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cfgrib broke netCDF4 #7

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rabernat opened this issue Sep 11, 2019 · 4 comments
Closed

cfgrib broke netCDF4 #7

rabernat opened this issue Sep 11, 2019 · 4 comments

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@rabernat
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Thanks for providing this very valuable conda package!

I tried to use it for the first time to help with pydata/xarray#3199. I had a perfectly working relatively recent conda environment. Then I ran conda install -c conda-forge cfgrib. It brought along dozens of new binaries which broke my netCDF4 library.

>>> import netCDF4
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-2-f731da2de255> in <module>()
----> 1 import netCDF4

~/miniconda3/envs/geo_scipy/lib/python3.6/site-packages/netCDF4/__init__.py in <module>()
      1 # init for netCDF4. package
      2 # Docstring comes from extension module _netCDF4.
----> 3 from ._netCDF4 import *
      4 # Need explicit imports for names beginning with underscores
      5 from ._netCDF4 import __doc__, __pdoc__

ImportError: dlopen(/Users/rpa/miniconda3/envs/geo_scipy/lib/python3.6/site-packages/netCDF4/_netCDF4.cpython-36m-darwin.so, 2): Library not loaded: @rpath/libssl.1.0.0.dylib
  Referenced from: /Users/rpa/miniconda3/envs/geo_scipy/lib/libssh2.1.dylib
  Reason: image not found

I tried conda update -c conda-forge netCDF4, but it told me I already had the latest version.

I would prefer not to have to choose between cfgrib and netCDF4, as these are both common file formats.

Would appreciate any advice for how to resolve this dependency mess.


Environment (conda list): 
$ conda list
# packages in environment at /Users/rpa/miniconda3/envs/geo_scipy:
#
# Name                    Version                   Build  Channel
absl-py                   0.5.0                      py_0    conda-forge
affine                    2.1.0                      py_1    conda-forge
aiohttp                   3.5.4                    pypi_0    pypi
alabaster                 0.7.10                   py36_1    conda-forge
alembic                   1.1.0                    pypi_0    pypi
appdirs                   1.4.3                      py_1    conda-forge
appnope                   0.1.0                    py36_0    conda-forge
argh                      0.26.2                   pypi_0    pypi
arrow                     0.12.1                   pypi_0    pypi
asciitree                 0.3.3                    pypi_0    pypi
asks                      2.2.0                    pypi_0    pypi
asn1crypto                0.24.0                py36_1003    conda-forge
aspy-yaml                 1.3.0                    pypi_0    pypi
astor                     0.7.1                      py_0    conda-forge
async-generator           1.10                     pypi_0    pypi
async-timeout             3.0.1                    pypi_0    pypi
atomicwrites              1.2.1                      py_0    conda-forge
attrs                     18.2.0                   pypi_0    pypi
automat                   0.5.0                    py36_0  
babel                     2.5.1                    py36_0    conda-forge
backports                 1.0                      py36_1    conda-forge
backports.functools_lru_cache 1.4                      py36_1    conda-forge
basemap                   1.1.0                    py36_4    conda-forge
beautifulsoup4            4.6.3                    pypi_0    pypi
bibtexparser              1.0.1                    pypi_0    pypi
binaryornot               0.4.4                    pypi_0    pypi
bkcharts                  0.2                      py36_0    conda-forge
black                     19.3b0                     py_0    conda-forge
blas                      2.4                    openblas    conda-forge
bleach                    2.0.0                    py36_0    conda-forge
blinker                   1.4                      pypi_0    pypi
bokeh                     1.0.4                 py36_1000    conda-forge
boost                     1.65.1                   py36_0    conda-forge
boost-cpp                 1.65.1                        1    conda-forge
boto                      2.48.0                   pypi_0    pypi
boto3                     1.4.7                    py36_0    conda-forge
botocore                  1.5.92                   py36_0    conda-forge
bottleneck                1.2.1            py36h7eb728f_1    conda-forge
bzip2                     1.0.6                         1    conda-forge
c-ares                    1.14.0               h470a237_0    conda-forge
ca-certificates           2019.6.16            hecc5488_0    conda-forge
cachetools                2.0.1                    pypi_0    pypi
cairo                     1.14.12              he56eebe_3    conda-forge
cartopy                   0.17.0          py36h707127b_1000    conda-forge
certifi                   2018.10.15               pypi_0    pypi
cffi                      1.12.3           py36hccf1714_0    conda-forge
cfgrib                    0.9.7.1                    py_0    conda-forge
cfgv                      2.0.0                    pypi_0    pypi
cftime                    1.0.1                     dev_0    <develop>
chardet                   3.0.4                 py36_1003    conda-forge
click                     7.0                      pypi_0    pypi
click-plugins             1.0.3                    py36_0    conda-forge
cligj                     0.4.0                    py36_0    conda-forge
cloudpickle               0.5.2                      py_0    conda-forge
coards                    1.0.5                    pypi_0    pypi
colorcet                  1.0.0                      py_0    conda-forge
commonmark                0.9.0                    pypi_0    pypi
configobj                 5.0.6                    py36_0  
constantly                15.1.0                   py36_0  
contextvars               2.3                      pypi_0    pypi
cookiecutter              1.6.0                    pypi_0    pypi
coverage                  4.5.1                    pypi_0    pypi
cryptography              2.7              py36h212c5bf_0    conda-forge
cssselect                 1.0.1                    py36_0  
curl                      7.64.0               heae2a1f_2    conda-forge
cycler                    0.10.0                   py36_0    conda-forge
cython                    0.26                     py36_0    conda-forge
cytoolz                   0.9.0.1                  py36_0    conda-forge
dask                      0.20.2                     py_0    conda-forge
dask-core                 0.20.2                     py_0    conda-forge
dask-kubernetes           0.0.1                    pypi_0    pypi
datashader                0.6.5                      py_0    conda-forge
datashape                 0.5.4                    py36_0    conda-forge
decorator                 4.1.2                    py36_0    conda-forge
deprecated                1.2.5                    pypi_0    pypi
descartes                 1.1.0                      py_2    conda-forge
dill                      0.2.7.1                  pypi_0    pypi
distributed               1.24.2                py36_1000    conda-forge
docker                    3.7.0                    pypi_0    pypi
docker-pycreds            0.4.0                    pypi_0    pypi
docopt                    0.6.2                    pypi_0    pypi
docrep                    0.1.2                    pypi_0    pypi
doctr                     1.8.0                      py_0    conda-forge
docutils                  0.14                     pypi_0    pypi
eccodes                   2.12.3               hac8aea4_1    conda-forge
entrypoints               0.2.3                    py36_1    conda-forge
eofs                      1.3.1                    pypi_0    pypi
escapism                  1.0.0                    pypi_0    pypi
expat                     2.2.6                h0a44026_0  
fastcache                 1.1.0            py36h01d97ff_0    conda-forge
fasteners                 0.14.1                   py36_2    conda-forge
feedgenerator             1.9                      pypi_0    pypi
fiona                     1.7.13           py36hb00a9d7_3    conda-forge
flake8                    3.5.0                    pypi_0    pypi
floater                   0.1                       dev_0    <develop>
fontconfig                2.13.0               h8c010e7_5    conda-forge
fpzip                     1.1.1                    pypi_0    pypi
freetype                  2.8.1                hfa320df_1    conda-forge
freexl                    1.0.5             h1de35cc_1002    conda-forge
fsspec                    0.4.1                    pypi_0    pypi
future                    0.16.0                   py36_0    conda-forge
futures-compat            1.0                       py3_0  
fuzzywuzzy                0.17.0                   pypi_0    pypi
gapic-google-cloud-datastore-v1 0.15.3                   pypi_0    pypi
gapic-google-cloud-error-reporting-v1beta1 0.15.3                   pypi_0    pypi
gapic-google-cloud-logging-v2 0.91.3                   pypi_0    pypi
gast                      0.2.0                      py_0    conda-forge
gcdistance                0.0.1                     dev_0    <develop>
gcsfs                     0.1.2                      py_0    conda-forge
gdal                      2.3.3            py36hbe65578_0  
geopandas                 0.4.0                      py_1    conda-forge
geos                      3.7.1             h0a44026_1000    conda-forge
geotiff                   1.4.3             h113155d_1001    conda-forge
geoviews                  1.6.2                      py_0    conda-forge
geoviews-core             1.6.2                      py_0    conda-forge
gettext                   0.19.8.1                      0    conda-forge
ghp-import                0.5.5                    pypi_0    pypi
giflib                    5.1.4                         0    conda-forge
glib                      2.55.0               h464dc38_2    conda-forge
gmp                       6.1.2             h0a44026_1000    conda-forge
gmpy2                     2.0.8           py36h3aece09_1002    conda-forge
google-api-core           0.1.4                    pypi_0    pypi
google-auth               1.4.1                    pypi_0    pypi
google-auth-oauthlib      0.2.0                    pypi_0    pypi
google-cloud              0.32.0                   pypi_0    pypi
google-cloud-bigquery     0.28.0                   pypi_0    pypi
google-cloud-bigquery-datatransfer 0.1.1                    pypi_0    pypi
google-cloud-bigtable     0.28.1                   pypi_0    pypi
google-cloud-container    0.1.1                    pypi_0    pypi
google-cloud-core         0.28.1                   pypi_0    pypi
google-cloud-datastore    1.4.0                    pypi_0    pypi
google-cloud-dns          0.28.0                   pypi_0    pypi
google-cloud-error-reporting 0.28.0                   pypi_0    pypi
google-cloud-firestore    0.28.0                   pypi_0    pypi
google-cloud-language     1.0.1                    pypi_0    pypi
google-cloud-logging      1.4.0                    pypi_0    pypi
google-cloud-monitoring   0.28.1                   pypi_0    pypi
google-cloud-pubsub       0.30.1                   pypi_0    pypi
google-cloud-resource-manager 0.28.1                   pypi_0    pypi
google-cloud-runtimeconfig 0.28.1                   pypi_0    pypi
google-cloud-spanner      0.29.0                   pypi_0    pypi
google-cloud-speech       0.30.0                   pypi_0    pypi
google-cloud-storage      1.6.0                    pypi_0    pypi
google-cloud-trace        0.17.0                   pypi_0    pypi
google-cloud-translate    1.3.1                    pypi_0    pypi
google-cloud-videointelligence 1.0.1                    pypi_0    pypi
google-cloud-vision       0.29.0                   pypi_0    pypi
google-gax                0.15.16                  pypi_0    pypi
google-resumable-media    0.3.1                    pypi_0    pypi
googleapis-common-protos  1.5.3                    pypi_0    pypi
graphviz                  2.38.0               hbeef861_8    conda-forge
grpc-google-iam-v1        0.11.4                   pypi_0    pypi
grpcio                    1.10.0                   pypi_0    pypi
gsw                       3.0.6                    pypi_0    pypi
gunicorn                  19.9.0                   pypi_0    pypi
h11                       0.8.1                    pypi_0    pypi
h5netcdf                  0.4.1                      py_0    conda-forge
h5py                      2.7.1                    py36_2    conda-forge
hdf4                      4.2.13            hf3c6af0_1002    conda-forge
hdf5                      1.10.4          nompi_h0cbb7df_1106    conda-forge
heapdict                  1.0.0                    py36_0    conda-forge
holoviews                 1.11.2                     py_0    conda-forge
html5lib                  0.999999999              py36_0    conda-forge
httplib2                  0.11.1                   pypi_0    pypi
hubploy                   0.1.0                     dev_0    <develop>
hvplot                    0.4.0                    pypi_0    pypi
hyperlink                 17.1.1                   py36_0  
icu                       58.2              h0a44026_1000    conda-forge
identify                  1.4.5                    pypi_0    pypi
idna                      2.7                      pypi_0    pypi
idna-ssl                  1.1.0                    pypi_0    pypi
imageio                   2.2.0                    py36_0    conda-forge
imagesize                 0.7.1                    py36_0    conda-forge
immutables                0.6                      pypi_0    pypi
importlib-metadata        0.18                     pypi_0    pypi
importlib-resources       1.0.2                    pypi_0    pypi
incremental               16.10.1                  py36_0  
intake                    0.4.4                      py_0    conda-forge
intake-xarray             0.3.0                      py_0    conda-forge
ipaddress                 1.0.22                   pypi_0    pypi
ipykernel                 4.6.1                    py36_0    conda-forge
ipython                   6.1.0                    py36_0    conda-forge
ipython_genutils          0.2.0                    py36_0    conda-forge
ipywidgets                7.4.2                      py_0    conda-forge
jasper                    1.900.1           h636a363_1006    conda-forge
jedi                      0.11.0                   pypi_0    pypi
jinja2                    2.10                     pypi_0    pypi
jinja2-time               0.2.0                    pypi_0    pypi
jmespath                  0.9.3                    py36_0    conda-forge
jpeg                      9c                h1de35cc_1001    conda-forge
json-c                    0.13.1            h1de35cc_1001    conda-forge
jsonschema                2.6.0                    py36_0    conda-forge
jupyter                   1.0.0                      py_1    conda-forge
jupyter-book              0.5.2                    pypi_0    pypi
jupyter-contrib-core      0.3.3                    pypi_0    pypi
jupyter-contrib-nbextensions 0.5.1                    pypi_0    pypi
jupyter-highlight-selected-word 0.2.0                    pypi_0    pypi
jupyter-latex-envs        1.4.6                    pypi_0    pypi
jupyter-nbextensions-configurator 0.4.1                    pypi_0    pypi
jupyter-notebook-gist     0.4.0                    pypi_0    pypi
jupyter-repo2docker       0.8.0                    pypi_0    pypi
jupyter_client            5.2.3                    py36_0    conda-forge
jupyter_console           5.1.0                    py36_0    conda-forge
jupyter_core              4.4.0                      py_0    conda-forge
jupyterlab                0.33.11                  py36_0    conda-forge
jupyterlab_launcher       0.11.2                     py_0    conda-forge
kealib                    1.4.10            hecf890f_1003    conda-forge
keras                     2.2.4                    py36_0    conda-forge
keras-applications        1.0.4                      py_1    conda-forge
keras-preprocessing       1.0.2                      py_1    conda-forge
kiwisolver                1.0.1           py36h04f5b5a_1002    conda-forge
krb5                      1.16.3            hcfa6398_1001    conda-forge
kubernetes                6.0.0                    pypi_0    pypi
lancet                    0.9.0                    py36_0    conda-forge
latexcodec                1.0.7                    pypi_0    pypi
libaec                    1.0.4                h0a44026_0    conda-forge
libblas                   3.8.0                4_openblas    conda-forge
libboost                  1.67.0               hebc422b_4  
libcblas                  3.8.0                4_openblas    conda-forge
libcurl                   7.64.0               he376013_2    conda-forge
libcxx                    7.0.0                h2d50403_0    conda-forge
libdap4                   3.19.1            hae55d67_1000    conda-forge
libedit                   3.1.20170329      hcfe32e1_1001    conda-forge
libffi                    3.2.1                         3    conda-forge
libgdal                   2.3.3                h0950a36_0  
libgfortran               3.0.1                         0    conda-forge
libgpuarray               0.7.6                h470a237_3    conda-forge
libiconv                  1.15                          0    conda-forge
libkml                    1.3.0                hbe12b63_4  
liblapack                 3.8.0                4_openblas    conda-forge
liblapacke                3.8.0                4_openblas    conda-forge
libnetcdf                 4.6.2             h6b88ef6_1001    conda-forge
libpng                    1.6.37               h2573ce8_0    conda-forge
libpq                     11.4                 h56406e1_0    conda-forge
libprotobuf               3.6.1                hd28b015_0    conda-forge
libsodium                 1.0.10                        0    conda-forge
libspatialindex           1.8.5             h0a44026_1003    conda-forge
libspatialite             4.3.0a            h0cd9627_1026    conda-forge
libssh2                   1.8.0                         1    conda-forge
libtiff                   4.0.9             h79f4b77_1002    conda-forge
libxml2                   2.9.9                hd80cff7_2    conda-forge
libxslt                   1.1.29                        5    conda-forge
livereload                2.6.1                    pypi_0    pypi
llvm-meta                 7.0.0                         0    conda-forge
llvmlite                  0.25.0          py36h3fea490_1001    conda-forge
locket                    0.2.0                    py36_1    conda-forge
lxml                      3.8.0                    py36_0    conda-forge
mako                      1.0.7                      py_1    conda-forge
markdown                  2.6.9                    pypi_0    pypi
markupsafe                1.0                      py36_0    conda-forge
matplotlib                2.2.2                    py36_1    conda-forge
mccabe                    0.6.1                    pypi_0    pypi
mistune                   0.7.4                    py36_0    conda-forge
mkl                       2017.0.3                      0  
mock                      2.0.0                 py36_1000    conda-forge
monotonic                 1.3                      py36_0    conda-forge
more-itertools            4.1.0                      py_0    conda-forge
mpc                       1.1.0             h3aece09_1006    conda-forge
mpfr                      4.0.2                h0a95893_0    conda-forge
mpmath                    1.1.0                      py_0    conda-forge
msgpack-numpy             0.4.4.2                    py_0    conda-forge
msgpack-python            0.4.8                    py36_0    conda-forge
multidict                 4.5.2                    pypi_0    pypi
multio                    0.2.4                    pypi_0    pypi
multipledispatch          0.4.9                    py36_0    conda-forge
munch                     2.3.2                      py_0    conda-forge
nbclean                   0.3.2                    pypi_0    pypi
nbconvert                 5.2.1                    py36_1    conda-forge
nbformat                  4.3.0                    py36_0    conda-forge
nbgrader                  0.6.0                    pypi_0    pypi
nbsphinx                  0.3.1                      py_0    conda-forge
ncurses                   6.1               h0a44026_1002    conda-forge
netcdf4                   1.5.1.2          py36h58b02fa_0    conda-forge
networkx                  1.11                     py36_0    conda-forge
nodeenv                   1.3.3                    pypi_0    pypi
nodejs                    9.11.1                        0    conda-forge
notebook                  5.4.1                    py36_0    conda-forge
numba                     0.40.0           py36hf8a1672_0    conda-forge
numcodecs                 0.6.3                    pypi_0    pypi
numexpr                   2.6.8            py36hf8a1672_0    conda-forge
numpy                     1.15.4                   pypi_0    pypi
numpydoc                  0.7.0                    py36_0    conda-forge
oauth2client              3.0.0                    pypi_0    pypi
oauthlib                  2.0.6                    pypi_0    pypi
odo                       0.5.1                    py36_0    conda-forge
olefile                   0.44                     py36_0    conda-forge
openblas                  0.3.5             h436c29b_1001    conda-forge
openjpeg                  2.3.0             h3bf0609_1003    conda-forge
openssl                   1.1.1c               h01d97ff_0    conda-forge
ordereddict               1.1                      pypi_0    pypi
oset                      0.1.3                    pypi_0    pypi
outcome                   1.0.0                    pypi_0    pypi
owslib                    0.14.0                   py36_1    conda-forge
packaging                 17.1                       py_0    conda-forge
palettable                3.1.1                      py_0    conda-forge
pandas                    0.25.1           py36h86efe34_0    conda-forge
pandoc                    1.19.2                        0    conda-forge
pandocfilters             1.4.1                    py36_0    conda-forge
param                     1.8.2                      py_0    conda-forge
parsel                    1.2.0                    py36_0  
parso                     0.1.0                    pypi_0    pypi
partd                     0.3.8                    py36_0    conda-forge
pastedeploy               1.5.2                    pypi_0    pypi
pathtools                 0.1.2                    pypi_0    pypi
patsy                     0.4.1                    py36_0    conda-forge
pbr                       4.2.0                      py_0    conda-forge
pcre                      8.43                 h0a44026_0  
pelican                   3.7.1                    pypi_0    pypi
pexpect                   4.2.1                    py36_0    conda-forge
pickleshare               0.7.4                    py36_0    conda-forge
pillow                    5.2.0            py36h2dc6135_1    conda-forge
pip                       18.1                     pypi_0    pypi
pixman                    0.34.0                        1    conda-forge
pluggy                    0.8.0                      py_0    conda-forge
ply                       3.8                      pypi_0    pypi
poppler                   0.67.0               hb55ee21_1    conda-forge
poppler-data              0.4.8                         0    conda-forge
port-for                  0.3.1                    pypi_0    pypi
poyo                      0.4.2                    pypi_0    pypi
pre-commit                1.17.0                   pypi_0    pypi
proj4                     5.2.0             h6de7cb9_1006    conda-forge
prompt_toolkit            1.0.15                   py36_0    conda-forge
proto-google-cloud-datastore-v1 0.90.4                   pypi_0    pypi
proto-google-cloud-error-reporting-v1beta1 0.15.3                   pypi_0    pypi
proto-google-cloud-logging-v2 0.91.3                   pypi_0    pypi
protobuf                  3.5.2.post1              pypi_0    pypi
psutil                    5.4.3                    pypi_0    pypi
psycopg2                  2.6.2                    py36_0  
ptyprocess                0.5.2                    py36_0    conda-forge
py                        1.5.3                      py_0    conda-forge
pyasn1                    0.4.2                    pypi_0    pypi
pyasn1-modules            0.2.1                    pypi_0    pypi
pybtex                    0.22.2                   pypi_0    pypi
pybtex-docutils           0.2.1                    pypi_0    pypi
pycodestyle               2.3.1                    pypi_0    pypi
pycparser                 2.19                     py36_1    conda-forge
pyct                      0.4.6                      py_0    conda-forge
pyct-core                 0.4.6                      py_0    conda-forge
pydap                     3.2.2                     dev_0    <develop>
pydispatcher              2.0.5                    py36_0  
pyepsg                    0.3.2                    py36_0    conda-forge
pyflakes                  1.6.0                    pypi_0    pypi
pygithub                  1.43.5                   pypi_0    pypi
pygments                  2.2.0                    py36_0    conda-forge
pygpu                     0.7.6            py36h7eb728f_0    conda-forge
pyjwt                     1.6.4                      py_0    conda-forge
pykdtree                  1.2.2                    py36_1    conda-forge
pymongo                   3.6.1                    pypi_0    pypi
pyopenssl                 19.0.0                   py36_0    conda-forge
pyparsing                 2.2.0                    py36_0    conda-forge
pyproj                    1.9.5.1                  py36_0    conda-forge
pyqt                      5.6.0                    py36_4    conda-forge
pyresample                1.9.3                    py36_0    conda-forge
pysal                     2.0.0                      py_0    conda-forge
pyshp                     1.2.12                     py_0    conda-forge
pysocks                   1.7.0                    py36_0    conda-forge
pytables                  3.4.2                    py36_7    conda-forge
pytest                    4.0.0                 py36_1000    conda-forge
pytest-attrib             0.1.3                    pypi_0    pypi
pytest-cov                2.6.0                    pypi_0    pypi
python                    3.6.8                haf84260_0  
python-dateutil           2.7.5                    pypi_0    pypi
python-editor             1.0.4                    pypi_0    pypi
python-graphviz           0.8                      py36_0    conda-forge
python-json-logger        0.1.10                   pypi_0    pypi
python-snappy             0.5.3            py36h00d4201_0    conda-forge
pytz                      2018.3                   pypi_0    pypi
pyviz_comms               0.7.0                      py_0    conda-forge
pywavelets                1.0.1            py36h7eb728f_0    conda-forge
pyyaml                    5.1.2            py36h01d97ff_0    conda-forge
pyzmq                     17.0.0                   py36_4    conda-forge
qt                        5.6.2                h9e3eb04_4    conda-forge
qtconsole                 4.3.1                    py36_0    conda-forge
queuelib                  1.4.2                    py36_0  
rasterio                  0.36.0                   py36_2    conda-forge
readline                  7.0               hcfe32e1_1001    conda-forge
recommonmark              0.5.0                    pypi_0    pypi
requests                  2.19.1                   pypi_0    pypi
requests-mock             1.5.2                    pypi_0    pypi
requests-oauthlib         0.8.0                    pypi_0    pypi
rise                      5.0.0                    py36_0    damianavila82
rsa                       3.4.2                    pypi_0    pypi
rstcloth                  0.2.6                    pypi_0    pypi
rtree                     0.8.3                 py36_1000    conda-forge
ruamel.yaml               0.15.81          py36h470a237_0    conda-forge
s3transfer                0.1.11                   py36_0    conda-forge
sat-stac                  0.1.0rc5                 pypi_0    pypi
scikit-image              0.13.0                   py36_1    conda-forge
scikit-learn              0.20.3           py36hca23c92_1    conda-forge
scipy                     1.2.1            py36hbd7caa9_1    conda-forge
scrapy                    1.3.3                    py36_0  
seaborn                   0.8.1                    py36_0    conda-forge
send2trash                1.5.0                      py_0    conda-forge
service_identity          17.0.0                   py36_0  
setuptools                39.0.1                   pypi_0    pypi
shapely                   1.6.4           py36h79c6f3e_1005    conda-forge
simplegeneric             0.8.1                    py36_0    conda-forge
sip                       4.18                     py36_1    conda-forge
six                       1.11.0                   pypi_0    pypi
snakeviz                  0.4.2                    pypi_0    pypi
snappy                    1.1.7                hfc679d8_2    conda-forge
sniffio                   1.0.0                    pypi_0    pypi
snowballstemmer           1.2.1                    py36_0    conda-forge
snuggs                    1.4.1                    py36_0    conda-forge
sortedcontainers          1.5.7                    py36_0    conda-forge
sphinx                    1.6.5                    py36_0    conda-forge
sphinx-autobuild          0.7.1                    pypi_0    pypi
sphinx-bootstrap-theme    0.6.4                    pypi_0    pypi
sphinx-copybutton         0.2.4                    pypi_0    pypi
sphinx-execute-code       0.2a2                    pypi_0    pypi
sphinx-fontawesome        0.0.6                    pypi_0    pypi
sphinx-gallery            0.1.12                   py36_0    conda-forge
sphinx-markdown-tables    0.0.9                    pypi_0    pypi
sphinx-modern-theme       1.0.5                    pypi_0    pypi
sphinx-nbexamples         0.3.0                    pypi_0    pypi
sphinx-pangeo-theme       0+untagged.9.g6e68f92.dirty          pypi_0    pypi
sphinx-rtd-theme          0.2.4                    pypi_0    pypi
sphinxbootstrap4theme     0.6.0                    pypi_0    pypi
sphinxcontrib-bibtex      0.4.2                    pypi_0    pypi
sphinxcontrib-srclinks    0.2.4                    pypi_0    pypi
sphinxcontrib-websupport  1.0.1                    py36_0    conda-forge
sqlalchemy                1.2.18           py36h1de35cc_0    conda-forge
sqlite                    3.26.0            h1765d9f_1000    conda-forge
stac-validator            0.0.1                    pypi_0    pypi
statsmodels               0.9.0            py36h7eb728f_0    conda-forge
sympy                     1.4                      py36_0    conda-forge
tblib                     1.3.2                    py36_0    conda-forge
tensorboard               1.10.0                   py36_0    conda-forge
tensorflow                1.1.0                    py36_0    conda-forge
termcolor                 1.1.0                      py_2    conda-forge
terminado                 0.8.1                    py36_0    conda-forge
testpath                  0.3.1                    py36_0    conda-forge
theano                    1.0.3                    py36_0    conda-forge
tk                        8.6.9             ha441bb4_1000    conda-forge
toml                      0.10.0                     py_0    conda-forge
toolz                     0.8.2                    py36_0    conda-forge
tornado                   4.5.3                    py36_0    conda-forge
tqdm                      4.31.1                   pypi_0    pypi
traitlets                 4.3.2                    py36_0    conda-forge
trio                      0.9.0                    pypi_0    pypi
twine                     1.13.0                   pypi_0    pypi
twisted                   17.5.0                   py36_0  
typing                    3.6.2                    py36_0    conda-forge
typing-extensions         3.7.4                    pypi_0    pypi
unidecode                 0.04.21                  pypi_0    pypi
urllib3                   1.25.3                   py36_0    conda-forge
versioneer                0.18                     pypi_0    pypi
virtualenv                16.6.1                   pypi_0    pypi
w3lib                     1.17.0                   py36_0  
waitress                  1.1.0                    pypi_0    pypi
watchdog                  0.9.0                    pypi_0    pypi
wcwidth                   0.1.7                    py36_0    conda-forge
webencodings              0.5                      py36_0    conda-forge
webob                     1.8.4                    pypi_0    pypi
websocket-client          0.48.0                   pypi_0    pypi
webtest                   2.0.32                   pypi_0    pypi
werkzeug                  0.14.1                     py_0    conda-forge
wheel                     0.33.6                   py36_0    conda-forge
whichcraft                0.5.2                    pypi_0    pypi
widgetsnbextension        3.4.2                 py36_1000    conda-forge
wrapt                     1.11.1                   pypi_0    pypi
xarray                    0.10.0                   pypi_0    pypi
xbatcher                  0.1.0                     dev_0    <develop>
xerces-c                  3.2.2             h4db8090_1003    conda-forge
xgcm                      0.2.0                     dev_0    <develop>
xhistogram                0.1.1                     dev_0    <develop>
xmitgcm                   0.4.1                     dev_0    <develop>
xrft                      0.1                       dev_0    <develop>
xz                        5.2.4             h1de35cc_1001    conda-forge
yaml                      0.1.7                         0    conda-forge
yarl                      1.3.0                    pypi_0    pypi
zarr                      2.3.2                     dev_0    <develop>
zeromq                    4.2.5                         1    conda-forge
zict                      0.1.3                      py_0    conda-forge
zipp                      0.5.2                    pypi_0    pypi
zlib                      1.2.11                        0    conda-forge
zope                      1.0                      py36_0  
zope.interface            4.4.2                    py36_0

Details about conda and system ( conda info ): 
$ conda info
     active environment : geo_scipy
    active env location : /Users/rpa/miniconda3/envs/geo_scipy
            shell level : 1
       user config file : /Users/rpa/.condarc
 populated config files : /Users/rpa/.condarc
          conda version : 4.6.7
    conda-build version : not installed
         python version : 3.6.7.final.0
       base environment : /Users/rpa/miniconda3  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/osx-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/rpa/miniconda3/pkgs
                          /Users/rpa/.conda/pkgs
       envs directories : /Users/rpa/miniconda3/envs
                          /Users/rpa/.conda/envs
               platform : osx-64
             user-agent : conda/4.6.7 requests/2.21.0 CPython/3.6.7 Darwin/16.7.0 OSX/10.12.6
                UID:GID : 501:20
             netrc file : None
           offline mode : False
@alexamici
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@rabernat I'm not able to reproduce this with a brand new environment.

This are the steps I used:

$ conda create -t tmp
$ conda activate tmp
$ conda install xarray netcdf4 ipython
$ # can open a netCDF4 file with  in ipyhton
$ conda install -c conda-forge cfgrib
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /Users/amici/devel/conda3/envs/tmp

  added / updated specs:
    - cfgrib

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2019.6.16          |           py36_1         149 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         149 KB

The following NEW packages will be INSTALLED:

  attrs              conda-forge/noarch::attrs-19.1.0-py_0
  cffi               conda-forge/osx-64::cffi-1.12.3-py36hccf1714_0
  cfgrib             conda-forge/noarch::cfgrib-0.9.7.1-py_0
  click              conda-forge/noarch::click-7.0-py_0
  eccodes            conda-forge/osx-64::eccodes-2.12.3-hac8aea4_1
  jasper             conda-forge/osx-64::jasper-1.900.1-h636a363_1006
  libaec             conda-forge/osx-64::libaec-1.0.4-h0a44026_0
  libpng             conda-forge/osx-64::libpng-1.6.37-h2573ce8_0
  pycparser          conda-forge/osx-64::pycparser-2.19-py36_1

The following packages will be UPDATED:

  ca-certificates    pkgs/main::ca-certificates-2019.5.15-1 --> conda-forge::ca-certificates-2019.6.16-hecc5488_0
  jpeg                        pkgs/main::jpeg-9b-he5867d9_2 --> conda-forge::jpeg-9c-h1de35cc_1001
  libnetcdf           pkgs/main::libnetcdf-4.6.1-hd5207e6_2 --> conda-forge::libnetcdf-4.6.2-h6b88ef6_1001

The following packages will be SUPERSEDED by a higher-priority channel:

  certifi                                         pkgs/main --> conda-forge
  openssl              pkgs/main::openssl-1.1.1d-h1de35cc_0 --> conda-forge::openssl-1.1.1c-h01d97ff_0

Downloading and Extracting Packages
certifi-2019.6.16    | 149 KB    | ########################################################################################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

After that I can open both netCDF4 and GRIB files with xarray in IPyhton.

Note that eccodes appears to depend on the conda-forge version of the netCDF4 package that in turns appear to update openssl.

This issue should probably be moved to https://github.com/conda-forge/eccodes-feedstock as it is dpoesn't appear to be cfgrib-specific. cc @StephanSiemen

@rabernat
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Thanks @alexamici for checking on this.

It's good to know that everything works in a fresh environment. What puzzles me is that I have the same exact library versions (libnetcdf, openssl) as your environment.

libnetcdf                 4.6.2             h6b88ef6_1001    conda-forge
openssl                   1.1.1c               h01d97ff_0    conda-forge

I would prefer not to completely abandon my old environment if possible. This sounds like a problem for binary dependency guru @ocefpaf.

I am happy if you want to transfer the issue to eccodes.

@ocefpaf
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ocefpaf commented Sep 11, 2019

I would prefer not to completely abandon my old environment if possible. This sounds like a problem for binary dependency guru @ocefpaf.

I don't have a macOS available to debug that env but I tried something similar on Linux and everything worked. See the command and list of packages below.

Can you try to force conda install libssh2=1.8.2 and see if that helps? Also, I would update to conda 4.7 and activate strict in your .condarc before trying that.

> conda create --name TEST xarray netcdf4 ipython cfgrib --yes
The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main
  attrs              conda-forge/noarch::attrs-19.1.0-py_0
  backcall           conda-forge/noarch::backcall-0.1.0-py_0
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h516909a_1
  ca-certificates    conda-forge/linux-64::ca-certificates-2019.6.16-hecc5488_0
  certifi            conda-forge/linux-64::certifi-2019.6.16-py37_1
  cffi               conda-forge/linux-64::cffi-1.12.3-py37h8022711_0
  cfgrib             conda-forge/noarch::cfgrib-0.9.7.1-py_0
  cftime             conda-forge/linux-64::cftime-1.0.3.4-py37hd352d35_1001
  click              conda-forge/noarch::click-7.0-py_0
  curl               conda-forge/linux-64::curl-7.65.3-hf8cf82a_0
  decorator          conda-forge/noarch::decorator-4.4.0-py_0
  eccodes            conda-forge/linux-64::eccodes-2.13.1-hec26673_1
  hdf4               conda-forge/linux-64::hdf4-4.2.13-h9a582f1_1002
  hdf5               conda-forge/linux-64::hdf5-1.10.5-nompi_h3c11f04_1103
  ipython            conda-forge/linux-64::ipython-7.8.0-py37h5ca1d4c_0
  ipython_genutils   conda-forge/noarch::ipython_genutils-0.2.0-py_1
  jasper             conda-forge/linux-64::jasper-1.900.1-h07fcdf6_1006
  jedi               conda-forge/linux-64::jedi-0.15.1-py37_0
  jpeg               conda-forge/linux-64::jpeg-9c-h14c3975_1001
  krb5               conda-forge/linux-64::krb5-1.16.3-h05b26f9_1001
  libaec             conda-forge/linux-64::libaec-1.0.4-hf484d3e_0
  libblas            conda-forge/linux-64::libblas-3.8.0-12_openblas
  libcblas           conda-forge/linux-64::libcblas-3.8.0-12_openblas
  libcurl            conda-forge/linux-64::libcurl-7.65.3-hda55be3_0
  libedit            conda-forge/linux-64::libedit-3.1.20170329-hf8c457e_1001
  libffi             conda-forge/linux-64::libffi-3.2.1-he1b5a44_1006
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0
  libgfortran-ng     pkgs/main/linux-64::libgfortran-ng-7.3.0-hdf63c60_0
  liblapack          conda-forge/linux-64::liblapack-3.8.0-12_openblas
  libnetcdf          conda-forge/linux-64::libnetcdf-4.6.2-h303dfb8_1003
  libopenblas        conda-forge/linux-64::libopenblas-0.3.7-h6e990d7_1
  libpng             conda-forge/linux-64::libpng-1.6.37-hed695b0_0
  libssh2            conda-forge/linux-64::libssh2-1.8.2-h22169c7_2
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0
  ncurses            conda-forge/linux-64::ncurses-6.1-hf484d3e_1002
  netcdf4            conda-forge/linux-64::netcdf4-1.5.1.2-py37h73a1b54_1
  numpy              conda-forge/linux-64::numpy-1.17.2-py37h95a1406_0
  openssl            conda-forge/linux-64::openssl-1.1.1c-h516909a_0
  pandas             conda-forge/linux-64::pandas-0.25.1-py37hb3f55d8_0
  parso              conda-forge/noarch::parso-0.5.1-py_0
  pexpect            conda-forge/linux-64::pexpect-4.7.0-py37_0
  pickleshare        conda-forge/linux-64::pickleshare-0.7.5-py37_1000
  pip                conda-forge/linux-64::pip-19.2.3-py37_0
  prompt_toolkit     conda-forge/noarch::prompt_toolkit-2.0.9-py_0
  ptyprocess         conda-forge/noarch::ptyprocess-0.6.0-py_1001
  pycparser          conda-forge/linux-64::pycparser-2.19-py37_1
  pygments           conda-forge/noarch::pygments-2.4.2-py_0
  python             conda-forge/linux-64::python-3.7.3-h33d41f4_1
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.0-py_0
  pytz               conda-forge/noarch::pytz-2019.2-py_0
  readline           conda-forge/linux-64::readline-8.0-hf8c457e_0
  setuptools         conda-forge/linux-64::setuptools-41.2.0-py37_0
  six                conda-forge/linux-64::six-1.12.0-py37_1000
  sqlite             conda-forge/linux-64::sqlite-3.29.0-hcee41ef_1
  tk                 conda-forge/linux-64::tk-8.6.9-hed695b0_1002
  traitlets          conda-forge/linux-64::traitlets-4.3.2-py37_1000
  wcwidth            conda-forge/noarch::wcwidth-0.1.7-py_1
  wheel              conda-forge/linux-64::wheel-0.33.6-py37_0
  xarray             conda-forge/noarch::xarray-0.12.3-py_0
  xz                 conda-forge/linux-64::xz-5.2.4-h14c3975_1001
  zlib               conda-forge/linux-64::zlib-1.2.11-h516909a_1006

@rabernat
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Thanks for the suggestions @ocefpaf! But I just bit the bullet and created a fresh environment.

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@alexamici @ocefpaf @rabernat