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Fix Astropy and scikit-learn test #3

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Fix Astropy and scikit-learn test #3

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dorbanianas
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I fixed the issues related to Astropy, and the dependencies issue of scikit-learn

@libowen2121
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Hey @dorbanianas, I still encountered the following issues.

For the astropy repo:

2024-04-01 17:32:16,498 - INFO - [Testbed] Installing pip packages for astropy__astropy__5.0; Command: source /home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpuchbg2ds/miniconda3/bin/activate astropy__astropy__5.0 && pip install pytest
/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmphjupapih/astropy__astropy__5.0: 1 instances
2024-04-01 17:32:18,219 - INFO - [astropy__astropy__5.0] [astropy__astropy-13745] Reset task environment to 0446f168dc6e34996482394f00770b52756b8f9c
2024-04-01 17:32:18,225 - INFO - [astropy__astropy__5.0] [astropy__astropy-13745] Apply patch successful (pred_try)
2024-04-01 17:32:18,230 - INFO - [astropy__astropy__5.0] [astropy__astropy-13745] Revert patch successful (pred_try)
2024-04-01 17:32:18,230 - INFO - [astropy__astropy__5.0] [astropy__astropy-13745] Installing with command: source /home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpuchbg2ds/miniconda3/bin/activate astropy__astropy__5.0 && echo 'activate successful' && python setup.py install
2024-04-01 17:32:18,370 - ERROR - Error: Command 'source /home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpuchbg2ds/miniconda3/bin/activate astropy__astropy__5.0 && echo 'activate successful' && python setup.py install' returned non-zero exit status 1.
2024-04-01 17:32:18,370 - ERROR - Error stdout: activate successful

2024-04-01 17:32:18,370 - ERROR - Error stderr: Traceback (most recent call last):
  File "/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmphjupapih/astropy__astropy__5.0/setup.py", line 67, in <module>
    from extension_helpers import get_extensions  # noqa: E402
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named 'extension_helpers'

2024-04-01 17:32:18,371 - ERROR - Error traceback: Traceback (most recent call last):
  File "/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness/context_manager.py", line 49, in __call__
    output = subprocess.run(cmd, **combined_args)
  File "/home/PJLAB/libowen/miniconda3/envs/swe-bench/lib/python3.9/subprocess.py", line 528, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'source /home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpuchbg2ds/miniconda3/bin/activate astropy__astropy__5.0 && echo 'activate successful' && python setup.py install' returned non-zero exit status 1.

2024-04-01 17:32:18,371 - ERROR - [astropy__astropy__5.0] [astropy__astropy-13745] Installation failed

For the scikit-learn repo:

2024-04-01 17:34:26,741 - INFO - [scikit-learn__scikit-learn__0.21] [scikit-learn__scikit-learn-13496] Reset task environment to 3aefc834dce72e850bff48689bea3c7dff5f3fad
2024-04-01 17:34:26,747 - INFO - [scikit-learn__scikit-learn__0.21] [scikit-learn__scikit-learn-13496] Apply patch successful (pred_try)
2024-04-01 17:34:26,753 - INFO - [scikit-learn__scikit-learn__0.21] [scikit-learn__scikit-learn-13496] Revert patch successful (pred_try)
2024-04-01 17:34:26,753 - INFO - [scikit-learn__scikit-learn__0.21] [scikit-learn__scikit-learn-13496] Installing with command: source /home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.21/tmpjomf167r/miniconda3/bin/activate scikit-learn__scikit-learn__0.21 && echo 'activate successful' && pip install -v --no-use-pep517 --no-build-isolation -e .
2024-04-01 17:34:27,345 - ERROR - Error: Command 'source /home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.21/tmpjomf167r/miniconda3/bin/activate scikit-learn__scikit-learn__0.21 && echo 'activate successful' && pip install -v --no-use-pep517 --no-build-isolation -e .' returned non-zero exit status 1.
2024-04-01 17:34:27,345 - ERROR - Error stdout: activate successful
Using pip 23.3.1 from /home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.21/tmpjomf167r/miniconda3/lib/python3.11/site-packages/pip (python 3.11)
Obtaining file:///home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.21/tmp8upww50n/scikit-learn__scikit-learn__0.21
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'error'

2024-04-01 17:34:27,345 - ERROR - Error stderr:   Running command python setup.py egg_info
  /home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.21/tmp8upww50n/scikit-learn__scikit-learn__0.21/setup.py:12: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
    from pkg_resources import parse_version
  Partial import of sklearn during the build process.
  /home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.21/tmp8upww50n/scikit-learn__scikit-learn__0.21/setup.py:139: DeprecationWarning:

    `numpy.distutils` is deprecated since NumPy 1.23.0, as a result
    of the deprecation of `distutils` itself. It will be removed for
    Python >= 3.12. For older Python versions it will remain present.
    It is recommended to use `setuptools < 60.0` for those Python versions.
    For more details, see:
      https://numpy.org/devdocs/reference/distutils_status_migration.html


    from numpy.distutils.command.build_ext import build_ext  # noqa
  error: Multiple top-level packages discovered in a flat-layout: ['sklearn', 'build_tools', 'maint_tools'].

  To avoid accidental inclusion of unwanted files or directories,
  setuptools will not proceed with this build.

  If you are trying to create a single distribution with multiple packages
  on purpose, you should not rely on automatic discovery.
  Instead, consider the following options:

  1. set up custom discovery (`find` directive with `include` or `exclude`)
  2. use a `src-layout`
  3. explicitly set `py_modules` or `packages` with a list of names

  To find more information, look for "package discovery" on setuptools docs.
  error: subprocess-exited-with-error
  
  × python setup.py egg_info 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.
  full command: /home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.21/tmpjomf167r/miniconda3/bin/python -c '
  exec(compile('"'"''"'"''"'"'
  # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
  #
  # - It imports setuptools before invoking setup.py, to enable projects that directly
  #   import from `distutils.core` to work with newer packaging standards.
  # - It provides a clear error message when setuptools is not installed.
  # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so
  #   setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning:
  #     manifest_maker: standard file '"'"'-c'"'"' not found".
  # - It generates a shim setup.py, for handling setup.cfg-only projects.
  import os, sys, tokenize
  
  try:
      import setuptools
  except ImportError as error:
      print(
          "ERROR: Can not execute `setup.py` since setuptools is not available in "
          "the build environment.",
          file=sys.stderr,
      )
      sys.exit(1)
  
  __file__ = %r
  sys.argv[0] = __file__
  
  if os.path.exists(__file__):
      filename = __file__
      with tokenize.open(__file__) as f:
          setup_py_code = f.read()
  else:
      filename = "<auto-generated setuptools caller>"
      setup_py_code = "from setuptools import setup; setup()"
  
  exec(compile(setup_py_code, filename, "exec"))
  '"'"''"'"''"'"' % ('"'"'/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.21/tmp8upww50n/scikit-learn__scikit-learn__0.21/setup.py'"'"',), "<pip-setuptools-caller>", "exec"))' egg_info --egg-base /tmp/pip-pip-egg-info-9ezjf262
  cwd: /home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.21/tmp8upww50n/scikit-learn__scikit-learn__0.21/
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

2024-04-01 17:34:27,345 - ERROR - Error traceback: Traceback (most recent call last):
  File "/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness/context_manager.py", line 49, in __call__
    output = subprocess.run(cmd, **combined_args)
  File "/home/PJLAB/libowen/miniconda3/envs/swe-bench/lib/python3.9/subprocess.py", line 528, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'source /home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.21/tmpjomf167r/miniconda3/bin/activate scikit-learn__scikit-learn__0.21 && echo 'activate successful' && pip install -v --no-use-pep517 --no-build-isolation -e .' returned non-zero exit status 1.

2024-04-01 17:34:27,346 - ERROR - [scikit-learn__scikit-learn__0.21] [scikit-learn__scikit-learn-13496] Installation failed

@dorbanianas
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@libowen2121 for the astropy I guess we should add extension_helpers to the requirements it may solve the problem for version 5.0, for scikit-learn I face this problem from time to time I found that it's related to the project structure so the solution that I found is by restructuring the scikit-learn project which is not possible or by modifying on the setup.py

@libowen2121
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For astropy, I added some missing packages and still had the following error.

creating build/lib.linux-x86_64-cpython-311/astropy/config/tests/data
copying astropy/config/tests/data/not_empty.cfg -> build/lib.linux-x86_64-cpython-311/astropy/config/tests/data
copying astropy/config/tests/data/empty.cfg -> build/lib.linux-x86_64-cpython-311/astropy/config/tests/data
copying astropy/config/tests/data/deprecated.cfg -> build/lib.linux-x86_64-cpython-311/astropy/config/tests/data
copying astropy/config/tests/data/alias.cfg -> build/lib.linux-x86_64-cpython-311/astropy/config/tests/data
running build_ext
building 'astropy.convolution._convolve' extension
creating build/temp.linux-x86_64-cpython-311
creating build/temp.linux-x86_64-cpython-311/astropy
creating build/temp.linux-x86_64-cpython-311/astropy/convolution
creating build/temp.linux-x86_64-cpython-311/astropy/convolution/src
gcc -pthread -B /home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpj3c6dosk/miniconda3/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpj3c6dosk/miniconda3/include -fPIC -O2 -isystem /home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpj3c6dosk/miniconda3/include -fPIC -I/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpj3c6dosk/miniconda3/lib/python3.11/site-packages/numpy/core/include -I/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpj3c6dosk/miniconda3/include/python3.11 -c astropy/convolution/src/convolve.c -o build/temp.linux-x86_64-cpython-311/astropy/convolution/src/convolve.o -UNDEBUG -fPIC
gcc -pthread -B /home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpj3c6dosk/miniconda3/compiler_compat -shared -Wl,-rpath,/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpj3c6dosk/miniconda3/lib -Wl,-rpath-link,/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpj3c6dosk/miniconda3/lib -L/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpj3c6dosk/miniconda3/lib -Wl,-rpath,/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpj3c6dosk/miniconda3/lib -Wl,-rpath-link,/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpj3c6dosk/miniconda3/lib -L/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpj3c6dosk/miniconda3/lib build/temp.linux-x86_64-cpython-311/astropy/convolution/src/convolve.o -o build/lib.linux-x86_64-cpython-311/astropy/convolution/_convolve.cpython-311-x86_64-linux-gnu.so
building 'astropy.table._np_utils' extension
creating build/temp.linux-x86_64-cpython-311/astropy/table
gcc -pthread -B /home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpj3c6dosk/miniconda3/compiler_compat -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpj3c6dosk/miniconda3/include -fPIC -O2 -isystem /home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpj3c6dosk/miniconda3/include -fPIC -I/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpj3c6dosk/miniconda3/lib/python3.11/site-packages/numpy/core/include -I/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpj3c6dosk/miniconda3/include/python3.11 -c astropy/table/_np_utils.c -o build/temp.linux-x86_64-cpython-311/astropy/table/_np_utils.o

2024-04-01 20:02:36,872 - ERROR - Error stderr: Extension astropy.io.fits.compression contains source files (astropy/io/fits/src/compressionmodule.c) that are specified using an absolute path, which will not be supported in future.
/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpj3c6dosk/miniconda3/lib/python3.11/site-packages/setuptools/config/setupcfg.py:293: _DeprecatedConfig: Deprecated config in `setup.cfg`
!!

        ********************************************************************************
        The license_file parameter is deprecated, use license_files instead.

        This deprecation is overdue, please update your project and remove deprecated
        calls to avoid build errors in the future.

        See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
        ********************************************************************************

!!
  parsed = self.parsers.get(option_name, lambda x: x)(value)
/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpj3c6dosk/miniconda3/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` directly.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
        ********************************************************************************

!!
  self.initialize_options()
/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpj3c6dosk/miniconda3/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` and ``easy_install``.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://github.com/pypa/setuptools/issues/917 for details.
        ********************************************************************************

!!
  self.initialize_options()
warning: no files found matching '*.templ' under directory 'astropy'
warning: no files found matching 'astropy/astropy.cfg'
warning: no files found matching '*' under directory 'scripts'
warning: no files found matching '*' under directory 'static'
no previously-included directories found matching 'astropy/_dev'
no previously-included directories found matching 'docs/_build'
no previously-included directories found matching 'build'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.o' found anywhere in distribution
gcc: error: astropy/table/_np_utils.c: No such file or directory
gcc: fatal error: no input files
compilation terminated.
error: command '/usr/bin/gcc' failed with exit code 1

2024-04-01 20:02:36,872 - ERROR - Error traceback: Traceback (most recent call last):
  File "/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness/context_manager.py", line 49, in __call__
    output = subprocess.run(cmd, **combined_args)
  File "/home/PJLAB/libowen/miniconda3/envs/swe-bench/lib/python3.9/subprocess.py", line 528, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'source /home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/astropy__astropy/5.0/tmpj3c6dosk/miniconda3/bin/activate astropy__astropy__5.0 && echo 'activate successful' && python setup.py install' returned non-zero exit status 1.

2024-04-01 20:02:36,872 - ERROR - [astropy__astropy__5.0] [astropy__astropy-13745] Installation failed

For scikit-learn, I changed the installation command to python setup.py develop and it seemed to resolve the issue of multiple top-level packages. But I got some new errors.

/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.20/tmpynho64be/miniconda3/lib/python3.11/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: /home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.20/tmphvbk3k79/scikit-learn__scikit-learn__0.20/sklearn/ensemble/_gradient_boosting.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)
warning: sklearn/tree/_tree.pxd:61:68: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
warning: sklearn/tree/_tree.pxd:62:59: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
warning: sklearn/tree/_tree.pxd:63:63: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
warning: sklearn/tree/_splitter.pxd:89:72: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
warning: sklearn/tree/_splitter.pxd:94:68: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
warning: sklearn/tree/_criterion.pxd:58:45: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
warning: sklearn/tree/_criterion.pxd:59:40: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
warning: sklearn/tree/_criterion.pxd:60:48: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
warning: sklearn/tree/_criterion.pxd:61:57: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
warning: sklearn/tree/_utils.pxd:48:75: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
warning: sklearn/tree/_utils.pxd:86:61: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
warning: sklearn/tree/_utils.pxd:118:56: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
warning: sklearn/tree/_utils.pxd:136:40: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
warning: sklearn/tree/_utils.pxd:138:71: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
warning: sklearn/tree/_utils.pxd:159:71: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
warning: sklearn/tree/_utils.pxd:160:40: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.

Error compiling Cython file:
------------------------------------------------------------
...

# See _utils.pyx for details.

import numpy as np
cimport numpy as np
from _tree cimport Node
^
------------------------------------------------------------

sklearn/tree/_utils.pxd:13:0: '_tree.pxd' not found

Error compiling Cython file:
------------------------------------------------------------
...

# See _utils.pyx for details.

import numpy as np
cimport numpy as np
from _tree cimport Node
^
------------------------------------------------------------

sklearn/tree/_utils.pxd:13:0: '_tree/Node.pxd' not found
warning: sklearn/neighbors/quad_tree.pxd:75:59: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
warning: sklearn/neighbors/quad_tree.pxd:94:51: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
warning: sklearn/neighbors/quad_tree.pxd:97:59: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
warning: sklearn/neighbors/quad_tree.pxd:98:63: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.
warning: sklearn/neighbors/quad_tree.pxd:99:80: The keyword 'nogil' should appear at the end of the function signature line. Placing it before 'except' or 'noexcept' will be disallowed in a future version of Cython.

Error compiling Cython file:
------------------------------------------------------------
...
    (SIZE_t*)
    (unsigned char*)
    (WeightedPQueueRecord*)
    (DOUBLE_t*)
    (DOUBLE_t**)
    (Node*)
     ^
------------------------------------------------------------

sklearn/tree/_utils.pxd:42:5: 'Node' is not a type identifier

Error compiling Cython file:
------------------------------------------------------------
...
    (WeightedPQueueRecord*)
    (DOUBLE_t*)
    (DOUBLE_t**)
    (Node*)
    (Cell*)
    (Node**)
     ^
------------------------------------------------------------

sklearn/tree/_utils.pxd:44:5: 'Node' is not a type identifier

Error compiling Cython file:
------------------------------------------------------------
...
    (WeightedPQueueRecord*)
    (DOUBLE_t*)
    (DOUBLE_t**)
    (Node*)
    (Cell*)
    (Node**)
    ^
------------------------------------------------------------

sklearn/tree/_utils.pxd:44:4: Type specified multiple times

Error compiling Cython file:
------------------------------------------------------------
...

    cdef Tree tree
    cdef Node** nodes = NULL
    cdef double** values = NULL
    safe_realloc(&nodes, n_stages * n_outputs)
    safe_realloc(&values, n_stages * n_outputs)
                ^
------------------------------------------------------------

sklearn/ensemble/_gradient_boosting.pyx:134:16: ambiguous overloaded method

Error compiling Cython file:
------------------------------------------------------------
...
    # feature_to_sample as a data structure records the last seen sample
    # for each feature; functionally, it is an efficient way to identify
    # which features are nonzero in the present sample.
    cdef SIZE_t* feature_to_sample = NULL

    safe_realloc(&X_sample, n_features)
                ^
------------------------------------------------------------

sklearn/ensemble/_gradient_boosting.pyx:150:16: ambiguous overloaded method

Error compiling Cython file:
------------------------------------------------------------
...
    # for each feature; functionally, it is an efficient way to identify
    # which features are nonzero in the present sample.
    cdef SIZE_t* feature_to_sample = NULL

    safe_realloc(&X_sample, n_features)
    safe_realloc(&feature_to_sample, n_features)
                ^
------------------------------------------------------------

sklearn/ensemble/_gradient_boosting.pyx:151:16: ambiguous overloaded method

Error compiling Cython file:
------------------------------------------------------------
...

    cdef Tree tree
    cdef Node** nodes = NULL
    cdef double** values = NULL
    safe_realloc(&nodes, n_stages * n_outputs)
    safe_realloc(&values, n_stages * n_outputs)
    ^
------------------------------------------------------------

sklearn/ensemble/_gradient_boosting.pyx:134:4: Invalid use of fused types, type cannot be specialized

Error compiling Cython file:
------------------------------------------------------------
...
    # feature_to_sample as a data structure records the last seen sample
    # for each feature; functionally, it is an efficient way to identify
    # which features are nonzero in the present sample.
    cdef SIZE_t* feature_to_sample = NULL

    safe_realloc(&X_sample, n_features)
    ^
------------------------------------------------------------

sklearn/ensemble/_gradient_boosting.pyx:150:4: Invalid use of fused types, type cannot be specialized

Error compiling Cython file:
------------------------------------------------------------
...
    # for each feature; functionally, it is an efficient way to identify
    # which features are nonzero in the present sample.
    cdef SIZE_t* feature_to_sample = NULL

    safe_realloc(&X_sample, n_features)
    safe_realloc(&feature_to_sample, n_features)
    ^
------------------------------------------------------------

sklearn/ensemble/_gradient_boosting.pyx:151:4: Invalid use of fused types, type cannot be specialized
Traceback (most recent call last):
  File "/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.20/tmphvbk3k79/scikit-learn__scikit-learn__0.20/setup.py", line 241, in <module>
    setup_package()
  File "/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.20/tmphvbk3k79/scikit-learn__scikit-learn__0.20/setup.py", line 237, in setup_package
    setup(**metadata)
  File "/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.20/tmpynho64be/miniconda3/lib/python3.11/site-packages/numpy/distutils/core.py", line 136, in setup
    config = configuration()
             ^^^^^^^^^^^^^^^
  File "/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.20/tmphvbk3k79/scikit-learn__scikit-learn__0.20/setup.py", line 136, in configuration
    config.add_subpackage('sklearn')
  File "/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.20/tmpynho64be/miniconda3/lib/python3.11/site-packages/numpy/distutils/misc_util.py", line 1050, in add_subpackage
    config_list = self.get_subpackage(subpackage_name, subpackage_path,
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.20/tmpynho64be/miniconda3/lib/python3.11/site-packages/numpy/distutils/misc_util.py", line 1016, in get_subpackage
    config = self._get_configuration_from_setup_py(
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.20/tmpynho64be/miniconda3/lib/python3.11/site-packages/numpy/distutils/misc_util.py", line 958, in _get_configuration_from_setup_py
    config = setup_module.configuration(*args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.20/tmphvbk3k79/scikit-learn__scikit-learn__0.20/sklearn/setup.py", line 82, in configuration
    maybe_cythonize_extensions(top_path, config)
  File "/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.20/tmphvbk3k79/scikit-learn__scikit-learn__0.20/sklearn/_build_utils/__init__.py", line 84, in maybe_cythonize_extensions
    config.ext_modules = cythonize(config.ext_modules)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.20/tmpynho64be/miniconda3/lib/python3.11/site-packages/Cython/Build/Dependencies.py", line 1154, in cythonize
    cythonize_one(*args)
  File "/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.20/tmpynho64be/miniconda3/lib/python3.11/site-packages/Cython/Build/Dependencies.py", line 1321, in cythonize_one
    raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: sklearn/ensemble/_gradient_boosting.pyx

2024-04-01 20:07:26,441 - ERROR - Error traceback: Traceback (most recent call last):
  File "/home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness/context_manager.py", line 49, in __call__
    output = subprocess.run(cmd, **combined_args)
  File "/home/PJLAB/libowen/miniconda3/envs/swe-bench/lib/python3.9/subprocess.py", line 528, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'source /home/PJLAB/libowen/Documents/Projects/codellm/OD/SWE-bench/harness_materials/testbeds/Devin/scikit-learn__scikit-learn/0.20/tmpynho64be/miniconda3/bin/activate scikit-learn__scikit-learn__0.20 && echo 'activate successful' && python setup.py develop' returned non-zero exit status 1.

2024-04-01 20:07:26,441 - ERROR - [scikit-learn__scikit-learn__0.20] [scikit-learn__scikit-learn-10297] Installation failed

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