cmdoret
commented
17 hours ago It seems that pysam indeed does not work on windows, however it should work using WSL (see https://github.com/pysam-developers/pysam/issues/575).
Is using WSL a major issue? If so we can look into something else, but AFAIK pysam is the only implementation of CRAM parsing / manipulation in python.
htmonkey
Contact Details
No response
What happened?
I tried several times to install via pip and poetry in clean venvs, on 3.10 and 3.12, but it always fails because of pysam-0.22.1 and PEP517. PS: I can install it on Ubuntu. PS2: pip, wheel, setuptools, etc are all updated.
This is the cleanest error log:
PS D:\SW\modo-test> poetry add modos Using version ^0.2.2 for modos
Updating dependencies Resolving dependencies... (2.2s)
Package operations: 67 installs, 0 updates, 0 removals
Installing pysam (0.22.1): Failed
ChefBuildError
Backend subprocess exited when trying to invoke get_requires_for_build_wheel
pysam: cython is available - using cythonize if necessary
pysam: htslib mode is shared
pysam: HTSLIB_CONFIGURE_OPTIONS=None
'.' is not recognized as an internal or external command, operable program or batch file. '.' is not recognized as an internal or external command, operable program or batch file.
pysam: htslib configure options: None
Traceback (most recent call last): File "C:\Users\nzamboni\pipx\venvs\poetry\Lib\site-packages\pyproject_hooks_in_process_in_process.py", line 373, in
main()
File "C:\Users\nzamboni\pipx\venvs\poetry\Lib\site-packages\pyproject_hooks_in_process_in_process.py", line 357, in main
json_out["return_val"] = hook(hook_input["kwargs"])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\nzamboni\pipx\venvs\poetry\Lib\site-packages\pyproject_hooks_in_process_in_process.py", line 134, in get_requires_for_build_wheel
return hook(config_settings)
^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\nzamboni\AppData\Local\Temp\tmpve2z1hdi.venv\Lib\site-packages\setuptools\build_meta.py", line 334, in get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=[])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\nzamboni\AppData\Local\Temp\tmpve2z1hdi.venv\Lib\site-packages\setuptools\build_meta.py", line 304, in _get_build_requires
self.run_setup()
File "C:\Users\nzamboni\AppData\Local\Temp\tmpve2z1hdi.venv\Lib\site-packages\setuptools\build_meta.py", line 522, in run_setup
super().run_setup(setup_script=setup_script)
File "C:\Users\nzamboni\AppData\Local\Temp\tmpve2z1hdi.venv\Lib\site-packages\setuptools\build_meta.py", line 320, in run_setup
exec(code, locals())
File "", line 437, in
File "", line 81, in run_make_print_config
File "D:\libs\Python312\Lib\subprocess.py", line 466, in check_output
return run(popenargs, stdout=PIPE, timeout=timeout, check=True,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\libs\Python312\Lib\subprocess.py", line 548, in run
with Popen(popenargs, kwargs) as process:
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\libs\Python312\Lib\subprocess.py", line 1026, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "D:\libs\Python312\Lib\subprocess.py", line 1538, in _execute_child
hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [WinError 2] The system cannot find the file specified
at ~\pipx\venvs\poetry\Lib\site-packages\poetry\installation\chef.py:164 in _prepare 160│ 161│ error = ChefBuildError("\n\n".join(message_parts)) 162│ 163│ if error is not None: → 164│ raise error from None 165│ 166│ return path 167│ 168│ def _prepare_sdist(self, archive: Path, destination: Path | None = None) -> Path:
Note: This error originates from the build backend, and is likely not a problem with poetry but with pysam (0.22.1) not supporting PEP 517 builds. You can verify this by running 'pip wheel --no-cache-dir --use-pep517 "pysam (==0.22.1)"'.
Installing zarr (2.18.3) PS D:\SW\modo-test> pip wheel --no-cache-dir --use-pep517 "pysam (==0.22.1)
× Getting requirements to build wheel did not run successfully. │ exit code: 1 ╰─> [40 lines of output]
pysam: cython is available - using cythonize if necessary
pysam: htslib mode is shared
pysam: HTSLIB_CONFIGURE_OPTIONS=None
'.' is not recognized as an internal or external command, operable program or batch file. '.' is not recognized as an internal or external command, operable program or batch file.
pysam: htslib configure options: None
Traceback (most recent call last): File "D:\libs\Python312\Lib\site-packages\pip_vendor\pyproject_hooks_in_process_in_process.py", line 353, in
main()
File "D:\libs\Python312\Lib\site-packages\pip_vendor\pyproject_hooks_in_process_in_process.py", line 335, in main
json_out['return_val'] = hook(hook_input['kwargs'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\libs\Python312\Lib\site-packages\pip_vendor\pyproject_hooks_in_process_in_process.py", line 118, in get_requires_for_build_wheel
return hook(config_settings)
^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\nzamboni\AppData\Local\Temp\pip-build-env-vxmt1xno\overlay\Lib\site-packages\setuptools\build_meta.py", line 334, in get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=[])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\nzamboni\AppData\Local\Temp\pip-build-env-vxmt1xno\overlay\Lib\site-packages\setuptools\build_meta.py", line 304, in _get_build_requires
self.run_setup()
File "C:\Users\nzamboni\AppData\Local\Temp\pip-build-env-vxmt1xno\overlay\Lib\site-packages\setuptools\build_meta.py", line 522, in run_setup
super().run_setup(setup_script=setup_script)
File "C:\Users\nzamboni\AppData\Local\Temp\pip-build-env-vxmt1xno\overlay\Lib\site-packages\setuptools\build_meta.py", line 320, in run_setup
exec(code, locals())
File "", line 437, in
File "", line 81, in run_make_print_config
File "D:\libs\Python312\Lib\subprocess.py", line 466, in check_output
return run(popenargs, stdout=PIPE, timeout=timeout, check=True,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\libs\Python312\Lib\subprocess.py", line 548, in run
with Popen(popenargs, kwargs) as process:
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\libs\Python312\Lib\subprocess.py", line 1026, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "D:\libs\Python312\Lib\subprocess.py", line 1538, in _execute_child
hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [WinError 2] The system cannot find the file specified
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully. │ exit code: 1 ╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
What system are you using?
Microsoft Windows
Relevant log output
No response