HDF5 Based Install Error

Hello,

I’m trying to install pymc3 again after failing before. I used the below code from the install guide for Windows.

conda create -n pymc_env -c conda-forge python libpython mkl-service m2w64-toolchain numba python-graphviz scipy

That seems to run fine.

Then I run this:

conda activate pymc_env
pip install pymc3

And I get the below error. I’m not sure how to fix it. i see this has something to do with hdf5 but I’m not sure where to go from here.

Preparing metadata (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: 'C:\Users\JORDAN.HOWELL.GITDIR\AppData\Local\Continuum\anaconda3\envs\pymc_env\python.exe' -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\\Users\\JORDAN.HOWELL.GITDIR\\AppData\\Local\\Temp\\pip-install-ih5_4wrt\\netcdf4_6946b2fe78694a31b93f1c5cea666d01\\setup.py'"'"'; __file__='"'"'C:\\Users\\JORDAN.HOWELL.GITDIR\\AppData\\Local\\Temp\\pip-install-ih5_4wrt\\netcdf4_6946b2fe78694a31b93f1c5cea666d01\\setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base 'C:\Users\JORDAN.HOWELL.GITDIR\AppData\Local\Temp\pip-pip-egg-info-m4hq86wf'
       cwd: C:\Users\JORDAN.HOWELL.GITDIR\AppData\Local\Temp\pip-install-ih5_4wrt\netcdf4_6946b2fe78694a31b93f1c5cea666d01\
  Complete output (30 lines):
  Package hdf5 was not found in the pkg-config search path.
  Perhaps you should add the directory containing `hdf5.pc'
  to the PKG_CONFIG_PATH environment variable
  No package 'hdf5' found
  Traceback (most recent call last):
    File "<string>", line 1, in <module>
    File "C:\Users\JORDAN.HOWELL.GITDIR\AppData\Local\Temp\pip-install-ih5_4wrt\netcdf4_6946b2fe78694a31b93f1c5cea666d01\setup.py", line 419, in <module>
      _populate_hdf5_info(dirstosearch, inc_dirs, libs, lib_dirs)
    File "C:\Users\JORDAN.HOWELL.GITDIR\AppData\Local\Temp\pip-install-ih5_4wrt\netcdf4_6946b2fe78694a31b93f1c5cea666d01\setup.py", line 360, in _populate_hdf5_info
      raise ValueError('did not find HDF5 headers')
  ValueError: did not find HDF5 headers
  reading from setup.cfg...

      HDF5_DIR environment variable not set, checking some standard locations ..
  checking C:\Users\JORDAN.HOWELL.GITDIR\AppData\Local\Continuum\anaconda3\envs\pymc_env\include ...
  hdf5 headers not found in C:\Users\JORDAN.HOWELL.GITDIR\AppData\Local\Continuum\anaconda3\envs\pymc_env\include
  checking C:\Users\JORDAN.HOWELL.GITDIR\AppData\Local\Continuum\anaconda3\envs\pymc_env\Library\include ...
  hdf5 headers not found in C:\Users\JORDAN.HOWELL.GITDIR\AppData\Local\Continuum\anaconda3\envs\pymc_env\Library\include
  checking C:\Users\JORDAN.HOWELL.GITDIR\include ...
  hdf5 headers not found in C:\Users\JORDAN.HOWELL.GITDIR\include
  checking /usr/local\include ...
  hdf5 headers not found in /usr/local\include
  checking /sw\include ...
  hdf5 headers not found in /sw\include
  checking /opt\include ...
  hdf5 headers not found in /opt\include
  checking /opt/local\include ...
  hdf5 headers not found in /opt/local\include
  checking /usr\include ...
  hdf5 headers not found in /usr\include
  ----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/e4/09/c7582134adb67b2ef136b954344d0522e9e3e1c7a292004eec0e8f8b1f0d/netCDF4-1.5.8.tar.gz#sha256=ca3d468f4812c0999df86e3f428851fb0c17ac34ce0827115c246b0b690e4e84 (from https://pypi.org/simple/netcdf4/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.