[INF] simplify a bit linting, use pre-commit as CI linting checker #892

Zeroto521 · 2021-08-25T02:39:38Z

PR Description

Please describe the changes proposed in the pull request:

There is two similar linting CIs (pre-commit and code-checks) but also have tiny differences.
We should use one of them as the standard, not both. Otherwise, we would get confused.

PR Checklist

Please ensure that you have done the following:

PR in from a fork off your branch. Do not PR from <your_username>:dev, but rather from <your_username>:<feature-branch_name>.

If you're not on the contributors list, add yourself to AUTHORS.rst.

Add a line to CHANGELOG.md under the latest version header (i.e. the one that is "on deck") describing the contribution.
- Do use some discretion here; if there are multiple PRs that are related, keep them in a single line.

Automatic checks

There will be automatic checks run on the PR. These include:

Building a preview of the docs on Netlify
Automatically linting the code
Making sure the code is documented
Making sure that all tests are passed
Making sure that code coverage doesn't go down.

Relevant Reviewers

Please tag maintainers to review.

@ericmjl

There is two similar linting CIs (pre-commit and code-checks) but also have tiny differences. We should use one of them as the standard, not both.

Zeroto521 · 2021-08-25T02:41:15Z

.pre-commit-config.yaml

+  rev: 3.9.2
+  hooks:
+    - id: flake8
+      args: [--exclude, nbconvert_config.py]


code-checks.yml has flake8, but pre-commit doesn't.

.pre-commit-config.yaml

codecov · 2021-08-25T02:48:35Z

Codecov Report

Merging #892 (a9a7c8c) into dev (36d6a6b) will decrease coverage by 0.04%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##              dev     #892      +/-   ##
==========================================
- Coverage   95.66%   95.62%   -0.05%     
==========================================
  Files          19       19              
  Lines        2448     2448              
==========================================
- Hits         2342     2341       -1     
- Misses        106      107       +1

Zeroto521 · 2021-08-25T02:53:07Z

Because the linting standard is different, so https://github.com/pyjanitor-devs/pyjanitor/pull/892/checks is red.

Now we should determine to use which linting is the standard.
code-checks.yml or pre-commit?

ericmjl · 2021-08-25T10:36:13Z

@Zeroto521 thanks for handling this! In the interest of minimizing the diff, I think we should defer to the codechecks.yml file for the settings, but use pre-commit as our actual code checker. Would you be open to making that happen please?

`-c` = `--code TEXT`, Format the code passed in as a string.

keep the same with the old code-checks.yml

…21/pyjanitor into simplify-code-checks.yml

Zeroto521

Now use the old code-checks.yml as the base standard and pre-commit as the lining checker.

But these hooks weren't removed. They changed a little. Just remove some whitespace when lint.

hooks:
  - id: trailing-whitespace
  - id: end-of-file-fixer
  - id: check-yaml
  - id: check-added-large-files

Zeroto521 · 2021-08-26T02:48:55Z

.pre-commit-config.yaml

- repo: https://github.com/kynan/nbstripout
-  rev: 0.5.0
-  hooks:
-  - id: nbstripout
-    files: ".ipynb"


nbstripout should be removed.
It changed a lot, even would make ipynb outputs become empty.

Got it, thanks @Zeroto521.

We can remove it for now. In a future setting, though, I think we'd want to do the notebooks such that they are built in the CI system and deployed.

I see conf.py already adds nbsphinx, but no a .rst file index these notebooks.

Right. Regarding the notebooks (and docs more generally), I have been debating, btw, to switch the docs over to mkdocs + mkdocs-material. It is much easier to maintain in the long-run than Sphinx; I know I have been hesitant to make any changes to the docs as it stands right now because of a lot of magic that happens behind the scenes that I'm just not well-versed in, whereas MkDocs and mkdocs-material are much easier to maintain combined. (It feels... flatter.)

ericmjl · 2021-08-26T10:36:16Z

Let's get one more review in before merging. Tagging @loganthomas and @hectormz, whom I think might take an interest in the PR.

ericmjl · 2021-09-04T14:00:08Z

@Zeroto521 I'm going to merge as I'd like to have these changes present in #897. Thanks for your contributions here, much appreciated!

* [INF] simplify a bit linting, use pre-commit as CI linting checker (#892) * [INF] simplify a bit linting There is two similar linting CIs (pre-commit and code-checks) but also have tiny differences. We should use one of them as the standard, not both. * Update CHANGELOG.md * should be `--config` not `-c` `-c` = `--code TEXT`, Format the code passed in as a string. * remove nbstripout keep the same with the old code-checks.yml * lint via pre-commit * Update CHANGELOG.md Co-authored-by: Eric Ma <[email protected]> * [DOC] mkdocs updates to ml module * [DOC] mkdocs updates to ml module * [DOC] mkdocs updates to ml module * [DOC] mkdocs updates to ml module; black formatting Co-authored-by: Zero <[email protected]> Co-authored-by: Eric Ma <[email protected]>

* [INF] simplify a bit linting, use pre-commit as CI linting checker (#892) * [INF] simplify a bit linting There is two similar linting CIs (pre-commit and code-checks) but also have tiny differences. We should use one of them as the standard, not both. * Update CHANGELOG.md * should be `--config` not `-c` `-c` = `--code TEXT`, Format the code passed in as a string. * remove nbstripout keep the same with the old code-checks.yml * lint via pre-commit * Update CHANGELOG.md Co-authored-by: Eric Ma <[email protected]> * [DOC] mkdocs updates to read_csv() in io * [DOC] mkdocs updates to incldue io in docs Co-authored-by: Zero <[email protected]> Co-authored-by: Eric Ma <[email protected]>

* [INF] simplify a bit linting, use pre-commit as CI linting checker (#892) * [INF] simplify a bit linting There is two similar linting CIs (pre-commit and code-checks) but also have tiny differences. We should use one of them as the standard, not both. * Update CHANGELOG.md * should be `--config` not `-c` `-c` = `--code TEXT`, Format the code passed in as a string. * remove nbstripout keep the same with the old code-checks.yml * lint via pre-commit * Update CHANGELOG.md Co-authored-by: Eric Ma <[email protected]> * [DOC] mkdocs updates to log() in math * [DOC] mkdocs updates to ecdf() in math * [DOC] mkdocs updates to exp() in math * [DOC] mkdocs updates to logit() in math * [DOC] mkdocs updates to normal_cdf() in math * [DOC] mkdocs updates to probit() in math * [DOC] mkdocs updates to single line docstrings in math * [DOC] mkdocs updates to z_score() in math Co-authored-by: Zero <[email protected]> Co-authored-by: Eric Ma <[email protected]>

* mkdocstrings on chemistry functions * Minor update to biology.py * Proper config for syntax highlighting * Switch to nord theme for syntax highlighting * [INF] simplify a bit linting, use pre-commit as CI linting checker (#892) * [INF] simplify a bit linting There is two similar linting CIs (pre-commit and code-checks) but also have tiny differences. We should use one of them as the standard, not both. * Update CHANGELOG.md * should be `--config` not `-c` `-c` = `--code TEXT`, Format the code passed in as a string. * remove nbstripout keep the same with the old code-checks.yml * lint via pre-commit * Update CHANGELOG.md Co-authored-by: Eric Ma <[email protected]> * FLake8 fix. Co-authored-by: Zero <[email protected]>

* [INF] simplify a bit linting, use pre-commit as CI linting checker (#892) * [INF] simplify a bit linting There is two similar linting CIs (pre-commit and code-checks) but also have tiny differences. We should use one of them as the standard, not both. * Update CHANGELOG.md * should be `--config` not `-c` `-c` = `--code TEXT`, Format the code passed in as a string. * remove nbstripout keep the same with the old code-checks.yml * lint via pre-commit * Update CHANGELOG.md Co-authored-by: Eric Ma <[email protected]> * [CLN] remove README.rst in favor of mkdocs/index.md * [CLN] remove CONTRIBUTING.rst in favor of mkdocs/devguide.md * [DOC] add symlink to mkdocs/devguide.md for CONTRIBUTING.md * [FIX] remove file CONTRIBUTING.md * [DOC] add symlink to mkdocs/devguide.md for CONTRIBUTING.md * [INF] update setup.py to replace README.rst with mkdocs/index.md Co-authored-by: Zero <[email protected]> Co-authored-by: Eric Ma <[email protected]>

* [INF] simplify a bit linting, use pre-commit as CI linting checker (#892) * [INF] simplify a bit linting There is two similar linting CIs (pre-commit and code-checks) but also have tiny differences. We should use one of them as the standard, not both. * Update CHANGELOG.md * should be `--config` not `-c` `-c` = `--code TEXT`, Format the code passed in as a string. * remove nbstripout keep the same with the old code-checks.yml * lint via pre-commit * Update CHANGELOG.md Co-authored-by: Eric Ma <[email protected]> * [DOC] mkdocs updates to convert_units() in engineering Co-authored-by: Zero <[email protected]> Co-authored-by: Eric Ma <[email protected]>

* [INF] simplify a bit linting, use pre-commit as CI linting checker (#892) * [INF] simplify a bit linting There is two similar linting CIs (pre-commit and code-checks) but also have tiny differences. We should use one of them as the standard, not both. * Update CHANGELOG.md * should be `--config` not `-c` `-c` = `--code TEXT`, Format the code passed in as a string. * remove nbstripout keep the same with the old code-checks.yml * lint via pre-commit * Update CHANGELOG.md Co-authored-by: Eric Ma <[email protected]> * [DOC] mkdocs updates to refactored_function() in utils * [DOC] mkdocs updates to rename_kwargs() in utils * [DOC] mkdocs updates to check_column() in utils * [DOC] mkdocs updates to skipna() in utils * [DOC] mkdocs updates to skiperror() in utils Co-authored-by: Zero <[email protected]> Co-authored-by: Eric Ma <[email protected]>

* [INF] simplify a bit linting, use pre-commit as CI linting checker (#892) * [INF] simplify a bit linting There is two similar linting CIs (pre-commit and code-checks) but also have tiny differences. We should use one of them as the standard, not both. * Update CHANGELOG.md * should be `--config` not `-c` `-c` = `--code TEXT`, Format the code passed in as a string. * remove nbstripout keep the same with the old code-checks.yml * lint via pre-commit * Update CHANGELOG.md Co-authored-by: Eric Ma <[email protected]> * [DOC] mkdocs updates to check() in utils * [DOC] mkdocs updates to _strip_underscores() in utils * [DOC] mkdocs updates to import_message() in utils * [DOC] mkdocs updates to idempotent() in utils * [DOC] mkdocs updates to deprecated_alias() in utils Co-authored-by: Zero <[email protected]> Co-authored-by: Eric Ma <[email protected]>

* [INF] simplify a bit linting, use pre-commit as CI linting checker (#892) * [INF] simplify a bit linting There is two similar linting CIs (pre-commit and code-checks) but also have tiny differences. We should use one of them as the standard, not both. * Update CHANGELOG.md * should be `--config` not `-c` `-c` = `--code TEXT`, Format the code passed in as a string. * remove nbstripout keep the same with the old code-checks.yml * lint via pre-commit * Update CHANGELOG.md Co-authored-by: Eric Ma <[email protected]> * DOC: update _sub_expand_grid(pd.DataFrame) in utils * DOC: update _sub_expand_grid(pd.Index) in utils * DOC: update _data_checks_complete() in utils * DOC: update _computations_complete() in utils * DOC: update _create_indexer_for_complete() in utils Co-authored-by: Zero <[email protected]> Co-authored-by: Eric Ma <[email protected]>

* [INF] simplify a bit linting, use pre-commit as CI linting checker (#892) * [INF] simplify a bit linting There is two similar linting CIs (pre-commit and code-checks) but also have tiny differences. We should use one of them as the standard, not both. * Update CHANGELOG.md * should be `--config` not `-c` `-c` = `--code TEXT`, Format the code passed in as a string. * remove nbstripout keep the same with the old code-checks.yml * lint via pre-commit * Update CHANGELOG.md Co-authored-by: Eric Ma <[email protected]> * DOC: update _computations_expand_grid() in utils * DOC: update _expand_grid() in utils * DOC: update _sub_expand_grid() in utils * DOC: update _sub_expand_grid(np.ndarray) in utils * DOC: update _sub_expand_grid(pd.Series) in utils * [DOC] fix NumPy Co-authored-by: Zero <[email protected]> Co-authored-by: Eric Ma <[email protected]>

Zeroto521 added 2 commits August 25, 2021 10:35

[INF] simplify a bit linting

57c979a

There is two similar linting CIs (pre-commit and code-checks) but also have tiny differences. We should use one of them as the standard, not both.

Update CHANGELOG.md

f876e73

Zeroto521 commented Aug 25, 2021

View reviewed changes

.pre-commit-config.yaml Outdated Show resolved Hide resolved

Merge branch 'dev' into simplify-code-checks.yml

cdd5af9

samukweku assigned Zeroto521 Aug 25, 2021

samukweku requested a review from loganthomas August 25, 2021 04:43

Zeroto521 added 3 commits August 26, 2021 09:54

should be --config not -c

729a96b

`-c` = `--code TEXT`, Format the code passed in as a string.

remove nbstripout

365422d

keep the same with the old code-checks.yml

lint via pre-commit

869159e

Zeroto521 changed the title ~~[INF] simplify a bit linting, use pre-commit as the standard~~ [INF] simplify a bit linting Aug 26, 2021

Update CHANGELOG.md

086908f

Zeroto521 changed the title ~~[INF] simplify a bit linting~~ [INF] simplify a bit linting, use pre-commit as the CI linting checker Aug 26, 2021

Zeroto521 changed the title ~~[INF] simplify a bit linting, use pre-commit as the CI linting checker~~ [INF] simplify a bit linting, use pre-commit as CI linting checker Aug 26, 2021

Merge branch 'simplify-code-checks.yml' of https://github.com/Zeroto5…

71fee7c

…21/pyjanitor into simplify-code-checks.yml

Zeroto521 commented Aug 26, 2021

View reviewed changes

ericmjl approved these changes Aug 26, 2021

View reviewed changes

Merge branch 'dev' into simplify-code-checks.yml

a9a7c8c

ericmjl merged commit f4b4f8e into pyjanitor-devs:dev Sep 4, 2021

Zeroto521 deleted the simplify-code-checks.yml branch September 6, 2021 01:50

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