audit-generic-fixes

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Next steps for #34
Identifiers are from PullRequest.com report
https://github.com/quiltdata/nf-quilt/files/10470527/reportgen.zip

= A.Generic Fixes
== PRComment_001, PRComment_026

• rename all fields and methods to camelCase [PRComment_014, PRComment_020]
• run a code formatter [PRComment_013]
• try running a code coverage tool to see what remaining paths may be uncovered

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Formatter Options

• https://www.npmjs.com/package/prettier-plugin-groovy
• https://www.npmjs.com/package/npm-groovy-lint
  • https://github.com/nvuillam/npm-groovy-lint
• https://github.com/diffplug/spotless [requires maven/gradle integration]
• https://github.com/uncrustify/uncrustify
• https://github.com/penberg/groovyfmt [3 years dead]

Code Coverage

• https://www.eclemma.org/jacoco/ (for Groovy: https://stackoverflow.com/questions/67974282/can-jacoco-instrument-groovy-scripts )
• https://openclover.org
• http://cobertura.github.io/cobertura/

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The GitHub action nf-core uses is codecov
https://about.codecov.io/language/groovy/

• cf Improve test coverage of sync.py nf-core/tools#1936
• https://github.com/nf-core/tools/tree/master/.github/workflows
• https://github.com/nf-core/tools/blob/master/.github/.coveragerc

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Actions

• https://mskelton.dev/blog/auto-formatting-code-using-prettier-and-github-actions
• https://github.com/marketplace/actions/prettier-action
• https://github.com/marketplace/actions/actionsx-prettier

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https://www.npmjs.com/package/npm-groovy-lint
Based on CodeNarc , this out of the box package allows to track groovy errors and correct a part of them

Use option --format to format & prettify source code
Use option --fix to activate autofixing of fixable rules

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npm install -g npm-groovy-lint
npm-groovy-lint 

Hangs on JRE install...

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Use via mega-linter?!
https://nvuillam.github.io/mega-linter
https://github.com/marketplace/actions/megalinter

[drernie]

Intriguing. I was getting a PlugIn error withmake png-test. It went away when I reverted the 'exclude', but then I got the coverage error back.
I think I should pull out the test issue for now, and focus on the mega-lint.