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Edinburgh-Genome-Foundry / DnaChisel

:pencil2: A versatile DNA sequence optimizer
https://edinburgh-genome-foundry.github.io/DnaChisel/
MIT License
219 stars 40 forks source link

Spelling #48

Closed jsoref closed 3 years ago

jsoref commented 3 years ago

This PR corrects misspellings identified by the check-spelling action.

The misspellings have been reported at https://github.com/jsoref/DnaChisel/commit/df5c1ec886b3b8b02f93bb63e8c14a1ad01f0350#commitcomment-45566687

The action reports that the changes in this PR would make it happy: https://github.com/jsoref/DnaChisel/commit/a0e31fdbf1937feb1e1fc58d3d1f7a0ee186dcfa

Note: this PR does not include the action. If you're interested in running a spell check on every PR and push, that can be offered separately.

Zulko commented 3 years ago

Oh wow that's a lot of typos, thanks @jsoref for this spell-checking tool! @veghp sorry for the typos. Most corrections in this PR look good, but it looks like I have consistently written occurence with a single r, and unfortunately fixing that will require an API change + version bump (to correct class EnforcePatternOccurence to EnforcePatternOccurrence).

jsoref commented 3 years ago

This should fix the build -- I have tooling for renames, but apparently not for git, and I haven't integrated renaming into my tooling...

As API bumps are major things, I'm going to drop it from this PR. I could try to make the actual PR for it, but as I'm not precisely sure what it'll entail, it might make more sense for me to give you some commits and let you write the API compat bits you require.

coveralls commented 3 years ago

Coverage Status

Coverage remained the same at 89.084% when pulling a51790d5665725ecdfc045ebf2efba7719fc4e14 on jsoref:spelling into 726b2b0254a8dbd9f51a78998cbb4e43cb096057 on Edinburgh-Genome-Foundry:master.

veghp commented 3 years ago

Thank you for these corrections. I reviewed most of the other packages for spelling, but not this one. I merged your commits into the dev branch and they will be included in the next release, except for the change in the spelling of 'palindromic'. I stored that in branch palindromic, and will be applied together with other API changes in the next major release. As the change to default value "unnamed" affects the name of the report only, I left that in.

Please note that the tool introduced one spelling error ('respectivelyy', which I corrected): https://github.com/Edinburgh-Genome-Foundry/DnaChisel/pull/48/files#diff-2d7660d970eabc63831ad1b44104bc87976f5f6d15acc187354d3a1aef578d35R40

jsoref commented 3 years ago

oops. I'm still working on improving those edges. I actually added a thing to my tool between this PR and today to try to avoid eating my own tail.

veghp commented 3 years ago

Sounds good. I'll close this PR as the commits are already in the dev and palindromic branches.

jsoref commented 3 years ago

@veghp: note that https://github.com/jsoref/DnaChisel/tree/spelling-occurrence is currently floating outside as @Zulko identified it as problematic and I excluded it from this PR. (Maybe I shouldn't have.)

veghp commented 3 years ago

Yes, thanks, it has been noted in the todo list. We will do this change "manually" with an IDE, as DNA Chisel has many dependents.