Add opencadd.databases.klifs module

[dominiquesydow]

Description

Integrate klifs_utils package into opencadd in the form of the opencadd.databases.klifs module.

Todos

• [x] Move klifs_utils code to opencadd.databases.klifs
  • Code from https://github.com/volkamerlab/klifs_utils/tree/extend_coordinates, i.e. the extend_coordinates branch with simplifications of the coordinates module as described in PR https://github.com/volkamerlab/klifs_utils/pull/10
• [x] Update imports and __init__.py files.
• [x] Update and run tutorial (instead of running unit test, which do not exist yet): docs/tutorials/klifs.ipydb
• [x] Update devtools/conda-envs/test_env.yml
• [x] Add klifs tests (skeleton) to opencadd.tests.databases.test_databases_klifs.py and test data to opencadd/tests/databases/data/
• [x] Run black reformatter
• [x] Add sphinx documentation to docs/index.rst
  • Description: docs/databases_klifs.rst
  • Tutorial: docs/tutorials/databases_klifs.rst

Questions

• [x] Where to add module dependencies? Currently devtools/conda-envs/test_env.yml.
• [x] Where to add unit tests and data for klifs module? Currently opencadd.tests.databases.
• [x] Where to add a README for the opencadd.databases.klifs module? opencadd/databases/klifs/README.md? > Added in the form of a sphinx documentation in docs/databases_klifs.rst.

Status

• [ ] Ready to go

[codecov-commenter]

Codecov Report

Merging #38 into master will decrease coverage by 19.41%. The diff coverage is 27.68%.

[dominiquesydow]

@jaimergp, whenever the test checks are done (they are in waiting mode for quite a while already), could you review this PR, please? The main aim here is to integrate the existing klifs_utils code into the opencadd package.

In the next PR, I plan to simplify the API a bit and add unit testing, thus I suggest reviewing here only the package-level part - and the API next time.

[dominiquesydow]

My main question is if I put the testing and environment bits at the right position within the package (see PR Questions).

[dominiquesydow]

@jaimergp, coming back to the still pending checks. Is it possible that the checks "test (xxx)" are outdated? https://github.community/t/expected-waiting-for-status-to-be-reported/16727

When I look into the protected branch settings, I see (only part of it shown): https://github.com/volkamerlab/opencadd/settings/branches

The "Test on xxx" checks match with the ci.yaml configs: https://github.com/volkamerlab/opencadd/blob/master/.github/workflows/ci.yaml

Maybe we need to check those instead?

[jaimergp]

Yep, good catch, this was inherited from the previous superposer configs. Reviewing now.

[jaimergp]

All good! This was an excellent PR. Thanks for your contribution!