Fix bugs

[JunCEEE]

• Add local GAPD package to avoid unstable network.
• Add hint to remember source simex_vars.sh in develop install mode.
• Add numpy importing into diffr_diagnostics.py
• Freeze scipy version at 1.3.1 in requirement files.

[CFGrote]

@ejcjason, can you also fix the tests? see https://travis-ci.org/eucall-software/simex_platform/jobs/648439779 for details (scroll down to the bottom).

[JunCEEE]

From the FAIL information, it's the problem of PhotonBeamParametersTest.PhotonBeamParametersTest """ testSerialize (SimExTest.Parameters.PhotonBeamParametersTest.PhotonBeamParametersTest) Test the serialization of a PhotonBeamParameters instance. ... FAIL testSerializeToFile (SimExTest.Parameters.PhotonBeamParametersTest.PhotonBeamParametersTest) Test the serialization of a PhotonBeamParameters instance to file. ... FAIL testSerializeToFileName (SimExTest.Parameters.PhotonBeamParametersTest.PhotonBeamParametersTest) Test the serialization of a PhotonBeamParameters instance to file given the filename. ... FAIL """ When I tried to run the test with python PhotonBeamParametersTest.py on Maxwell, I got error

======================================================================
ERROR: testPropToBeamParameters (__main__.PhotonBeamParametersTest)
Test the utility function to construct a PhotonBeamParameters instance from prop output (wavefront file).
----------------------------------------------------------------------
Traceback (most recent call last):
  File "PhotonBeamParametersTest.py", line 206, in testPropToBeamParameters
    beam_parameters = propToBeamParameters(TestUtilities.generateTestFilePath("prop_out_0000001.h5"))
  File "/gpfs/exfel/data/user/juncheng/panoscProject/src/simex_platform/Sources/python/SimEx/Parameters/PhotonBeamParameters.py", line 183, in propToBeamParameters
    wavefront.load_hdf5( prop_output_path )
  File "/gpfs/exfel/data/user/juncheng/panoscProject/src/simex_platform/lib/python3.6/wpg/wavefront.py", line 184, in load_hdf5
    self._update_from_dict(utils.load_dict_slash_hdf5(file_name))
  File "/gpfs/exfel/data/user/juncheng/panoscProject/src/simex_platform/lib/python3.6/wpg/utils.py", line 93, in load_dict_slash_hdf5
    with h5py.File(hdf5_file_name, 'r') as h5_file:
  File "/home/juncheng/.conda/envs/simex-dev/lib/python3.6/site-packages/h5py/_hl/files.py", line 408, in __init__
    swmr=swmr)
  File "/home/juncheng/.conda/envs/simex-dev/lib/python3.6/site-packages/h5py/_hl/files.py", line 173, in make_fid
    fid = h5f.open(name, flags, fapl=fapl)
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5f.pyx", line 88, in h5py.h5f.open
OSError: Unable to open file (file signature not found)

The data is src/simex_platform/Tests/python/unittest/TestFiles/prop_out_0000001.h5, but I cannot read it by h5ls and h5dump:

prop_out_0000001.h5: unable to open file

It seems the hdf5 is corrupted or not compatible to newer version of hdf5. Do you think is this directly related to the problem?