[MNT] Add codespell support (config, workflow to detect/not fix) and make it fix a "few" typos

[yarikoptic]

More about codespell: https://github.com/codespell-project/codespell .

I personally introduced it to dozens if not hundreds of projects already and so far only positive feedback.

CI workflow has 'permissions' set only to 'read' so also should be safe.

This is just a draft: due to large number of typos detected, so before tuning up config and skips, I decided first to check with you either you would be interested/willing to eventually review/accept such a PR. But if you spot false positive -- alert or introduce into pyproject.toml config for codespell and let's work together to make aeon "typos free"!

TODOs

• ...
• [ ] run round of interactive fixes for ambiguous typos -- I didn't do yet

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[MatthewMiddlehurst]

@yarikoptic anything you need for this? No issue if you're just busy.

[yarikoptic]

@MatthewMiddlehurst thanks for the review!

There are a few concerns that would mean I would not want it editing my code/docs on its own, but making PRs or suggestions is fine, and I could see it being helpful.

this would not do any changes -- it would just detect and annotate like at https://github.com/aeon-toolkit/aeon/pull/2653/files#diff-55dd3e1949bcb682be343ce038cc8afa221db3fd5d3096eee878870ca6b34543 you can now see

which you would not get if you have only pre-commit. Up to you to either leave a dedicated CI as well, or just resort to pre-commit. I personally prefer a dedicated one for this and other reasons such as immediately becomes clear that likely culprit is just a typo ;)

[yarikoptic]

@yarikoptic anything you need for this? No issue if you're just busy.

ideally

1. someone going through those ambigous ones to see if anything to skip at files level or just for specific words or ...

❯ codespell
./aeon/benchmarking/results_loaders.py:254: ot ==> to, of, or, not, it
./aeon/classification/deep_learning/_disjoint_cnn.py:57: ot ==> to, of, or, not, it
./aeon/classification/deep_learning/_fcn.py:39: ot ==> to, of, or, not, it
./aeon/classification/dictionary_based/_tde.py:619: propotion ==> proportion, promotion
./aeon/classification/ordinal_classification/_ordinal_tde.py:593: propotion ==> proportion, promotion
./aeon/clustering/deep_learning/_ae_dcnn.py:49: ot ==> to, of, or, not, it
./aeon/clustering/deep_learning/_ae_fcn.py:47: ot ==> to, of, or, not, it
./aeon/networks/_ae_fcn.py:37: ot ==> to, of, or, not, it
./aeon/networks/_disjoint_cnn.py:51: ot ==> to, of, or, not, it
./aeon/networks/_fcn.py:32: ot ==> to, of, or, not, it
./aeon/regression/deep_learning/_disjoint_cnn.py:57: ot ==> to, of, or, not, it
./aeon/regression/deep_learning/_fcn.py:39: ot ==> to, of, or, not, it
./aeon/segmentation/_ggs.py:66: interative ==> interactive, iterative
./aeon/segmentation/_ggs.py:129: fo ==> of, for, to, do, go
./aeon/segmentation/_ggs.py:390: interative ==> interactive, iterative
./aeon/segmentation/_hidalgo.py:540: lik ==> like, lick, link
./aeon/segmentation/_hidalgo.py:541: lik ==> like, lick, link
./aeon/segmentation/_hidalgo.py:625: lik ==> like, lick, link
./aeon/segmentation/_hidalgo.py:627: lik ==> like, lick, link
./aeon/segmentation/_hidalgo.py:629: lik ==> like, lick, link
./aeon/segmentation/_hmm.py:246: preceeding ==> preceding, proceeding
./aeon/similarity_search/base.py:199: interable ==> iterable, interactable, integrable, intolerable
./aeon/similarity_search/query_search.py:163: Interable ==> Iterable, Interactable, Integrable, Intolerable
./aeon/transformations/collection/channel_selection/_channel_scorer.py:25: fro ==> for, from
./aeon/transformations/collection/convolution_based/_minirocket.py:142: dependend ==> dependent, depended, depend
./aeon/transformations/collection/convolution_based/_multirocket.py:164: dependend ==> dependent, depended, depend
./aeon/transformations/collection/tests/test_pad.py:69: padd ==> pad, padded
./aeon/utils/tags/_tags.py:3: contrained ==> constrained, contained
./aeon/visualisation/estimator/_shapelets.py:262: macth ==> match, math, mach
./aeon/visualisation/estimator/_shapelets.py:515: macth ==> match, math, mach
./aeon/visualisation/estimator/_shapelets.py:1117: macth ==> match, math, mach
./aeon/visualisation/results/_mcm.py:141: ot ==> to, of, or, not, it
./aeon/visualisation/results/_scatter.py:291: wil ==> will, well
./aeon/visualisation/results/_scatter.py:296: wil ==> will, well
./docs/conf.py:591: buttom ==> button, bottom
./docs/changelogs/v0/v0.1.md:54: coverting ==> converting, covering, coveting
./docs/changelogs/v0/v0.6.md:126: ot ==> to, of, or, not, it
./examples/clustering/partitional_clustering.ipynb:142: proably ==> probably, provably
./examples/datasets/provided_data.ipynb:496: flourescent ==> fluorescent, florescent
./examples/distances/distances.ipynb:418: constained ==> constrained, contained
./examples/networks/deep_learning.ipynb:257: throught ==> thought, through, throughout
./examples/transformations/sast.ipynb:2152: considere ==> consider, considered
./examples/transformations/tsfresh.ipynb:9: extacting ==> extracting, exacting

2. add those and other false positives to ignore to pyproject.toml config: https://github.com/aeon-toolkit/aeon/pull/2653/files#diff-50c86b7ed8ac2cf95bd48334961bf0530cdc77b5a56f852c5c61b89d735fd711 .

then we could rerun that commit with codespell -w and fall it up with the codespell -w -i 3 -C 2 to address outstanding "ambiguous" ones and be done and make aeon typos free!

[MatthewMiddlehurst]

Hi, @yarikoptic I went ahead and did the above. I think It would fit better into our current setup going through pre-commit. Can you just do the annotations without the other action? Would be helpful if you could take a look at the setup for any issues. Don't have to go through all the typos 🙂

[MatthewMiddlehurst]

Also, I am a fan of skipping .git don't think we want to skip .github, .git* will do both I believe, tried a few ways to do one but not the other but didn't work. Not sure if you could help with that @yarikoptic

[yarikoptic]

Hi, @yarikoptic I went ahead and did the above. I think It would fit better into our current setup going through pre-commit. Can you just do the annotations without the other action? Would be helpful if you could take a look at the setup for any issues. Don't have to go through all the typos 🙂

I am not sure that annotation action alone, without codespell one, would work. Could we push some TEMP commit with a typo and see if it gets properly annotated? (and then drop that commit and force-push; let me know if you need help on that) I think there is overall little to no harm to have additional codespell step.

Also, I am a fan of skipping .git don't think we want to skip .github, .git* will do both I believe, tried a few ways to do one but not the other but didn't work. Not sure if you could help with that @yarikoptic

replace .git* with just .git in skip, or am I missing something ?

[MatthewMiddlehurst]

No, not missing anything. I must have missed the simplest option while trying to fix that 🙂. Agreed, no harm in having an additional step/failing check for the annotations.

I am fine with this now but will let other developers comment if they want. Thank you for putting this up and for the help @yarikoptic.