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Attempt to import numpy.ma.rank failing with numpy 1.18.1 #384

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xylar opened this issue Feb 3, 2020 · 6 comments · Fixed by #386
Closed

Attempt to import numpy.ma.rank failing with numpy 1.18.1 #384

xylar opened this issue Feb 3, 2020 · 6 comments · Fixed by #386
Labels
pending-release Fix is included in a pending release of CDAT metapackage.
Milestone
8.2.1

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@xylar
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xylar commented Feb 3, 2020

Describe the bug
With the latest cdms2 from conda-forge, I'm getting an import error related to numpy.ma.rank, which appears not to exist.

To Reproduce
Steps to reproduce the behavior:

conda create -y -n test -c conda-forge cdms2=3.1.4
conda activate test
python -c "import cdms2.tvariable"

The result is:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/xylar/miniconda3/envs/test/lib/python3.7/site-packages/cdms2/__init__.py", line 8, in <module>
    from . import dataset
  File "/home/xylar/miniconda3/envs/test/lib/python3.7/site-packages/cdms2/dataset.py", line 24, in <module>
    from .coord import FileAxis2D, DatasetAxis2D
  File "/home/xylar/miniconda3/envs/test/lib/python3.7/site-packages/cdms2/coord.py", line 17, in <module>
    from .fvariable import FileVariable
  File "/home/xylar/miniconda3/envs/test/lib/python3.7/site-packages/cdms2/fvariable.py", line 7, in <module>
    from .variable import DatasetVariable
  File "/home/xylar/miniconda3/envs/test/lib/python3.7/site-packages/cdms2/variable.py", line 17, in <module>
    from .avariable import AbstractVariable
  File "/home/xylar/miniconda3/envs/test/lib/python3.7/site-packages/cdms2/avariable.py", line 1933, in <module>
    from . import MV2 as MV  # noqa
  File "/home/xylar/miniconda3/envs/test/lib/python3.7/site-packages/cdms2/MV2.py", line 12, in <module>
    from numpy.ma import indices, innerproduct, masked, put, putmask, rank, ravel  # noqa
ImportError: cannot import name 'rank' from 'numpy.ma' (/home/xylar/miniconda3/envs/test/lib/python3.7/site-packages/numpy/ma/__init__.py)

Expected behavior
Import should succeed.

Desktop (please complete the following information):

  • OS: linux

Environment Information

`conda info`

     active environment : test
    active env location : /home/xylar/miniconda3/envs/test
            shell level : 2
       user config file : /home/xylar/.condarc
 populated config files : /home/xylar/.condarc
          conda version : 4.8.2
    conda-build version : 3.18.11
         python version : 3.7.3.final.0
       virtual packages : __glibc=2.23
       base environment : /home/xylar/miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/xylar/miniconda3/pkgs
                          /home/xylar/.conda/pkgs
       envs directories : /home/xylar/miniconda3/envs
                          /home/xylar/.conda/envs
               platform : linux-64
             user-agent : conda/4.8.2 requests/2.22.0 CPython/3.7.3 Linux/4.4.0-171-generic ubuntu/16.04.6 glibc/2.23
                UID:GID : 1001:1001
             netrc file : None
           offline mode : False

`conda config --show-sources`

==> /home/xylar/.condarc <==
channel_priority: strict
channels:
  - conda-forge
  - defaults

`conda list --show-channel-urls`

# packages in environment at /home/xylar/miniconda3/envs/test:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       0_gnu    conda-forge
attrs                     19.3.0                     py_0    conda-forge
bzip2                     1.0.8                h516909a_2    conda-forge
ca-certificates           2019.11.28           hecc5488_0    conda-forge
cdat_info                 8.2                        py_7    conda-forge
cdms2                     3.1.4                    pypi_0    pypi
cdtime                    3.1.3            py38h1ac8016_0    conda-forge
certifi                   2019.11.28               py38_0    conda-forge
cffi                      1.13.2           py38h8022711_0    conda-forge
chardet                   3.0.4                 py38_1003    conda-forge
cryptography              2.8              py38h72c5cf5_1    conda-forge
curl                      7.65.3               hf8cf82a_0    conda-forge
decorator                 4.4.1                      py_0    conda-forge
distarray                 2.12.2                     py_1    conda-forge
esmf                      8.0.0           nompi_he6d0a24_4    conda-forge
esmpy                     8.0.0           nompi_py38hf0e99fa_1    conda-forge
future                    0.18.2                   py38_0    conda-forge
g2clib                    1.6.0                hf3f1b0b_9    conda-forge
hdf4                      4.2.13            hf30be14_1003    conda-forge
hdf5                      1.10.5          nompi_h3c11f04_1104    conda-forge
idna                      2.8                   py38_1000    conda-forge
importlib_metadata        1.5.0                    py38_0    conda-forge
inflect                   4.0.0                    py38_1    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jaraco.itertools          5.0.0                      py_0    conda-forge
jasper                    1.900.1           h07fcdf6_1006    conda-forge
jpeg                      9c                h14c3975_1001    conda-forge
jsonschema                3.2.0                    py38_0    conda-forge
jupyter_core              4.6.1                    py38_0    conda-forge
krb5                      1.16.4               h2fd8d38_0    conda-forge
lazy-object-proxy         1.4.3            py38h516909a_1    conda-forge
ld_impl_linux-64          2.33.1               h53a641e_8    conda-forge
libblas                   3.8.0               11_openblas    conda-forge
libcblas                  3.8.0               11_openblas    conda-forge
libcdms                   3.1.2                ha54dda3_8    conda-forge
libcf                     1.0.3            py38hdee1361_5    conda-forge
libcurl                   7.65.3               hda55be3_0    conda-forge
libdrs                    3.1.2                h9b7ed86_9    conda-forge
libdrs_f                  3.1.2                h322d3c2_5    conda-forge
libedit                   3.1.20170329      hf8c457e_1001    conda-forge
libffi                    3.2.1             he1b5a44_1006    conda-forge
libgcc-ng                 9.2.0                h24d8f2e_2    conda-forge
libgfortran-ng            7.3.0                hdf63c60_5    conda-forge
libgomp                   9.2.0                h24d8f2e_2    conda-forge
liblapack                 3.8.0               11_openblas    conda-forge
libnetcdf                 4.7.3           nompi_h9f9fd6a_101    conda-forge
libopenblas               0.3.6                h6e990d7_6    conda-forge
libpng                    1.6.37               hed695b0_0    conda-forge
libssh2                   1.8.2                h22169c7_2    conda-forge
libstdcxx-ng              9.2.0                hdf63c60_2    conda-forge
libtiff                   4.1.0                hc3755c2_3    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
lz4-c                     1.8.3             he1b5a44_1001    conda-forge
more-itertools            8.2.0                      py_0    conda-forge
nbformat                  5.0.4                      py_0    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
netcdf-fortran            4.5.2           nompi_h09cde99_103    conda-forge
numpy                     1.18.1           py38h95a1406_0    conda-forge
openblas                  0.3.6                h6e990d7_6    conda-forge
openssl                   1.1.1d               h516909a_0    conda-forge
pip                       20.0.2                   py38_1    conda-forge
pycparser                 2.19                     py38_1    conda-forge
pyopenssl                 19.1.0                   py38_0    conda-forge
pyrsistent                0.15.7           py38h516909a_0    conda-forge
pysocks                   1.7.1                    py38_0    conda-forge
python                    3.8.1                h357f687_2    conda-forge
readline                  8.0                  hf8c457e_0    conda-forge
regrid2                   3.1.4                    pypi_0    pypi
requests                  2.22.0                   py38_1    conda-forge
setuptools                45.1.0                   py38_0    conda-forge
six                       1.14.0                   py38_0    conda-forge
sqlite                    3.30.1               hcee41ef_0    conda-forge
tk                        8.6.10               hed695b0_0    conda-forge
traitlets                 4.3.3                    py38_0    conda-forge
urllib3                   1.25.7                   py38_0    conda-forge
wheel                     0.34.2                   py38_0    conda-forge
xz                        5.2.4             h14c3975_1001    conda-forge
zipp                      2.1.0                      py_0    conda-forge
zlib                      1.2.11            h516909a_1006    conda-forge
zstd                      1.4.4                h3b9ef0a_1    conda-forge

Additional context
I think numpy.rank might work fine, and that numpy.ma.rank was eliminated in the most recent release of numpy.
@xylar
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xylar commented Feb 3, 2020

I can confirm that I do not see this issue with numpy<1.18:

conda create -y -n test -c conda-forge cdms2=3.1.4 numpy=1.17
conda activate test
python -c "import cdms2"

(No output)

@xylar xylar mentioned this issue Feb 4, 2020
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@muryanto1 muryanto1 mentioned this issue Feb 4, 2020
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@muryanto1 muryanto1 reopened this Feb 4, 2020
@muryanto1
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fix was not correct -- working on the fix and adding a testcase.

@xylar
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xylar commented Feb 4, 2020

@muryanto1, could you explain what was wrong with the fix?

By the way, my test environment is still picking up cdms2 build 4 (rather than build 7 that we just merged) but I think that's because of a different dependency not being up-to-date with conda-forge pinnings. So as far as I know, conda-forge/cdms2-feedstock#47 should have fixed things from my perspective. But maybe there's something more subtle?

@xylar xylar mentioned this issue Feb 4, 2020
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@xylar
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xylar commented Feb 5, 2020

As we discussed, the issue is that numpy.rank isn't the right replacement, and numpy.ndims is actually what's needed.

It's odd to me that the old numpy.ma.rank is equivalent to numpy.ndims but whatever works...

@muryanto1
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@xylar correct, I am replacing calls to numpy.rank() with numpy.ndims(), @jasonb5 helped me with the fix. we are testing the fix.

@muryanto1 muryanto1 mentioned this issue Feb 6, 2020
Merged
@jasonb5 jasonb5 added this to the 3.1.5 milestone Jul 6, 2020
@jasonb5 jasonb5 added the pending-release Fix is included in a pending release of CDAT metapackage. label Jul 8, 2020
@xylar
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xylar commented Jul 19, 2020

I believe this was addressed by #387 and can be closed.

@xylar xylar closed this as completed Jul 19, 2020
@jasonb5 jasonb5 modified the milestones: 3.1.5, 8.2.1 Jul 27, 2020
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fixed https://github.com/CDAT/cdms/issues/384 CDAT/cdms
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@jasonb5 @xylar @muryanto1