Moved from markdownlint-cli to pymarkdown

.pre-commit-config.yaml

@@ -71,11 +71,10 @@ repos:
     hooks:
       - id: nb-clean
         args: [--preserve-cell-outputs, --remove-empty-cells]
-  - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.45.0
+  - repo: https://github.com/jackdewinter/pymarkdown
+    rev: v0.9.31
     hooks:
-      - id: markdownlint
-        args: [--config=pyproject.toml, --configPointer=/tool/markdownlint]
+      - id: pymarkdown
         exclude: docs/tutorials/
   - repo: https://github.com/tcort/markdown-link-check
     rev: v3.12.2

README.md

@@ -1,5 +1,7 @@
 # PaperQA2
 
+<!-- pyml disable-num-lines 6 line-length -->
+
 [![GitHub](https://img.shields.io/badge/GitHub-black?logo=github&logoColor=white)](https://github.com/Future-House/paper-qa)
 [![PyPI version](https://badge.fury.io/py/paper-qa.svg)](https://badge.fury.io/py/paper-qa)
 [![tests](https://github.com/Future-House/paper-qa/actions/workflows/tests.yml/badge.svg)](https://github.com/Future-House/paper-qa)

packages/paper-qa-pymupdf/README.md

@@ -1,5 +1,7 @@
 # paper-qa-pymupdf
 
+<!-- pyml disable-num-lines 6 line-length -->
+
 [![GitHub](https://img.shields.io/badge/GitHub-black?logo=github&logoColor=white)](https://github.com/Future-House/paper-qa/tree/main/packages/paper-qa-pymupdf)
 [![PyPI version](https://badge.fury.io/py/paper-qa-pymupdf.svg)](https://badge.fury.io/py/paper-qa-pymupdf)
 [![tests](https://github.com/Future-House/paper-qa/actions/workflows/tests.yml/badge.svg)](https://github.com/Future-House/paper-qa)

packages/paper-qa-pypdf/README.md

@@ -1,5 +1,7 @@
 # paper-qa-pypdf
 
+<!-- pyml disable-num-lines 6 line-length -->
+
 [![GitHub](https://img.shields.io/badge/GitHub-black?logo=github&logoColor=white)](https://github.com/Future-House/paper-qa/tree/main/packages/paper-qa-pypdf)
 [![PyPI version](https://badge.fury.io/py/paper-qa-pypdf.svg)](https://badge.fury.io/py/paper-qa-pypdf)
 [![tests](https://github.com/Future-House/paper-qa/actions/workflows/tests.yml/badge.svg)](https://github.com/Future-House/paper-qa)

pyproject.toml

@@ -127,15 +127,6 @@ skip = [
     "tests/stub_data/*",
 ]
 
-[tool.markdownlint]
-no-inline-html = false
-
-[tool.markdownlint.line-length]
-code_block_line_length = 88  # Match ruff line-length
-line_length = 120  # Match ruff max-doc-length
-stern = true
-tables = false
-
 [tool.mypy]
 # Type-checks the interior of functions without type annotations.
 check_untyped_defs = true
@@ -305,6 +296,16 @@ score = false
 # Minimum lines number of a similarity.
 min-similarity-lines = 12
 
+[tool.pymarkdown]
+plugins.line-length.code_block_line_length = 88  # Match ruff line-length
+plugins.line-length.enabled = true
+plugins.line-length.line_length = 120  # Match ruff max-doc-length
+plugins.line-length.stern = true
+plugins.line-length.tables = false
+plugins.no-duplicate-heading.siblings_only = true  # GitHub appends -X for duplicated headings
+plugins.no-emphasis-as-heading.enabled = false
+plugins.no-inline-html.enabled = false
+
 [tool.pytest.ini_options]
 # Add the specified OPTS to the set of command line arguments as if they had been
 # specified by the user.