Resolve 30 skipped tests after all dependencies are installed and released correctly

[bobleesj]

30 tests are skipped when pyobjcryst, diffpy.structure, diffpy.srreal, sas are not installed.

Current result without installing the dependencies mentioned above:

conda create -n diffpy.srfit_312 python=3.12
conda activate diffpy.srfit_312
pip install -r requirement/run.txt  # scipy, numpy, matplotlib (at the moment)
pip install . --no-deps
pytest

====== 80 passed, 30 skipped, 1 warning in 0.43s =====

[sbillinge]

I think we don't want to skip these, so we just have CI install these things?

[bobleesj]

yes we don't want to, while we re-cookiecut, i will add these dependencies under run.txt and see what happens.

[bobleesj]

Discussed with @sbillinge in #89

• include optional dependencies such as diffpy.structure under run-ext.txt

[sbillinge]

reopening. Let's close when it is merged into main and fully resolved.

[zmx27]

I suggest that we move this issue to a later release because this can only be done when all of our other packages are released. Additionally, we are facing problems with sasmodels right now as discussed in #126

[sbillinge]

Please can you review how many skips we have left now, and how many are related to the sas issue, just for review.

[zmx27]

Here is the result of running pytest after the changes in #126:

========================================== warnings summary ==========================================
tests/test_sas.py::test_generator
tests/test_sas.py::testGenerator2
  /Users/zhimingxu/miniconda3/envs/srfit-env/lib/python3.13/site-packages/pyopencl/cache.py:496: CompilerWarning: Non-empty compiler output encountered. Set the environment variable PYOPENCL_COMPILER_OUTPUT=1 to see more.
    _create_built_program_from_source_cached(

tests/test_sas.py::test_generator
tests/test_sas.py::testGenerator2
  /Users/zhimingxu/miniconda3/envs/srfit-env/lib/python3.13/site-packages/pyopencl/cache.py:500: CompilerWarning: Non-empty compiler output encountered. Set the environment variable PYOPENCL_COMPILER_OUTPUT=1 to see more.
    prg.build(options_bytes, devices)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
============================= 84 passed, 27 skipped, 4 warnings in 5.24s =============================

Although I'm still in progress with refactoring the code to use the updated sasview api, I dealt with the three tests in test_sas.py that were initially skipped. Next, there are four more tests in test_characteristicfunctions.py that has to be skipped because the calculate_ER function raises a NotImplementedError. This makes for a total of 7 tests total out of the original 30 skipped tests that are related to the sas issue.

[ycexiao]

I have successfully run other tests. There are two similar errors

        stru = PDFFitStructure()
        ciffile = datafile("ni.cif")
>       stru.read(ciffile)

tests/test_pdf.py:163: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
../diffpy.structure/src/diffpy/structure/pdffitstructure.py:75: in read
    p = Structure.read(self, filename, format)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
../diffpy.structure/src/diffpy/structure/structure.py:285: in read
    new_structure = p.parseFile(filename)
                    ^^^^^^^^^^^^^^^^^^^^^
../diffpy.structure/src/diffpy/structure/parsers/p_auto.py:146: in parseFile
    return self._wrapParseMethod("parseFile", filename)

The reason is that the current version of diffpy.structure accepts a filename string, not a filename pathlib.Path. It is also mentioned in diffpy/diffpy.structure#124

[sbillinge]

Great, thanks. Let's make sure that any unmerged issues from this list have their own issue on diffpy.structure or diffpy.srfit for us to fix later (for example, but not limited to, the sas issues). Then we can close this.