BUG: 2.2.2 pep517 build fails

[kloczek]

Pandas version checks

• I have checked that this issue has not already been reported.

• I have confirmed this bug exists on the latest version of pandas.

• I have confirmed this bug exists on the main branch of pandas.

Reproducible Example

- clone repo
- `python3 -sBm build -w --no-isolation`

Issue Description

Looks like something is wrong and pep517 based build fails

Build fails with

+ /usr/bin/python3 -sBm build -w --no-isolation
* Getting build dependencies for wheel...
* Building wheel...
+ meson setup /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2 /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/.mesonpy-3bx4fkmn -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --vsenv --native-file=/home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/.mesonpy-3bx4fkmn/meson-python-native-file.ini
The Meson build system
Version: 1.4.0
Source dir: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2
Build dir: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/.mesonpy-3bx4fkmn
Build type: native build
Project name: pandas
Project version: 2.2.2
C compiler for the host machine: /usr/bin/gcc (gcc 14.0.1 "gcc (GCC) 14.0.1 20240411 (Red Hat 14.0.1-0)")
C linker for the host machine: /usr/bin/gcc ld.bfd 2.42.50.20240318
C++ compiler for the host machine: /usr/bin/g++ (gcc 14.0.1 "g++ (GCC) 14.0.1 20240411 (Red Hat 14.0.1-0)")
C++ linker for the host machine: /usr/bin/g++ ld.bfd 2.42.50.20240318
Cython compiler for the host machine: cython (cython 3.0.10)
Host machine cpu family: x86_64
Host machine cpu: x86_64
Program python found: YES (/usr/bin/python3)
Found pkg-config: YES (/usr/bin/pkg-config) 2.1.1
Run-time dependency python found: YES 3.10
Build targets in project: 54

pandas 2.2.2

  User defined options
    Native files: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/.mesonpy-3bx4fkmn/meson-python-native-file.ini
    buildtype   : release
    vsenv       : true
    b_ndebug    : if-release
    b_vscrt     : md

Found ninja-1.12.0 at /usr/bin/ninja

Visual Studio environment is needed to run Ninja. It is recommended to use Meson wrapper:
/usr/bin/meson compile -C .
+ /usr/bin/ninja
[34/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/conversion.pyx
FAILED: pandas/_libs/tslibs/conversion.cpython-310-x86_64-linux-gnu.so.p/pandas/_libs/tslibs/conversion.pyx.c
cython -M --fast-fail -3 --include-dir /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/.mesonpy-3bx4fkmn/pandas/_libs/tslibs '-X always_allow_keywords=true' /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/conversion.pyx -o pandas/_libs/tslibs/conversion.cpython-310-x86_64-linux-gnu.so.p/pandas/_libs/tslibs/conversion.pyx.c

Error compiling Cython file:
------------------------------------------------------------
...
        ts = datetime.combine(ts, time())
        return convert_datetime_to_tsobject(
            ts, tz, nanos=0, reso=NPY_DATETIMEUNIT.NPY_FR_s
        )
    else:
        pandas_libs.tslibs.period import Period
                                  ^
------------------------------------------------------------

/home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/conversion.pyx:421:34: Syntax error in simple statement list
[37/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/testing.pyx
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
[38/152] Compiling C object pandas/_libs/byteswap.cpython-310-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_byteswap.pyx.c.o
pandas/_libs/byteswap.cpython-310-x86_64-linux-gnu.so.p/pandas/_libs/byteswap.pyx.c: In function ‘__pyx_pf_6pandas_5_libs_8byteswap_read_float_with_byteswap’:
pandas/_libs/byteswap.cpython-310-x86_64-linux-gnu.so.p/pandas/_libs/byteswap.pyx.c:2477:61: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘Py_ssize_t’ {aka ‘long int’} [-Wsign-compare]
 2477 |     __pyx_t_2 = ((__pyx_v_offset + (sizeof(__pyx_v_value))) < __pyx_t_1);
      |                                                             ^
pandas/_libs/byteswap.cpython-310-x86_64-linux-gnu.so.p/pandas/_libs/byteswap.pyx.c: In function ‘__pyx_pf_6pandas_5_libs_8byteswap_2read_double_with_byteswap’:
pandas/_libs/byteswap.cpython-310-x86_64-linux-gnu.so.p/pandas/_libs/byteswap.pyx.c:2747:61: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘Py_ssize_t’ {aka ‘long int’} [-Wsign-compare]
 2747 |     __pyx_t_2 = ((__pyx_v_offset + (sizeof(__pyx_v_value))) < __pyx_t_1);
      |                                                             ^
pandas/_libs/byteswap.cpython-310-x86_64-linux-gnu.so.p/pandas/_libs/byteswap.pyx.c: In function ‘__pyx_pf_6pandas_5_libs_8byteswap_4read_uint16_with_byteswap’:
pandas/_libs/byteswap.cpython-310-x86_64-linux-gnu.so.p/pandas/_libs/byteswap.pyx.c:3015:59: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘Py_ssize_t’ {aka ‘long int’} [-Wsign-compare]
 3015 |     __pyx_t_2 = ((__pyx_v_offset + (sizeof(__pyx_v_res))) < __pyx_t_1);
      |                                                           ^
pandas/_libs/byteswap.cpython-310-x86_64-linux-gnu.so.p/pandas/_libs/byteswap.pyx.c: In function ‘__pyx_pf_6pandas_5_libs_8byteswap_6read_uint32_with_byteswap’:
pandas/_libs/byteswap.cpython-310-x86_64-linux-gnu.so.p/pandas/_libs/byteswap.pyx.c:3265:59: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘Py_ssize_t’ {aka ‘long int’} [-Wsign-compare]
 3265 |     __pyx_t_2 = ((__pyx_v_offset + (sizeof(__pyx_v_res))) < __pyx_t_1);
      |                                                           ^
pandas/_libs/byteswap.cpython-310-x86_64-linux-gnu.so.p/pandas/_libs/byteswap.pyx.c: In function ‘__pyx_pf_6pandas_5_libs_8byteswap_8read_uint64_with_byteswap’:
pandas/_libs/byteswap.cpython-310-x86_64-linux-gnu.so.p/pandas/_libs/byteswap.pyx.c:3515:59: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘Py_ssize_t’ {aka ‘long int’} [-Wsign-compare]
 3515 |     __pyx_t_2 = ((__pyx_v_offset + (sizeof(__pyx_v_res))) < __pyx_t_1);
      |                                                           ^
[39/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/nattype.pyx
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/nattype.pyx:79:0: Global name __nat_unpickle matched from within class scope in contradiction to to Python 'class private name' rules. This may change in a future release.
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/nattype.pyx:79:0: Global name __nat_unpickle matched from within class scope in contradiction to to Python 'class private name' rules. This may change in a future release.
[40/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/np_datetime.pyx
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
[44/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/tzconversion.pyx
FAILED: pandas/_libs/tslibs/tzconversion.cpython-310-x86_64-linux-gnu.so.p/pandas/_libs/tslibs/tzconversion.pyx.c
cython -M --fast-fail -3 --include-dir /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/.mesonpy-3bx4fkmn/pandas/_libs/tslibs '-X always_allow_keywords=true' /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/tzconversion.pyx -o pandas/_libs/tslibs/tzconversion.cpython-310-x86_64-linux-gnu.so.p/pandas/_libs/tslibs/tzconversion.pyx.c

Error compiling Cython file:
------------------------------------------------------------
...
    elif nonexistent == "shift_forward":
        shift_forward = True
    elif nonexistent == "shift_backward":
        shift_backward = True
    elif PyDelta_Check(nonexistent):
        pandas_libs.tslibs.timedeltas import delta_to_nanoseconds
                                      ^
------------------------------------------------------------

/home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/tzconversion.pyx:283:38: Syntax error in simple statement list
[45/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/missing.pyx
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
[48/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/hashing.pyx
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
[49/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/timezones.pyx
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
[53/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/ops.pyx
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
[55/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/parsing.pyx
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
[58/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslib.pyx
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
[59/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/strptime.pyx
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
[61/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/parsers.pyx
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/parsers.pyx:1605:18: noexcept clause is ignored for function returning Python object
[62/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/internals.pyx
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
[65/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/timedeltas.pyx
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
[66/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/timestamps.pyx
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
[67/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/period.pyx
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
[68/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/offsets.pyx
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
[69/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/index.pyx
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
[70/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/lib.pyx
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
[72/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/interval.pyx
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
[74/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/hashtable.pyx
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
[75/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/algos.pyx
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
[76/152] Compiling Cython source /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/groupby.pyx
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
warning: /home/tkloczko/rpmbuild/BUILD/pandas-2.2.2/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
ninja: build stopped: subcommand failed.

ERROR Backend subprocess exited when trying to invoke build_wheel

Expected Behavior

pep517 build should not fail.

Installed Versions

List of installed modules in build env:

Package            Version
------------------ -----------
arrow              1.3.0
attrs              23.2.0
beautifulsoup4     4.12.3
build              1.2.1
contourpy          1.2.1
cycler             0.12.1
Cython             3.0.10
et_xmlfile         1.1.0
exceptiongroup     1.1.3
execnet            2.0.2
fonttools          4.51.0
gitdb              4.0.11
GitPython          3.1.43
greenlet           3.0.3
hypothesis         6.100.0
importlib_metadata 7.1.0
iniconfig          2.0.0
installer          0.7.0
Jinja2             3.1.3
kiwisolver         1.4.5
lxml               5.2.1
MarkupSafe         2.1.5
matplotlib         3.8.4
numpy              1.26.5
olefile            0.47
openpyxl           3.1.2
packaging          24.0
pillow             10.3.0
pluggy             1.4.0
pyparsing          3.1.2
pyproject_hooks    1.0.0
pyproject-metadata 0.7.1
pytest             8.1.1
pytest-asyncio     0.23.6
pytest-xdist       3.5.0
python-dateutil    2.9.0.post0
pytz               2024.1
setuptools         69.4.0
smmap              5.0.0
sortedcontainers   2.4.0
soupsieve          2.5
SQLAlchemy         2.0.29
tokenize_rt        5.2.0
tomli              2.0.1
typing_extensions  4.11.0
versioneer         0.29
wheel              0.43.0
xlrd               2.0.1
zipp               3.18.1

[lithomas1]

else:
        pandas_libs.tslibs.period import Period

This line looks suspicious.

It looks like this line is from pandas/_libs/tslibs/conversion.pyx, but it doesn't seem to match the pandas source code on github.

Can you make sure your local copy of pandas isn't corrupted?

[priyapandey26]

Hi @kloczek could you please share the steps in more detail? For me the steps you share clone and build its work as accepted.

[kloczek]

I'm building all binaries with LTO enabled so maybe some symbols are not correctly exported 🤔
Will try to have look on that in hour or two when will back home.
Another possible cause could be use relative imports which always causes some issues on testing with procedure which I've described as commonly used on packaging (not only in my distro but in Fedora and few other which needs some procedure working from non-root account possibly without tox/venv).
if you have any propositions of of any diagnostics please rop some line or two so when I'll back home will try to test that as well.

PS. BTW: As your module is using cython .. did you try to use cython-lint? 🤔 (maybe this could show something)

[kloczek]

My typical packaging procedure consist out of few steps:

• python3 -sBm build -w --no-isolation
• because I'm calling build with --no-isolation I'm using during all processes only locally installed modules
• install .whl file in </install/prefix> using installer module
• run pytest with $PYTHONPATH pointing to sitearch and sitelib inside </install/prefix>
• build is performed in env which is cut off from access to the public network (pytest is executed with -m "not network")

[lithomas1]

Hm, it could be the issue with relative imports.

I had a look at the second error and it does something like

pandas/pandas/_libs/tslibs/tzconversion.pyx

Lines 282 to 284 in 8131381

	elif PyDelta_Check(nonexistent):
	from .timedeltas import delta_to_nanoseconds
	shift_delta = delta_to_nanoseconds(nonexistent, reso=creso)

Can you try patching the sources to do from pandas._libs.tslibs.timedeltas import delta_to_nanoseconds here?
(and from pandas._libs.tslibs.period import Period) for the other one?

(If this works, I'll try to put up a fix for the next release).

I'm curious how the relative import gets butchered like that though.