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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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broken installation with astropy v5 #43

Closed jpinedaf closed 2 years ago

jpinedaf commented 2 years ago

I am trying to install it, but there seems to be an important issue with the newer astropy.

I cloned the casa-formats-io repo, and tried to install it with both pip and python setup.py and got a similar error message. See below.

python setup.py develop did not run successfully.
â exit code: 1
â°â> [36 lines of output]
    running develop
    /private/var/folders/2n/6gk_yf0d1zvdwj6wy12h_klr0000gn/T/pip-build-env-pidylk7f/overlay/lib/python3.9/site-packages/setuptools/command/easy_install.py:144: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
      warnings.warn(
    /private/var/folders/2n/6gk_yf0d1zvdwj6wy12h_klr0000gn/T/pip-build-env-pidylk7f/overlay/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 casa_formats_io.egg-info/PKG-INFO
    writing dependency_links to casa_formats_io.egg-info/dependency_links.txt
    writing entry points to casa_formats_io.egg-info/entry_points.txt
    writing requirements to casa_formats_io.egg-info/requires.txt
    writing top-level names to casa_formats_io.egg-info/top_level.txt
    reading manifest template 'MANIFEST.in'
    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
    adding license file 'LICENSE'
    writing manifest file 'casa_formats_io.egg-info/SOURCES.txt'
    running build_ext
    building 'casa_formats_io._casa_chunking' extension
    x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/jpineda/miniconda3/envs/py3/include -fPIC -O2 -isystem /Users/jpineda/miniconda3/envs/py3/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/jpineda/miniconda3/envs/py3/include -D_FORTIFY_SOURCE=2 -isystem /Users/jpineda/miniconda3/envs/py3/include -I/private/var/folders/2n/6gk_yf0d1zvdwj6wy12h_klr0000gn/T/pip-build-env-pidylk7f/overlay/lib/python3.9/site-packages/numpy/core/include -I/Users/jpineda/miniconda3/envs/py3/include/python3.9 -c casa_formats_io/_casa_chunking.c -o build/temp.macosx-10.9-x86_64-cpython-39/casa_formats_io/_casa_chunking.o
    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: command '/Users/jpineda/miniconda3/envs/py3/bin/x86_64-apple-darwin13.4.0-clang' failed with exit code 1
    [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.

I am using python 3.9.10 and astropy 5.0.2. This is the version of GCC installed

(py3) bash-3.2$ gcc -v
Apple clang version 13.1.6 (clang-1316.0.21.2.3)

and the main python environment is managed with conda. What else would you like me to check? Because this is breaking both SpectralCube and Turbustat for me. :-(

@keflavich @e-koch

e-koch commented 2 years ago

Fix here for building py39, py310 wheels: https://github.com/radio-astro-tools/casa-formats-io/pull/44