).

I'm pretty sure the C code can acquire the GIL for itself when it needs it so nogil isn't needed?

cc @WillAyd

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Yea it looks like the C code does ensure the GIL. I'm a little unclear then though - isn't marking this nogil incorrect since it actually uses the GIL?

return buffer_rd_bytes(source, nbytes, bytes_read, status, encoding_errors)

cdef int del_rd_source_wrapper(void *src) noexcept:
Expand Down
2 changes: 1 addition & 1 deletion pandas/_libs/tslibs/meson.build
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Expand Up @@ -23,7 +23,7 @@ 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: cython_args,
include_directories: [inc_np, inc_pd],
dependencies: ext_dict.get('deps', ''),
subdir: 'pandas/_libs/tslibs',
Expand Down
4 changes: 2 additions & 2 deletions pandas/_libs/window/meson.build
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@@ -1,7 +1,7 @@
py.extension_module(
'aggregations',
['aggregations.pyx'],
cython_args: ['-X always_allow_keywords=true'],
cython_args: cython_args,
include_directories: [inc_np, inc_pd],
dependencies: [py_dep],
subdir: 'pandas/_libs/window',
Expand All @@ -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',
Expand Down
2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -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
Expand Down
2 changes: 1 addition & 1 deletion requirements-dev.txt
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Expand Up @@ -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
Expand Down