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Minor refactoring of the structure.py module #170

Merged
merged 6 commits into from
Jun 29, 2023
Merged

Minor refactoring of the structure.py module #170

merged 6 commits into from
Jun 29, 2023

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andthum
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@andthum andthum commented Jun 29, 2023

Minor refactoring of the structure.py module

Type of change

  • Change of core package.
  • Change of scripts.
  • Bug fix.
  • New feature.
  • Code refactoring.
  • Dependency update.
  • Documentation update.
  • Maintenance.
  • Other: Description.
  • Non-breaking (backward-compatible) change.
  • Breaking (non-backward-compatible) change.

Proposed changes

  • Update some pre-commit hooks.
  • Update/correct documentation and run-time information of some functions in the structure.py module.
  • Function mdtools.structure.contact_matrix: Raise a DeprecationWarning when using the debug argument.

PR checklist

  • I followed the guidelines in the Developer's guide.
  • New/changed code is properly tested.
  • [~] New/changed code is properly documented.
  • The CI workflow is passing.

@andthum
[.pre-commit-config.yaml]: Update
8163204 
Updates:

* https://github.com/python-jsonschema/check-jsonschema from `0.22.0` to
`0.23.2`.
* https://github.com/shellcheck-py/shellcheck-py from `v0.9.0.2` to
`v0.9.0.5`.

Downgrades:

* https://github.com/markdownlint/markdownlint from `v0.11.0` to
`v0.9.0`, because `v0.11.0` and `v0.10.0` somehow now require ruby2.6,
but openSUSE only provides ruby2.5.
@andthum
[structure.py]: Function natms_per_cmp: Correct Docstring
cbf2e91
@andthum
[structure.py]: Function contact_matrix: Raise DeprecationWarning W…
3722a5a 
…hen Using `debug` Argument
@andthum
[structure.py]: Function contact_matrices: Update Docstring And Run…
3ecaa2f 
… Time Info
@andthum
[structure.py]: Function discrete_pos_trj: Update Run Time Info
a5ffc78
@andthum
[structure.py]: Function contact_hist_refcmp_same_selcmp: Add Comment
2d0226b
@github-actions github-actions bot added documentation Improvements or additions to documentation maintenance Project maintenance patch Change that results in a new patch version refactoring Code refactoring labels Jun 29, 2023
@andthum andthum merged commit 3a03398 into main Jun 29, 2023
30 checks passed
@andthum andthum deleted the ref/src/mdtools/structure branch June 29, 2023 15:14
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