feat: added news section, small updates

[m-jahn]

Summary by CodeRabbit

• New Features

  • Automatic Tube Map visualization when executable test cases exist.
  • Automatic Workflow Parameter Table generation from configuration schema files.

• Style

  • Centered, block image display and new rounded-corner image styling.
  • Adjusted layout of workflow cards for improved visual arrangement.

• Documentation

  • Added a News announcement for new renderings and fixed internal doc links.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: ab6e37c3-a2d5-491e-81ea-17069a04d15c

📥 Commits

Reviewing files that changed from the base of the PR and between 79a9252 and 9c47e08.

📒 Files selected for processing (2)

• source/_templates/workflows_by.md
• source/index.md

✅ Files skipped from review due to trivial changes (2)

• source/_templates/workflows_by.md
• source/index.md

---

📝 Walkthrough

Walkthrough

Adjusted catalog script logging range formatting, updated image reference CSS with centered block display and a new rounded-image class, and added a dated News section plus minor layout/link tweaks in documentation announcing automatic renderings.

Changes

Cohort / File(s)	Summary
Catalog logging scripts/generate-catalog.py	Added end_log to format repository search range in initial log and changed progress messages to use len(repo_list) for periodic updates.
CSS styling source/_static/custom.css	Changed .image-reference img from display: inline to display: block with text-align: center; added .rounded-img { border-radius: 10px; overflow: hidden; }.
Documentation — index & templates source/index.md, source/_templates/workflows_by.md	Replaced top logo with a dated News item (2026-04-13) describing Tube Maps and Workflow Parameter Tables; adjusted grid layout (::::{grid} 1 2 3 3), inserted a blank line before an iframe, and removed angle-bracket wrappers from several internal links in Contributing.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'added news section, small updates' accurately reflects the main changes: a new news section was added to the homepage (source/index.md), alongside CSS styling updates and a logging script modification.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

---

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[coderabbitai]

Actionable comments posted: 3

🧹 Nitpick comments (1)

source/_static/custom.css (1)

2-3: text-align: center will not center this block image

On Line 3, text-align on img is ineffective for centering the image itself after Line 2 sets display: block. Use auto horizontal margins on the image (or apply text-align on the parent).

Suggested CSS adjustment

 .image-reference img {
   display: block;
-  text-align: center;
+  margin-left: auto;
+  margin-right: auto;
 }

🤖 Prompt for AI Agents

Verify each finding against the current code and only fix it if needed.

In `@source/_static/custom.css` around lines 2 - 3, The img rule currently sets
display: block and text-align: center, but text-align on the img itself does
nothing; change the centering approach for the image selector (the img rule) by
replacing the ineffective text-align with auto horizontal margins (margin-left
and margin-right set to auto) to center the block image, or alternatively remove
text-align from the img rule and apply text-align: center to the parent
container selector instead to achieve centering.

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@scripts/generate-catalog.py`:
- Line 124: The logged upper bound end_log is computed incorrectly for
exclusive-end ranges: change the test-mode assignment of end_log (and the later
computation that sets end_log when end == total_count) to reflect that
range(offset, end) excludes end by using end_log = end - 1 (or end_log =
max(offset, end - 1)) instead of end_log = end or end_log = 1; update both
occurrences that set end_log (the test-mode branch and the runtime branch that
currently checks end == total_count) so the log that prints "offset-end_log"
shows the correct inclusive upper index when using range(offset, end).

In `@source/index.md`:
- Line 28: The News subsection heading currently uses "#### 2026-04-13" which
jumps the hierarchy from "##" to "####"; update that heading to "### 2026-04-13"
so the heading level remains consistent with the surrounding "##" News section
(replace the line containing "#### 2026-04-13" with "### 2026-04-13").
- Line 119: Replace the generic link text "here" on the line that links to
docs/snakemake with a descriptive phrase such as "Snakemake workflow authoring
guide" (or "Snakemake workflow examples"), so the sentence reads e.g. "Resources
for creating new workflows can be found in the Snakemake workflow authoring
guide (docs/snakemake) or in more detail on the Snakemake documentation
(https://snakemake.readthedocs.io/en/stable/index.html)"; update the visible
link text pointing to docs/snakemake accordingly.

---

Nitpick comments:
In `@source/_static/custom.css`:
- Around line 2-3: The img rule currently sets display: block and text-align:
center, but text-align on the img itself does nothing; change the centering
approach for the image selector (the img rule) by replacing the ineffective
text-align with auto horizontal margins (margin-left and margin-right set to
auto) to center the block image, or alternatively remove text-align from the img
rule and apply text-align: center to the parent container selector instead to
achieve centering.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 92e55f31-5dfa-4584-ba6e-f188aa71714e

📥 Commits

Reviewing files that changed from the base of the PR and between 10115bc and 79a9252.

⛔ Files ignored due to path filters (2)

• source/_static/news_item1.png is excluded by !**/*.png
• source/_static/news_item2.png is excluded by !**/*.png

📒 Files selected for processing (3)

• scripts/generate-catalog.py
• source/_static/custom.css
• source/index.md