FileNotFoundError METADATA

[nprime496]

Hey, I get this weird error each time the first time I try to use bio_embeddings package, then it disappears the next times.

[nprime496]

Complete stacktrace

AttributeError                            Traceback (most recent call last)
/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py in _dep_map(self)
   3015         try:
-> 3016             return self.__dep_map
   3017         except AttributeError:

19 frames
/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py in __getattr__(self, attr)
   2812         if attr.startswith('_'):
-> 2813             raise AttributeError(attr)
   2814         return getattr(self._provider, attr)

AttributeError: _DistInfoDistribution__dep_map

During handling of the above exception, another exception occurred:

AttributeError                            Traceback (most recent call last)
/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py in _parsed_pkg_info(self)
   3006         try:
-> 3007             return self._pkg_info
   3008         except AttributeError:

/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py in __getattr__(self, attr)
   2812         if attr.startswith('_'):
-> 2813             raise AttributeError(attr)
   2814         return getattr(self._provider, attr)

AttributeError: _pkg_info

During handling of the above exception, another exception occurred:

FileNotFoundError                         Traceback (most recent call last)
<ipython-input-36-284220267b6b> in <module>()
----> 1 import bio_embeddings
      2 bio_embeddings.__version__

/usr/local/lib/python3.7/dist-packages/bio_embeddings/__init__.py in <module>()
     12 import bio_embeddings.embed
     13 import bio_embeddings.extract
---> 14 import bio_embeddings.project
     15 import bio_embeddings.utilities
     16 import bio_embeddings.visualize

/usr/local/lib/python3.7/dist-packages/bio_embeddings/project/__init__.py in <module>()
      3 from bio_embeddings.project.pb_tucker import PBTucker, PBTuckerModel
      4 from bio_embeddings.project.tsne import tsne_reduce
----> 5 from bio_embeddings.project.umap import umap_reduce
      6 
      7 __all__ = [

/usr/local/lib/python3.7/dist-packages/bio_embeddings/project/umap.py in <module>()
----> 1 from umap import UMAP
      2 
      3 
      4 def umap_reduce(embeddings, **kwargs):
      5     """Wrapper around :meth:`umap.UMAP` with defaults for bio_embeddings"""

/usr/local/lib/python3.7/dist-packages/umap/__init__.py in <module>()
      1 from warnings import warn, catch_warnings, simplefilter
----> 2 from .umap_ import UMAP
      3 
      4 try:
      5     with catch_warnings():

/usr/local/lib/python3.7/dist-packages/umap/umap_.py in <module>()
     45 )
     46 
---> 47 from pynndescent import NNDescent
     48 from pynndescent.distances import named_distances as pynn_named_distances
     49 from pynndescent.sparse import sparse_named_distances as pynn_sparse_named_distances

/usr/local/lib/python3.7/dist-packages/pynndescent/__init__.py in <module>()
     13         numba.config.THREADING_LAYER = "workqueue"
     14 
---> 15 __version__ = pkg_resources.get_distribution("pynndescent").version

/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py in get_distribution(dist)
    464         dist = Requirement.parse(dist)
    465     if isinstance(dist, Requirement):
--> 466         dist = get_provider(dist)
    467     if not isinstance(dist, Distribution):
    468         raise TypeError("Expected string, Requirement, or Distribution", dist)

/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py in get_provider(moduleOrReq)
    340     """Return an IResourceProvider for the named module or requirement"""
    341     if isinstance(moduleOrReq, Requirement):
--> 342         return working_set.find(moduleOrReq) or require(str(moduleOrReq))[0]
    343     try:
    344         module = sys.modules[moduleOrReq]

/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py in require(self, *requirements)
    884         included, even if they were already activated in this working set.
    885         """
--> 886         needed = self.resolve(parse_requirements(requirements))
    887 
    888         for dist in needed:

/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py in resolve(self, requirements, env, installer, replace_conflicting, extras)
    778 
    779             # push the new requirements onto the stack
--> 780             new_requirements = dist.requires(req.extras)[::-1]
    781             requirements.extend(new_requirements)
    782 

/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py in requires(self, extras)
   2732     def requires(self, extras=()):
   2733         """List of Requirements needed for this distro if `extras` are used"""
-> 2734         dm = self._dep_map
   2735         deps = []
   2736         deps.extend(dm.get(None, ()))

/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py in _dep_map(self)
   3016             return self.__dep_map
   3017         except AttributeError:
-> 3018             self.__dep_map = self._compute_dependencies()
   3019             return self.__dep_map
   3020 

/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py in _compute_dependencies(self)
   3025         reqs = []
   3026         # Including any condition expressions
-> 3027         for req in self._parsed_pkg_info.get_all('Requires-Dist') or []:
   3028             reqs.extend(parse_requirements(req))
   3029 

/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py in _parsed_pkg_info(self)
   3007             return self._pkg_info
   3008         except AttributeError:
-> 3009             metadata = self.get_metadata(self.PKG_INFO)
   3010             self._pkg_info = email.parser.Parser().parsestr(metadata)
   3011             return self._pkg_info

/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py in get_metadata(self, name)
   1405             return ""
   1406         path = self._get_metadata_path(name)
-> 1407         value = self._get(path)
   1408         try:
   1409             return value.decode('utf-8')
/usr/local/lib/python3.7/dist-packages/pkg_resources/__init__.py in _get(self, path)
   1609 
   1610     def _get(self, path):
-> 1611         with open(path, 'rb') as stream:
   1612             return stream.read()
   1613 

FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/lib/python3.7/dist-packages/scikit_learn-0.22.2.post1.dist-info/METADATA'

[sacdallago]

Yeah, I guess this happens on Colab? I don't know, Colab remains a mistery to me, it does weird things. I happen to get some "errors" on there, too, and upon re-executing the same cell: error's gone. REALLY difficult to debug :(

[konstin]

This is essentially the same as #123, but with another package. I've filed lmcinnes/pynndescent#137 to fix this upstream. If required I can also add some hacky solution to work around this before we get the upstream fix.