From 4090df2ca7d6d0d0bf41a6da8ba4ec38e8e6faba Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 5 Jan 2024 10:07:00 +0100
Subject: [PATCH 1/6] use pre-commit for all linting jobs

# Conflicts:
#	.github/workflows/lint-code.yml
#	.pre-commit-config.yaml
---
 .github/workflows/create-lint-wf.yml          | 25 +------
 .../create-test-lint-wf-template.yml          | 19 +-----
 .github/workflows/fix-linting.yml             | 24 ++-----
 .github/workflows/lint-code.yml               | 27 +-------
 .pre-commit-config.yaml                       | 11 +++-
 .../.github/workflows/fix-linting.yml         | 29 ++++-----
 .../.github/workflows/linting.yml             | 65 ++-----------------
 .../pipeline-template/.pre-commit-config.yaml |  7 +-
 8 files changed, 46 insertions(+), 161 deletions(-)

diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 786a9a7f79..98e887b36b 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -35,6 +35,7 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: 3.11
+          cache: pip
 
       - name: Install python dependencies
         run: |
@@ -47,19 +48,6 @@ jobs:
         with:
           version: ${{ matrix.NXF_VER }}
 
-      # Install the Prettier linting tools
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install Prettier and editorconfig-checker
-        run: npm install -g prettier editorconfig-checker
-
-      - name: Install ruff
-        run: |
-          python -m pip install --upgrade pip
-          pip install ruff
-
       # Build a pipeline from the template
       - name: nf-core create
         run: |
@@ -78,15 +66,8 @@ jobs:
         working-directory: create-lint-wf
 
       # Run code style linting
-      - name: Run Prettier --check
-        run: prettier --check create-lint-wf/nf-core-testpipeline
-
-      - name: Run Ruff check
-        run: ruff check create-lint-wf/nf-core-testpipeline
-      - name: Run Ruff format
-        run: ruff format create-lint-wf/nf-core-testpipeline
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(find nf-core-testpipeline/.* -type f | grep -v '.git\|.py\|md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
+      - name: run pre-commit
+        run: pre-commit run --all-files
         working-directory: create-lint-wf
 
       # Update modules to the latest version
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
index 37cbf65c7d..0dba0543d2 100644
--- a/.github/workflows/create-test-lint-wf-template.yml
+++ b/.github/workflows/create-test-lint-wf-template.yml
@@ -51,18 +51,6 @@ jobs:
         with:
           version: latest-everything
 
-      # Install the Prettier linting tools
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install Prettier
-        run: npm install -g prettier
-
-      # Install the editorconfig linting tools
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
-
       # Create template files
       - name: Create template skip all (except github)
         run: |
@@ -107,11 +95,8 @@ jobs:
         run: nf-core --log-file log.txt sync --dir create-test-lint-wf/my-prefix-testpipeline/
 
       # Run code style linting
-      - name: Run Prettier --check
-        run: prettier --check create-test-lint-wf/my-prefix-testpipeline
-
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(find my-prefix-testpipeline/.* -type f | grep -v '.git\|.py\|md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
+      - name: Run pre-commit
+        run: pre-commit run --all-files
         working-directory: create-test-lint-wf
 
       # Remove TODO statements
diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index ad3383097a..cb7cf47187 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -24,29 +24,17 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install Prettier
-        run: npm install -g prettier @prettier/plugin-php
-
-      - name: Run 'prettier --write'
-        run: prettier --write ${GITHUB_WORKSPACE}
-
       - name: Set up Python 3.11
         uses: actions/setup-python@v4
         with:
           python-version: 3.11
+          cache: "pip"
 
-      - name: Install Ruff
-        run: |
-          python -m pip install --upgrade pip
-          pip install ruff
-      - name: Run Ruff
-        run: |
-          ruff check --fix .
-          ruff format .
+      - name: Install pre-commit
+        run: pip install pre-commit
+
+      - name: Run pre-commit
+        run: pre-commit run --all-files
 
       - name: Commit & push changes
         run: |
diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index 43311848ad..cc69408334 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -100,28 +100,5 @@ jobs:
           python -m pip install --upgrade pip -r requirements-dev.txt
           pip install -e .
 
-      - name: Cache nf-test installation
-        id: cache-software
-        uses: actions/cache@v3
-        with:
-          path: |
-            /usr/local/bin/nf-test
-            /home/runner/.nf-test/nf-test.jar
-          key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest
-
-      - name: Install nf-test
-        if: steps.cache-software.outputs.cache-hit != 'true'
-        run: |
-          wget -qO- https://code.askimed.com/install/nf-test | bash
-          sudo mv nf-test /usr/local/bin/
-
-      - name: Get Python changed files
-        id: changed-py-files
-        uses: tj-actions/changed-files@v23
-        with:
-          files: |
-            *.py
-            **/*.py
-      - name: Run if any of the listed files above is changed
-        if: steps.changed-py-files.outputs.any_changed == 'true'
-        run: mypy ${{ steps.changed-py-files.outputs.all_changed_files }}
+      - name: Run pre-commit
+        run: pre-commit run --all-files
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 8dc52f06fe..fb2a67bace 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -6,11 +6,18 @@ repos:
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
       - id: ruff-format # formatter
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v2.7.1"
+    rev: "v3.1.0"
     hooks:
       - id: prettier
+
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "2.7.3"
+    hooks:
+      - id: editorconfig-checker
+        alias: ec
+
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.8.0" # Use the sha / tag you want to point at
+    rev: "v1.8.0"
     hooks:
       - id: mypy
         additional_dependencies:
diff --git a/nf_core/pipeline-template/.github/workflows/fix-linting.yml b/nf_core/pipeline-template/.github/workflows/fix-linting.yml
index 31e8cd2b36..d9986bd30f 100644
--- a/nf_core/pipeline-template/.github/workflows/fix-linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/fix-linting.yml
@@ -24,32 +24,25 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v4
-
-      - name: Install Prettier
-        run: npm install -g prettier @prettier/plugin-php
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+          cache: "pip"
 
-      # Check that we actually need to fix something
-      - name: Run 'prettier --check'
-        id: prettier_status
-        run: |
-          if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "result=pass" >> $GITHUB_OUTPUT
-          else
-            echo "result=fail" >> $GITHUB_OUTPUT
-          fi
+      - name: Install pre-commit
+        run: pip install pre-commit
 
-      - name: Run 'prettier --write'
-        if: steps.prettier_status.outputs.result == 'fail'
-        run: prettier --write ${GITHUB_WORKSPACE}
+      - name: Run pre-commit
+        run: pre-commit run --all-files || echo "status=fail" >> $GITHUB_ENV
 
       - name: Commit & push changes
-        if: steps.prettier_status.outputs.result == 'fail'
+        if: env.status == 'fail'
         run: |
           git config user.email "core@nf-co.re"
           git config user.name "nf-core-bot"
           git config push.default upstream
           git add .
           git status
-          git commit -m "[automated] Fix linting with Prettier"
+          git commit -m "[automated] Fix linting with pre-commit"
           git push {%- endraw %}
diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml
index 1cd46a1920..da6726a441 100644
--- a/nf_core/pipeline-template/.github/workflows/linting.yml
+++ b/nf_core/pipeline-template/.github/workflows/linting.yml
@@ -11,73 +11,22 @@ on:
     types: [published]
 
 jobs:
-  EditorConfig:
+  pre-commit:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v4
-
-      - 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@v4
-
-      - uses: actions/setup-node@v4
-
-      - name: Install Prettier
-        run: npm install -g prettier
-
-      - name: Run Prettier --check
-        run: prettier --check ${GITHUB_WORKSPACE}
-
-  Ruff:
-    runs-on: ["self-hosted"]
-    steps:
-      - name: Check out source-code repository
-        uses: actions/checkout@v4
-
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
-      - name: Install Ruff
-        run: |
-          python -m pip install --upgrade pip
-          pip install ruff
-      - name: Run Ruff check
-        run: ruff check .
-
-      - name: Run Ruff format
-        run: ruff format .
-
-      # 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@v2
-        with:
-          message: |
-            ## Python linting (`ruff`) 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 [`ruff`](https://github.com/astral-sh/ruff): `pip install ruff`
-            * Fix formatting errors in your pipeline: `ruff check --fix .` and `ruff format .`
-
-            Once you push these changes the test should pass, and you can hide this comment :+1:
+          cache: "pip"
 
-            We highly recommend setting up Ruff 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/nf_core/pipeline-template/.pre-commit-config.yaml b/nf_core/pipeline-template/.pre-commit-config.yaml
index 0c31cdb99f..984321ff26 100644
--- a/nf_core/pipeline-template/.pre-commit-config.yaml
+++ b/nf_core/pipeline-template/.pre-commit-config.yaml
@@ -1,5 +1,10 @@
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v2.7.1"
+    rev: "v3.1.1"
     hooks:
       - id: prettier
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "2.7.3"
+    hooks:
+      - id: editorconfig-checker
+        alias: ec

From f58fd5cff57a050b93d26f0d66c93c43257d8233 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 5 Jan 2024 10:07:16 +0100
Subject: [PATCH 2/6] fix editorconfig

---
 .editorconfig                           | 4 ++++
 docs/api/Makefile                       | 4 ++--
 nf_core/pipeline-template/.editorconfig | 8 ++++++++
 3 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/.editorconfig b/.editorconfig
index 014c2383bd..eaf7834976 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -10,3 +10,7 @@ indent_style = space
 
 [*.{md,yml,yaml,html,css,scss,js,cff}]
 indent_size = 2
+
+# ignore python and markdown files
+[*.{py,md}]
+indent_style = unset
diff --git a/docs/api/Makefile b/docs/api/Makefile
index f961e4ded1..69f3987065 100644
--- a/docs/api/Makefile
+++ b/docs/api/Makefile
@@ -9,11 +9,11 @@ BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".
 help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+    @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 .PHONY: help Makefile
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
\ No newline at end of file
+    @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/nf_core/pipeline-template/.editorconfig b/nf_core/pipeline-template/.editorconfig
index b6b3190776..9b990088ab 100644
--- a/nf_core/pipeline-template/.editorconfig
+++ b/nf_core/pipeline-template/.editorconfig
@@ -22,3 +22,11 @@ indent_size = unset
 
 [/assets/email*]
 indent_size = unset
+
+# ignore Readme
+[README.md]
+indent_style = unset
+
+# ignore python
+[*.{py}]
+indent_style = unset

From 8d9c38116075a8bc032013bee3cfc62fee40666a Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 5 Jan 2024 10:12:20 +0100
Subject: [PATCH 3/6] fix .editorconfig and makefile

---
 .editorconfig     | 8 +++++++-
 docs/api/Makefile | 4 ++--
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/.editorconfig b/.editorconfig
index eaf7834976..449f446a3b 100644
--- a/.editorconfig
+++ b/.editorconfig
@@ -12,5 +12,11 @@ indent_style = space
 indent_size = 2
 
 # ignore python and markdown files
-[*.{py,md}]
+[*.py]
+indent_style = unset
+
+[**/{CONTRIBUTING,README}.md]
+indent_style = unset
+
+[**/Makefile]
 indent_style = unset
diff --git a/docs/api/Makefile b/docs/api/Makefile
index 69f3987065..ab30a5051e 100644
--- a/docs/api/Makefile
+++ b/docs/api/Makefile
@@ -9,11 +9,11 @@ BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".
 help:
-    @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 .PHONY: help Makefile
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-    @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

From 3fad2329418fe22cfe8d9d04943a3a905cd79611 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 5 Jan 2024 10:19:54 +0100
Subject: [PATCH 4/6] use pre-commit for tools job as well

---
 .github/workflows/lint-code.yml | 78 ++-------------------------------
 1 file changed, 3 insertions(+), 75 deletions(-)

diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
index cc69408334..69ad009851 100644
--- a/.github/workflows/lint-code.yml
+++ b/.github/workflows/lint-code.yml
@@ -13,81 +13,9 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  EditorConfig:
-    runs-on: ["self-hosted"]
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install editorconfig-checker
-        run: npm install -g editorconfig-checker
-
-      # Run editor config check only on files not covered by a linter
-      - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v 'test\|.py\|md\|json\|yml\|yaml\|html\|css\|Makefile')
-
-  Prettier:
-    runs-on: ["self-hosted"]
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: actions/setup-node@v4
-        with:
-          node-version: "20"
-
-      - name: Install Prettier
-        run: npm install -g prettier
-
-      - name: Run Prettier --check
-        run: prettier --check ${GITHUB_WORKSPACE}
-
-  Ruff:
-    runs-on: ["self-hosted"]
-    steps:
-      - name: Check out source-code repository
-        uses: actions/checkout@v4
-
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v4
-        with:
-          python-version: 3.11
-      - name: Install Ruff
-        run: |
-          python -m pip install --upgrade pip
-          pip install ruff
-      - name: Run Ruff check
-        run: ruff check .
-
-      - name: Run Ruff format
-        run: ruff format .
-
-      # 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@v2
-        with:
-          message: |
-            ## Python linting (`ruff`) 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 [`ruff`](https://github.com/astral-sh/ruff): `pip install ruff`
-            * Fix formatting errors in your pipeline: `ruff check --fix .` and `ruff format .`
-
-            Once you push these changes the test should pass, and you can hide this comment :+1:
-
-            We highly recommend setting up Ruff in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
-
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
-
-  static-type-check:
-    runs-on: ["self-hosted"]
+  Pre-commit:
+    name: Pre-commit
+    runs-on: ["ubuntu-latest"]
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v4

From f05b8643ca6304d721b393cf2d49ead4ba4974bf Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 5 Jan 2024 10:53:24 +0100
Subject: [PATCH 5/6] set python version in changelog job

---
 .github/workflows/changelog.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml
index 11db7939d9..01d86fad98 100644
--- a/.github/workflows/changelog.yml
+++ b/.github/workflows/changelog.yml
@@ -35,6 +35,8 @@ jobs:
           gh pr checkout $PR_NUMBER
 
       - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
 
       - name: Install packages
         run: |

From acfb4f7ac91217ffc0bc12bfac3916dffb9218c6 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 5 Jan 2024 10:58:44 +0100
Subject: [PATCH 6/6] update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9a88a14265..2c8f522fe4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -24,6 +24,7 @@
 
 - Rename `release-announcments.yml` to `release-announcements.yml` ([#2610](https://github.com/nf-core/tools/pull/2610))
 - Fix `nextflow.config` `docker.runOptions` ([#2607](https://github.com/nf-core/tools/pull/2607))
+- Use `pre-commit` to lint files in GitHub CI ([#2635](https://github.com/nf-core/tools/pull/2635))
 
 ### General