fishers_exact_test
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brentp
pip install fails in python 3.12
Hi, very recently, in Linux only, pip install fails:
mamba create -yn test_pr_fisher python
mamba activate test_pr_fisher
pip install fisher
The error:
Collecting fisher
Downloading fisher-0.1.14.tar.gz (22 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting numpy (from fisher)
Using cached numpy-2.0.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
Using cached numpy-2.0.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (19.0 MB)
Building wheels for collected packages: fisher
Building wheel for fisher (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for fisher (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [118 lines of output]
Failed to load config from /tmp/pip-install-1cwg4ln9/fisher_35c0d6f414c145cd88a7eebf3afda6d3/pyproject.toml: 'tool'
Try to load it from setup.cfg
running bdist_wheel
running build
running build_py
Failed to load config from /tmp/pip-install-1cwg4ln9/fisher_35c0d6f414c145cd88a7eebf3afda6d3/pyproject.toml: 'tool'
Try to load it from setup.cfg
Failed to load config from /tmp/pip-install-1cwg4ln9/fisher_35c0d6f414c145cd88a7eebf3afda6d3/pyproject.toml: 'tool'
Try to load it from setup.cfg
creating build
creating build/lib.linux-x86_64-cpython-312
creating build/lib.linux-x86_64-cpython-312/fisher
copying fisher/tableprinter.py -> build/lib.linux-x86_64-cpython-312/fisher
copying fisher/_version.py -> build/lib.linux-x86_64-cpython-312/fisher
copying fisher/__init__.py -> build/lib.linux-x86_64-cpython-312/fisher
running egg_info
writing fisher.egg-info/PKG-INFO
writing dependency_links to fisher.egg-info/dependency_links.txt
writing requirements to fisher.egg-info/requires.txt
writing top-level names to fisher.egg-info/top_level.txt
reading manifest file 'fisher.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'README.rst'
adding license file 'LICENSE'
writing manifest file 'fisher.egg-info/SOURCES.txt'
Failed to load config from /tmp/pip-install-1cwg4ln9/fisher_35c0d6f414c145cd88a7eebf3afda6d3/pyproject.toml: 'tool'
Try to load it from setup.cfg
UPDATING build/lib.linux-x86_64-cpython-312/fisher/_version.py
set build/lib.linux-x86_64-cpython-312/fisher/_version.py to '0.1.14'
running build_ext
/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /tmp/pip-install-1cwg4ln9/fisher_35c0d6f414c145cd88a7eebf3afda6d3/src/cfisher.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
Error compiling Cython file:
------------------------------------------------------------
...
return pvalue(k, n - k, K - k, N - K - n + k)
@cython.boundscheck(False)
def pvalue_npy(
np.ndarray[np.uint_t] a_true,
^
------------------------------------------------------------
src/cfisher.pyx:129:21: Invalid type.
Failed to load config from /tmp/pip-install-1cwg4ln9/fisher_35c0d6f414c145cd88a7eebf3afda6d3/pyproject.toml: 'tool'
Try to load it from setup.cfg
Failed to load config from /tmp/pip-install-1cwg4ln9/fisher_35c0d6f414c145cd88a7eebf3afda6d3/pyproject.toml: 'tool'
Try to load it from setup.cfg
Compiling src/cfisher.pyx because it changed.
[1/1] Cythonizing src/cfisher.pyx
Traceback (most recent call last):
File "/home/mmariotti/miniforge3/envs/test_pr_fisher/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/home/mmariotti/miniforge3/envs/test_pr_fisher/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mmariotti/miniforge3/envs/test_pr_fisher/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
return _build_backend().build_wheel(wheel_directory, config_settings,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 415, in build_wheel
return self._build_with_temp_dir(
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 397, in _build_with_temp_dir
self.run_setup()
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 313, in run_setup
exec(code, locals())
File "<string>", line 67, in <module>
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/setuptools/__init__.py", line 103, in setup
return distutils.core.setup(**attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/setuptools/_distutils/core.py", line 184, in setup
return run_commands(dist)
^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/setuptools/_distutils/core.py", line 200, in run_commands
dist.run_commands()
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
self.run_command(cmd)
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/setuptools/dist.py", line 976, in run_command
super().run_command(command)
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/setuptools/command/bdist_wheel.py", line 373, in run
self.run_command("build")
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command
self.distribution.run_command(command)
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/setuptools/dist.py", line 976, in run_command
super().run_command(command)
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/setuptools/_distutils/command/build.py", line 132, in run
self.run_command(cmd_name)
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command
self.distribution.run_command(command)
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/setuptools/dist.py", line 976, in run_command
super().run_command(command)
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "<string>", line 1974, in run
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/setuptools/command/build_ext.py", line 93, in run
_build_ext.run(self)
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/setuptools/_distutils/command/build_ext.py", line 359, in run
self.build_extensions()
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/setuptools/_distutils/command/build_ext.py", line 479, in build_extensions
self._build_extensions_serial()
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/setuptools/_distutils/command/build_ext.py", line 505, in _build_extensions_serial
self.build_extension(ext)
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/setuptools/command/build_ext.py", line 254, in build_extension
_build_ext.build_extension(self, ext)
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/Cython/Distutils/build_ext.py", line 130, in build_extension
new_ext = cythonize(
^^^^^^^^^^
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/Cython/Build/Dependencies.py", line 1154, in cythonize
cythonize_one(*args)
File "/tmp/pip-build-env-sx33scse/overlay/lib/python3.12/site-packages/Cython/Build/Dependencies.py", line 1321, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: src/cfisher.pyx
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for fisher
Failed to build fisher
ERROR: Could not build wheels for fisher, which is required to install pyproject.toml-based projects
You can also see the error in this action fail in pyranges, a package that imports fisher: https://github.com/pyranges/pyranges_1.x/actions/runs/9593389507/job/26453746122
fisher version 0.1.14, python 3.12.4 (but same error on python 3.12.0)
The same version installed correctly some time ago, so I'm guessing it's something about its dependencies that changed (???)
btw thanks for your package!
looks like this is due to numpy 2.0. We could change the type to np.uint32_t, I think. Would accept a PR
@brentp while this works when installed from github, and also surprisingly from pip, the jobs that requires fisher still fail at github and RTD. I see that the version number didn't change. So perhaps it's a problem of github etc still caching the old version?
Please bump version number and update pypi
thanks
@brentp did you have a chance to look into this? Our repo workflows have been stuck on this small bug for a long time. If we can't fix this in fisher, we'll need to remove it from our dependencies.
How do I do it 'manually'?
Ah, this works (which is what @marco-mariotti probably meant when he said, "this works when installed from github, and also surprisingly from pip):
pip install git+https://github.com/marco-mariotti/fishers_exact_test
Hi, I'd accept a PR to fix this, but am not able to keep up with python packaging issues lately
Thanks @brentp, as far as I can tell, the issue is 100% fixed. The problem is that pip finds the old, unfixed version. I'm honestly not sure what the process is for updating the version that pip uses... Seems like @marco-mariotti knows? He has provided a PR which fixes it for me.
I think bumping the version number is all that is left to do. I couldn't understand how to do it in this package, since it relies on some automated system which I couldn't grasp. Marco Mariotti
On Sat, Mar 15, 2025, 12:49 Dan Bolser @.***> wrote:
Thanks @brentp https://github.com/brentp, as far as I can tell, the issue is 100% fixed. The problem is that pip finds the old, unfixed version. I'm honestly not sure what the process is for updating the version that pip uses... Seems like @marco-mariotti https://github.com/marco-mariotti knows? He has provided a PR which fixes it for me.
— Reply to this email directly, view it on GitHub https://github.com/brentp/fishers_exact_test/issues/48#issuecomment-2726471764, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACTXRIA3U3TEYYEOEN5H7IT2UQHV7AVCNFSM6AAAAABZANRN2OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDOMRWGQ3TCNZWGQ . You are receiving this because you were mentioned.Message ID: @.***> [image: dbolser]dbolser left a comment (brentp/fishers_exact_test#48) https://github.com/brentp/fishers_exact_test/issues/48#issuecomment-2726471764
Thanks @brentp https://github.com/brentp, as far as I can tell, the issue is 100% fixed. The problem is that pip finds the old, unfixed version. I'm honestly not sure what the process is for updating the version that pip uses... Seems like @marco-mariotti https://github.com/marco-mariotti knows? He has provided a PR which fixes it for me.
— Reply to this email directly, view it on GitHub https://github.com/brentp/fishers_exact_test/issues/48#issuecomment-2726471764, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACTXRIA3U3TEYYEOEN5H7IT2UQHV7AVCNFSM6AAAAABZANRN2OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDOMRWGQ3TCNZWGQ . You are receiving this because you were mentioned.Message ID: @.***>
https://github.com/brentp/fishers_exact_test/blob/master/.github/workflows/package.yml
I wonder why the package doesn't fail?
Here is my update to package.yml, but not sure how to trigger it on my fork. https://github.com/brentp/fishers_exact_test/pull/52
OK, now we need to debug the build 😅
As I said, I couldn't figure out how to trigger an action on my own fork of the repo, so I couldn't test the PR before pushing... I'm not an expert, but I'll poke around...
I think this is the latest run: https://github.com/brentp/fishers_exact_test/actions/runs/13970828167
This is the latest build: https://github.com/brentp/fishers_exact_test/actions/runs/13974734435 I have it working except that the MacOS builds are not running
GitHub want some money I guess?
On Sat, 22 Mar 2025 at 13:06, Brent Pedersen @.***> wrote:
This is the latest build: https://github.com/brentp/fishers_exact_test/actions/runs/13974734435 I have it working except that the MacOS builds are not running
— Reply to this email directly, view it on GitHub https://github.com/brentp/fishers_exact_test/issues/48#issuecomment-2745259770, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAA7NE6MIWL7U33PCB4IJIT2VVN4NAVCNFSM6AAAAABZANRN2OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDONBVGI2TSNZXGA . You are receiving this because you commented.Message ID: @.***> [image: brentp]brentp left a comment (brentp/fishers_exact_test#48) https://github.com/brentp/fishers_exact_test/issues/48#issuecomment-2745259770
This is the latest build: https://github.com/brentp/fishers_exact_test/actions/runs/13974734435 I have it working except that the MacOS builds are not running
— Reply to this email directly, view it on GitHub https://github.com/brentp/fishers_exact_test/issues/48#issuecomment-2745259770, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAA7NE6MIWL7U33PCB4IJIT2VVN4NAVCNFSM6AAAAABZANRN2OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDONBVGI2TSNZXGA . You are receiving this because you commented.Message ID: @.***>