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conda-forge / cfgrib-feedstock

A conda-smithy repository for cfgrib.
BSD 3-Clause "New" or "Revised" License
2 stars 4 forks source link

cfgrib broke netCDF4 #7

Closed rabernat closed 4 years ago

rabernat commented 5 years ago

Thanks for providing this very valuable conda package!

I tried to use it for the first time to help with https://github.com/pydata/xarray/pull/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 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 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 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 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 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 xerces-c 3.2.2 h4db8090_1003 conda-forge xgcm 0.2.0 dev_0 xhistogram 0.1.1 dev_0 xmitgcm 0.4.1 dev_0 xrft 0.1 dev_0 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 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 commented 5 years ago

@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 commented 5 years ago

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 commented 5 years ago

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 commented 4 years ago

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