Conda skeleton pypi fails with pmdarima -- AttributeError numpy disutils

Question

I'm trying to install pmdarima package in a conda env as it requires statsmodels <0.12 and I would also like to use statmodels latest release for this project. My understanding is limited, but I first tried

conda skeleton pypi pmdarima

This failed with the same AttributeError related to numpy disutils described below.

Similarly to the questioner in this question: Conda skeleton pypi: ModuleNotFoundError: No module named 'numpy' I was unable to get this to work either.

conda install -n _build numpy

I then tried the advice laid out in the above-linked SO question and ran:

conda skeleton pypi --extra-specs numpy pmdarima

This results in pretty long output but the key piece as far as I can tell is:

Applying patch: '/var/folders/7f/8d7rz34522gcq4z774n9v91r0000gn/T/tmp8tv1gdnxconda_skeleton_pmdarima-1.7.1.tar.gz/pypi-distutils.patch'
patching file core.py
Hunk #1 succeeded at 168 with fuzz 2 (offset 1 line).
Partial import of pmdarima during the build process.
Requirements: ['joblib>=0.11', 'Cython>=0.29,<0.29.18', 'numpy>=1.17.3', 'pandas>=0.19', 'scikit-learn>=0.22', 'scipy>=1.3.2', 'statsmodels>=0.11,<0.12', 'urllib3', 'setuptools<50.0.0']
Setting up with numpy.distutils.core
Traceback (most recent call last):
  File "setup.py", line 324, in <module>
    do_setup()
  File "setup.py", line 320, in do_setup
    setup(**metadata)
  File "/opt/anaconda3/conda-bld/skeleton_1599410605346/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.7/site-packages/numpy/distutils/core.py", line 130, in setup
    if dist.help or not _command_line_ok():
AttributeError: 'NoneType' object has no attribute 'help'
$PYTHONPATH = /var/folders/7f/8d7rz34522gcq4z774n9v91r0000gn/T/tmp8tv1gdnxconda_skeleton_pmdarima-1.7.1.tar.gz/pmdarima-1.7.1

Leaving build/test directories:
  Work:
 /opt/anaconda3/conda-bld/skeleton_1599410605346/work 
  Test:
 /opt/anaconda3/conda-bld/skeleton_1599410605346/test_tmp 
Leaving build/test environments:
  Test:
source activate  /opt/anaconda3/conda-bld/skeleton_1599410605346/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place 
  Build:
source activate  /opt/anaconda3/conda-bld/skeleton_1599410605346/_build_env 


Error: command failed: /opt/anaconda3/conda-bld/skeleton_1599410605346/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/bin/python setup.py install

Any ideas? Thank you so much in advance, very much appreciated!

score 1 · Answer 1 · answered Sep 07 '20 at 06:14

Not sure what the proper resolution is for the NumPy-based build, but the setup.py does check for an sdist argument, which branches to use setuptools for the build instead of numpy. Hence, the following seems to avoid the code causing the issue:

conda skeleton pypi --setup-options sdist pmdarima

I suspect the downside to this workaround is that there is no Cython compilation done, but not totally sure.

You may want to file an issue on the pmdarima GitHub to see if any of the devs have ideas. Otherwise, it might just be more efficient to pip install the package in the environment you want it (as long as that environment is not base).

To the extent you are interested there is an existing thread that I asked on, and thought I'd share the fairly detailed and useful response for future reference: https://github.com/alkaline-ml/pmdarima/issues/326 — jmillerbrooks, Sep 08 '20 at 01:50

score 0 · Answer 2 · answered Sep 07 '20 at 17:44

@merv thank you for your help! Interestingly, this works for the skeleton, but fails when running conda-build with the following (truncated until the errors) output:

0 location(s) to search for versions of sdist:
Given no hashes to check 0 links for project 'sdist': discarding no candidates
ERROR: Could not find a version that satisfies the requirement sdist (from versions: none)
ERROR: No matching distribution found for sdist
Exception information:
Traceback (most recent call last):
  File "$PREFIX/lib/python3.7/site-packages/pip/_internal/cli/base_command.py", line 216, in _main
    status = self.run(options, args)
  File "$PREFIX/lib/python3.7/site-packages/pip/_internal/cli/req_command.py", line 182, in wrapper
    return func(self, options, args)
  File "$PREFIX/lib/python3.7/site-packages/pip/_internal/commands/install.py", line 325, in run
    reqs, check_supported_wheels=not options.target_dir
  File "$PREFIX/lib/python3.7/site-packages/pip/_internal/resolution/legacy/resolver.py", line 183, in resolve
    discovered_reqs.extend(self._resolve_one(requirement_set, req))
  File "$PREFIX/lib/python3.7/site-packages/pip/_internal/resolution/legacy/resolver.py", line 388, in _resolve_one
    abstract_dist = self._get_abstract_dist_for(req_to_install)
  File "$PREFIX/lib/python3.7/site-packages/pip/_internal/resolution/legacy/resolver.py", line 339, in _get_abstract_dist_for
    self._populate_link(req)
  File "$PREFIX/lib/python3.7/site-packages/pip/_internal/resolution/legacy/resolver.py", line 305, in _populate_link
    req.link = self._find_requirement_link(req)
  File "$PREFIX/lib/python3.7/site-packages/pip/_internal/resolution/legacy/resolver.py", line 270, in _find_requirement_link
    best_candidate = self.finder.find_requirement(req, upgrade)
  File "$PREFIX/lib/python3.7/site-packages/pip/_internal/index/package_finder.py", line 928, in find_requirement
    req)
pip._internal.exceptions.DistributionNotFound: No matching distribution found for sdist
Removed build tracker: '/private/tmp/pip-req-tracker-umxriyi2'
Traceback (most recent call last):
  File "/opt/anaconda3/bin/conda-build", line 11, in <module>
    sys.exit(main())
  File "/opt/anaconda3/lib/python3.7/site-packages/conda_build/cli/main_build.py", line 474, in main
    execute(sys.argv[1:])
  File "/opt/anaconda3/lib/python3.7/site-packages/conda_build/cli/main_build.py", line 465, in execute
    verify=args.verify, variants=args.variants)
  File "/opt/anaconda3/lib/python3.7/site-packages/conda_build/api.py", line 210, in build
    notest=notest, variants=variants)
  File "/opt/anaconda3/lib/python3.7/site-packages/conda_build/build.py", line 3036, in build_tree
    notest=notest,
  File "/opt/anaconda3/lib/python3.7/site-packages/conda_build/build.py", line 2155, in build
    cwd=src_dir, stats=build_stats)
  File "/opt/anaconda3/lib/python3.7/site-packages/conda_build/utils.py", line 407, in check_call_env
    return _func_defaulting_env_to_os_environ('call', *popenargs, **kwargs)
  File "/opt/anaconda3/lib/python3.7/site-packages/conda_build/utils.py", line 387, in _func_defaulting_env_to_os_environ
    raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/anaconda3/conda-bld/pmdarima_1599500058832/work/conda_build.sh']' returned non-zero exit status 1.

I'll confess we're well above my head at this point, (do I need to edit the meta.yaml file somehow? Is that crazy?) but will try opening an issue as you suggested, once again really appreciate it.

Conda skeleton pypi fails with pmdarima -- AttributeError numpy disutils

2 Answers2