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:

• [x] 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
• [ ] #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)... :slightly_frowning_face:
• [ ] 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

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

@ShiveshM

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

@atrettin

• [x] pisa.utils.hypersurface.test_hypersurface_uncertainty makes plots that require latex: Failed to process string with tex because latex could not be found
• [x] 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