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radio-astro-tools / casa-formats-io

Code to handle I/O from/to data in CASA format
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Installation/import issue #23

Open keflavich opened 3 years ago

keflavich commented 3 years ago

Reported by @dmehring

https://github.com/radio-astro-tools/uvcombine/issues/24

astrofrog commented 2 years ago

See https://github.com/radio-astro-tools/uvcombine/issues/24#issuecomment-970846954 - I think somehow it is because casa-formats-io was not installed with pip and it is being imported from the source tree without the extension compiled.

jpinedaf commented 2 years ago

I cannot get spetral_cube to work because of this issue with casa-formats-io. I installed it using pip, 

pip install spectral-cube

but then I get the following error:

In [1]: from spectral_cube import SpectralCube as sc
---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
Input In [1], in <cell line: 1>()
----> 1 from spectral_cube import SpectralCube as sc

File ~/miniconda3/envs/py38/lib/python3.8/site-packages/spectral_cube/__init__.py:16, in <module>
     13 from .lower_dimensional_structures import (OneDSpectrum, Projection, Slice)
     15 # Import the following sub-packages to make sure the I/O functions are registered
---> 16 from .io import casa_image
     17 del casa_image
     18 from .io import class_lmv

File ~/miniconda3/envs/py38/lib/python3.8/site-packages/spectral_cube/io/casa_image.py:14, in <module>
     11 from .. utils import BeamWarning
     12 from .. import wcs_utils
---> 14 from casa_formats_io import getdesc, coordsys_to_astropy_wcs, image_to_dask
     16 # Read and write from a CASA image. This has a few
     17 # complications. First, by default CASA does not return the
     18 # "python order" and so we either have to transpose the cube on
   (...)
     22 # when writing but don't want them in memory. By default, try to
     23 # yield the same array in memory that we would get from astropy.
     26 def is_casa_image(origin, filepath, fileobj, *args, **kwargs):
     27 
     28     # See note before StringWrapper definition

File ~/code/python_code/casa-formats-io/casa_formats_io/__init__.py:9, in <module>
      1 # For convenience, we import the astropy Table class here which
      2 # allows one to do:
      3 #     >>> from casa_formats_io import Table
      4 # instead of:
      5 #     >>> import casa_formats_io
      6 #     >>> from astropy.table import Table
      7 from astropy.table import Table  # noqa
----> 9 from .casa_dask import *  # noqa
     10 from .casa_low_level_io import *  # noqa
     11 from .casa_wcs import *  # noqa

File ~/code/python_code/casa-formats-io/casa_formats_io/casa_dask.py:13, in <module>
     10 import dask.array
     12 from .casa_low_level_io.table import CASATable
---> 13 from ._casa_chunking import _combine_chunks
     15 __all__ = ['image_to_dask']
     18 def combine_chunks(array_1d, itemsize, shape, oversample):

ModuleNotFoundError: No module named 'casa_formats_io._casa_chunking'

This is in a fresh environment, with python 3.8 and ipython installed. I also tried installing casa-formats-io via

pip install casa-formats-io

but I get the same error.

Any suggestion of how to solve this? BTW, I also tried cloning the repo and installing using python setup.py develop without any difference.

astrofrog commented 2 years ago

@jpinedaf - it looks like it is trying to import from a local code path:

~/code/python_code/casa-formats-io/casa_formats_io

can you try using pip install and then importing casa_formats_io from an empty directory?

jpinedaf commented 2 years ago

@astrofrog you are right, that was messing it up... and now I remembered why, I am using python 3.9 and I cannot install 

(py3) bash-3.2$ python setup.py develop
/Users/jpineda/miniconda3/envs/py3/lib/python3.9/site-packages/setuptools/dist.py:738: UserWarning: Usage of dash-separated 'upload-dir' will not be supported in future versions. Please use the underscore name 'upload_dir' instead
  warnings.warn(
/Users/jpineda/miniconda3/envs/py3/lib/python3.9/site-packages/setuptools/dist.py:738: UserWarning: Usage of dash-separated 'show-response' will not be supported in future versions. Please use the underscore name 'show_response' instead
  warnings.warn(
/Users/jpineda/miniconda3/envs/py3/lib/python3.9/site-packages/setuptools/_distutils/dist.py:275: UserWarning: Unknown distribution option: 'use_scm_version'
  warnings.warn(msg)
running develop
/Users/jpineda/miniconda3/envs/py3/lib/python3.9/site-packages/setuptools/command/easy_install.py:160: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
/Users/jpineda/miniconda3/envs/py3/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
running egg_info
writing spectral_cube.egg-info/PKG-INFO
writing dependency_links to spectral_cube.egg-info/dependency_links.txt
writing requirements to spectral_cube.egg-info/requires.txt
writing top-level names to spectral_cube.egg-info/top_level.txt
reading manifest file 'spectral_cube.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'README.md'
warning: no files found matching '*.c' under directory '*.pyx'
warning: no files found matching '*.pxd' under directory '*.pyx'
warning: no files found matching '*' under directory 'licenses'
warning: no files found matching '*' under directory 'cextern'
warning: no files found matching '*' under directory 'scripts'
no previously-included directories found matching 'build'
no previously-included directories found matching 'docs/_build'
no previously-included directories found matching 'docs/api'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.o' found anywhere in distribution
adding license file 'LICENSE.rst'
writing manifest file 'spectral_cube.egg-info/SOURCES.txt'
running build_ext
Creating /Users/jpineda/miniconda3/envs/py3/lib/python3.9/site-packages/spectral-cube.egg-link (link to .)
spectral-cube 0.0.0 is already the active version in easy-install.pth

Installed /Users/jpineda/code/python_code/spectral-cube
Processing dependencies for spectral-cube==0.0.0
Searching for casa-formats-io
Reading https://pypi.org/simple/casa-formats-io/
/Users/jpineda/miniconda3/envs/py3/lib/python3.9/site-packages/pkg_resources/__init__.py:122: PkgResourcesDeprecationWarning: formats-io-0.1 is an invalid version and will not be supported in a future release
  warnings.warn(
/Users/jpineda/miniconda3/envs/py3/lib/python3.9/site-packages/pkg_resources/__init__.py:122: PkgResourcesDeprecationWarning: io-0.1 is an invalid version and will not be supported in a future release
  warnings.warn(
/Users/jpineda/miniconda3/envs/py3/lib/python3.9/site-packages/pkg_resources/__init__.py:122: PkgResourcesDeprecationWarning:  is an invalid version and will not be supported in a future release
  warnings.warn(
Downloading https://files.pythonhosted.org/packages/4f/9b/6411821cad6c502403c2447c14a55a92d8c2517c7161d9cf85f49604dd1f/casa-formats-io-0.1.tar.gz#sha256=3ad18e72fb732137b0fb49ef4d5c3468773a4c990bba4e63eedd355e8cbc3e9b
Best match: casa-formats-io 0.1
Processing casa-formats-io-0.1.tar.gz
Writing /var/folders/2n/6gk_yf0d1zvdwj6wy12h_klr0000gn/T/easy_install-fgemcgoq/casa-formats-io-0.1/setup.cfg
Running casa-formats-io-0.1/setup.py -q bdist_egg --dist-dir /var/folders/2n/6gk_yf0d1zvdwj6wy12h_klr0000gn/T/easy_install-fgemcgoq/casa-formats-io-0.1/egg-dist-tmp-r9nkg621
/Users/jpineda/miniconda3/envs/py3/lib/python3.9/site-packages/setuptools/_distutils/dist.py:275: UserWarning: Unknown distribution option: 'use_scm_version'
  warnings.warn(msg)
warning: no files found matching 'README.md'
warning: no files found matching 'LICENSE.rst'
warning: no files found matching '*.c' under directory '*.pyx'
warning: no files found matching '*.pxd' under directory '*.pyx'
warning: no files found matching '*' under directory 'licenses'
warning: no files found matching '*' under directory 'cextern'
warning: no files found matching '*' under directory 'scripts'
no previously-included directories found matching 'build'
no previously-included directories found matching 'docs/_build'
no previously-included directories found matching 'docs/api'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.o' found anywhere in distribution
/Users/jpineda/miniconda3/envs/py3/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
In file included from casa_formats_io/_casa_chunking.c:3:
In file included from /Users/jpineda/miniconda3/envs/py3/include/python3.9/Python.h:91:
/Users/jpineda/miniconda3/envs/py3/include/python3.9/bytearrayobject.h:9:10: fatal error: 'stdarg.h' file not found
#include <stdarg.h>
         ^~~~~~~~~~
1 error generated.
error: Setup script exited with error: command '/Users/jpineda/miniconda3/envs/py3/bin/x86_64-apple-darwin13.4.0-clang' failed with exit code 1
(py3) bash-3.2$

It installs very well in python 3.8, but with 3.9 I got this problem.

Any idea?

astrofrog commented 2 years ago

@jpinedaf - sorry for the delay, could you send me the output of conda list for the environment in which this fails?

astrofrog commented 2 years ago

I wonder if we should add a CI job with the conda compilers as it might be related to that.

astrofrog commented 2 years ago

@jpinedaf - could you try and pip install casa-formats-io as we have now published new wheels?