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Cannot complie current specutils master in new conda environment #464

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hamogu opened this issue Apr 25, 2019 · 4 comments
Closed

Cannot complie current specutils master in new conda environment #464

hamogu opened this issue Apr 25, 2019 · 4 comments

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@hamogu
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hamogu commented Apr 25, 2019

I'm failing to run the tests on a recent (yesterday) checkout of the specutils master. I'm installing python 3.7, astropy, and scipy through conda and then specutils with python setup.py. That stops for missing gwcs, so I pip install the last released gwcs version, but installing specutils fails with ValueError: Don't know how to write out ASDF version 1.3.0. Full output of the session is below:

[Hanss-MacBook-Air:~/code/specutils] hamogu% conda create -n specutils python scipy astropy ipython
Collecting package metadata: done
Solving environment: done

## Package Plan ##

  environment location: /Users/hamogu/anaconda/envs/specutils

  added / updated specs:
    - astropy
    - ipython
    - python
    - scipy


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    appnope-0.1.0              |           py37_0           8 KB
    backcall-0.1.0             |           py37_0          20 KB
    decorator-4.4.0            |           py37_1          18 KB
    ipython-7.4.0              |   py37h39e3cac_0         1.1 MB
    ipython_genutils-0.2.0     |           py37_0          39 KB
    jedi-0.13.3                |           py37_0         236 KB
    more-itertools-7.0.0       |           py37_0          93 KB
    numpy-1.16.3               |   py37hacdab7b_0          49 KB
    numpy-base-1.16.3          |   py37h6575580_0         4.2 MB
    pexpect-4.7.0              |           py37_0          82 KB
    pickleshare-0.7.5          |           py37_0          12 KB
    prompt_toolkit-2.0.9       |           py37_0         488 KB
    ptyprocess-0.6.0           |           py37_0          23 KB
    pygments-2.3.1             |           py37_0         1.3 MB
    pytest-4.4.1               |           py37_0         355 KB
    scipy-1.2.1                |   py37h1410ff5_0        15.6 MB
    traitlets-4.3.2            |           py37_0         133 KB
    wcwidth-0.1.7              |           py37_0          23 KB
    ------------------------------------------------------------
                                           Total:        23.8 MB

The following NEW packages will be INSTALLED:

  appnope            pkgs/main/osx-64::appnope-0.1.0-py37_0
  astropy            pkgs/main/osx-64::astropy-3.1.2-py37h1de35cc_0
  atomicwrites       pkgs/main/osx-64::atomicwrites-1.3.0-py37_1
  attrs              pkgs/main/osx-64::attrs-19.1.0-py37_1
  backcall           pkgs/main/osx-64::backcall-0.1.0-py37_0
  blas               pkgs/main/osx-64::blas-1.0-mkl
  ca-certificates    pkgs/main/osx-64::ca-certificates-2019.1.23-0
  certifi            pkgs/main/osx-64::certifi-2019.3.9-py37_0
  decorator          pkgs/main/osx-64::decorator-4.4.0-py37_1
  intel-openmp       pkgs/main/osx-64::intel-openmp-2019.3-199
  ipython            pkgs/main/osx-64::ipython-7.4.0-py37h39e3cac_0
  ipython_genutils   pkgs/main/osx-64::ipython_genutils-0.2.0-py37_0
  jedi               pkgs/main/osx-64::jedi-0.13.3-py37_0
  libcxx             pkgs/main/osx-64::libcxx-4.0.1-hcfea43d_1
  libcxxabi          pkgs/main/osx-64::libcxxabi-4.0.1-hcfea43d_1
  libedit            pkgs/main/osx-64::libedit-3.1.20181209-hb402a30_0
  libffi             pkgs/main/osx-64::libffi-3.2.1-h475c297_4
  libgfortran        pkgs/main/osx-64::libgfortran-3.0.1-h93005f0_2
  mkl                pkgs/main/osx-64::mkl-2019.3-199
  mkl_fft            pkgs/main/osx-64::mkl_fft-1.0.10-py37h5e564d8_0
  mkl_random         pkgs/main/osx-64::mkl_random-1.0.2-py37h27c97d8_0
  more-itertools     pkgs/main/osx-64::more-itertools-7.0.0-py37_0
  ncurses            pkgs/main/osx-64::ncurses-6.1-h0a44026_1
  numpy              pkgs/main/osx-64::numpy-1.16.3-py37hacdab7b_0
  numpy-base         pkgs/main/osx-64::numpy-base-1.16.3-py37h6575580_0
  openssl            pkgs/main/osx-64::openssl-1.1.1b-h1de35cc_1
  parso              pkgs/main/noarch::parso-0.4.0-py_0
  pexpect            pkgs/main/osx-64::pexpect-4.7.0-py37_0
  pickleshare        pkgs/main/osx-64::pickleshare-0.7.5-py37_0
  pip                pkgs/main/osx-64::pip-19.0.3-py37_0
  pluggy             pkgs/main/osx-64::pluggy-0.9.0-py37_0
  prompt_toolkit     pkgs/main/osx-64::prompt_toolkit-2.0.9-py37_0
  psutil             pkgs/main/osx-64::psutil-5.6.1-py37h1de35cc_0
  ptyprocess         pkgs/main/osx-64::ptyprocess-0.6.0-py37_0
  py                 pkgs/main/osx-64::py-1.8.0-py37_0
  pygments           pkgs/main/osx-64::pygments-2.3.1-py37_0
  pytest             pkgs/main/osx-64::pytest-4.4.1-py37_0
  pytest-arraydiff   pkgs/main/osx-64::pytest-arraydiff-0.3-py37h39e3cac_0
  pytest-astropy     pkgs/main/osx-64::pytest-astropy-0.5.0-py37_0
  pytest-doctestplus pkgs/main/osx-64::pytest-doctestplus-0.3.0-py37_0
  pytest-openfiles   pkgs/main/osx-64::pytest-openfiles-0.3.2-py37_0
  pytest-remotedata  pkgs/main/osx-64::pytest-remotedata-0.3.1-py37_0
  python             pkgs/main/osx-64::python-3.7.3-h359304d_0
  readline           pkgs/main/osx-64::readline-7.0-h1de35cc_5
  scipy              pkgs/main/osx-64::scipy-1.2.1-py37h1410ff5_0
  setuptools         pkgs/main/osx-64::setuptools-41.0.0-py37_0
  six                pkgs/main/osx-64::six-1.12.0-py37_0
  sqlite             pkgs/main/osx-64::sqlite-3.28.0-ha441bb4_0
  tk                 pkgs/main/osx-64::tk-8.6.8-ha441bb4_0
  traitlets          pkgs/main/osx-64::traitlets-4.3.2-py37_0
  wcwidth            pkgs/main/osx-64::wcwidth-0.1.7-py37_0
  wheel              pkgs/main/osx-64::wheel-0.33.1-py37_0
  xz                 pkgs/main/osx-64::xz-5.2.4-h1de35cc_4
  zlib               pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3


Proceed ([y]/n)? 


Downloading and Extracting Packages
scipy-1.2.1          | 15.6 MB   | ########################################################################################################### | 100% 
ipython-7.4.0        | 1.1 MB    | ########################################################################################################### | 100% 
decorator-4.4.0      | 18 KB     | ########################################################################################################### | 100% 
wcwidth-0.1.7        | 23 KB     | ########################################################################################################### | 100% 
pickleshare-0.7.5    | 12 KB     | ########################################################################################################### | 100% 
pexpect-4.7.0        | 82 KB     | ########################################################################################################### | 100% 
jedi-0.13.3          | 236 KB    | ########################################################################################################### | 100% 
pygments-2.3.1       | 1.3 MB    | ########################################################################################################### | 100% 
numpy-1.16.3         | 49 KB     | ########################################################################################################### | 100% 
ptyprocess-0.6.0     | 23 KB     | ########################################################################################################### | 100% 
appnope-0.1.0        | 8 KB      | ########################################################################################################### | 100% 
more-itertools-7.0.0 | 93 KB     | ########################################################################################################### | 100% 
traitlets-4.3.2      | 133 KB    | ########################################################################################################### | 100% 
numpy-base-1.16.3    | 4.2 MB    | ########################################################################################################### | 100% 
backcall-0.1.0       | 20 KB     | ########################################################################################################### | 100% 
ipython_genutils-0.2 | 39 KB     | ########################################################################################################### | 100% 
pytest-4.4.1         | 355 KB    | ########################################################################################################### | 100% 
prompt_toolkit-2.0.9 | 488 KB    | ########################################################################################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use:
# > conda activate specutils
#
# To deactivate an active environment, use:
# > conda deactivate
#

[Hanss-MacBook-Air:~/code/specutils] hamogu% conda_activate specutils
basename: illegal option -- t
usage: basename string [suffix]
       basename [-a] [-s suffix] string [...]
Your Python environment has been changed to the 'specutils' conda environment. Here's the active version of Python:
/Users/hamogu/anaconda/envs/specutils/bin/python
Python 3.7.3
To switch back to your default Python environment, type 'source deactivate.csh'
(specutils)~/code/specutils% python setup.py test
running test
Searching for gwcs
Reading https://pypi.org/simple/gwcs/
Downloading https://files.pythonhosted.org/packages/15/16/022cd5349f5f0987b5b62bd031b7b1b59559fcee20e79631841d4f1c7f3c/gwcs-0.10.0.tar.gz#sha256=976bfbe52c1eb895f48d4c2beeee196a216edb34bd0a9da480caee7dff591ed3
Best match: gwcs 0.10.0
Processing gwcs-0.10.0.tar.gz
Writing /var/folders/ml/hv25mzgx3k3bqzr21krjs5bw0000gn/T/easy_install-bey7wauy/gwcs-0.10.0/setup.cfg
Running gwcs-0.10.0/setup.py -q bdist_egg --dist-dir /var/folders/ml/hv25mzgx3k3bqzr21krjs5bw0000gn/T/easy_install-bey7wauy/gwcs-0.10.0/egg-dist-tmp-giiduj2n
creating /Users/hamogu/code/specutils/.eggs/gwcs-0.10.0-py3.7.egg
Extracting gwcs-0.10.0-py3.7.egg to /Users/hamogu/code/specutils/.eggs

Installed /Users/hamogu/code/specutils/.eggs/gwcs-0.10.0-py3.7.egg
Searching for asdf
Reading https://pypi.org/simple/asdf/
Downloading https://files.pythonhosted.org/packages/fb/20/f2277af8f18587fa5b5d1319765d9fe5c67e778c29e206478ce68c4bc1d0/asdf-2.3.3.tar.gz#sha256=d02e936a83abd206e7bc65050d94e8848da648344dbec9e49dddc2bdc3bd6870
Best match: asdf 2.3.3
Processing asdf-2.3.3.tar.gz
Writing /var/folders/ml/hv25mzgx3k3bqzr21krjs5bw0000gn/T/easy_install-vkpuj9ha/asdf-2.3.3/setup.cfg
Running asdf-2.3.3/setup.py -q bdist_egg --dist-dir /var/folders/ml/hv25mzgx3k3bqzr21krjs5bw0000gn/T/easy_install-vkpuj9ha/asdf-2.3.3/egg-dist-tmp-f3onhghb
package init file 'asdf-standard/schemas/__init__.py' not found (or not a regular file)
package init file 'asdf-standard/reference_files/__init__.py' not found (or not a regular file)
creating /Users/hamogu/code/specutils/.eggs/asdf-2.3.3-py3.7.egg
Extracting asdf-2.3.3-py3.7.egg to /Users/hamogu/code/specutils/.eggs

Installed /Users/hamogu/code/specutils/.eggs/asdf-2.3.3-py3.7.egg
Searching for jsonschema<=2.6,>=2.3
Reading https://pypi.org/simple/jsonschema/
Downloading https://files.pythonhosted.org/packages/77/de/47e35a97b2b05c2fadbec67d44cfcdcd09b8086951b331d82de90d2912da/jsonschema-2.6.0-py2.py3-none-any.whl#sha256=000e68abd33c972a5248544925a0cae7d1125f9bf6c58280d37546b946769a08
Best match: jsonschema 2.6.0
Processing jsonschema-2.6.0-py2.py3-none-any.whl
Installing jsonschema-2.6.0-py2.py3-none-any.whl to /Users/hamogu/code/specutils/.eggs
writing requirements to /Users/hamogu/code/specutils/.eggs/jsonschema-2.6.0-py3.7.egg/EGG-INFO/requires.txt

Installed /Users/hamogu/code/specutils/.eggs/jsonschema-2.6.0-py3.7.egg
Searching for pyyaml>=3.10
Reading https://pypi.org/simple/pyyaml/
Downloading https://files.pythonhosted.org/packages/9f/2c/9417b5c774792634834e730932745bc09a7d36754ca00acf1ccd1ac2594d/PyYAML-5.1.tar.gz#sha256=436bc774ecf7c103814098159fbb84c2715d25980175292c648f2da143909f95
Best match: PyYAML 5.1
Processing PyYAML-5.1.tar.gz
Writing /var/folders/ml/hv25mzgx3k3bqzr21krjs5bw0000gn/T/easy_install-3nmk0j36/PyYAML-5.1/setup.cfg
Running PyYAML-5.1/setup.py -q bdist_egg --dist-dir /var/folders/ml/hv25mzgx3k3bqzr21krjs5bw0000gn/T/easy_install-3nmk0j36/PyYAML-5.1/egg-dist-tmp-ih3xzvjv
In file included from ext/_yaml.c:591:
ext/_yaml.h:2:10: fatal error: 'yaml.h' file not found
#include <yaml.h>
         ^~~~~~~~
1 error generated.
Error compiling module, falling back to pure Python
zip_safe flag not set; analyzing archive contents...
Copying PyYAML-5.1-py3.7-macosx-10.7-x86_64.egg to /Users/hamogu/code/specutils/.eggs

Installed /Users/hamogu/code/specutils/.eggs/PyYAML-5.1-py3.7-macosx-10.7-x86_64.egg
Searching for semantic_version>=2.3.1
Reading https://pypi.org/simple/semantic_version/
Downloading https://files.pythonhosted.org/packages/28/be/3a7241d731ba89063780279a5433f5971c1cf41735b64a9f874b7c3ff995/semantic_version-2.6.0-py3-none-any.whl#sha256=2d06ab7372034bcb8b54f2205370f4aa0643c133b7e6dbd129c5200b83ab394b
Best match: semantic-version 2.6.0
Processing semantic_version-2.6.0-py3-none-any.whl
Installing semantic_version-2.6.0-py3-none-any.whl to /Users/hamogu/code/specutils/.eggs

Installed /Users/hamogu/code/specutils/.eggs/semantic_version-2.6.0-py3.7.egg
installing to temporary directory: /private/var/folders/ml/hv25mzgx3k3bqzr21krjs5bw0000gn/T/specutils-test-1xnffycc
warning: no files found matching 'ez_setup.py'
warning: no files found matching '*.pyx' under directory 'specutils'
warning: no files found matching '*.pxd' under directory 'specutils'
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'
warning: no files found matching 'astropy_helpers/ez_setup.py'
warning: no files found matching '*.pyx' under directory 'astropy_helpers/astropy_helpers'
warning: no files found matching '*.h' under directory 'astropy_helpers/astropy_helpers'
no previously-included directories found matching 'astropy_helpers/build'
warning: no previously-included files matching '*.o' found anywhere in distribution
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/private/var/folders/ml/hv25mzgx3k3bqzr21krjs5bw0000gn/T/specutils-test-1xnffycc/lib/python3.7/site-packages/specutils/__init__.py", line 29, in <module>
    from .spectra import *
  File "/private/var/folders/ml/hv25mzgx3k3bqzr21krjs5bw0000gn/T/specutils-test-1xnffycc/lib/python3.7/site-packages/specutils/spectra/__init__.py", line 5, in <module>
    from .spectrum1d import *  # noqa
  File "/private/var/folders/ml/hv25mzgx3k3bqzr21krjs5bw0000gn/T/specutils-test-1xnffycc/lib/python3.7/site-packages/specutils/spectra/spectrum1d.py", line 8, in <module>
    from ..wcs import WCSWrapper, WCSAdapter
  File "/private/var/folders/ml/hv25mzgx3k3bqzr21krjs5bw0000gn/T/specutils-test-1xnffycc/lib/python3.7/site-packages/specutils/wcs/__init__.py", line 1, in <module>
    from .wcs_wrapper import WCSWrapper
  File "/private/var/folders/ml/hv25mzgx3k3bqzr21krjs5bw0000gn/T/specutils-test-1xnffycc/lib/python3.7/site-packages/specutils/wcs/wcs_wrapper.py", line 1, in <module>
    import gwcs
ModuleNotFoundError: No module named 'gwcs'
(specutils)~/code/specutils% pip install gwcs
Collecting gwcs
  Using cached https://files.pythonhosted.org/packages/15/16/022cd5349f5f0987b5b62bd031b7b1b59559fcee20e79631841d4f1c7f3c/gwcs-0.10.0.tar.gz
Requirement already satisfied: astropy in /Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages (from gwcs) (3.1.2)
Collecting asdf (from gwcs)
  Using cached https://files.pythonhosted.org/packages/fb/20/f2277af8f18587fa5b5d1319765d9fe5c67e778c29e206478ce68c4bc1d0/asdf-2.3.3.tar.gz
Requirement already satisfied: numpy>=1.13.0 in /Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages (from astropy->gwcs) (1.16.3)
Collecting semantic_version>=2.3.1 (from asdf->gwcs)
  Using cached https://files.pythonhosted.org/packages/28/be/3a7241d731ba89063780279a5433f5971c1cf41735b64a9f874b7c3ff995/semantic_version-2.6.0-py3-none-any.whl
Collecting pyyaml>=3.10 (from asdf->gwcs)
  Using cached https://files.pythonhosted.org/packages/9f/2c/9417b5c774792634834e730932745bc09a7d36754ca00acf1ccd1ac2594d/PyYAML-5.1.tar.gz
Collecting jsonschema<=2.6,>=2.3 (from asdf->gwcs)
  Downloading https://files.pythonhosted.org/packages/77/de/47e35a97b2b05c2fadbec67d44cfcdcd09b8086951b331d82de90d2912da/jsonschema-2.6.0-py2.py3-none-any.whl
Requirement already satisfied: six>=1.9.0 in /Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages (from asdf->gwcs) (1.12.0)
Building wheels for collected packages: gwcs, asdf, pyyaml
  Building wheel for gwcs (setup.py) ... done
  Stored in directory: /Users/hamogu/Library/Caches/pip/wheels/70/c3/6f/f976c7390a4f73d34830cd0bd41d707e4118da6664aaef6a61
  Building wheel for asdf (setup.py) ... done
  Stored in directory: /Users/hamogu/Library/Caches/pip/wheels/1d/20/c6/2823bd2cdbf8b4e53bc583e5d3bd1dc316dc2a09c3d5625bda
  Building wheel for pyyaml (setup.py) ... done
  Stored in directory: /Users/hamogu/Library/Caches/pip/wheels/ad/56/bc/1522f864feb2a358ea6f1a92b4798d69ac783a28e80567a18b
Successfully built gwcs asdf pyyaml
Installing collected packages: semantic-version, pyyaml, jsonschema, asdf, gwcs
Successfully installed asdf-2.3.3 gwcs-0.10.0 jsonschema-2.6.0 pyyaml-5.1 semantic-version-2.6.0
(specutils)~/code/specutils% python setup.py test
running test
installing to temporary directory: /private/var/folders/ml/hv25mzgx3k3bqzr21krjs5bw0000gn/T/specutils-test-zfzkg7nr
warning: no files found matching 'ez_setup.py'
warning: no files found matching '*.pyx' under directory 'specutils'
warning: no files found matching '*.pxd' under directory 'specutils'
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'
warning: no files found matching 'astropy_helpers/ez_setup.py'
warning: no files found matching '*.pyx' under directory 'astropy_helpers/astropy_helpers'
warning: no files found matching '*.h' under directory 'astropy_helpers/astropy_helpers'
no previously-included directories found matching 'astropy_helpers/build'
warning: no previously-included files matching '*.o' found anywhere in distribution
Traceback (most recent call last):
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/_pytest/config/__init__.py", line 435, in _importconftest
    return self._conftestpath2mod[conftestpath]
KeyError: local('/private/var/folders/ml/hv25mzgx3k3bqzr21krjs5bw0000gn/T/specutils-test-zfzkg7nr/lib/python3.7/site-packages/specutils/conftest.py')

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File ".eggs/asdf-2.3.3-py3.7.egg/asdf/versioning.py", line 52, in get_version_map
    with generic_io.get_file(version_map_path, 'r') as fd:
  File ".eggs/asdf-2.3.3-py3.7.egg/asdf/generic_io.py", line 1198, in get_file
    fd = open(realpath, realmode)
FileNotFoundError: [Errno 2] No such file or directory: '/.eggs/asdf-2.3.3-py3.7.egg/asdf/schemas/stsci.edu/asdf/version_map-1.3.0.yaml'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File ".eggs/asdf-2.3.3-py3.7.egg/asdf/type_index.py", line 57, in __init__
    version_map = get_version_map(self._version)
  File ".eggs/asdf-2.3.3-py3.7.egg/asdf/versioning.py", line 57, in get_version_map
    "Could not load version map for version {0}".format(version))
ValueError: Could not load version map for version 1.3.0

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/astropy/utils/decorators.py", line 860, in test
    func = make_function_with_signature(func, name=name, **wrapped_args)
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/astropy/tests/runner.py", line 260, in test
    return runner.run_tests(**kwargs)
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/astropy/tests/runner.py", line 605, in run_tests
    return super().run_tests(**kwargs)
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/astropy/tests/runner.py", line 242, in run_tests
    return pytest.main(args=args, plugins=plugins)
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/_pytest/config/__init__.py", line 60, in main
    config = _prepareconfig(args, plugins)
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/_pytest/config/__init__.py", line 201, in _prepareconfig
    pluginmanager=pluginmanager, args=args
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/pluggy/hooks.py", line 289, in __call__
    return self._hookexec(self, self.get_hookimpls(), kwargs)
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/pluggy/manager.py", line 68, in _hookexec
    return self._inner_hookexec(hook, methods, kwargs)
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/pluggy/manager.py", line 62, in <lambda>
    firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/pluggy/callers.py", line 203, in _multicall
    gen.send(outcome)
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/_pytest/helpconfig.py", line 93, in pytest_cmdline_parse
    config = outcome.get_result()
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/pluggy/callers.py", line 80, in get_result
    raise ex[1].with_traceback(ex[2])
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/pluggy/callers.py", line 187, in _multicall
    res = hook_impl.function(*args)
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/_pytest/config/__init__.py", line 679, in pytest_cmdline_parse
    self.parse(args)
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/_pytest/config/__init__.py", line 896, in parse
    self._preparse(args, addopts=addopts)
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/_pytest/config/__init__.py", line 851, in _preparse
    early_config=self, args=args, parser=self._parser
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/pluggy/hooks.py", line 289, in __call__
    return self._hookexec(self, self.get_hookimpls(), kwargs)
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/pluggy/manager.py", line 68, in _hookexec
    return self._inner_hookexec(hook, methods, kwargs)
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/pluggy/manager.py", line 62, in <lambda>
    firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/pluggy/callers.py", line 208, in _multicall
    return outcome.get_result()
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/pluggy/callers.py", line 80, in get_result
    raise ex[1].with_traceback(ex[2])
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/pluggy/callers.py", line 187, in _multicall
    res = hook_impl.function(*args)
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/_pytest/config/__init__.py", line 742, in pytest_load_initial_conftests
    self.pluginmanager._set_initial_conftests(early_config.known_args_namespace)
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/_pytest/config/__init__.py", line 378, in _set_initial_conftests
    self._try_load_conftest(anchor)
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/_pytest/config/__init__.py", line 384, in _try_load_conftest
    self._getconftestmodules(anchor)
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/_pytest/config/__init__.py", line 419, in _getconftestmodules
    mod = self._importconftest(conftestpath.realpath())
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/_pytest/config/__init__.py", line 469, in _importconftest
    self.consider_conftest(mod)
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/_pytest/config/__init__.py", line 519, in consider_conftest
    self.register(conftestmodule, name=conftestmodule.__file__)
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/_pytest/config/__init__.py", line 323, in register
    self.consider_module(plugin)
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/_pytest/config/__init__.py", line 525, in consider_module
    self._import_plugin_specs(getattr(mod, "pytest_plugins", []))
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/_pytest/config/__init__.py", line 530, in _import_plugin_specs
    self.import_plugin(import_spec)
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/_pytest/config/__init__.py", line 557, in import_plugin
    __import__(importspec)
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 668, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 638, in _load_backward_compatible
  File "/Users/hamogu/anaconda/envs/specutils/lib/python3.7/site-packages/_pytest/assertion/rewrite.py", line 299, in load_module
    six.exec_(co, mod.__dict__)
  File "/private/var/folders/ml/hv25mzgx3k3bqzr21krjs5bw0000gn/T/specutils-test-zfzkg7nr/lib/python3.7/site-packages/.eggs/asdf-2.3.3-py3.7.egg/asdf/tests/schema_tester.py", line 23, in <module>
    _ctx = AsdfFile()
  File ".eggs/asdf-2.3.3-py3.7.egg/asdf/asdf.py", line 137, in __init__
    self.tree = {}
  File ".eggs/asdf-2.3.3-py3.7.egg/asdf/asdf.py", line 395, in tree
    self._validate(asdf_object, custom=bool(tree))
  File ".eggs/asdf-2.3.3-py3.7.egg/asdf/asdf.py", line 416, in _validate
    tree, self)
  File ".eggs/asdf-2.3.3-py3.7.egg/asdf/yamlutil.py", line 234, in custom_tree_to_tagged_tree
    return treeutil.walk_and_modify(tree, walker)
  File ".eggs/asdf-2.3.3-py3.7.egg/asdf/treeutil.py", line 206, in walk_and_modify
    return recurse(top)
  File ".eggs/asdf-2.3.3-py3.7.egg/asdf/treeutil.py", line 158, in recurse
    result = callback(result)
  File ".eggs/asdf-2.3.3-py3.7.egg/asdf/yamlutil.py", line 229, in walker
    tag = ctx.type_index.from_custom_type(type(node), ctx.version_string)
  File ".eggs/asdf-2.3.3-py3.7.egg/asdf/type_index.py", line 255, in from_custom_type
    write_type_index = _AsdfWriteTypeIndex(version, self)
  File ".eggs/asdf-2.3.3-py3.7.egg/asdf/type_index.py", line 63, in __init__
    self._version))
ValueError: Don't know how to write out ASDF version 1.3.0
@hamogu hamogu mentioned this issue Apr 25, 2019
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@nmearl
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nmearl commented Apr 25, 2019

Curious. Can you try the following commands instead in your specutils directory

$ pip install -e .
$ pytest specutils

@hamogu
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hamogu commented Apr 25, 2019

Will try tonight. (It's on my laptop and that's at home.)

@hamogu
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hamogu commented Apr 25, 2019

Curiously the same setup for a fresh conda environment that failed for my mac (see above) works on my CentOS machine.

@hamogu
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hamogu commented Apr 26, 2019

pip install -e . etc. works. Mmm. So, I remembered git clean and now python setup.py test also works. So, it must have been some old stuff that was sitting around in my tree. I've not seen it before that that made python setup.py install fail, in particular with such a seemingly unrelated error message, but there is no use in investigating this further; solved! Thanks for your advice @nmearl which brought me on the right track.

@hamogu hamogu closed this as completed Apr 26, 2019
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