Failing and "bad" unit tests, imports, etc

[jllanfranchi]

Full build log is here for reference: 1_build (3.6).txt, which you can see directly here

General issues:

• matplotlib.use(backend) warnings everywhere (I'll look into this, might not be too hard to fix) -- solution: remove all calls to use() and just use MPLBACKEND env var, which is far more well behaved
• "pandas", "emcee", "pycuda", "ROOT", "libPyROOT", "MCEq", "nuSQUIDSpy" optional dependencies are being ignored right now, but it would be nice to have these installed (if fast enough to be practical) for all unit tests to be able to run #788
• not enough unit tests
• no hypo testing test right now
• no higher-level tests (can we do some simple high-level physics things w/ publicly-available data?)
• pisa.utils.kde_hist.test_kde_histogramdd... missing pycuda (but pycuda precludes use of numba on gpu). Module probably needs a numba re-write moving forward (if it will be used)... 🙁
• Use black to make your code PEP8 compliant, minimizes diffs between git commits, and formatting should be ~ reproducible

@philippeller

• pisa.core.container.test_container outputs a lot of stuff

@jllanfranchi

• pisa.core.distribution_maker.test_DistributionMaker missing configs (at least)
• pisa.core.pipeline.test_Pipeline depends on missing tests/settings/test_Pipeline.cfg
• pisa.core.prior.test_Prior_plot missing 1 required positional argument: 'ts_fname'
• pisa.utils.random_numbers.test_get_random_state not implemented
• pisa.utils.flavInt.test_CombinedFlavIntData not implemented
• pisa.utils.cross_sections.test_CrossSections root dependency?
• test_parse_pipeline_config uses set_verbosity?
• pisa.utils.format.test_timestamp prints stuff to screen

@ShiveshM

• pisa.core.events.test_Data missing (proprietary) data files
• pisa.stages.xsec.genie.test_standard_plots test function requires an argument
• pisa.stages.xsec.genie.test_per_e_plot requires an argument

@atrettin

• pisa.utils.hypersurface.test_hypersurface_uncertainty makes plots that require latex: Failed to process string with tex because latex could not be found
• pisa/utils/hypersurface.py warnings:

[ WARNING] /home/justin/src/pisa/pisa/utils/hypersurface.py:701: RuntimeWarning: overflow encountered in exp
  output_factors = np.exp(out) if self.log else out

[ WARNING] /home/justin/src/pisa/pisa/utils/hypersurface.py:1048: RuntimeWarning: overflow encountered in square
  return np.sum(((fvals - y_to_use)/y_sigma_to_use)**2) + np.sum((inv_param_sigma*p)**2)

GPU failures:

  pisa.stages.flux.pi_mceq_barr, pisa.stages.absorption.pi_earth_absorption
8 unit test(s) failed:
  pisa.stages.osc.prob3numba.numba_osc.test_get_H_vac, pisa.stages.osc.prob3numba.numba_osc.test_get_H_mat, pisa.stages.osc.prob3numba.numba_osc.test_get_dms, pisa.stages.osc.prob3numba.numba_osc.test_get_product, pisa.stages.osc.prob3numba.numba_osc.test_get_transition_matrix_massbasis, pisa.stages.osc.prob3numba.numba_osc.test_convert_from_mass_eigenstate, pisa.stages.osc.prob3numba.numba_osc.test_get_transition_matrix, pisa.stages.osc.prob3numba.numba_osc.test_osc_probs_layers_kernel