Merge pull request #4 from CCBR/tests

Setup unit tests with pytest & nf-test

.github/check_duplicate_md5s.py

@@ -0,0 +1,82 @@
+#!/usr/bin/env python
+
+from rich import print
+from rich.table import Table
+import click
+import glob
+import os
+import yaml
+
+
+@click.command()
+@click.option(
+    "--min_dups",
+    default=5,
+    show_default=True,
+    help="Minimum number of duplicates to report",
+)
+@click.option(
+    "--search_dir",
+    default=f"{os.path.dirname(__file__)}/../tests/**/test.yml",
+    show_default=True,
+    help="Glob directory pattern used to find test YAML files",
+)
+def find_duplicate_md5s(min_dups, search_dir):
+    """
+    Find duplicate file MD5 sums in test YAML files.
+    """
+    md5_filenames = {}
+    md5_output_fn_counts = {}
+    module_counts = {}
+
+    # Loop through all files in tests/ called test.yml
+    for test_yml in glob.glob(search_dir, recursive=True):
+        # Open file and parse YAML
+        with open(test_yml, "r") as fh:
+            test_config = yaml.safe_load(fh)
+            # Loop through tests and check for duplicate md5s
+            for test in test_config:
+                for test_file in test.get("files", []):
+                    if "md5sum" in test_file:
+                        md5 = test_file["md5sum"]
+                        md5_filenames[md5] = md5_filenames.get(md5, []) + [
+                            os.path.basename(test_file.get("path"))
+                        ]
+                        md5_output_fn_counts[md5] = md5_output_fn_counts.get(md5, 0) + 1
+                        # Log the module that this md5 was in
+                        modname = os.path.basename(os.path.dirname(test_yml))
+                        # If tool/subtool show the whole thing
+                        # Ugly code but trying to stat os-agnostic
+                        if os.path.basename(
+                            os.path.dirname(os.path.dirname(test_yml))
+                        ) not in ["modules", "config", "subworkflows"]:
+                            modname = "{}/{}".format(
+                                os.path.basename(
+                                    os.path.dirname(os.path.dirname(test_yml))
+                                ),
+                                os.path.basename(os.path.dirname(test_yml)),
+                            )
+                        module_counts[md5] = module_counts.get(md5, []) + [modname]
+
+    # Set up rich table
+    table = Table(title="Duplicate MD5s", row_styles=["dim", ""])
+    table.add_column("MD5", style="cyan", no_wrap=True)
+    table.add_column("Count", style="magenta", justify="right")
+    table.add_column("Num modules", style="blue", justify="right")
+    table.add_column("Filenames", style="green")
+
+    # Add rows - sort md5_output_fn_counts by value
+    for md5 in sorted(md5_output_fn_counts, key=md5_output_fn_counts.get):
+        if md5_output_fn_counts[md5] >= min_dups:
+            table.add_row(
+                md5,
+                str(md5_output_fn_counts[md5]),
+                str(len(set(module_counts[md5]))),
+                ", ".join(set(md5_filenames[md5])),
+            )
+
+    print(table)
+
+
+if __name__ == "__main__":
+    find_duplicate_md5s()

.github/workflows/fix-linting.yml

@@ -0,0 +1,72 @@
+name: fix-linting
+run-name: fix linting (automated)
+on:
+  issue_comment:
+    types: [created]
+
+jobs:
+  fix-linting:
+    # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
+    if: >
+      contains(github.event.comment.html_url, '/pull/') &&
+      contains(github.event.comment.body, '/fix linting') &&
+      (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') &&
+      github.repository == 'CCBR/nf-modules'
+    runs-on: ubuntu-latest
+    steps:
+      # Use the @nf-core-bot token to check out so we can push later
+      - uses: actions/checkout@v3
+        with:
+          token: ${{ secrets.GH_PAT }}
+
+      # indication that the linting is being fixed
+      - name: React on comment
+        uses: peter-evans/create-or-update-comment@v2
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: eyes
+
+      # Action runs on the issue comment, so we don't get the PR by default
+      # Use the gh cli to check out the PR
+      - name: Checkout Pull Request
+        run: gh pr checkout ${{ github.event.issue.number }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GH_PAT }}
+
+      - uses: actions/setup-node@v2
+
+      - name: Install Prettier
+        run: npm install -g prettier @prettier/plugin-php
+
+      # Check that we actually need to fix something
+      - name: Run 'prettier --check'
+        id: prettier_status
+        run: |
+          if prettier --check ${GITHUB_WORKSPACE}; then
+            echo "::set-output name=result::pass"
+          else
+            echo "::set-output name=result::fail"
+          fi
+      - name: Run 'prettier --write'
+        if: steps.prettier_status.outputs.result == 'fail'
+        run: prettier --write ${GITHUB_WORKSPACE}
+
+      - name: Post nothing-to-do comment
+        if: steps.prettier_status.outputs.result == 'pass'
+        uses: peter-evans/create-or-update-comment@v2
+        with:
+          issue-number: ${{ github.event.issue.number }}
+          body: |
+            Nothing for me to do here! :shrug:
+            This is probably because the linting errors come from `nf-core lint` and have to be fixed manually (or with `nf-core lint --fix`).
+
+      - name: Commit & push changes
+        if: steps.prettier_status.outputs.result == 'fail'
+        run: |
+          git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git config --local user.name "github-actions[bot]"
+          git config push.default upstream
+          git add .
+          git status
+          git commit -m "🤖 Fix linting with Prettier"
+          git push