Code

Lint refactoring#809

Code

Merged

ewels merged 73 commits intonf-core:devnf-core/tools:devfrom ewels:lint-refactoringewels/nf-core-tools:lint-refactoringCopy head branch name to clipboardDec 14, 2020

+3,394-3,182

Commits

Commits on Dec 5, 2020

• Rename test functions to exclude check_ prefix

  ewels

  committed
  993ef82

• Start playing around with improving the sphinx docs for linting

  ewels

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  eafa914

• Fight with sphinx a bit more

  ewels

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  70dd0d4

• Make each lint test return its results instead of updating the object

  ewels

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  a99b7f4

• Don't use numeric test IDs

  ewels

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  7a52fef

• Added ability to optionally load a pipeline lint config file

  ewels

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  15d4f5e

• Config: skip test if named and is false

  ewels

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  3b494ce

• Rename .nf-core-lint-config.yml to .nf-core-lint.yml

  ewels

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  c01e9e4

• Log / report ignored tests

  ewels

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  89df655

• Make module directory for linting

  ewels

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  44ad230

• Break lint functions out into their own files

  ewels

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  0f7f023

• Testing and tidying of the newly split linting code

  ewels

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  0abffb4

• Add sphinx docs .rst files for all new lint test functions

  ewels

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  f9093cb

• More bugfixes as I start working on tests

  ewels

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  558c1d6

• Deleted lint examples, started rewriting lint tests

  ewels

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  0a4319c

• Remove somewhat pointless lint test 'docker'

  ewels

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  99ad455

Commits on Dec 6, 2020

• Spinx docs - move function reference into a subdir called 'API Reference'

  ewels

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  abd4544

• Lint pytests - comment out old tests

  ewels

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  664895e

• Lint tests - more core tests

  Show description for 6046bde
  ewels

  committed
  6046bde

• Lint tests - more core functions, slight simplification

  ewels

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  094ca66

• Update lint function names in nf-core licences

  ewels

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  3c3debd

• Clean up missing self. references in simplification of test code

  ewels

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  02aa6dd

• Fix old references to lint_pipeline() function

  ewels

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  1f0e4cf

• Set the pipeline name in the helper function, not a test

  ewels

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  0eec578

• Bump versions - run all linting load functions

  ewels

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  43cd4ba

• Try to disentangle nf_core.lint from rest of nf_core package

  ewels

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  9603afb

• Rewrite bump-version to not using linting code.

  Show description for fe268d1
  ewels

  committed
  fe268d1

• Rewrite tests for bump-version

  ewels

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  dc60c20

• Make test_download.py use created wf instead of PATH_WORKING_EXAMPLE

  ewels

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  f833c8e

• Update lint pytests for refactored code and fix a bug in the process

  ewels

  committed
  9eed44a

• Move some pytests from lint to utils

  ewels

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  851abe5

• Added / rewrote pytests for first couple of lint tests

  ewels

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  2fd086a

• Split lint pytest tests into files too

  ewels

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  7b5a0b3

• Wrote helper script to auto-generate sphinx docs .rst files for lint tests

  ewels

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  cef17b7

• Added documentation to function docstrings for awstest lint tests

  ewels

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  cc43e6a

Commits on Dec 7, 2020

• Added ignoring option for 'files_exist' test

  KevinMenden

  committed
  b4c7177

• Lint tests - add test to check that all sphinx .rst files are present for all lint tests

  ewels

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  500fcaf

• updated changes

  KevinMenden

  committed
  527766c

• Port over lint documentation for actions_branch_protection

  ewels

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  025b268

• Added 'files_exist' tests

  KevinMenden

  committed
  25414a7

• Remove docs from errors.md that has been ported into docstrings

  ewels

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  440a619

• Added pytests for actions_branch_protection lint test

  ewels

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  541a2c0

• Auto-black formatting didn't work. Try again..

  ewels

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  37418e8

• actions_ci lint - return ignored message if file not found

  ewels

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  7fddb25

• Moved docs to docstring for actions_ci test

  ewels

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  d1bdeb6

• Write pytests for actions_ci lint test

  ewels

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  d1e4fed

• actions_ci pytests - more granular

  ewels

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  e459973

Commits on Dec 8, 2020

• small edit

  KevinMenden

  committed
  03ac603

• added logging of ignored files/configs

  KevinMenden

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  aac25e9

• added licence tests

  KevinMenden

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  c5c07da

• added branch protection test

  KevinMenden

  committed
  c5b7489

• Merge branch 'lint-refactoring' into lint-refactoring

  KevinMenden

  authored
  efd82b1

• Apply suggestions from code review

  Show description for d6309e7
  

  KevinMenden

  and

  ewels

  authored
  d6309e7

• removed nextflow_config; added passing test (files_exist)

  KevinMenden

  committed
  7228e3d

• Merge pull request #2 from KevinMenden/lint-refactoring

  Show description for 2986826
  ewels

  authored
  2986826

• Run black for #2

  ewels

  committed
  e668d85

Commits on Dec 10, 2020

• Lint test actions_lint - docs + functionality

  Show description for fe9ab0a
  ewels

  committed
  fe9ab0a

• Add requirements.txt for Sphinx docs generation

  ewels

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  cb14fc7

• Docs: Small intro for tools docs homepage

  ewels

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  6268eb8

• Ported lint error docs to docstring: conda_dockerfile

  ewels

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  5368414

• errors to docstrings - conda_env_yaml

  ewels

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  e8c34f0

• Fixup more lenient make_lint_rst.py helper script

  ewels

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  364a340

• Errors to docstring - cookiecutter_strings

  ewels

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  c4d9b59

Commits on Dec 11, 2020

• Files exist docs - minor tweaks

  ewels

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  bf58a60

• Errors to docstring - licence lint test

  ewels

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  daae3dd

• Errors to docstring - pipeline name conventions

  ewels

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  d399079

• Errors to docstring - pipeline todos

  ewels

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  b28eb12

• Errors to docstring - readme lint test

  ewels

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  d2f63cd

• Errors to docstring - schema lint

  ewels

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  117ba8f

• Errors to docstring - schema params

  ewels

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  f9bef03

• Errors to docstring - version consistency

  ewels

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  b6e64b4

• Errors to docstring - nextflow config

  ewels

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  1a8b4b4

• Remove docs/lint_errors.md

  ewels

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  135fb8b