Merge pull request #65 from seqeralabs/ECLINT

Fix Eclint
seqeralabs · Oct 23, 2024 · 08a907f · 08a907f
2 parents e85cb21 + a832d10
commit 08a907f
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Showing 8 changed files with 178 additions and 215 deletions.
diff --git a/.editorconfig b/.editorconfig
@@ -31,3 +31,7 @@ indent_size = unset
 # ignore python and markdown
 [*.{py,md}]
 indent_style = unset
+
+# ignore multiqc example
+[/assets/multiqc_report.html]
+indent_style = unset
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -11,61 +11,21 @@ on:
     types: [published]
 
 jobs:
-  EditorConfig:
+  pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - uses: actions/setup-node@v3
-
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
-
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
-
-  Prettier:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-
-      - uses: actions/setup-node@v3
-
-      - name: Install Prettier
-        run: npm install -g prettier
-
-      - name: Run Prettier --check
-        run: prettier --check ${GITHUB_WORKSPACE}
-
-  PythonBlack:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: Check code lints with Black
-        uses: psf/black@stable
-
-      # If the above check failed, post a comment on the PR explaining the failure
-      - name: Post PR comment
-        if: failure()
-        uses: mshick/add-pr-comment@v1
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          message: |
-            ## Python linting (`black`) is failing
-
-            To keep the code consistent with lots of contributors, we run automated code consistency checks.
-            To fix this CI test, please run:
-
-            * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
-            * Fix formatting errors in your pipeline: `black .`
-
-            Once you push these changes the test should pass, and you can hide this comment :+1:
+          python-version: "3.12"
 
-            We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
+      - name: Run pre-commit
+        run: pre-commit run --all-files
 
   nf-core:
     runs-on: ubuntu-latest

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -18,6 +18,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 
 [PR #61](https://github.com/seqeralabs/nf-aggregate/pull/61) - Remove dependency on external library/grape
 [PR #63](https://github.com/seqeralabs/nf-aggregate/pull/63) - Add `maxForks` setting for Seqera CLI to overcome API issues
+[PR #65](https://github.com/seqeralabs/nf-aggregate/pull/65) - Replace eclint GHA by pre-commit
 
 ## [[0.4.0](https://github.com/seqeralabs/nf-aggregate/releases/tag/0.4.0)] - 2024-07-26
 

diff --git a/assets/multiqc_report.html b/assets/multiqc_report.html
diff --git a/modules/local/plot_run_gantt/nextflow.config b/modules/local/plot_run_gantt/nextflow.config
@@ -6,4 +6,4 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-}
+}
diff --git a/subworkflows/local/utils_nf_aggregate/main.nf b/subworkflows/local/utils_nf_aggregate/main.nf
@@ -78,7 +78,7 @@ def getWorkflowPublishDir(json_file, outdir) {
         def workdir = getWorkflowWorkDir(json_file)
         if (workdir.startsWith('s3://')) {
             path = Paths.get(workdir, path)
-        }  
+        }
     }
     return path
 }
@@ -99,8 +99,8 @@ def getProcessVersions(yaml_file) {
 def getWorkflowVersions() {
     return """
     'Workflow':
-      "Nextflow": "$workflow.nextflow.version"
-      "$workflow.manifest.name": "$workflow.manifest.version"
+        "Nextflow": "$workflow.nextflow.version"
+        "$workflow.manifest.name": "$workflow.manifest.version"
     """.stripIndent().trim()
 }
 

diff --git a/subworkflows/local/utils_nf_aggregate/tests/main.nf.test b/subworkflows/local/utils_nf_aggregate/tests/main.nf.test
@@ -6,7 +6,7 @@ nextflow_workflow {
 
     tag "subworkflows"
     tag "subworkflows_local_utils_nf_aggregate"
-    
+
     stage {
         symlink "nextflow_schema.json"
         symlink "workflows/nf_aggregate/assets/test_run_ids.csv"
@@ -28,10 +28,8 @@ nextflow_workflow {
                 { assert workflow.success },
                 { assert snapshot(
                     workflow.out.ids
-                 ).match() }
+                ).match() }
             )
         }
-
     }
-
 }
diff --git a/workflows/nf_aggregate/nextflow.config b/workflows/nf_aggregate/nextflow.config
@@ -1,3 +1,3 @@
 includeConfig '../../modules/local/seqera_runs_dump/nextflow.config'
 includeConfig '../../modules/local/plot_run_gantt/nextflow.config'
-includeConfig '../../modules/nf-core/multiqc/nextflow.config'
+includeConfig '../../modules/nf-core/multiqc/nextflow.config'