feat: Add section validation warnings for recommended manuscript sections

src/rxiv_maker/engines/operations/validate.py

@@ -25,6 +25,7 @@
     from ...validators.latex_error_parser import LaTeXErrorParser
     from ...validators.math_validator import MathValidator
     from ...validators.reference_validator import ReferenceValidator
+    from ...validators.section_validator import SectionValidator
     from ...validators.syntax_validator import SyntaxValidator
 
     VALIDATORS_AVAILABLE = True
@@ -42,6 +43,7 @@
         from rxiv_maker.validators.latex_error_parser import LaTeXErrorParser  # type: ignore
         from rxiv_maker.validators.math_validator import MathValidator  # type: ignore
         from rxiv_maker.validators.reference_validator import ReferenceValidator  # type: ignore
+        from rxiv_maker.validators.section_validator import SectionValidator  # type: ignore
         from rxiv_maker.validators.syntax_validator import SyntaxValidator  # type: ignore
 
         VALIDATORS_AVAILABLE = True
@@ -95,6 +97,7 @@ def validate_all(self) -> bool:
             print()
 
         validators = [
+            ("Structure", SectionValidator),
             ("Citations", CitationValidator),
             ("Cross-references", ReferenceValidator),
             ("Figures", FigureValidator),

src/rxiv_maker/validators/section_validator.py

@@ -0,0 +1,139 @@
+"""Section validator for checking recommended manuscript sections.
+
+This validator checks if manuscripts include important sections that are
+commonly required by journals, such as:
+- Data Availability
+- Code Availability
+- Author Contributions
+- Acknowledgements
+- Funding
+- Competing Interests
+
+Missing sections generate warnings (not errors) to help authors ensure
+their manuscript is complete before submission.
+"""
+
+import re
+
+from ..utils.file_helpers import find_manuscript_md
+from .base_validator import BaseValidator, ValidationError, ValidationLevel, ValidationResult
+
+
+class SectionValidator(BaseValidator):
+    """Validator for checking recommended manuscript sections."""
+
+    # Required sections that should generate warnings if missing
+    RECOMMENDED_SECTIONS = {
+        "data availability": {
+            "patterns": [
+                r"##\s+Data\s+Availability",
+                r"##\s+Data\s+and\s+Code\s+Availability",
+            ],
+            "suggestion": "Add a '## Data Availability' section describing where your data can be accessed",
+        },
+        "code availability": {
+            "patterns": [
+                r"##\s+Code\s+Availability",
+                r"##\s+Data\s+and\s+Code\s+Availability",
+                r"##\s+Software\s+Availability",
+            ],
+            "suggestion": "Add a '## Code Availability' section with links to code repositories",
+        },
+        "author contributions": {
+            "patterns": [
+                r"##\s+Author\s+Contributions?",
+                r"##\s+Contributions?",
+            ],
+            "suggestion": "Add an '## Author Contributions' section describing each author's role",
+        },
+        "acknowledgements": {
+            "patterns": [
+                r"##\s+Acknowledgements?",
+                r"##\s+Acknowledgments?",
+            ],
+            "suggestion": "Add an '## Acknowledgements' section to thank contributors",
+        },
+        "funding": {
+            "patterns": [
+                r"##\s+Funding",
+                r"##\s+Financial\s+Support",
+                r"##\s+Grant\s+Information",
+            ],
+            "suggestion": "Add a '## Funding' section declaring funding sources or stating 'This research received no external funding.'",
+        },
+        "competing interests": {
+            "patterns": [
+                r"##\s+Competing\s+Interests?",
+                r"##\s+Conflicts?\s+of\s+Interest",
+                r"##\s+Disclosure",
+            ],
+            "suggestion": "Add a '## Competing Interests' section, even if just to state 'The authors declare no competing interests.'",
+        },
+    }
+
+    def validate(self) -> ValidationResult:
+        """Check for recommended manuscript sections.
+
+        Returns:
+            ValidationResult with warnings for missing sections
+        """
+        errors: list[ValidationError] = []
+        metadata = {
+            "missing_sections": [],
+            "found_sections": [],
+        }
+
+        # Find manuscript file
+        try:
+            manuscript_file = find_manuscript_md(self.manuscript_path)
+        except (FileNotFoundError, ValueError) as e:
+            return ValidationResult(
+                validator_name=self.name,
+                errors=[
+                    self._create_error(
+                        level=ValidationLevel.ERROR,
+                        message=f"Could not find manuscript file: {e}",
+                    )
+                ],
+                metadata=metadata,
+            )
+
+        # Read manuscript content
+        content = self._read_file_safely(manuscript_file)
+        if content is None:
+            return ValidationResult(
+                validator_name=self.name,
+                errors=[
+                    self._create_error(
+                        level=ValidationLevel.ERROR,
+                        message=f"Could not read manuscript file: {manuscript_file}",
+                    )
+                ],
+                metadata=metadata,
+            )
+
+        # Check for each recommended section
+        for section_name, section_info in self.RECOMMENDED_SECTIONS.items():
+            found = False
+            for pattern in section_info["patterns"]:
+                if re.search(pattern, content, re.IGNORECASE):
+                    found = True
+                    metadata["found_sections"].append(section_name)
+                    break
+
+            if not found:
+                metadata["missing_sections"].append(section_name)
+                errors.append(
+                    self._create_error(
+                        level=ValidationLevel.WARNING,
+                        message=f"Recommended section '{section_name.title()}' not found",
+                        file_path=manuscript_file,
+                        suggestion=section_info["suggestion"],
+                    )
+                )
+
+        return ValidationResult(
+            validator_name=self.name,
+            errors=errors,
+            metadata=metadata,
+        )