Template: switch to new image syntax in readme (and fix changelog action)

.github/workflows/changelog.py

@@ -16,7 +16,6 @@
 
 import os
 import re
-import subprocess
 import sys
 from pathlib import Path
 from typing import List
@@ -51,39 +50,33 @@
     sys.exit(0)
 
 
-def _run_cmd(cmd):
-    print(cmd)
-    result = subprocess.run(cmd, shell=True, capture_output=True, text=True)
-    if result.returncode != 0:
-        raise RuntimeError(f"Error executing command: {result.stderr}")
-    return result
-
-
-def _determine_change_type(pr_title) -> 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.
     """
     sections = {
-        "Template": "### Template updates",
-        "Download": "### Download updates",
-        "Linting": "### Linting updates",
+        "Template": "### Template",
+        "Download": "### Download",
+        "Linting": "### Linting",
         "Modules": "### Modules",
         "Subworkflows": "### Subworkflows",
     }
-    current_section = "### General"
+    current_section_header = "### General"
+    current_section = "General"
 
     # Check if the PR in any of the sections.
     for section, section_header in sections.items():
         # check if the PR title contains any of the section headers, with some loose matching, e.g. removing plural and suffixes
         if re.sub(r"s$", "", section.lower().replace("ing", "")) in pr_title.lower():
-            current_section = section_header
-
-    return current_section
+            current_section_header = section_header
+            current_section = section
+    print(f"Detected section: {current_section}")
+    return current_section, current_section_header
 
 
-# Determine the type of the PR: new module, module update, or core update.
-section = _determine_change_type(pr_title)
+# Determine the type of the PR
+section, section_header = _determine_change_type(pr_title)
 
 # Remove section indicator from the PR title.
 pr_title = re.sub(rf"{section}[:\s]*", "", pr_title, flags=re.IGNORECASE)
@@ -93,11 +86,14 @@ def _determine_change_type(pr_title) -> str:
 
 # Handle manual changelog entries through comments.
 if comment := comment.removeprefix("@nf-core-bot changelog").strip():
+    print(f"Adding manual changelog entry: {comment}")
     pr_title = comment
 new_lines = [
     f"- {pr_title} {pr_link}\n",
 ]
 
+print(f"Adding new lines into section '{section}':\n" + "".join(new_lines))
+
 # Finally, updating the changelog.
 # Read the current changelog lines. We will print them back as is, except for one new
 # entry, corresponding to this new PR.
@@ -108,6 +104,7 @@ def _determine_change_type(pr_title) -> str:
 
 def _skip_existing_entry_for_this_pr(line: str, same_section: bool = True) -> str:
     if line.strip().endswith(pr_link):
+        print(f"Found existing entry for this pull request #{pr_number}:")
         existing_lines = [line]
         if new_lines and new_lines == existing_lines and same_section:
             print(f"Found existing identical entry for this pull request #{pr_number} in the same section:")
@@ -126,7 +123,7 @@ def _skip_existing_entry_for_this_pr(line: str, same_section: bool = True) -> st
     return line
 
 
-# Find the next line in the change log that matches the pattern "## MultiQC v.*dev"
+# Find the next line in the change log that matches the pattern "# nf-core/tools v.*dev"
 # If it doesn't exist, exist with code 1 (let's assume that a new section is added
 # manually or by CI when a release is pushed).
 # Else, find the next line that matches the `section` variable, and insert a new line
@@ -140,6 +137,7 @@ def _skip_existing_entry_for_this_pr(line: str, same_section: bool = True) -> st
     line = _skip_existing_entry_for_this_pr(line, same_section=False)
 
     if line.startswith("# ") and not line.strip() == "# nf-core/tools: Changelog":  # Version header, e.g. "# v2.12dev"
+        print(f"Found version header: {line.strip()}")
         updated_lines.append(line)
 
         # Parse version from the line `# v2.12dev` or
@@ -175,8 +173,11 @@ def _skip_existing_entry_for_this_pr(line: str, same_section: bool = True) -> st
                     updated_lines.append(line)
             break
         continue
-
-    if inside_version_dev and line.lower().startswith(section.lower()):  # Section of interest header
+    print(f"Found line: {line.strip()}")
+    print(f"inside_version_dev: {inside_version_dev}")
+    print(f"section_header: {section_header}")
+    if inside_version_dev and line.lower().startswith(section_header.lower()):  # Section of interest header
+        print(f"Found section header: {line.strip()}")
         if already_added_entry:
             print(
                 f"Already added new lines into section {section}, is the section duplicated?",
@@ -189,6 +190,7 @@ def _skip_existing_entry_for_this_pr(line: str, same_section: bool = True) -> st
         while True:
             line = orig_lines.pop(0)
             if line.startswith("#"):
+                print(f"Found the next section header: {line.strip()}")
                 # Found the next section header, so need to put all the lines we collected.
                 updated_lines.append("\n")
                 _updated_lines = [_l for _l in section_lines + new_lines if _l.strip()]

CHANGELOG.md

@@ -6,6 +6,8 @@
 
 - Add a Github Action Workflow to the pipeline template that tests a successful download with 'nf-core download' ([#2618](https://github.com/nf-core/tools/pull/2618))
 - Use `pre-commit` to lint files in GitHub CI ([#2635](https://github.com/nf-core/tools/pull/2635))
+- Use pdiff also on gitpod for nf-test ([#2640](https://github.com/nf-core/tools/pull/2640))
+- 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))
 
 ### Download

README.md

@@ -1,4 +1,7 @@
-# ![nf-core/tools](docs/images/nfcore-tools_logo_light.png#gh-light-mode-only) ![nf-core/tools](docs/images/nfcore-tools_logo_dark.png#gh-dark-mode-only) <!-- omit in toc -->
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="docs/images/nfcore-tools_logo_dark.png">
+  <img alt="nf-core/tools logo" src="docs/images/nfcore-tools_logo_light.png">
+</picture><!-- omit in toc -->
 
 [![Python tests](https://github.com/nf-core/tools/workflows/Python%20tests/badge.svg?branch=master&event=push)](https://github.com/nf-core/tools/actions?query=workflow%3A%22Python+tests%22+branch%3Amaster)
 [![codecov](https://codecov.io/gh/nf-core/tools/branch/master/graph/badge.svg)](https://codecov.io/gh/nf-core/tools)

nf_core/pipeline-template/README.md

@@ -1,7 +1,9 @@
 {% if branded -%}
+<picture>
 
-# ![{{ name }}](docs/images/{{ logo_light }}#gh-light-mode-only) ![{{ name }}](docs/images/{{ logo_dark }}#gh-dark-mode-only)
-
+  <source media="(prefers-color-scheme: dark)" srcset="docs/images/{{ logo_dark }}">
+  <img alt="{{ name }} logo" src="docs/images/{{ logo_light }}">
+</picture>
 {% endif -%}
 {% if github_badges -%}
 [![GitHub Actions CI Status](https://github.com/{{ name }}/workflows/nf-core%20CI/badge.svg)](https://github.com/{{ name }}/actions?query=workflow%3A%22nf-core+CI%22)