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Move linting configuration to .cicd-env file #50

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merged 1 commit into from
Oct 4, 2023
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@nwiltsie nwiltsie commented Oct 4, 2023

Description

This is a super-simple change that moves the setting of the PYTHON_PYLINT_CONFIG_FILE envvar from the workflow file to a new .cicd-env file. That enables the new bllint script from https://github.com/uclahs-cds/docker-CICD-base/pull/60 to lint a local checkout:

tool-NFTest $ ~/src/docker-CICD-base/bin/bllint
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
-------- COMMON ---------
No links to confluence.mednet.ucla.edu in Markdown files........
      [LICENSE.md]..............................................    ok
      [CHANGELOG.md]............................................    ok
      [README.md]...............................................    ok
      ..........................................................    ok
The repository name should not be public or private.............    ok
The organization and repository names must meet the standard....    ok
The templated files must exist..................................
      (filename='README.md')....................................    ok
      (filename='metadata.yaml')................................    ok
      (filename='.gitignore')...................................    ok
      ..........................................................    ok
-------- LINTER ---------
CPP files must be lint-free.....................................    ok
Dockerfiles must be lint-free...................................    ok
JSON files must be lint-free....................................    ok
Perl files must be lint-free....................................    ok
Python files must be lint-free..................................    ok
R files must be lint-free.......................................    ok
YAML files must be lint-free....................................    ok
-------- README ---------
All of the templated text should be removed from the README.....    ok

----------------------------------------------------------------------
Ran 12 tests in 17.147s

OK

Checklist

  • This PR does NOT contain Protected Health Information (PHI). A repo may need to be deleted if such data is uploaded.
    Disclosing PHI is a major problem1 - Even a small leak can be costly2.

  • This PR does NOT contain germline genetic data3, RNA-Seq, DNA methylation, microbiome or other molecular data4.

  • This PR does NOT contain other non-plain text files, such as: compressed files, images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other output files.

  To automatically exclude such files using a .gitignore file, see here for example.

  • I have read the code review guidelines and the code review best practice on GitHub check-list.

  • I have set up or verified the main branch protection rule following the github standards before opening this pull request.

  • The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].

  • I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

Footnotes

  1. UCLA Health reaches $7.5m settlement over 2015 breach of 4.5m patient records

  2. The average healthcare data breach costs $2.2 million, despite the majority of breaches releasing fewer than 500 records.

  3. Genetic information is considered PHI.
    Forensic assays can identify patients with as few as 21 SNPs

  4. RNA-Seq, DNA methylation, microbiome, or other molecular data can be used to predict genotypes (PHI) and reveal a patient's identity.

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@yashpatel6 yashpatel6 left a comment

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Looks good!

@nwiltsie nwiltsie merged commit d096b96 into main Oct 4, 2023
1 check passed
@nwiltsie nwiltsie deleted the nwiltsie_fix_linting branch October 4, 2023 21:48
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2 participants