use mdformat to format Markdown

[njzjz-bot]

Follow up deepmodeling/deepmd-kit@69eb0c3, use mdformat to format Markdown.

• Replace blacken-docs with mdformat

Summary by CodeRabbit

• Chores
  • Updated development configuration to enhance code and markdown formatting capabilities.

[codspeed-hq]

Merging this PR will not alter performance

⚠️ Unknown Walltime execution environment detected

Using the Walltime instrument on standard Hosted Runners will lead to inconsistent data.

For the most accurate results, we recommend using CodSpeed Macro Runners: bare-metal machines fine-tuned for performance measurement consistency.

✅ 2 untouched benchmarks
⏩ 2 skipped benchmarks¹

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_{Comparing njzjz-bothub:use-mdformat (9e9fcba) with devel (d6b44e7)}

Footnotes

1. 2 benchmarks were skipped, so the baseline results were used instead. If they were deleted from the codebase, click here and archive them to remove them from the performance reports. ↩

[coderabbitai]

📝 Walkthrough

Walkthrough

The .pre-commit-config.yaml is updated to replace the blacken-docs hook with mdformat for Markdown formatting. The mdformat hook (version 1.0.0) is configured with multiple plugins including mdformat-myst, mdformat-ruff, mdformat-web, mdformat-config, mdformat-beautysh, and mdformat-gfm-alerts.

Changes

Cohort / File(s)	Summary
Pre-commit Configuration .pre-commit-config.yaml	Removed blacken-docs hook and added mdformat hook (v1.0.0) with six additional dependencies for Markdown formatting across various formats and linting integrations.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~5 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 'use mdformat to format Markdown' directly describes the main change: replacing blacken-docs with mdformat for Markdown formatting in pre-commit configuration.
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
• Post copyable unit tests in a comment

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[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

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

Inline comments:
In @.pre-commit-config.yaml:
- Around line 43-45: The pre-commit config currently fetches mdformat-myst from
an unofficial git fork using the dependency string
"git+https://github.com/njzjz-bothub/mdformat-myst@d9c414e", which is a
supply-chain risk; replace this git+ URL with the official PyPI release
"mdformat-myst==0.3.0" (or a documented, signed internal package name) and add a
short comment explaining the temporary decision, or if the fork is required
long-term, publish the patched fork to PyPI (or an internal index) and update
the dependency to that published package name so CI and scanners can verify
artifacts.

---

ℹ️ Review info

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between d6b44e7 and 9e9fcba.

📒 Files selected for processing (1)

• .pre-commit-config.yaml

[coderabbitai]

⚠️ Potential issue | 🟠 Major

🧩 Analysis chain

🏁 Script executed:

#!/bin/bash
# Fetch commit d9c414e details from the fork
curl -s "https://api.github.com/repos/njzjz-bothub/mdformat-myst/commits/d9c414e" | jq -r '{sha: .sha, message: .commit.message, author_name: .commit.author.name, date: .commit.author.date, url: .html_url}'

Repository: deepmodeling/dpdata

Length of output: 731

---

🌐 Web query:

executablebooks mdformat-myst issue #13 status 2025 2026

💡 Result:

executablebooks/mdformat-myst Issue #13 (“colon fence syntax is broken by escape character”) is still Open as of February 24, 2026. It was opened Nov 29, 2021 by @arwedus, labeled enhancement, with no assignee, milestone, or linked PRs shown on the issue page. [1]

---

🌐 Web query:

mdformat-myst pypi latest version releases

💡 Result:

mdformat-myst (PyPI) latest version: 0.3.0 — released Nov 27, 2025. [1]

Recent releases (newest → oldest): [1]

• 0.3.0 — Nov 27, 2025
• 0.2.2 — Aug 19, 2025
• 0.2.1 — Nov 14, 2024
• 0.2.0 — Oct 16, 2024
• 0.1.5 — Feb 2, 2022
• 0.1.4 — Jun 23, 2021

Install: pip install mdformat-myst [1]

Sources: [1]

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Supply-chain risk: git+ fork dependency for mdformat-myst

Installing a package via git+https://github.com/njzjz-bothub/mdformat-myst@d9c414e bypasses PyPI's artifact integrity checks and vulnerability scanning pipeline. Even though the dependency is pinned to a specific commit hash, it pulls from an unofficial, unpublished fork rather than the verified PyPI release (0.3.0, released Nov 27, 2025). This is a meaningful supply-chain risk for any project contributor or CI runner that consumes this pre-commit config.

The commit fixes an indentation preservation issue for non-MyST directive content (as described in its message), which is different from the original issue #13 (colon fence syntax broken by escape character) that remains unresolved upstream. Consider:

• Tracking when upstream resolves the underlying issues and reverting to the official PyPI release.
• If the fork must be used long-term, consider formally publishing the patched version to PyPI under a scoped name to improve transparency and enable vulnerability scanning.

🤖 Prompt for AI Agents

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

In @.pre-commit-config.yaml around lines 43 - 45, The pre-commit config
currently fetches mdformat-myst from an unofficial git fork using the dependency
string "git+https://github.com/njzjz-bothub/mdformat-myst@d9c414e", which is a
supply-chain risk; replace this git+ URL with the official PyPI release
"mdformat-myst==0.3.0" (or a documented, signed internal package name) and add a
short comment explaining the temporary decision, or if the fork is required
long-term, publish the patched fork to PyPI (or an internal index) and update
the dependency to that published package name so CI and scanners can verify
artifacts.

[njzjz-bot]

pre-commit.ci autofix

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 86.37%. Comparing base (d6b44e7) to head (9e9fcba).

Additional details and impacted files

@@           Coverage Diff           @@
##            devel     #940   +/-   ##
=======================================
  Coverage   86.37%   86.37%           
=======================================
  Files          86       86           
  Lines        8086     8086           
=======================================
  Hits         6984     6984           
  Misses       1102     1102           

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