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cdms2 in python3 has issue with eofs #101

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lee1043 opened this issue Dec 4, 2018 · 6 comments
Closed

cdms2 in python3 has issue with eofs #101

lee1043 opened this issue Dec 4, 2018 · 6 comments

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@lee1043
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lee1043 commented Dec 4, 2018

CDAT/cdms#294
@lee1043
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lee1043 commented Dec 4, 2018

Describe the bug
Updated version of cdms2 which use Python 3 has issue eofs (version below).

# Name                    Version                   Build  Channel
cdms2                     3.1.0.2018.11.14.22.42.g7e8de8f  py36h481b005_0    cdat/label/nightly
eofs                      1.3.0                      py_1    conda-forge

To Reproduce
python simple_test.py (use below two files, rename to remove .txt)
simple_test.py.txt
sample_input.nc.txt

Error message:

Traceback (most recent call last):
  File "simple_test.py", line 8, in <module>
    solver = Eof(d)
  File "/export_backup/lee1043/anaconda2/envs/pmp_nightly_20181128/lib/python3.6/site-packages/eofs/cdms.py", line 165, in __init__
    self._dataset_name = cdms2_name(dataset).replace(' ', '_')
  File "/export_backup/lee1043/anaconda2/envs/pmp_nightly_20181128/lib/python3.6/site-packages/eofs/tools/cdms.py", line 149, in cdms2_name
    return filter(None, names)[0]
TypeError: 'filter' object is not subscriptable

Expected behavior
It should return below image without having any error. It has been okay using previous version of cdms2 as below:

# Name                    Version                   Build  Channel
cdms2                     3.0.2018.08.30.01.24.ge41c556  py27h14c3975_0    cdat/label/nightly

simple_test

Desktop (please complete the following information):

  • OS: Linux (on Crunchy), Mac

Environment Information

`conda info`

     active environment : pmp_nightly_20181128
    active env location : /export_backup/lee1043/anaconda2/envs/pmp_nightly_20181128
            shell level : 2
       user config file : /export_backup/lee1043/.condarc
 populated config files : /export_backup/lee1043/.condarc
          conda version : 4.5.11
    conda-build version : not installed
         python version : 2.7.13.final.0
       base environment : /export_backup/lee1043/anaconda2  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /export_backup/lee1043/anaconda2/pkgs
                          /export_backup/lee1043/.conda/pkgs
       envs directories : /export_backup/lee1043/anaconda2/envs
                          /export_backup/lee1043/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.11 requests/2.14.2 CPython/2.7.13 Linux/2.6.32-696.30.1.el6.x86_64 rhel/6.10 glibc/2.12
                UID:GID : 55431:1026
             netrc file : None
           offline mode : False

`conda list --show-channel-urls`

# packages in environment at /export_backup/lee1043/anaconda2/envs/pmp_nightly_20181128:
#
# Name                    Version                   Build  Channel
asn1crypto                0.24.0                   py36_3    cdat-forge
blas                      1.0                         mkl    defaults
bokeh                     0.13.0                   py36_0    cdat-forge
bzip2                     1.0.6                h470a237_2    cdat-forge
ca-certificates           2018.8.24            ha4d7672_0    conda-forge
cdat_info                 8.0.2018.10.30.14.29.gc2e9630          py36_0    cdat/label/nightly
cdms2                     3.1.0.2018.11.14.22.42.g7e8de8f  py36h481b005_0    cdat/label/nightly
cdp                       1.3.3.2018.11.14.15.52          py36_0    cdat/label/nightly
cdtime                    3.1.0.2018.11.01.17.45.gb8c370e  py36h9ac9557_0    cdat/label/nightly
cdutil                    8.0.2018.11.12.19.20.g3bd6383            py_0    cdat/label/nightly
certifi                   2018.8.24                py36_1    conda-forge
cffi                      1.11.5           py36h5e8e0c9_1    cdat-forge
chardet                   3.0.4                    py36_3    cdat-forge
cia                       0.0.6                         0    cdat-forge
clapack                   3.2.1                h470a237_1    cdat-forge
click                     6.7                        py_1    cdat-forge
cloudpickle               0.5.5                      py_0    cdat-forge
cryptography              2.3.1            py36hdffb7b8_0    cdat-forge
cryptography-vectors      2.3.1                    py36_0    cdat-forge
curl                      7.61.0               h93b3f91_2    cdat-forge
cycler                    0.10.0           py36h93f1223_0    defaults
cytoolz                   0.9.0.1          py36h470a237_0    cdat-forge
dask                      0.19.1                     py_0    cdat-forge
dask-core                 0.19.1                     py_0    cdat-forge
dbus                      1.13.2               h714fa37_1    defaults
decorator                 4.3.0                    py36_0    defaults
distarray                 2.12.2                   py36_0    cdat-forge
distributed               1.23.1                   py36_0    cdat-forge
dv3d                      8.0.2018.10.25.14.21.g4afbd51            py_0    cdat/label/nightly
eofs                      1.3.0                      py_1    conda-forge
esmf                      7.1.0r                        1    cdat-forge
esmpy                     7.1.0r                   py36_1    cdat-forge
expat                     2.2.5                hfc679d8_2    cdat-forge
ffmpeg                    4.0                  hc8c182b_0    cdat-forge
fontconfig                2.12.6               h49f89f6_0    defaults
freetype                  2.8.1                hfa320df_1    cdat-forge
future                    0.16.0                   py36_2    cdat-forge
g2clib                    1.6.0                         3    cdat-forge
genutil                   8.1.2018.07.24.00.41.gc18c308.npy1.14  py36hb3ffb1f_0    cdat/label/nightly
glib                      2.56.1               h000015b_0    defaults
gmp                       6.1.2                hfc679d8_0    cdat-forge
gnutls                    3.5.19               h2a4e5f8_1    cdat-forge
gst-plugins-base          1.14.0               hbbd80ab_1    defaults
gstreamer                 1.14.0               hb453b48_1    defaults
hdf4                      4.2.13               h951d187_2    cdat-forge
hdf5                      1.10.1                        2    cdat-forge
heapdict                  1.0.0                    py36_0    cdat-forge
icu                       58.2                 h9c2bf20_1    defaults
idna                      2.7                      py36_2    cdat-forge
intel-openmp              2018.0.3                      0    cdat-forge
ipython_genutils          0.2.0                    py36_0    defaults
jasper                    1.900.1              hff1ad4c_5    cdat-forge
jinja2                    2.10                       py_1    cdat-forge
jpeg                      9c                   h470a237_1    cdat-forge
jsonschema                2.6.0                    py36_0    defaults
jupyter_core              4.4.0                    py36_0    defaults
kiwisolver                1.0.1            py36hf484d3e_0    defaults
krb5                      1.14.6                        0    cdat-forge
lapack                    3.6.1                         1    cdat-forge
libcdms                   3.0.2018.10.17.21.09.g4f79235      h9ac9557_0    cdat/label/nightly
libcf                     3.0.2018.06.28.01.19.g994aa30  py36h14c3975_0    cdat/label/nightly
libdrs                    3.0.2018.10.18.21.40.g36264ac      h9ac9557_0    cdat/label/nightly
libdrs_f                  3.0.2018.10.18.21.40.g36264ac      h9ac9557_0    cdat/label/nightly
libffi                    3.2.1                hfc679d8_5    cdat-forge
libgcc                    7.2.0                h69d50b8_2    cdat-forge
libgcc-ng                 8.2.0                hdf63c60_1    defaults
libgfortran               3.0.0                         1    cdat-forge
libgfortran-ng            7.2.0                hdf63c60_3    cdat-forge
libiconv                  1.15                 h470a237_3    cdat-forge
libnetcdf                 4.6.1                         2    cdat-forge
libpng                    1.6.35               ha92aebf_2    cdat-forge
libssh2                   1.8.0                h5b517e9_2    cdat-forge
libstdcxx-ng              7.2.0                hdf63c60_3    cdat-forge
libtiff                   4.0.9                he6b73bb_2    cdat-forge
libxcb                    1.13                 h1bed415_1    defaults
libxml2                   2.9.8                h26e45fe_1    defaults
locket                    0.2.0                      py_2    cdat-forge
markupsafe                1.0              py36h470a237_1    cdat-forge
matplotlib                2.2.2            py36h0e671d2_1    defaults
mkl                       2018.0.3                      1    cdat-forge
mkl_fft                   1.0.6                    py36_0    cdat-forge
mkl_random                1.0.1                    py36_0    cdat-forge
modes_of_variability-v0.1-68 g37ed74e                  <pip>
modes_of_variability-v0.1-70 gdbc6e4b                  <pip>
modes_of_variability-v0.1-71 ga2c8992                  <pip>
mpi                       1.0                       mpich    cdat-forge
mpich                     3.2.1                h26a2512_4    cdat-forge
msgpack-python            0.5.6            py36h2d50403_2    cdat-forge
nbformat                  4.4.0                    py36_0    defaults
ncurses                   6.1                  hfc679d8_1    cdat-forge
netcdf-fortran            4.4.4                         7    cdat-forge
nettle                    3.3                           0    cdat-forge
numpy                     1.15.0           py36h1b885b7_0    cdat-forge
numpy-base                1.15.0           py36h3dfced4_0    cdat-forge
openssl                   1.0.2p               h470a237_0    conda-forge
ossuuid                   1.6.2                hfc679d8_0    cdat-forge
output_viewer             1.2.5                    py36_0    cdat-forge
packaging                 17.1                       py_0    cdat-forge
pandas                    0.23.4           py36hf8a1672_0    cdat-forge
partd                     0.3.8                      py_1    cdat-forge
pcmdi_metrics             1.2.2018.11.15.19.02.g9cf5870    pyh39e3cac_0    pcmdi/label/nightly
pcre                      8.42                 h439df22_0    defaults
pip                       18.0                     py36_1    cdat-forge
proj4                     4.9.3                h470a237_8    cdat-forge
psutil                    5.4.7            py36h470a237_1    cdat-forge
pycparser                 2.18                       py_1    cdat-forge
pyopenssl                 18.0.0                   py36_0    cdat-forge
pyparsing                 2.2.0                      py_1    cdat-forge
pyqt                      5.9.2            py36h751905a_0    defaults
pysocks                   1.6.8                    py36_2    cdat-forge
python                    3.6.6                h5001a0f_0    cdat-forge
python-dateutil           2.7.3                      py_0    cdat-forge
pytz                      2018.5                     py_0    cdat-forge
pyyaml                    3.13             py36h470a237_1    cdat-forge
qt                        5.9.5                h7e424d6_0    defaults
readline                  7.0                  haf1bffa_1    cdat-forge
requests                  2.19.1                   py36_1    cdat-forge
setuptools                40.2.0                   py36_0    cdat-forge
sip                       4.19.8           py36hf484d3e_0    defaults
six                       1.11.0                   py36_1    cdat-forge
sortedcontainers          2.0.4                      py_1    cdat-forge
sqlite                    3.24.0               h2f33b56_1    cdat-forge
tblib                     1.3.2                      py_1    cdat-forge
tk                        8.6.8                         0    cdat-forge
toolz                     0.9.0                      py_0    cdat-forge
tornado                   5.1              py36h470a237_1    cdat-forge
traitlets                 4.3.2            py36h674d592_0    defaults
udunits2                  2.2.27.6             h3a4f0e9_1    cdat-forge
urllib3                   1.23                     py36_1    cdat-forge
vcs                       8.0.2018.11.12.23.15.gd5511950            py_0    cdat/label/nightly
vcsaddons                 8.0.2018.11.06.13.49.gca89c17  py36h14c3975_0    cdat/label/nightly
vtk-cdat                  8.0.1.8.0                py36_2    cdat/label/nightly
wheel                     0.31.1                   py36_1    cdat-forge
x264                      20131218                      0    cdat-forge
xz                        5.2.4                h470a237_1    cdat-forge
yaml                      0.1.7                h470a237_1    cdat-forge
zict                      0.1.3                      py_0    cdat-forge
zlib                      1.2.11               h470a237_3    cdat-forge

@ajdawson
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ajdawson commented Dec 4, 2018 •
edited
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Hi @lee1043 - thanks for moving this issue over. I've made a fix on the v1.3.x branch (#102), and updated the CI testing so that the cdms interface is tested on Python 3.6 and 3.7 as well as 2.7. I have not yet made a new release containing the fix, but I intend to to a v1.3.1 very soon.

@lee1043
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lee1043 commented Dec 4, 2018

@ajdawson Very nice, thank you for the immediate update. I look for release of v1.3.1, during the mean time I will use that branch.

@lee1043
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lee1043 commented Dec 4, 2018

The updated code works like a charm on my side.

@ajdawson
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ajdawson commented Dec 5, 2018

I have made a v1.3.1 release with this fix. The PyPI package is uploaded, it will take a little time for the conda-forge package to be created and uploaded.

@ajdawson ajdawson closed this as completed Dec 5, 2018
@lee1043
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lee1043 commented Dec 5, 2018

@ajdawson thank you!

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