Merge pull request #3070 from mashehu/move-pipeline-linting

Restructure pipeline tests and move pipeline linting into subfolder

.editorconfig

@@ -21,7 +21,7 @@ indent_style = unset
 [**/Makefile]
 indent_style = unset
 
-[tests/__snapshots__/*]
+[tests/pipelines/__snapshots__/*]
 charset = unset
 end_of_line = unset
 insert_final_newline = unset

.github/workflows/changelog.py

@@ -1,3 +1,4 @@
+#! /usr/bin/env python3
 """
 Taken from https://github.com/MultiQC/MultiQC/blob/main/.github/workflows/changelog.py and updated for nf-core
 
@@ -18,7 +19,7 @@
 import re
 import sys
 from pathlib import Path
-from typing import List
+from typing import List, Tuple
 
 REPO_URL = "https://github.com/nf-core/tools"
 
@@ -32,7 +33,7 @@
 assert pr_number, pr_number
 
 # Trim the PR number added when GitHub squashes commits, e.g. "Template: Updated (#2026)"
-pr_title = pr_title.removesuffix(f" (#{pr_number})")
+pr_title = pr_title.removesuffix(f" (#{pr_number})")  # type: ignore
 
 changelog_path = workspace_path / "CHANGELOG.md"
 
@@ -50,7 +51,7 @@
     sys.exit(0)
 
 
-def _determine_change_type(pr_title) -> tuple[str, str]:
+def _determine_change_type(pr_title) -> Tuple[str, str]:
     """
     Determine the type of the PR: Template, Download, Linting, Modules, Subworkflows, or General
     Returns a tuple of the section name and the module info.
@@ -85,7 +86,7 @@ def _determine_change_type(pr_title) -> tuple[str, str]:
 pr_link = f"([#{pr_number}]({REPO_URL}/pull/{pr_number}))"
 
 # Handle manual changelog entries through comments.
-if comment := comment.removeprefix("@nf-core-bot changelog").strip():
+if comment := comment.removeprefix("@nf-core-bot changelog").strip():  # type: ignore
     print(f"Adding manual changelog entry: {comment}")
     pr_title = comment
 new_lines = [

.github/workflows/pytest.yml

@@ -67,7 +67,7 @@ jobs:
       - name: List tests
         id: list_tests
         run: |
-          echo "tests=$(find tests/test_* | tac | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT
+          echo "tests=$(find tests -type f -name "test_*.py" | tac | sed 's/tests\///g'  | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT
     outputs:
       tests: ${{ steps.list_tests.outputs.tests }}
 
@@ -149,10 +149,15 @@ jobs:
           name: Snapshot Report ${{ matrix.test }}
           path: ./snapshot_report.html
 
+      - name: remove slashes from test name
+        run: |
+          test=$(echo ${{ matrix.test }} | sed 's/\//__/g')
+          echo "test=${test}" >> $GITHUB_ENV
+
       - name: Upload coverage
         uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
-          name: coverage_${{ matrix.test }}
+          name: coverage_${{ env.test }}
           path: .coverage
 
   coverage:

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.4
+    rev: v0.5.6
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
@@ -10,7 +10,7 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.2.5
+          - prettier@3.3.3
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"
@@ -28,3 +28,4 @@ repos:
           - types-jsonschema
           - types-Markdown
           - types-setuptools
+          - pydantic

CHANGELOG.md

@@ -20,6 +20,7 @@
 
 - Fix linting fail on nfcore_external_java_deps if nf_schema is used ([#2976](https://github.com/nf-core/tools/pull/2976))
 - Conda module linting: Include package name in log file ([#3014](https://github.com/nf-core/tools/pull/3014))
+- Restructure pipeline tests and move pipeline linting into subfolder ([#3070](https://github.com/nf-core/tools/pull/3070))
 - Fix module linting warning for process_high_memory ([#3086](https://github.com/nf-core/tools/issues/3086))
 
 ### Download

mypy.ini

@@ -1,3 +1,4 @@
 [mypy]
 warn_unused_configs = True
 ignore_missing_imports = true
+plugins = pydantic.mypy