Style improvements

[m-jahn]

• closes update catalog test section with new pixi software dpeloyment #70
• closes Enhancement: can we search only Github repos that contain a Snakefile using the API? #71
• closes tube maps and config tables not present as expected #72
• regarding the tube maps, everything should work as expected. The more workflows are updated and WF pages rebuild in the catalog, the more maps should be added automatically
• the one prerequisite is that automatic workflow execution using the .test dir is enabled. Documentation was added.

Summary by CodeRabbit

Release Notes

• New Features

  • Added per-workflow documentation pages with visual diagrams, configuration and parameter details

• Documentation

  • Switched local development and contribution instructions to use pixi and predefined test/render commands
  • Shortened commit/PR guidance

• Bug Fixes

  • Faster, more reliable repository scanning with Snakefile-aware filtering and reduced delays
  • Improved workflow diagram styling

• Chores

  • Tightened and normalized dependency version constraints

[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: e4f83ccd-f689-44a8-8d77-f018fe7f868a

📥 Commits

Reviewing files that changed from the base of the PR and between e43eba1 and c48f343.

📒 Files selected for processing (1)

• scripts/common.py

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📝 Walkthrough

🚥 Pre-merge checks | ✅ 3 | ❌ 2

❌ Failed checks (1 warning, 1 inconclusive)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.
Title check	❓ Inconclusive	The title 'Style improvements' is vague and does not clearly convey the main objectives of the PR, which involve pixi migration, Snakefile filtering, and tube map generation.	Consider a more descriptive title that captures the primary changes, such as 'Replace conda with pixi and add Snakefile filtering' or 'Improve workflow catalog generation with pixi, Snakefile filtering, and style enhancements'.

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Linked Issues check	✅ Passed	All code changes directly address the three linked issues: pixi migration replaces conda [#70], Snakefile detection filters repos [#71], and styling improvements support tube maps [#72].
Out of Scope Changes check	✅ Passed	All changes are directly related to linked issues: dependency updates enable pixi, Snakefile filtering implements #71, and SVG styling supports tube maps from #72.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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[coderabbitai]

Actionable comments posted: 1

🧹 Nitpick comments (1)

scripts/generate-catalog.py (1)

142-142: Lambda captures loop variable by reference.

The lambda lambda: repo_search[i] captures i by reference. While this works correctly here because the lambda is called immediately within the same iteration, it's a common source of bugs if code is refactored.

Bind `i` explicitly

-        checked_repo = call_rate_limit_aware(lambda: repo_search[i], api_type="search")
+        checked_repo = call_rate_limit_aware(lambda idx=i: repo_search[idx], api_type="search")

🤖 Prompt for AI Agents

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

In `@scripts/generate-catalog.py` at line 142, The lambda passed to
call_rate_limit_aware captures the loop variable i by reference (checked_repo =
call_rate_limit_aware(lambda: repo_search[i], ...)), which is fragile; fix by
binding the current index or value when creating the callable—for example, pass
a lambda that captures the value like lambda v=repo_search[i]: v or use
functools.partial to pass repo_search[i] into call_rate_limit_aware—so that
call_rate_limit_aware receives a callable that closes over the concrete
repo_search element rather than the loop variable i.

🤖 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/common.py`:
- Around line 60-67: The has_snakefile function calls repo.get_contents directly
(for "Snakefile" and "workflow/Snakefile") and only catches
UnknownObjectException, which can leak other GithubException subclasses and
bypass rate-limit accounting; update has_snakefile to invoke repo.get_contents
inside call_rate_limit_aware (or wrap the get_contents call with the existing
rate-limit helper) and broaden the except clause to catch GithubException (or
Exception subclass appropriate) in addition to UnknownObjectException so
network/server errors are handled without crashing; keep the original return
semantics (True when found, False otherwise) and ensure any logged errors use
the existing logging pattern.

---

Nitpick comments:
In `@scripts/generate-catalog.py`:
- Line 142: The lambda passed to call_rate_limit_aware captures the loop
variable i by reference (checked_repo = call_rate_limit_aware(lambda:
repo_search[i], ...)), which is fragile; fix by binding the current index or
value when creating the callable—for example, pass a lambda that captures the
value like lambda v=repo_search[i]: v or use functools.partial to pass
repo_search[i] into call_rate_limit_aware—so that call_rate_limit_aware receives
a callable that closes over the concrete repo_search element rather than the
loop variable i.

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 91038cfd-6836-423d-bdba-94bbebb7759e

📥 Commits

Reviewing files that changed from the base of the PR and between 30d9042 and e43eba1.

⛔ Files ignored due to path filters (1)

• pixi.lock is excluded by !**/*.lock

📒 Files selected for processing (6)

• README.md
• pixi.toml
• scripts/common.py
• scripts/generate-catalog.py
• source/build_wf_pages.py
• source/modify_svg.py

💤 Files with no reviewable changes (1)

• source/modify_svg.py