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conda-forge / netcdf4-feedstock

A conda-smithy repository for netcdf4.
BSD 3-Clause "New" or "Revised" License
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conda-forge netCDF4 not recognizing CDF-5 support #67

Closed xylar closed 5 years ago

xylar commented 5 years ago

Issue: the conda-forge version of netCDF4 thinks it doesn't support CDF-5 format (see MPAS-Dev/MPAS-Analysis#459).

I believe the issue may be fixed via the following PR that was just merged: https://github.com/conda-forge/libnetcdf-feedstock/pull/59

After this fix, nc-config will give a correct path to the NetCDF include files. I believe this is needed for netCDF4 to find the correct include path: https://github.com/Unidata/netcdf4-python/blob/master/setup.py#L342-L353 and later to recognize that CDF-5 is supported: https://github.com/Unidata/netcdf4-python/blob/master/setup.py#L76-L77


Environment (conda list):

``` $ conda list # packages in environment at /global/project/projectdirs/acme/software/anaconda_envs/edison/base/envs/e3sm_unified_1.2.3_py2.7_nox: # # Name Version Build Channel alabaster 0.7.12 py_0 conda-forge asn1crypto 0.24.0 py27_1003 conda-forge astroid 1.6.5 py27_0 conda-forge atomicwrites 1.2.1 py_0 conda-forge attrs 18.2.0 py_0 conda-forge autopep8 1.4.1 py_0 conda-forge babel 2.6.0 py_1 conda-forge backports 1.0 py_2 conda-forge backports.functools_lru_cache 1.5 py_1 conda-forge backports.shutil_get_terminal_size 1.0.0 py_3 conda-forge backports_abc 0.5 py_1 conda-forge basemap 1.2.0 py27h50ae964_0 conda-forge bcrypt 3.1.4 py27h14c3975_0 beautifulsoup4 4.6.3 py27_1000 conda-forge blas 1.1 openblas conda-forge bleach 3.0.2 py_0 conda-forge bokeh 0.13.0 py27_1000 conda-forge boost-cpp 1.67.0 h3a22d5f_0 conda-forge bottleneck 1.2.1 py27h7eb728f_1 conda-forge bzip2 1.0.6 h470a237_2 conda-forge ca-certificates 2018.10.15 ha4d7672_0 conda-forge cairo 1.14.12 he6fea26_5 conda-forge cartopy 0.16.0 py27h81b52dc_2 conda-forge cdat 8.0 0 cdat cdat_info 8.0 py27_0 conda-forge cdms2 3.0.1 py27h6091dcd_1 conda-forge cdp 1.4.0 py27_0 cdat cdtime 3.0 py27h6091dcd_1 conda-forge cdutil 8.0 py27_1 conda-forge certifi 2018.10.15 py27_1000 conda-forge cffi 1.11.5 py27h5e8e0c9_1 conda-forge cftime 1.0.1 py27h7eb728f_1 conda-forge chardet 3.0.4 py27_1003 conda-forge cibots 0.2 py27_0 conda-forge click 7.0 py_0 conda-forge cloudpickle 0.6.1 py_0 conda-forge cmocean 1.2 py_0 conda-forge cmor 3.3.3 py27h18b3941_2 conda-forge configobj 5.0.6 py_0 conda-forge configparser 3.5.0 py27_1001 conda-forge cryptography 2.3.1 py27hdffb7b8_0 conda-forge cryptography-vectors 2.3.1 py27_1000 conda-forge curl 7.61.1 h74213dd_2 conda-forge cycler 0.10.0 py_1 conda-forge cyordereddict 1.0.0 py27h470a237_2 conda-forge cython 0.29 py27hfc679d8_0 conda-forge cytoolz 0.9.0.1 py27h470a237_1 conda-forge dask 0.18.2 py_0 conda-forge dask-core 0.18.2 py_0 conda-forge dbus 1.13.0 h3a4f0e9_0 conda-forge decorator 4.3.0 py_0 conda-forge distarray 2.12.2 py_1 conda-forge distributed 1.23.3 py27_1000 conda-forge docutils 0.14 py27_1001 conda-forge dv3d 8.0 py27_0 cdat e3sm-unified 1.2.3 0 e3sm e3sm_diags 1.4.0 py27_0 e3sm e3sm_nex 0.0.2 py27_0 cdat e3sm_to_cmip 0.0.4 1 e3sm entrypoints 0.2.3 py27_1002 conda-forge enum34 1.1.6 py27_1001 conda-forge eofs 1.3.0 py_1 conda-forge esmf 7.1.0r ha678704_2 conda-forge esmpy 7.1.0r py27_1 conda-forge evtk 1.1.1 py27_0 e3sm expat 2.2.5 hfc679d8_2 conda-forge f90nml 1.0.2 py27_1000 conda-forge fastcache 1.0.2 py27h470a237_1 conda-forge ffmpeg 3.4.1 0 conda-forge flake8 3.5.0 py27_1000 conda-forge flann 1.9.1 h57d4613_3 conda-forge fontconfig 2.13.1 h65d0f4c_0 conda-forge freetype 2.9.1 h6debe1e_4 conda-forge freexl 1.0.5 h470a237_2 conda-forge funcsigs 1.0.2 py_2 conda-forge functools32 3.2.3.2 py_3 conda-forge future 0.16.0 py27_1002 conda-forge futures 3.2.0 py27_1000 conda-forge g2clib 1.6.0 3 conda-forge genutil 8.0 py27_1 conda-forge geos 3.6.2 hfc679d8_3 conda-forge geotiff 1.4.2 h700e5ad_4 conda-forge gettext 0.19.8.1 h5e8e0c9_1 conda-forge giflib 5.1.4 h470a237_1 conda-forge glib 2.55.0 h464dc38_2 conda-forge globus-cli 1.1.2 py27hcbe4c9c_0 e3sm globus-sdk 1.1.1 py27h128db3a_0 e3sm gmp 6.1.2 hfc679d8_0 conda-forge gmpy2 2.0.8 py27hb705a9b_2 conda-forge gsl 2.2.1 h0c605f7_3 gst-plugins-base 1.12.5 hde13a9d_0 conda-forge gstreamer 1.12.5 h61a6719_0 conda-forge gsw 3.0.6 py27_0 conda-forge h5netcdf 0.6.2 py_0 conda-forge h5py 2.8.0 py27h7eb728f_3 conda-forge hdf4 4.2.13 h951d187_2 conda-forge hdf5 1.10.2 hc401514_2 conda-forge hdfeos2 2.20 h7a90ae3_0 conda-forge hdfeos5 5.1.16 h647bee3_2 conda-forge heapdict 1.0.0 py27_1000 conda-forge icu 58.2 hfc679d8_0 conda-forge idna 2.7 py27_1002 conda-forge imageio 2.3.0 py_1 conda-forge imagesize 1.1.0 py_0 conda-forge ipaddress 1.0.22 py_1 conda-forge ipykernel 4.10.0 py27_1 conda-forge ipython 5.8.0 py27_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 7.4.2 py_0 conda-forge isort 4.3.4 py27_1000 conda-forge jasper 1.900.1 hff1ad4c_5 conda-forge jedi 0.13.1 py27_1000 conda-forge jinja2 2.10 py_1 conda-forge jmespath 0.9.3 py_1 conda-forge jpeg 9c h470a237_1 conda-forge json-c 0.12.1 h470a237_1 conda-forge json_tricks 3.11.0 py_0 conda-forge jsonschema 2.6.0 py27_1002 conda-forge jupyter 1.0.0 py_1 conda-forge jupyter_client 5.2.3 py_1 conda-forge jupyter_console 5.2.0 py27_1 conda-forge jupyter_core 4.4.0 py_0 conda-forge kealib 1.4.9 h0bee7d0_2 conda-forge kiwisolver 1.0.1 py27h2d50403_2 conda-forge krb5 1.16.1 hbb41f41_0 conda-forge lazy-object-proxy 1.3.1 py27h470a237_0 conda-forge libcdms 3.0.1 hcacfb3f_4 conda-forge libcf 1.0.2 py27h426daee_5 conda-forge libcurl 7.61.1 hbdb9355_2 conda-forge libdap4 3.19.1 h8fe5423_1 conda-forge libdrs 3.0.1 h6e3784b_3 conda-forge libdrs_f 3.0.1 h2cd7f18_3 conda-forge libedit 3.1.20170329 haf1bffa_1 conda-forge libffi 3.2.1 hfc679d8_5 conda-forge libgcc 7.2.0 h69d50b8_2 conda-forge libgcc-ng 7.2.0 hdf63c60_3 conda-forge libgdal 2.2.4 hbd6f514_9 conda-forge libgfortran 3.0.0 1 conda-forge libgfortran-ng 7.2.0 hdf63c60_3 conda-forge libiconv 1.15 h470a237_3 conda-forge libkml 1.3.0 hccc92b1_8 conda-forge libnetcdf 4.6.1 he6cff42_8 conda-forge libpng 1.6.35 ha92aebf_2 conda-forge libpq 10.5 he29860b_0 conda-forge libsodium 1.0.16 h470a237_1 conda-forge libspatialite 4.3.0a hdfcc80b_23 conda-forge libssh2 1.8.0 h5b517e9_2 conda-forge libstdcxx-ng 7.2.0 hdf63c60_3 conda-forge libtiff 4.0.9 he6b73bb_2 conda-forge libuuid 2.32.1 h470a237_2 conda-forge libxcb 1.13 h470a237_2 conda-forge libxml2 2.9.8 h422b904_5 conda-forge libxslt 1.1.32 h88dbc4e_2 conda-forge linecache2 1.0.0 py_1 conda-forge livvkit 2.1.6 py_0 conda-forge locket 0.2.0 py_2 conda-forge lxml 4.2.5 py27hc9114bc_0 conda-forge markupsafe 1.0 py27h470a237_1 conda-forge matplotlib 2.2.3 py27h8e2386c_0 conda-forge mccabe 0.6.1 py_1 conda-forge mesalib 17.3.9 hdd5ec5b_0 conda-forge mistune 0.8.4 py27h470a237_0 conda-forge more-itertools 4.3.0 py27_1000 conda-forge mpas_analysis 1.0 py_0 e3sm mpc 1.1.0 hb705a9b_6 conda-forge mpfr 4.0.1 h16a7912_0 conda-forge mpi 1.0 mpich conda-forge mpich 3.2.1 h26a2512_5 conda-forge mpmath 1.0.0 py_1 conda-forge msgpack-python 0.5.6 py27h2d50403_3 conda-forge nb_conda 2.2.1 py27_0 conda-forge nb_conda_kernels 2.1.1 py27_1001 conda-forge nbconvert 5.3.1 py_1 conda-forge nbformat 4.4.0 py_1 conda-forge ncl 6.5.0 blas_openblashd40de8d_1 [blas_openblas] conda-forge nco 4.7.7 h16f6c37_200 conda-forge ncurses 6.1 hfc679d8_1 conda-forge netcdf-fortran 4.4.4 h4363f12_9 conda-forge netcdf4 1.4.1 py27h62672b6_0 conda-forge networkx 2.2 py_1 conda-forge notebook 5.7.0 py27_1000 conda-forge numpy 1.15.2 py27_blas_openblashb06ca3d_1 [blas_openblas] conda-forge numpydoc 0.8.0 py_1 conda-forge olefile 0.46 py_0 conda-forge openblas 0.3.3 ha44fe06_1 conda-forge openjpeg 2.3.0 h0e734dc_3 conda-forge openssl 1.0.2p h470a237_1 conda-forge ossuuid 1.6.2 hfc679d8_0 conda-forge output_viewer 1.2.5 py_0 conda-forge owslib 0.17.0 py_0 conda-forge packaging 18.0 py_0 conda-forge pandas 0.23.4 py27hf8a1672_0 conda-forge pandoc 2.3.1 0 conda-forge pandocfilters 1.4.2 py_1 conda-forge paramiko 2.4.1 py27_0 conda-forge parso 0.3.1 py_0 conda-forge partd 0.3.9 py_0 conda-forge pathlib2 2.3.2 py27_1000 conda-forge pcre 8.41 hfc679d8_3 conda-forge peewee 3.6.4 py27h65ede16_1000 conda-forge pexpect 4.6.0 py27_1000 conda-forge pickleshare 0.7.5 py27_1000 conda-forge pillow 5.3.0 py27hc736899_0 conda-forge pip 18.1 py27_1000 conda-forge pixman 0.34.0 h470a237_3 conda-forge plotly 3.3.0 py_0 conda-forge pluggy 0.8.0 py_0 conda-forge poppler 0.67.0 h4d7e492_3 conda-forge poppler-data 0.4.9 0 conda-forge postgresql 10.5 h66035e0_0 conda-forge processflow 2.1.0 0 e3sm progressbar2 3.38.0 py_1 conda-forge proj4 4.9.3 h470a237_8 conda-forge prometheus_client 0.4.2 py_0 conda-forge prompt_toolkit 1.0.15 py_1 conda-forge psutil 5.4.7 py27h470a237_1 conda-forge pthread-stubs 0.4 h470a237_1 conda-forge ptyprocess 0.6.0 py27_1000 conda-forge py 1.7.0 py_0 conda-forge pyasn1 0.4.4 py_0 conda-forge pycodestyle 2.4.0 py_1 conda-forge pycparser 2.19 py_0 conda-forge pyepsg 0.3.2 py_1 conda-forge pyflakes 1.6.0 py_1 conda-forge pyflann 1.9.1 py27h2d50403_2 conda-forge pygments 2.2.0 py_1 conda-forge pylint 1.9.2 py27_0 conda-forge pynacl 1.1.2 py27_0 conda-forge pyopenssl 18.0.0 py27_1000 conda-forge pyparsing 2.2.2 py_0 conda-forge pyproj 1.9.5.1 py27h508ed2a_5 conda-forge pyqt 5.6.0 py27h8210e8a_7 conda-forge pyshp 1.2.12 py_0 conda-forge pysocks 1.6.8 py27_1002 conda-forge pyspharm 1.0.9 py27h18b3941_3 conda-forge pytest 3.9.1 py27_1000 conda-forge pytest-runner 4.2 py_1 conda-forge python 2.7.15 h33da82c_4 conda-forge python-dateutil 2.7.3 py_0 conda-forge python-utils 2.3.0 py_1 conda-forge pytz 2018.5 py_0 conda-forge pywavelets 1.0.1 py27h7eb728f_0 conda-forge pyyaml 3.13 py27h470a237_1 conda-forge pyzmq 17.1.2 py27hae99301_1 conda-forge qt 5.6.2 hf70d934_9 conda-forge qtawesome 0.5.1 pyh8a2030e_1 conda-forge qtconsole 4.4.2 py_1 conda-forge qtpy 1.5.1 pyh8a2030e_0 conda-forge readline 7.0 haf1bffa_1 conda-forge requests 2.19.1 py27_1001 conda-forge retrying 1.3.3 py_2 conda-forge rope 0.10.7 py_1 conda-forge scandir 1.9.0 py27h470a237_0 conda-forge scikit-image 0.14.1 py27hfc679d8_0 conda-forge scipy 1.1.0 py27_blas_openblashb06ca3d_202 [blas_openblas] conda-forge send2trash 1.5.0 py_0 conda-forge setuptools 40.4.3 py27_0 conda-forge shapely 1.6.4 py27h164cb2d_1 conda-forge simplegeneric 0.8.1 py_1 conda-forge singledispatch 3.4.0.3 py27_1000 conda-forge sip 4.18.1 py27hfc679d8_0 conda-forge six 1.11.0 py27_1001 conda-forge snowballstemmer 1.2.1 py_1 conda-forge sortedcontainers 2.0.5 py_0 conda-forge sphinx 1.8.1 py27_1000 conda-forge sphinxcontrib-websupport 1.1.0 py_1 conda-forge spyder 3.3.1 py27_3 conda-forge spyder-kernels 0.2.6 py_1 conda-forge sqlite 3.25.2 hb1c47c0_0 conda-forge subprocess32 3.5.3 py27h470a237_0 conda-forge sympy 1.3 py27_1000 conda-forge tabulate 0.8.2 py_0 conda-forge tblib 1.3.2 py_1 conda-forge terminado 0.8.1 py27_1001 conda-forge testpath 0.4.2 py27_1000 conda-forge thermo 8.0 py27_0 cdat tk 8.6.8 ha92aebf_0 conda-forge toolz 0.9.0 py_1 conda-forge tornado 5.1.1 py27h470a237_0 conda-forge traceback2 1.4.0 py27_0 conda-forge traitlets 4.3.2 py27_1000 conda-forge typing 3.6.6 py27_1000 conda-forge udunits2 2.2.27.6 h3a4f0e9_1 conda-forge unittest2 1.1.0 py_0 conda-forge urllib3 1.23 py27_1001 conda-forge vcs 8.0 py27_0 cdat vcsaddons 8.0 py27_0 cdat vtk-cdat 8.0.1.8.0 py27_mesalib_1 [mesalib] cdat wcwidth 0.1.7 py_1 conda-forge webencodings 0.5.1 py_1 conda-forge wheel 0.32.1 py27_0 conda-forge widgetsnbextension 3.4.2 py27_1000 conda-forge windspharm 1.7.0 py27_1000 conda-forge wk 8.0 py27_0 cdat wrapt 1.10.11 py27h470a237_1 conda-forge x264 20131218 0 conda-forge xarray 0.10.8 py27_1 conda-forge xerces-c 3.2.0 h5d6a6da_2 conda-forge xorg-imake 1.0.7 0 conda-forge xorg-kbproto 1.0.7 h470a237_2 conda-forge xorg-libice 1.0.9 h470a237_4 conda-forge xorg-libsm 1.2.3 h8c8a85c_0 conda-forge xorg-libx11 1.6.6 h470a237_0 conda-forge xorg-libxau 1.0.8 h470a237_6 conda-forge xorg-libxaw 1.0.13 h470a237_2 conda-forge xorg-libxdmcp 1.1.2 h470a237_7 conda-forge xorg-libxext 1.3.3 h470a237_4 conda-forge xorg-libxmu 1.1.2 h470a237_2 conda-forge xorg-libxpm 3.5.12 h470a237_2 conda-forge xorg-libxrender 0.9.10 h470a237_2 conda-forge xorg-libxt 1.1.5 h470a237_2 conda-forge xorg-makedepend 1.0.5 0 conda-forge xorg-renderproto 0.11.1 h470a237_2 conda-forge xorg-xextproto 7.3.0 h470a237_2 conda-forge xorg-xproto 7.0.31 h470a237_7 conda-forge xz 5.2.4 h470a237_1 conda-forge yaml 0.1.7 h470a237_1 conda-forge zeromq 4.2.5 hfc679d8_6 conda-forge zict 0.1.3 py_0 conda-forge zlib 1.2.11 h470a237_3 conda-forge ```


Details about conda and system ( conda info ):

``` $ conda info active environment : e3sm_unified_1.2.3_py2.7_nox active env location : /global/project/projectdirs/acme/software/anaconda_envs/edison/base/envs/e3sm_unified_1.2.3_py2.7_nox shell level : 1 user config file : /global/homes/x/xylar/.condarc populated config files : /global/homes/x/xylar/.condarc conda version : 4.5.11 conda-build version : not installed python version : 2.7.15.final.0 base environment : /global/project/projectdirs/acme/software/anaconda_envs/edison/base (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/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 : /global/project/projectdirs/acme/software/anaconda_envs/edison/base/pkgs /global/homes/x/xylar/.conda/pkgs envs directories : /global/project/projectdirs/acme/software/anaconda_envs/edison/base/envs /global/homes/x/xylar/.conda/envs platform : linux-64 user-agent : conda/4.5.11 requests/2.19.1 CPython/2.7.15 Linux/4.4.143-94.47.1.16060.2.PTF.1107299-default sles/12.3 glibc/2.22 UID:GID : 32003:32003 netrc file : /global/homes/x/xylar/.netrc offline mode : False ```