Run PTCDA_single example with pytest

[yakutovicha]

fixes #118
supersedes #205

[yakutovicha]

Ok, with this, I declare a partial win against tests. To achieve it, I had to do two things:

• Disable test_vdw.py by renaming it to _test_vdw.py
• Disable tests for Python 3.8.

It looks to me that test_vdw.py interferes with the actual smoke tests through the common.py module that stores the current value of parameters. Therefore, it is now highly important to fix #232.

For the Python 3.8 issue, I don't know the origin of the problem.

[yakutovicha]

For your information, this is the current test coverage:

---------- coverage: platform linux, python 3.9.18-final-0 -----------
Name                                                  Stmts   Miss  Cover
-------------------------------------------------------------------------
examples/PTCDA_Hartree_dz2/example_ptcda_hartree.py      18      1    94%
examples/PTCDA_single/example_ptcda.py                   15      1    93%
ppafm/GridUtils.py                                      100     56    44%
ppafm/HighLevel.py                                      320    129    60%
ppafm/PPPlot.py                                         155    121    22%
ppafm/__init__.py                                         2      0   100%
ppafm/atomicUtils.py                                    203    180    11%
ppafm/cli/__init__.py                                     0      0   100%
ppafm/cli/generateElFF.py                               112     71    37%
ppafm/cli/generateElFF_point_charges.py                  11      1    91%
ppafm/cli/generateLJFF.py                                16      3    81%
ppafm/cli/plot_results.py                               174     73    58%
ppafm/cli/relaxed_scan.py                               138     47    66%
ppafm/common.py                                         500    267    47%
ppafm/core.py                                           217     69    68%
ppafm/cpp_utils.py                                       53     23    57%
ppafm/defaults/__init__.py                                0      0   100%
ppafm/defaults/d3.py                                     29     14    52%
ppafm/elements.py                                         7      0   100%
ppafm/fieldFFT.py                                       317    170    46%
ppafm/io.py                                             621    294    53%
ppafm/ocl/AFMulator.py                                  361    178    51%
ppafm/ocl/__init__.py                                     0      0   100%
ppafm/ocl/field.py                                     1078    773    28%
ppafm/ocl/oclUtils.py                                    64     32    50%
ppafm/ocl/relax.py                                      343    232    32%
ppafm/version.py                                          1      0   100%
tests/human_eye/test_TipForce.py                         29      0   100%
tests/human_eye/test_splines.py                          26      0   100%
tests/human_eye/test_vdwDamping.py                       67      1    99%
tests/test_afmulator.py                                  27      0   100%
tests/test_atomicUtils.py                                 5      0   100%
tests/test_common.py                                     12      0   100%
tests/test_datagrid.py                                   47      0   100%
tests/test_io.py                                         54      0   100%
-------------------------------------------------------------------------
TOTAL                                                  5122   2736    47%

47 % is not very good, but not catastrophic either.

[NikoOinonen]

@yakutovicha Do you think it would make more sense to put the example_*.py scripts under the tests folder? They don't really add any value as examples for the end user, so they are a kind of clutter. If you put them under tests then we also wouldn't need to put the underscore in any of the scripts under the examples folder.

[NikoOinonen]

I tried running the test with Python 3.8 locally, and interestingly the segfault only happens when running all tests with pytest. If run individually (with or without pytest), the test passes, so it seems that one of the other test functions is messing up the state somehow. No clue why it's only happening on 3.8, though.

[yakutovicha]

@yakutovicha Do you think it would make more sense to put the example_*.py scripts under the tests folder? They don't really add any value as examples for the end user, so they are a kind of clutter. If you put them under tests then we also wouldn't need to put the underscore in any of the scripts under the examples folder.

The rationale behind this is the separation of unit tests from smoke tests. Also, the way we run ppafm will undergo some transformation soon.

So, I would not worry about this now. We can revisit tests in the future when we have a clearer idea of where we are going.

[yakutovicha]

I tried running the test with Python 3.8 locally, and interestingly the segfault only happens when running all tests with pytest. If run individually (with or without pytest), the test passes, so it seems that one of the other test functions is messing up the state somehow. No clue why it's only happening on 3.8, though.

I believe it has to do with the fact that Python loads modules only once (which makes sense). If the same module is used for two different simulations, it creates problems. The params variable, for instance, will be shared among those runs.

This makes the case clear that storing some state variables inside a module is not a good idea. That is why I created #232.

That is also why tests are useful in general 👍

[NikoOinonen]

The rationale behind this is the separation of unit tests from smoke tests.

Makes sense, but I also kind of think that the examples directory is also not the right place for them. I would maybe put them into their own subdirectory in tests/smoke_tests or something, but it's not that important, so I will leave it up to you.