Merge pull request #134 from rhpvorderman/release_0.7.1

Release 0.7.1

.github/workflows/ci.yml

@@ -22,6 +22,7 @@ jobs:
           - docs
           - lint
           - pedantic_compile
+          - html5validator
     runs-on: ubuntu-20.04
     steps:
       - uses: actions/checkout@v4
@@ -49,15 +50,15 @@ jobs:
         os: ["ubuntu-latest"]
         include:
           # Macos X86
-          - os: "macos-13"
-            python-version: "3.8"
-          - os: "macos-13"
-            python-version: "3.12"
-          # Macos ARM m1
           - os: "macos-latest"
             python-version: "3.8"
           - os: "macos-latest"
             python-version: "3.12"
+          # Macos ARM m1
+          - os: "macos-14"
+            python-version: "3.10"
+          - os: "macos-14"
+            python-version: "3.12"
           - os: "windows-latest"
             python-version: "3.8"
           - os: "windows-latest"
@@ -97,12 +98,12 @@ jobs:
   deploy:
     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
     runs-on: ${{ matrix.os }}
-    needs: [package-checks, test]
+    needs: [package-checks, test, test-arch]
     strategy:
       matrix:
         os:
           - ubuntu-latest
-          - macos-13
+          - macos-14
           - macos-latest
           - windows-latest
         cibw_archs_linux: ["x86_64"]

CHANGELOG.rst

@@ -7,6 +7,12 @@ Changelog
 .. This document is user facing. Please word the changes in such a way
 .. that users understand how the changes affect the new version.
 
+version 0.7.1
+-----------------
++ Fix a small visual bug in the report sidebar.
++ PyGAL report htmls are now fully HTML5 compliant. HTML5 validation has been
+  made a part of the integration testing.
+
 version 0.7.0
 -----------------
 + Image files can now be saved as SVG files.

src/sequali/report_modules.py

@@ -140,10 +140,10 @@ def create_toc(content: str):
             if header_level != current_level:
                 if header_level > current_level:
                     for i in range(header_level - current_level):
-                        toc.write('<ul class="toc_list">')
+                        toc.write('<li><ul class="toc_list">')
                 else:
                     for i in range(current_level - header_level):
-                        toc.write("</ul>")
+                        toc.write("</ul></li>")
                 current_level = header_level
             toc.write(f'<li><a class="toclink" href="#{id}">{header}</a></li>')
     if current_level > 0:
@@ -152,8 +152,51 @@ def create_toc(content: str):
     return toc.getvalue()
 
 
+def make_series_unique(svg: str) -> str:
+    """
+    Processes a PyGAL SVG to have unique serie IDs to fix
+    https://github.com/Kozea/pygal/issues/563.
+    """
+    # TODO: Remove this once a fix is released in PyGAL and the PyGAL
+    # requirement is updated.
+    svg_element: xml.etree.ElementTree.Element = xml.etree.ElementTree.fromstring(svg)
+    if not svg_element.tag.endswith("svg"):
+        raise ValueError("This is not a svg xml")
+    namespace = svg_element.tag.rstrip("svg")
+    xml.etree.ElementTree.register_namespace("", namespace.strip("{}"))
+    chart_id = svg_element.attrib["id"]
+    for element in svg_element.iter():
+        if not element.tag == f"{namespace}g":
+            continue
+        id = element.get("id")
+        # Find activate-serie elements and append chart-id to their name to
+        # make them unique.
+        if id and id.startswith("activate-serie"):
+            element.set("id", f"{id}-{chart_id}")
+            continue
+
+        # Individual series have a class attribute serie-<NUMBER> format.
+        # Append the chart_id to make these unique.
+        cls = element.get("class")
+        if cls and "serie-" in cls:
+            classifiers = cls.split()
+            for classifier in classifiers:
+                if classifier.startswith("serie-"):
+                    to_replace = classifier
+                    break
+            else:  # No break
+                raise RuntimeError("serie classifier should exist")
+            classifiers.remove(to_replace)
+            new_classifier = f"{to_replace}-{chart_id}"
+            classifiers.append(new_classifier)
+            element.set("class", " ".join(classifiers))
+    return xml.etree.ElementTree.tostring(
+        svg_element, encoding="unicode", method="xml")
+
+
 def figurize_plot(plot: pygal.Graph):
     svg_unicode = plot.render(is_unicode=True)
+    svg_unicode = make_series_unique(svg_unicode)
     svg_tree: xml.etree.ElementTree.Element = (
         xml.etree.ElementTree.fromstring(svg_unicode))
     svg_id = svg_tree.get("id")
@@ -425,7 +468,7 @@ def distribution_table(self):
     def to_html(self):
         return f"""
             {html_header("Sequence length distribution", 1)}
-            <p>{self.distribution_table()}</p>
+            {self.distribution_table()}
             {figurize_plot(self.plot())}
         """
 
@@ -678,7 +721,7 @@ def plot(self) -> pygal.Graph:
     def to_html(self) -> str:
         return f"""
             {html_header("Per sequence average quality scores", 1)}
-            <p>{self.quality_scores_table()}</p>
+            {self.quality_scores_table()}
             {figurize_plot(self.plot())}
         """
 
@@ -1121,7 +1164,6 @@ def to_html(self):
         estimate the duplication rate. See
         <a href="https://sequali.readthedocs.io/#duplication-estimation-module">
         the documentation</a> for a complete explanation.</p>
-        <p>
         <table>
             <tr>
                 <td>Fingerprint front sequence length</td>
@@ -1158,7 +1200,6 @@ def to_html(self):
                 <td style="text-align:right;">{self.remaining_fraction:.2%}</td>
             </tr>
             </table>
-        </p>
         """
         return f"""
             {html_header("Duplication percentages", 1)}
@@ -1683,6 +1724,7 @@ def write_html_report(report_modules: Iterable[ReportModule],
             <!DOCTYPE html>
             <html lang="en">
             <head>
+                <meta charset="utf-8">
                 <script>
                     {SEQUALI_REPORT_JS_CONTENT}
                 </script>
@@ -1692,7 +1734,6 @@ def write_html_report(report_modules: Iterable[ReportModule],
                 <style>
                     {SEQUALI_REPORT_CSS_CONTENT}
                 </style>
-                <meta charset="utf-8">
                 <title>{os.path.basename(filename)}: Sequali Report</title>
             </head>
             <body>

src/sequali/static/sequali_report.css

@@ -1,6 +1,7 @@
 body {
     font-family: sans;
     width:100%;
+    margin: 0px;
 }
 
 /* Use h2 header settings for h1 etc. to have more understated headers. */

tox.ini

@@ -69,3 +69,14 @@ commands=
     # -a rebuilds everything. -W turns warnings into errors.
     # --keep-going makes sure we see al the errors that are there in one go.
     sphinx-build -a -W -n --keep-going docs docs/_build
+
+
+[testenv:html5validator]
+deps=html5validator
+allowlist_externals=bash
+                    mkdir
+commands=
+    mkdir -p reports
+    bash -c 'for FILE in tests/data/*.fastq tests/data/*.fastq.gz tests/data/*.bam; do sequali --outdir reports $FILE; done'
+    # || exit 1 needed to force crashes when html5validator fails with 255
+    bash -c 'html5validator -- reports/*.html || exit 1'