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replace editorconfig by pre-commit-hooks #3467

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merged 3 commits into from
Feb 25, 2025
Merged

replace editorconfig by pre-commit-hooks #3467

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c733833
replace editorconfig by pre-commit-hooks
mirpedrol Feb 25, 2025
3107d54
run pre-commit to format json files
mirpedrol Feb 25, 2025
9f8a4d6
update indent size in prettierrc.yml
mirpedrol Feb 25, 2025
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30 changes: 0 additions & 30 deletions .editorconfig
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25 changes: 19 additions & 6 deletions .pre-commit-config.yaml
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Expand Up @@ -11,13 +11,26 @@ repos:
- id: prettier
additional_dependencies:
- prettier@3.5.0

- repo: https://github.com/editorconfig-checker/editorconfig-checker.python
rev: "3.2.0"
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v5.0.0
hooks:
- id: editorconfig-checker
alias: ec

- id: trailing-whitespace
args: [--markdown-linebreak-ext=md]
exclude: |
(?x)^(
.*\.snap$|
nf_core/pipeline-template/subworkflows/.*|
nf_core/pipeline-template/modules/.*|
tests/pipelines/__snapshots__/.*
)$
- id: end-of-file-fixer
exclude: |
(?x)^(
.*\.snap$|
nf_core/pipeline-template/subworkflows/.*|
nf_core/pipeline-template/modules/.*|
tests/pipelines/__snapshots__/.*
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looks like we need to also exclude main.nf in modules and subworkflow template files

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I think modifying the template is good, no? What we should skip are the modules and subworkflows because they are handeled in the module repo

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i am just wondering about the introduced changes... how come they were not there with editorconfig?

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I can't see anywhere where we excluded these files... but I have tested creating a new pipeline and running pre-commit there and everything passes.

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okay, fine for me then. 🙂

)$
- repo: https://github.com/pre-commit/mirrors-mypy
rev: "v1.15.0"
hooks:
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1 change: 0 additions & 1 deletion .prettierignore
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Expand Up @@ -12,4 +12,3 @@ tests/data/pipeline_create_template_skip.yml
# don't run on things handled by ruff
*.py
*.pyc

5 changes: 5 additions & 0 deletions .prettierrc.yml
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@@ -1 +1,6 @@
printWidth: 120
tabWidth: 4
overrides:
- files: "*.{md,yml,yaml,html,css,scss,js,cff}"
options:
tabWidth: 2
2 changes: 1 addition & 1 deletion nf_core/assets/logo/placeholder_logo.svg
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41 changes: 0 additions & 41 deletions nf_core/pipeline-template/.editorconfig
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24 changes: 19 additions & 5 deletions nf_core/pipeline-template/.pre-commit-config.yaml
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Expand Up @@ -5,9 +5,23 @@ repos:
- id: prettier
additional_dependencies:
- prettier@3.5.0

- repo: https://github.com/editorconfig-checker/editorconfig-checker.python
rev: "3.2.0"
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v5.0.0
hooks:
- id: editorconfig-checker
alias: ec
- id: trailing-whitespace
args: [--markdown-linebreak-ext=md]
exclude: |
(?x)^(
.*ro-crate-metadata.json$|
modules/nf-core/.*|
subworkflows/nf-core/.*|
.*\.snap$
)$
- id: end-of-file-fixer
exclude: |
(?x)^(
.*ro-crate-metadata.json$|
modules/nf-core/.*|
subworkflows/nf-core/.*|
.*\.snap$
)$
5 changes: 5 additions & 0 deletions nf_core/pipeline-template/.prettierrc.yml
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@@ -1 +1,6 @@
printWidth: 120
tabWidth: 4
overrides:
- files: "*.{md,yml,yaml,html,css,scss,js,cff}"
options:
tabWidth: 2
2 changes: 1 addition & 1 deletion nf_core/pipeline-template/subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf
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Expand Up @@ -303,4 +303,4 @@ def methodsDescriptionText(mqc_methods_yaml) {

return description_html.toString()
}
{% endif %}
{%- endif %}
3 changes: 0 additions & 3 deletions nf_core/pipelines/create/template_features.yml
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Expand Up @@ -167,7 +167,6 @@ is_nfcore:
custom_pipelines: False
code_linters:
skippable_paths:
- ".editorconfig"
- ".pre-commit-config.yaml"
- ".prettierignore"
- ".prettierrc.yml"
Expand All @@ -180,11 +179,9 @@ code_linters:
The available code linters are:

- pre-commit (https://pre-commit.com/): used to run all code-linters on every PR and on ever commit if you run `pre-commit install` to install it in your local repository.
- editor-config (https://github.com/editorconfig-checker/editorconfig-checker): checks rules such as indentation or trailing spaces.
- prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc).
linting:
files_exist:
- ".editorconfig"
- ".prettierignore"
- ".prettierrc.yml"
nfcore_pipelines: False
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2 changes: 0 additions & 2 deletions nf_core/pipelines/lint/files_exist.py
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Expand Up @@ -23,7 +23,6 @@ def files_exist(self) -> Dict[str, List[str]]:
.gitattributes
.gitignore
.nf-core.yml
.editorconfig
.prettierignore
.prettierrc.yml
.github/.dockstore.yml
Expand Down Expand Up @@ -128,7 +127,6 @@ def files_exist(self) -> Dict[str, List[str]]:
[Path(".gitattributes")],
[Path(".gitignore")],
[Path(".nf-core.yml")],
[Path(".editorconfig")],
[Path(".prettierignore")],
[Path(".prettierrc.yml")],
[Path("CHANGELOG.md")],
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1 change: 0 additions & 1 deletion nf_core/subworkflow-template/main.nf
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Expand Up @@ -33,4 +33,3 @@ workflow {{ component_name_underscore|upper }} {

versions = ch_versions // channel: [ versions.yml ]
}

1 change: 0 additions & 1 deletion tests/data/testdata_remote_containers.txt
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Expand Up @@ -34,4 +34,3 @@
These entries should not be used:
On October 5, 2011, the 224-meter containership MV Rena struck a reef close to New Zealand’s coast and broke apart. That spells disaster, no?
MV Rena

1 change: 0 additions & 1 deletion tests/pipelines/test_create.py
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Expand Up @@ -134,7 +134,6 @@ def test_pipeline_creation_with_yml_skip(self, tmp_path):
assert not (pipeline.outdir / "CODE_OF_CONDUCT.md").exists()
assert not (pipeline.outdir / ".github").exists()
assert not (pipeline.outdir / "conf" / "igenomes.config").exists()
assert not (pipeline.outdir / ".editorconfig").exists()

def test_template_customisation_all_files_grouping(self):
"""Test that all pipeline template files are included in a pipeline customisation group."""
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