Merge branch 'dev' into renovate/peter-evans-create-or-update-comment…

…-4.x
nf-core · Jan 29, 2024 · 027c519 · 027c519
2 parents 8f0ecbd + b6eb508
commit 027c519
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Showing 18 changed files with 428 additions and 149 deletions.
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
@@ -38,6 +38,7 @@ jobs:
           - TEMPLATE: "template_skip_nf_core_configs.yml"
             runner: ubuntu-latest
             profile: "docker"
+      fail-fast: false
 
     steps:
       - name: go to working directory

diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
@@ -4,7 +4,7 @@ on:
     types: [created]
 
 jobs:
-  deploy:
+  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/') &&
@@ -13,7 +13,7 @@ jobs:
     runs-on: self-hosted
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -31,11 +31,10 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+      # Install and run pre-commit
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: 3.11
-          cache: "pip"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -47,15 +46,15 @@ jobs:
 
       # indication that the linting has finished
       - name: react if linting finished succesfully
-        if: ${{ steps.pre-commit.outcome }} == 'success'
+        if: steps.pre-commit.outcome == 'success'
         uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
         with:
           comment-id: ${{ github.event.comment.id }}
-          reactions: green_check_mark
+          reactions: "+1"
 
       - name: Commit & push changes
         id: commit-and-push
-        if: ${{ steps.pre-commit.outcome }} == 'failure'
+        if: steps.pre-commit.outcome == 'failure'
         run: |
           git config user.email "core@nf-co.re"
           git config user.name "nf-core-bot"
@@ -66,17 +65,25 @@ jobs:
           git push
 
       - name: react if linting errors were fixed
-        if: ${{ steps.commit-and-push.outcome }} == 'success'
+        id: react-if-fixed
+        if: steps.commit-and-push.outcome == 'success'
         uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
         with:
           comment-id: ${{ github.event.comment.id }}
-          reactions: pencil2
+          reactions: hooray
 
       - name: react if linting errors were not fixed
-        if: ${{ steps.commit-and-push.outcome }} == 'failure'
+        if: steps.commit-and-push.outcome == 'failure'
         uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4
         with:
           comment-id: ${{ github.event.comment.id }}
-          reactions: x
+          reactions: confused
+
+      - name: react if linting errors were not fixed
+        if: steps.commit-and-push.outcome  == 'failure'
+        uses: peter-evans/create-or-update-comment@23ff15729ef2fc348714a3bb66d2f655ca9066f2 # v3
+        with:
+          issue-number: ${{ github.event.issue.number }}
           body: |
             @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.
+            See [CI log](https://github.com/nf-core/tools/actions/runs/${{ github.run_id }}) for more details.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.13
+    rev: v0.1.14
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,7 +10,10 @@
 - switch to new image syntax in readme ([#2645](https://github.com/nf-core/tools/pull/2645))
 - Add conda channel order to nextflow.config ([#2094](https://github.com/nf-core/tools/pull/2094))
 - Fix tyop in pipeline nextflow.config ([#2664](https://github.com/nf-core/tools/pull/2664))
-- add function to check `-profile` is well formatted ([#2678](https://github.com/nf-core/tools/pull/2678))
+- Remove `nfcore_external_java_deps.jar` from lib directory in pipeline template ([#2675](https://github.com/nf-core/tools/pull/2675))
+- Add function to check `-profile` is well formatted ([#2678](https://github.com/nf-core/tools/pull/2678))
+- Add new pipeline error message pointing to docs when 'requirement exceeds available memory' error message ([#2680](https://github.com/nf-core/tools/pull/2680))
+- add 👀👍🏻🎉😕 reactions to fix-linting-bot action ([#2692](https://github.com/nf-core/tools/pull/2692))
 
 ### Download
 
@@ -19,6 +22,7 @@
 - Fix linting of a pipeline with patched custom module ([#2669](https://github.com/nf-core/tools/pull/2669))
 - linting a pipeline also lints the installed subworkflows ([#2677](https://github.com/nf-core/tools/pull/2677))
 - environment.yml name must be lowercase ([#2676](https://github.com/nf-core/tools/pull/2676))
+- lint `nextflow.config` default values match the ones specified in `nextflow_schema.json` ([#2684](https://github.com/nf-core/tools/pull/2684))
 
 ### Modules
 
@@ -39,7 +43,10 @@
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.1.13 ([#2660](https://github.com/nf-core/tools/pull/2660))
 - Add new subcommand: `nf-core logo-create` to output an nf-core logo for a pipeline (instead of going through the website) ([#2662](https://github.com/nf-core/tools/pull/2662))
 - Update actions/cache action to v4 ([#2666](https://github.com/nf-core/tools/pull/2666))
+- Handle api redirects from the old site ([#2672](https://github.com/nf-core/tools/pull/2672))
 - Remove redundanct v in pipeline version for emails ([#2667](https://github.com/nf-core/tools/pull/2667))
+- add function to check `-profile` is well formatted ([#2678](https://github.com/nf-core/tools/pull/2678))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.1.14 ([#2674](https://github.com/nf-core/tools/pull/2674))
 - Update peter-evans/create-or-update-comment action to v4 ([#2683](https://github.com/nf-core/tools/pull/2683))
 
 # [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20]

diff --git a/nf_core/create.py b/nf_core/create.py
@@ -505,10 +505,12 @@ def fix_linting(self):
     def make_pipeline_logo(self):
         """Fetch a logo for the new pipeline from the nf-core website"""
         email_logo_path = Path(self.outdir) / "assets"
-        create_logo(text=self.template_params["short_name"], dir=email_logo_path, theme="light")
+        create_logo(text=self.template_params["short_name"], dir=email_logo_path, theme="light", force=self.force)
         for theme in ["dark", "light"]:
             readme_logo_path = Path(self.outdir) / "docs" / "images"
-            create_logo(text=self.template_params["short_name"], dir=readme_logo_path, width=600, theme=theme)
+            create_logo(
+                text=self.template_params["short_name"], dir=readme_logo_path, width=600, theme=theme, force=self.force
+            )
 
     def git_init_pipeline(self):
         """Initialises the new pipeline as a Git repository and submits first commit.
@@ -537,8 +539,24 @@ def git_init_pipeline(self):
         repo.index.commit(f"initial template build from nf-core/tools, version {nf_core.__version__}")
         if default_branch:
             repo.active_branch.rename(default_branch)
-        repo.git.branch("TEMPLATE")
-        repo.git.branch("dev")
+        try:
+            repo.git.branch("TEMPLATE")
+            repo.git.branch("dev")
+
+        except git.GitCommandError as e:
+            if "already exists" in e.stderr:
+                log.debug("Branches 'TEMPLATE' and 'dev' already exist")
+                if self.force:
+                    log.debug("Force option set - deleting branches")
+                    repo.git.branch("-D", "TEMPLATE")
+                    repo.git.branch("-D", "dev")
+                    repo.git.branch("TEMPLATE")
+                    repo.git.branch("dev")
+                else:
+                    log.error(
+                        "Branches 'TEMPLATE' and 'dev' already exist. Use --force to overwrite existing branches."
+                    )
+                    sys.exit(1)
         log.info(
             "Done. Remember to add a remote and push to GitHub:\n"
             f"[white on grey23] cd {self.outdir} \n"

diff --git a/nf_core/create_logo.py b/nf_core/create_logo.py
@@ -5,6 +5,7 @@
 from PIL import Image, ImageDraw, ImageFont
 
 import nf_core
+from nf_core.utils import NFCORE_CACHE_DIR
 
 log = logging.getLogger(__name__)
 
@@ -26,7 +27,6 @@ def create_logo(
     if not dir.is_dir():
         log.debug(f"Creating directory {dir}")
         dir.mkdir(parents=True, exist_ok=True)
-
     assets = Path(nf_core.__file__).parent / "assets/logo"
 
     if format == "svg":
@@ -51,44 +51,56 @@ def create_logo(
     else:
         logo_filename = f"nf-core-{text}_logo_{theme}.png" if not filename else filename
         logo_filename = f"{logo_filename}.png" if not logo_filename.lower().endswith(".png") else logo_filename
+        cache_name = f"nf-core-{text}_logo_{theme}_{width}.png"
         logo_path = Path(dir, logo_filename)
 
         # Check if we haven't already created this logo
         if logo_path.is_file() and not force:
             log.info(f"Logo already exists at: {logo_path}. Use `--force` to overwrite.")
             return logo_path
-
-        log.debug(f"Creating logo for {text}")
-
-        # make sure the figure fits the text
-        font_path = assets / "MavenPro-Bold.ttf"
-        log.debug(f"Using font: {str(font_path)}")
-        font = ImageFont.truetype(str(font_path), 400)
-        text_length = font.getmask(text).getbbox()[2]  # get the width of the text based on the font
-
-        max_width = max(
-            2300, text_length + len(text) * 20
-        )  # need to add some more space to the text length to make sure it fits
-
-        template_fn = "nf-core-repo-logo-base-lightbg.png"
-        if theme == "dark":
-            template_fn = "nf-core-repo-logo-base-darkbg.png"
-
-        template_path = assets / template_fn
-        img = Image.open(str(template_path))
-        # get the height of the template image
-        height = img.size[1]
-
-        # Draw text
-        draw = ImageDraw.Draw(img)
-        color = theme == "dark" and (250, 250, 250) or (5, 5, 5)
-        draw.text((110, 465), text, color, font=font)
-
-        # Crop to max width
-        img = img.crop((0, 0, max_width, height))
-
-        # Resize
-        img = img.resize((width, int((width / max_width) * height)))
+        # cache file
+        cache_path = Path(NFCORE_CACHE_DIR, "logo", cache_name)
+        img = None
+        if cache_path.is_file():
+            log.debug(f"Logo already exists in cache at: {cache_path}. Reusing this file.")
+            img = Image.open(str(cache_path))
+        if not img:
+            log.debug(f"Creating logo for {text}")
+
+            # make sure the figure fits the text
+            font_path = assets / "MavenPro-Bold.ttf"
+            log.debug(f"Using font: {str(font_path)}")
+            font = ImageFont.truetype(str(font_path), 400)
+            text_length = font.getmask(text).getbbox()[2]  # get the width of the text based on the font
+
+            max_width = max(
+                2300, text_length + len(text) * 20
+            )  # need to add some more space to the text length to make sure it fits
+
+            template_fn = "nf-core-repo-logo-base-lightbg.png"
+            if theme == "dark":
+                template_fn = "nf-core-repo-logo-base-darkbg.png"
+
+            template_path = assets / template_fn
+            img = Image.open(str(template_path))
+            # get the height of the template image
+            height = img.size[1]
+
+            # Draw text
+            draw = ImageDraw.Draw(img)
+            color = theme == "dark" and (250, 250, 250) or (5, 5, 5)
+            draw.text((110, 465), text, color, font=font)
+
+            # Crop to max width
+            img = img.crop((0, 0, max_width, height))
+
+            # Resize
+            img = img.resize((width, int((width / max_width) * height)))
+
+            # Save to cache
+            Path(cache_path.parent).mkdir(parents=True, exist_ok=True)
+            log.debug(f"Saving logo to cache: {cache_path}")
+            img.save(cache_path, "PNG")
         # Save
         img.save(logo_path, "PNG")
 

diff --git a/nf_core/lint/__init__.py b/nf_core/lint/__init__.py
@@ -120,8 +120,10 @@ def run_linting(
     if subworkflow_lint_obj is not None:
         subworkflow_lint_obj.filter_tests_by_key(subworkflow_lint_tests)
 
-    # Set up files for modules linting test
+    # Set up files for component linting test
     module_lint_obj.set_up_pipeline_files()
+    if subworkflow_lint_obj is not None:
+        subworkflow_lint_obj.set_up_pipeline_files()
 
     # Run the pipeline linting tests
     try: