Add comments to test/ci files

[mfschubert]

Hi @polyanskiy --- as discussed in this thread, I'm adding some comments to test and CI files. Here's a quick summary:

• tests/test_parse.py: this test discovers all .yml files in the database and checks that they can be successfully parsed. It can be invoked using the pytest command, which automatically discovers and runs tests. (The pytest and parameterized python packages must be installed).
• .github/workflows/test.yml: this file defines a github action which checks out the repository, installs pytest and parameterized, and then runs pytest. The action is configured to run on pull requests and for pushes to the master branch.

I've also added a .github/dependabot.yml file, which will handle automatic security/version updates. For example, when a new version of the github checkout action is available, dependabot will create a PR proposing an update to the test.yml file.

Finally, in creating this PR I noticed that another .yml file error appeared. Going forward, to make the most of the automated test/ci capabilities, I would suggest authoring PRs rather than directly pushing to the master branch. Then, you will have a chance to catch any issues before you merge.

Let me know if you have any questions or if I can help otherwise.

[polyanskiy]

Thank you!

I’m not very familiar with the tools you are using, so it might take me a bit of time to figure out how to use them. At the moment, I’m having trouble understanding the output of pytest when I try running it on my local copy of the repository:

c:\Users\polyanskiy\Documents\GitHub\refractiveindex.info-database>pytest
================================================= test session starts =================================================
platform win32 -- Python 3.12.7, pytest-8.3.4, pluggy-1.5.0
rootdir: c:\Users\polyanskiy\Documents\GitHub\refractiveindex.info-database
collected 0 items / 1 error

======================================================= ERRORS ========================================================
________________________________________ ERROR collecting tests/test_parse.py _________________________________________
tests\test_parse.py:35: in
class ParseTest(unittest.TestCase):
tests\test_parse.py:36: in ParseTest
@parameterized.expand(PATHS, name_func=custom_name_func)
C:\Program Files\Python312\Lib\site-packages\parameterized\parameterized.py:594: in parameterized_expand_wrapper
name = name_func(f, "{num:0>{digits}}".format(digits=digits, num=num), p)
tests\test_parse.py:30: in custom_name_func
assert "/database/" in path
E AssertionError: assert '/database/' in 'C:\Users\polyanskiy\Documents\GitHub\refractiveindex.info-database\database\catalog-n2.yml'
=============================================== short test summary info ===============================================
ERROR tests/test_parse.py - AssertionError: assert '/database/' in 'C:\Users\polyanskiy\Documents\GitHub\refractiveindex.info-database\da...
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
================================================== 1 error in 1.87s ===================================================

[mfschubert]

Ah interesting, this seems to be a windows vs. linux issue. Linux will use / to indicate subdirectories, while windows seems to use \. We should be able to modify the test so that it works on both OSes. I could try to do this tomorrow, unless you prefer to do so.

[mfschubert]

Actually I just made a PR for this: #52

[polyanskiy]

Great! It's running now but it fails yaml files with certain Unicode characters (e.g., č):

C:\Program Files\Python312\Lib\encodings\cp1252.py:23: UnicodeDecodeError
============================================================= short test summary info =============================================================
FAILED tests/test_parse.py::ParseTest::test_can_parse_database_data_n2_main_AgGaS2_Jansonas_e_yml - UnicodeDecodeError: 'charmap' codec can't decode byte 0x8d in position 235: character maps to
FAILED tests/test_parse.py::ParseTest::test_can_parse_database_data_n2_main_AgGaS2_Jansonas_o_yml - UnicodeDecodeError: 'charmap' codec can't decode byte 0x8d in position 235: character maps to

[mfschubert]

Hmm, could you check which version of python you are using? I am using python 3.10.12 with yaml version 6.0.1. Is there any chance you are using a much older version?

[mfschubert]

Actually, maybe this could fix it. Swap out line 39/40 with the following:

with open(path, "r", encoding="utf8") as stream:
    yaml.safe_load(stream)

[polyanskiy]

That’s it! Adding encoding="utf8" fixed the problem.
Thank you!

[mfschubert]

Great! By the way, there seems to be an issue with dependabot, which I cannot debug because I don't have the appropriate permission.

Could you access the "more information" link on this page and paste it here? Then I might be able to tell what is wrong.
https://github.com/polyanskiy/refractiveindex.info-database/actions/runs/12145946006

Thanks!

[polyanskiy]

Dependabot couldn't find any dependency files in the directory
Dependabot couldn't find any dependency files in the configured directory

[mfschubert]

Ok, this can probably be fixed by updating the dependabot.yml file to remove the package-ecosystem: pip section. It would then read:

# This `dependabot.yml` file handles automatic security/version updates. In this repo,
# it may e.g. update the version of the checkout action used in the `test.yml` action.
# See https://github.com/dependabot/dependabot-core for additional info.

version: 2
updates:
  - package-ecosystem: github-actions
    directory: /
    schedule:
      interval: monthly