CR-Rejection wrapper for calstis — crrej_from_raw()

[sean-lockwood]

This code does the following:

• parse an input RAW STIS file for the CRREJTAB
• determine the appropriate row from the default CRREJTAB
• determine user overrides for the various CRREJTAB columns
• write a temporary CRREJTAB
• update the input RAW file to use the temporary CRREJTAB and add a HISTORY line
• run calstis on the RAW file
• revert the CRREJTAB and HISTORY in the RAW file

Note on testing:
The associated tests only check that input parameters do not fail immediately. The calls to calstis are terminated early by making the test data not contain a data table. So, output FITS products are not tested for the desired changes in the CRREJTAB.

@awfullerton: Let me know if you have any feedback on the interface or the routine name.

[sean-lockwood]

Documentation branch: https://stistools--159.org.readthedocs.build/en/159/override_crrej.html

Edit: Moved to here: https://stistools--159.org.readthedocs.build/en/159/crrej_from_raw.html

[sean-lockwood]

@stscirij -
I wasn't able to get the test code to work in the tests/ directory on my system, likely due to the conftest.py conflicting with the bare tests generated to test this routine. It does work fine when moved to another location.

Any thoughts on how to get this working properly would be appreciated.

UPDATE:
Testing issues have been resolved in the repo. The tests now work on my system locally.

[sean-lockwood]

Tests now look good:

pytest -vv test_crrej_from_raw.py

============================================================================= test session starts ==============================================================================
platform darwin -- Python 3.11.3, pytest-8.3.4, pluggy-1.5.0 -- /Users/lockwood/miniconda3/envs/stenv-macOS-ARM64-py3.11-2023.06.08/bin/python3
cachedir: .pytest_cache
rootdir: /Users/lockwood/git/stis/stistools-testing
configfile: pyproject.toml
plugins: asdf-2.15.0, jwst-1.10.2, ci_watson-0.8.0, xdist-3.3.1, anyio-3.7.0
collected 31 items

test_crrej_from_raw.py::Test_crrej_from_raw::test_user_crrejtab PASSED                                                                                                   [  3%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_meanexp_selection[1.2-4.4] PASSED                                                                                      [  6%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_meanexp_selection[4.4-4.4] PASSED                                                                                      [  9%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_bad_meanexp_selection PASSED                                                                                           [ 12%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_scalense PASSED                                                                                                        [ 16%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_initgues[minimum] PASSED                                                                                               [ 19%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_initgues[median] PASSED                                                                                                [ 22%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_bad_initgues PASSED                                                                                                    [ 25%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_skysub[none] PASSED                                                                                                    [ 29%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_skysub[mode] PASSED                                                                                                    [ 32%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_bad_skysub PASSED                                                                                                      [ 35%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_crsigmas[3] PASSED                                                                                                     [ 38%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_crsigmas[3,4] PASSED                                                                                                   [ 41%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_crsigmas[3,4.0] PASSED                                                                                                 [ 45%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_crsigmas[5] PASSED                                                                                                     [ 48%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_crsigmas[5.2] PASSED                                                                                                   [ 51%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_crradius PASSED                                                                                                        [ 54%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_crthresh[1.1] PASSED                                                                                                   [ 58%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_crthresh[3] PASSED                                                                                                     [ 61%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_crthresh[0] PASSED                                                                                                     [ 64%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_crthresh[-2.0] PASSED                                                                                                  [ 67%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_badinpdq[18] PASSED                                                                                                    [ 70%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_badinpdq[2.0001] PASSED                                                                                                [ 74%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_badinpdq[9600] PASSED                                                                                                  [ 77%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_crmask[True] PASSED                                                                                                    [ 80%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_crmask[False] PASSED                                                                                                   [ 83%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_crmask[None] PASSED                                                                                                    [ 87%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_crmask[1] PASSED                                                                                                       [ 90%]
test_crrej_from_raw.py::Test_crrej_from_raw::test_crmask[0] PASSED                                                                                                       [ 93%]
test_crrej_from_raw.py::Test_versions::test_version PASSED                                                                                                               [ 96%]
test_crrej_from_raw.py::Test_versions::test_revision PASSED                                                                                                              [100%]

=============================================================================== warnings summary ===============================================================================
../stistools/sshift.py:221
  /Users/lockwood/git/stis/stistools-testing/stistools/sshift.py:221: DeprecationWarning: invalid escape sequence '\.'
    outfile = re.sub('flt\.', 'sfl.', infile, count=1)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
======================================================================== 31 passed, 1 warning in 2.66s =========================================================================

The warning is unrelated to this code.

[sean-lockwood]

@stscirij, @Jackie-Brown -
This PR should be ready to review.

Update: Well, now after PEP8 updates.

[stscirij]

This looks good.
Maybe add a unit test to verify that the input file is left unchanged after running, since it looks like there's some writing to and removing from the file

[sean-lockwood]

@stscirij -
Thanks! I've added a test for that.

[stscirij]

Looks good!

[stscirij]

Maybe also fix the deprecation warning? I think it turns into a syntax error in 3.12. Just need to turn the string into an r-string I think...

[sean-lockwood]

Oh, that should be an easy fix. Will do today.

Update: PR #175