Hi，i used the command “pip install haplotype-plot” to install haplotype-plot，but always encountered the same error as follow：
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [203 lines of output]
performance hint: allel/opt/io_vcf_read.pyx:105:5: Exception check on 'CharVector_init' will always require the GIL to be acquired.
Possible solutions:
1. Declare 'CharVector_init' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'CharVector_init' to allow an error code to be returned.
performance hint: allel/opt/io_vcf_read.pyx:111:5: Exception check on 'CharVector_free' will always require the GIL to be acquired.
Possible solutions:
1. Declare 'CharVector_free' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'CharVector_free' to allow an error code to be returned.
performance hint: allel/opt/io_vcf_read.pyx:116:5: Exception check on 'CharVector_append' will always require the GIL to be acquired.
Possible solutions:
1. Declare 'CharVector_append' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'CharVector_append' to allow an error code to be returned.
performance hint: allel/opt/io_vcf_read.pyx:124:5: Exception check on 'CharVector_clear' will always require the GIL to be acquired.
Possible solutions:
1. Declare 'CharVector_clear' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'CharVector_clear' to allow an error code to be returned.
performance hint: allel/opt/io_vcf_read.pyx:128:5: Exception check on 'CharVector_terminate' will always require the GIL to be acquired.
Possible solutions:
1. Declare 'CharVector_terminate' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'CharVector_terminate' to allow an error code to be returned.
performance hint: allel/opt/io_vcf_read.pyx:154:5: Exception check on 'IntVector_init' will always require the GIL to be acquired.
Possible solutions:
1. Declare 'IntVector_init' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'IntVector_init' to allow an error code to be returned.
performance hint: allel/opt/io_vcf_read.pyx:160:5: Exception check on 'IntVector_free' will always require the GIL to be acquired.
Possible solutions:
1. Declare 'IntVector_free' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'IntVector_free' to allow an error code to be returned.
performance hint: allel/opt/io_vcf_read.pyx:165:5: Exception check on 'IntVector_append' will always require the GIL to be acquired.
Possible solutions:
1. Declare 'IntVector_append' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'IntVector_append' to allow an error code to be returned.
performance hint: allel/opt/io_vcf_read.pyx:173:5: Exception check on 'IntVector_clear' will always require the GIL to be acquired.
Possible solutions:
1. Declare 'IntVector_clear' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'IntVector_clear' to allow an error code to be returned.
performance hint: allel/opt/io_vcf_read.pyx:129:21: Exception check after calling 'CharVector_append' will always require the GIL to be acquired.
Possible solutions:
1. Declare 'CharVector_append' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'CharVector_append' to allow an error code to be returned.
[scikit-allel] setup extensions with cython
Compiling allel/opt/model.pyx because it changed.
Compiling allel/opt/stats.pyx because it changed.
Compiling allel/opt/io_vcf_read.pyx because it changed.
[1/3] Cythonizing allel/opt/io_vcf_read.pyx
[2/3] Cythonizing allel/opt/model.pyx
[3/3] Cythonizing allel/opt/stats.pyx
/tmp/pip-build-env-76m3o_f9/overlay/lib/python3.12/site-packages/setuptools/config/_apply_pyprojecttoml.py:76: _MissingDynamic: readme defined outside of pyproject.toml is ignored.
!!
********************************************************************************
The following seems to be defined outside of `pyproject.toml`:
`readme = '``scikit-allel``\n================\n\nA Python package for exploratory analysis of large scale genetic variation data.\n\n* Documentation: http://scikit-allel.readthedocs.org\n* Source code: https://github.com/cggh/scikit-allel\n* Download: https://pypi.python.org/pypi/scikit-allel\n\n.. image:: https://zenodo.org/badge/7890/cggh/scikit-allel.svg\n :target: https://zenodo.org/badge/latestdoi/7890/cggh/scikit-allel\n\n.. image:: https://readthedocs.org/projects/scikit-allel/badge/?version=latest\n :target: http://scikit-allel.readthedocs.io/en/latest/?badge=latest\n\n.. image:: https://travis-ci.org/cggh/scikit-allel.svg?branch=master\n :target: https://travis-ci.org/cggh/scikit-allel\n\n.. image:: https://ci.appveyor.com/api/projects/status/1fna2yr9uht0u296?svg=true\n :target: https://ci.appveyor.com/project/alimanfoo/scikit-allel\n\n\nDevelopment status\n******************\n\nPlease note that scikit-allel is no longer under active development\nand is now in "maintenance-only" mode. The intended successor\nproject is `sgkit <https://github.com/pystatgen/sgkit>`__ (the Statistical\nGenetics Toolkit) which should support all the functionality of sckit-allel,\nbut provide better scaling, performance and maintainability.\nSgkit is not yet at feature parity with scikit-allel and is therefore\nnot ready for all applications, but we welcome `contributions\n<https://pystatgen.github.io/sgkit/latest/contributing.html>`__!\n'`
According to the spec (see the link below), however, setuptools CANNOT
consider this value unless `readme` is listed as `dynamic`.
https://packaging.python.org/en/latest/specifications/pyproject-toml/#declaring-project-metadata-the-project-table
To prevent this problem, you can list `readme` under `dynamic` or alternatively
remove the `[project]` table from your file and rely entirely on other means of
configuration.
********************************************************************************
!!
_handle_missing_dynamic(dist, project_table)
/tmp/pip-build-env-76m3o_f9/overlay/lib/python3.12/site-packages/setuptools/config/_apply_pyprojecttoml.py:76: _MissingDynamic: `license` defined outside of `pyproject.toml` is ignored.
!!
********************************************************************************
The following seems to be defined outside of `pyproject.toml`:
`license = 'MIT'`
According to the spec (see the link below), however, setuptools CANNOT
consider this value unless `license` is listed as `dynamic`.
https://packaging.python.org/en/latest/specifications/pyproject-toml/#declaring-project-metadata-the-project-table
To prevent this problem, you can list `license` under `dynamic` or alternatively
remove the `[project]` table from your file and rely entirely on other means of
configuration.
********************************************************************************
!!
_handle_missing_dynamic(dist, project_table)
/tmp/pip-build-env-76m3o_f9/overlay/lib/python3.12/site-packages/setuptools/config/_apply_pyprojecttoml.py:76: _MissingDynamic: `maintainers` defined outside of `pyproject.toml` is ignored.
!!
********************************************************************************
The following seems to be defined outside of `pyproject.toml`:
`maintainers = 'Alistair Miles'`
According to the spec (see the link below), however, setuptools CANNOT
consider this value unless `maintainers` is listed as `dynamic`.
https://packaging.python.org/en/latest/specifications/pyproject-toml/#declaring-project-metadata-the-project-table
To prevent this problem, you can list `maintainers` under `dynamic` or alternatively
remove the `[project]` table from your file and rely entirely on other means of
configuration.
********************************************************************************
!!
_handle_missing_dynamic(dist, project_table)
/tmp/pip-build-env-76m3o_f9/overlay/lib/python3.12/site-packages/setuptools/config/_apply_pyprojecttoml.py:76: _MissingDynamic: `classifiers` defined outside of `pyproject.toml` is ignored.
!!
********************************************************************************
The following seems to be defined outside of `pyproject.toml`:
`classifiers = ['Development Status :: 4 - Beta', 'License :: OSI Approved :: MIT License', 'Intended Audience :: Developers', 'Intended Audience :: Science/Research', 'Programming Language :: Python', 'Topic :: Software Development :: Libraries :: Python Modules', 'Topic :: Scientific/Engineering', 'Operating System :: Microsoft :: Windows', 'Operating System :: POSIX', 'Operating System :: Unix', 'Operating System :: MacOS', 'Programming Language :: Python :: 3', 'Programming Language :: Python :: 3.8', 'Programming Language :: Python :: 3.9', 'Programming Language :: Python :: 3.10']`
According to the spec (see the link below), however, setuptools CANNOT
consider this value unless `classifiers` is listed as `dynamic`.
https://packaging.python.org/en/latest/specifications/pyproject-toml/#declaring-project-metadata-the-project-table
To prevent this problem, you can list `classifiers` under `dynamic` or alternatively
remove the `[project]` table from your file and rely entirely on other means of
configuration.
********************************************************************************
!!
_handle_missing_dynamic(dist, project_table)
/tmp/pip-build-env-76m3o_f9/overlay/lib/python3.12/site-packages/setuptools/config/_apply_pyprojecttoml.py:76: _MissingDynamic: `dependencies` defined outside of `pyproject.toml` is ignored.
!!
********************************************************************************
The following seems to be defined outside of `pyproject.toml`:
`dependencies = ['numpy', 'dask[array]']`
According to the spec (see the link below), however, setuptools CANNOT
consider this value unless `dependencies` is listed as `dynamic`.
https://packaging.python.org/en/latest/specifications/pyproject-toml/#declaring-project-metadata-the-project-table
To prevent this problem, you can list `dependencies` under `dynamic` or alternatively
remove the `[project]` table from your file and rely entirely on other means of
configuration.
********************************************************************************
!!
_handle_missing_dynamic(dist, project_table)
/tmp/pip-build-env-76m3o_f9/overlay/lib/python3.12/site-packages/setuptools/config/_apply_pyprojecttoml.py:76: _MissingDynamic: `optional-dependencies` defined outside of `pyproject.toml` is ignored.
!!
********************************************************************************
The following seems to be defined outside of `pyproject.toml`:
`optional-dependencies = {'full': ['scipy', 'matplotlib', 'seaborn', 'pandas', 'scikit-learn', 'h5py', 'numexpr', 'zarr', 'hmmlearn', 'pomegranate', 'nose']}`
According to the spec (see the link below), however, setuptools CANNOT
consider this value unless `optional-dependencies` is listed as `dynamic`.
https://packaging.python.org/en/latest/specifications/pyproject-toml/#declaring-project-metadata-the-project-table
To prevent this problem, you can list `optional-dependencies` under `dynamic` or alternatively
remove the `[project]` table from your file and rely entirely on other means of
configuration.
********************************************************************************
!!
_handle_missing_dynamic(dist, project_table)
Traceback (most recent call last):
File "/home/xiazq/miniconda3/envs/vcf_plot/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/home/xiazq/miniconda3/envs/vcf_plot/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/xiazq/miniconda3/envs/vcf_plot/lib/python3.12/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
return hook(config_settings)
^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-76m3o_f9/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 325, in get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=['wheel'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-76m3o_f9/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 295, in _get_build_requires
self.run_setup()
File "/tmp/pip-build-env-76m3o_f9/overlay/lib/python3.12/site-packages/setuptools/build_meta.py", line 311, in run_setup
exec(code, locals())
File "<string>", line 100, in <module>
File "<string>", line 96, in setup_package
File "/tmp/pip-build-env-76m3o_f9/overlay/lib/python3.12/site-packages/setuptools/__init__.py", line 104, in setup
return distutils.core.setup(**attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-76m3o_f9/overlay/lib/python3.12/site-packages/setuptools/_distutils/core.py", line 159, in setup
dist.parse_config_files()
File "/tmp/pip-build-env-76m3o_f9/overlay/lib/python3.12/site-packages/setuptools/dist.py", line 631, in parse_config_files
pyprojecttoml.apply_configuration(self, filename, ignore_option_errors)
File "/tmp/pip-build-env-76m3o_f9/overlay/lib/python3.12/site-packages/setuptools/config/pyprojecttoml.py", line 69, in apply_configuration
return _apply(dist, config, filepath)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/pip-build-env-76m3o_f9/overlay/lib/python3.12/site-packages/setuptools/config/_apply_pyprojecttoml.py", line 57, in apply
_apply_project_table(dist, config, root_dir)
File "/tmp/pip-build-env-76m3o_f9/overlay/lib/python3.12/site-packages/setuptools/config/_apply_pyprojecttoml.py", line 83, in _apply_project_table
corresp(dist, value, root_dir)
File "/tmp/pip-build-env-76m3o_f9/overlay/lib/python3.12/site-packages/setuptools/config/_apply_pyprojecttoml.py", line 164, in _long_description
file = val.get("file") or []
^^^^^^^
AttributeError: 'NoneType' object has no attribute 'get'
[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.
Hi，i used the command “pip install haplotype-plot” to install haplotype-plot，but always encountered the same error as follow：
$pip install haplotype-plot
Collecting haplotype-plot
Using cached haplotype_plot-1.1.3.tar.gz (13 kB)
Preparing metadata (setup.py) ... done
Collecting scikit-allel (from haplotype-plot)
Using cached scikit-allel-1.3.7.tar.gz (9.7 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... error
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [203 lines of output]
performance hint: allel/opt/io_vcf_read.pyx:105:5: Exception check on 'CharVector_init' will always require the GIL to be acquired.
Possible solutions:
1. Declare 'CharVector_init' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'CharVector_init' to allow an error code to be returned.
performance hint: allel/opt/io_vcf_read.pyx:111:5: Exception check on 'CharVector_free' will always require the GIL to be acquired.
Possible solutions:
1. Declare 'CharVector_free' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'CharVector_free' to allow an error code to be returned.
performance hint: allel/opt/io_vcf_read.pyx:116:5: Exception check on 'CharVector_append' will always require the GIL to be acquired.
Possible solutions:
1. Declare 'CharVector_append' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'CharVector_append' to allow an error code to be returned.
performance hint: allel/opt/io_vcf_read.pyx:124:5: Exception check on 'CharVector_clear' will always require the GIL to be acquired.
Possible solutions:
1. Declare 'CharVector_clear' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'CharVector_clear' to allow an error code to be returned.
performance hint: allel/opt/io_vcf_read.pyx:128:5: Exception check on 'CharVector_terminate' will always require the GIL to be acquired.
Possible solutions:
1. Declare 'CharVector_terminate' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'CharVector_terminate' to allow an error code to be returned.
performance hint: allel/opt/io_vcf_read.pyx:154:5: Exception check on 'IntVector_init' will always require the GIL to be acquired.
Possible solutions:
1. Declare 'IntVector_init' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'IntVector_init' to allow an error code to be returned.
performance hint: allel/opt/io_vcf_read.pyx:160:5: Exception check on 'IntVector_free' will always require the GIL to be acquired.
Possible solutions:
1. Declare 'IntVector_free' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'IntVector_free' to allow an error code to be returned.
performance hint: allel/opt/io_vcf_read.pyx:165:5: Exception check on 'IntVector_append' will always require the GIL to be acquired.
Possible solutions:
1. Declare 'IntVector_append' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'IntVector_append' to allow an error code to be returned.
performance hint: allel/opt/io_vcf_read.pyx:173:5: Exception check on 'IntVector_clear' will always require the GIL to be acquired.
Possible solutions:
1. Declare 'IntVector_clear' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'IntVector_clear' to allow an error code to be returned.
performance hint: allel/opt/io_vcf_read.pyx:129:21: Exception check after calling 'CharVector_append' will always require the GIL to be acquired.
Possible solutions:
1. Declare 'CharVector_append' as 'noexcept' if you control the definition and you're sure you don't want the function to raise exceptions.
2. Use an 'int' return type on 'CharVector_append' to allow an error code to be returned.
[scikit-allel] setup extensions with cython
Compiling allel/opt/model.pyx because it changed.
Compiling allel/opt/stats.pyx because it changed.
Compiling allel/opt/io_vcf_read.pyx because it changed.
[1/3] Cythonizing allel/opt/io_vcf_read.pyx
[2/3] Cythonizing allel/opt/model.pyx
[3/3] Cythonizing allel/opt/stats.pyx
/tmp/pip-build-env-76m3o_f9/overlay/lib/python3.12/site-packages/setuptools/config/_apply_pyprojecttoml.py:76: _MissingDynamic:
readmedefined outside ofpyproject.tomlis ignored.!!
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.