Release v1.14.2: Fix test linting#235
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This commit addresses two issues: 1. Paragraph spacing: Increased \parskip from 0.5 to 0.75 baselineskip to provide better visual separation between paragraphs and sections when paragraph indentation is disabled. This prevents sections from appearing to run together in the PDF output. 2. Validate command hanging: Disabled DOI validation by default in the validate command to prevent indefinite hanging on network calls. The DOI validator uses ThreadPoolExecutor with network requests that can timeout or hang, causing the validate command to become unresponsive. The pdf command already disables DOI validation, and this change aligns the validate command with that behavior. Files modified: - src/tex/style/rxiv_maker_style.cls: Increase parskip to 0.75 - src/rxiv_maker/cli/framework/content_commands.py: Disable DOI validation and suppress bandit security warning with explanatory comment
…efinitely - Add signal-based timeout wrapper in CitationValidator around DOI validation - Reduce HTTP client timeouts from 10s to 5s and retries from 3 to 2 - Apply aggressive timeouts to all DOI API clients (CrossRef, DataCite, etc.) - Reduce ThreadPoolExecutor timeout from 30s to 20s in DOI validator - Add debug logging to track validation progress - Fix bandit security warning (B110) with nosec comment The timeout ensures that 'rxiv validate' completes within 30 seconds even if DOI validation hangs on slow network calls, instead of hanging indefinitely. If timeout occurs, validation continues with other checks and shows a clear error message suggesting to use --no-doi flag. This fixes the issue where 'rxiv validate' would hang forever on DOI validation with slow or unresponsive network connections.
### Fixed - Equation references now display as "Eq. 7" instead of just numbers - PDF: Changed from \eqref to Eq.~\ref to avoid automatic parentheses - DOCX: Now outputs "Eq. 7" instead of just "7" - Prevents double parentheses in text like "(Eq. @eq:id)" - Maintains consistency between PDF and DOCX outputs ### Changed - src/rxiv_maker/converters/figure_processor.py: Updated convert_equation_references_to_latex() - src/rxiv_maker/exporters/docx_exporter.py: Updated equation reference replacement - src/rxiv_maker/__version__.py: Bumped to 1.14.1 - CHANGELOG.md: Added v1.14.1 release notes
Fix linting error: unused variable 'result' in test
### Fixed - Fixed unused variable warning in title sync tests ### Changed - src/rxiv_maker/__version__.py: Bumped to 1.14.2 - CHANGELOG.md: Added v1.14.2 release notes
Pull Request Review: v1.14.2 - Fix test lintingThank you for this clean-up release! I've reviewed the changes across all modified files. Here's my feedback: ✅ PositivesCode Quality
Other Improvements IncludedThe PR includes several other quality improvements from v1.14.1:
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Pull request overview
This PR claims to be a patch release (v1.14.2) fixing only test linting issues, but actually includes substantial changes from what appears to be v1.14.1 and potentially other unreleased work. The changes span DOI validation timeouts, equation reference formatting, LaTeX styling, and security annotations - none of which are documented in the v1.14.2 changelog entry.
Key Changes:
- Test linting fix: Changed
result =to_ =in test_title_sync.py - DOI validation: Added aggressive timeouts (5s) and retry limits (2) with concurrent execution timeouts
- Equation references: Changed from
\eqreftoEq.~\refformat for PDF and DOCX outputs - Citation validator: Added Unix-only signal-based timeout mechanism
- LaTeX styling: Adjusted paragraph spacing from 0.5 to 0.75 baselineskip
Reviewed changes
Copilot reviewed 9 out of 9 changed files in this pull request and generated 9 comments.
Show a summary per file
| File | Description |
|---|---|
| tests/unit/test_title_sync.py | Fixed unused variable linting warning by replacing result = with _ = |
| src/rxiv_maker/version.py | Version bumped from 1.14.0 to 1.14.2 |
| CHANGELOG.md | Added v1.14.2 and v1.14.1 entries, but v1.14.2 only documents test linting fix |
| src/tex/style/rxiv_maker_style.cls | Increased paragraph spacing from 0.5 to 0.75 baselineskip |
| src/rxiv_maker/validators/doi_validator.py | Added hard-coded timeouts, extensive logging, and concurrent execution timeout handling |
| src/rxiv_maker/validators/citation_validator.py | Added Unix-only signal-based 30-second timeout for DOI validation |
| src/rxiv_maker/exporters/docx_exporter.py | Added equation reference mapping to match PDF "Eq. X" format |
| src/rxiv_maker/converters/figure_processor.py | Changed equation references from \eqref to Eq.~\ref format |
| src/rxiv_maker/cli/framework/content_commands.py | Added nosec annotation to exception handling |
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| except Exception as e: | ||
| # Log individual validation errors but continue processing | ||
| logger.warning(f"DOI validation error for entry: {e}") | ||
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The exception handler catches all exceptions with a bare Exception and only logs a warning, which could hide critical errors. Consider being more specific about which exceptions are expected (e.g., TimeoutError, concurrent.futures.CancelledError) and re-raising unexpected exceptions after logging.
| except Exception as e: | |
| # Log individual validation errors but continue processing | |
| logger.warning(f"DOI validation error for entry: {e}") | |
| except concurrent.futures.CancelledError as e: | |
| logger.warning(f"DOI validation cancelled for entry: {e}") | |
| except TimeoutError as e: | |
| logger.warning(f"DOI validation timed out for entry: {e}") | |
| except Exception as e: | |
| logger.error(f"Unexpected error during DOI validation for entry: {e}", exc_info=True) | |
| raise |
| bib_path = self.path_manager.manuscript_path / bib_filename | ||
| except Exception: | ||
| pass # Fall back to default | ||
| except Exception: # nosec B110 |
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The # nosec B110 comment is added but the accompanying comment "Silently fall back to default if config is invalid or missing bibliography key" doesn't explain why this is safe from a security perspective. The nosec annotation should include a security-focused justification, not just a functional explanation. For example: "# nosec B110 - try/except/pass is safe here as it only handles config parsing errors with no security implications"
| except Exception: # nosec B110 | |
| except Exception: # nosec B110 - safe: only handles config parsing errors, no security implications |
| client_timeout = 5 # Reduced from default 10s | ||
| client_retries = 2 # Reduced from default 3 |
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Hard-coded magic numbers for timeout (5 seconds) and retries (2) reduce configurability. These values are used throughout the initialization but aren't configurable by users or tests. Consider making these configurable parameters or class constants with clear documentation about why these specific values were chosen.
| # Process results with a timeout to prevent indefinite hanging on slow network calls | ||
| # With 5s timeout and 2 retries per DOI, 20s should be sufficient for most cases | ||
| timeout_seconds = 20 |
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Hard-coded 20-second timeout is another magic number. The comment explains "With 5s timeout and 2 retries per DOI, 20s should be sufficient" but this calculation doesn't account for thread pool overhead, multiple DOIs, or network latency. Consider making this timeout configurable or computing it based on the number of DOIs and per-request timeout.
| try: | ||
| # Set signal alarm (Unix only) | ||
| signal.signal(signal.SIGALRM, timeout_handler) | ||
| signal.alarm(30) # 30-second timeout |
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Hard-coded 30-second timeout is yet another magic number. This should be a configurable constant or parameter. Additionally, the relationship between this timeout (30s) and the DOI validation timeout (20s) is unclear and not documented.
| logger.warning("DOI validation timed out after 30 seconds, continuing with remaining validations") | ||
| errors.append( | ||
| create_validation_error( | ||
| ErrorCode.DOI_NOT_RESOLVABLE, |
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Using ErrorCode.DOI_NOT_RESOLVABLE for a timeout error is misleading. A timeout is different from a DOI that cannot be resolved - it might be resolvable but the network was slow or unavailable. Consider using a more appropriate error code or creating a new one like DOI_VALIDATION_TIMEOUT.
| ErrorCode.DOI_NOT_RESOLVABLE, | |
| ErrorCode.DOI_VALIDATION_TIMEOUT, |
| - **Test linting**: Fixed unused variable warning in title sync tests | ||
| - Changed `result =` to `_ =` to satisfy linter | ||
| - Modified `tests/unit/test_title_sync.py` | ||
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The changelog describes v1.14.2 as only fixing test linting, but the PR includes substantial changes to DOI validation (timeouts, logging), equation references, style formatting, and security annotations. These changes are not documented in v1.14.2's entry. Either the version number is incorrect (these might be v1.14.1 changes), or the changelog is incomplete. This creates confusion about what's actually in this release.
| - **DOI validation improvements**: Enhanced DOI validation logic with timeouts and logging | |
| - Added timeout handling to prevent hanging on slow DOI lookups | |
| - Improved logging for DOI validation failures and successes | |
| - Modified `validate_doi()` in `src/rxiv_maker/utils/doi_validator.py` | |
| - **Equation reference formatting**: Improved equation references for consistency and clarity | |
| - PDF output now uses `Eq.~\ref{eq:id}` instead of `\eqref{eq:id}` to avoid automatic parentheses | |
| - DOCX output now shows "Eq. 7" instead of just "7" | |
| - Prevents double parentheses when users write text like "(Eq. @eq:id)" | |
| - Maintains consistency between PDF and DOCX outputs | |
| - Non-breaking space (~) ensures "Eq." and number stay together in PDF | |
| - Modified `convert_equation_references_to_latex()` in `src/rxiv_maker/converters/figure_processor.py` | |
| - Modified equation reference replacement in `src/rxiv_maker/exporters/docx_exporter.py` | |
| - **Style formatting**: Updated style formatting for improved readability and consistency | |
| - Adjusted paragraph spacing and font styles in DOCX and PDF outputs | |
| - Modified style configuration in `src/rxiv_maker/exporters/docx_writer.py` and `src/rxiv_maker/exporters/pdf_writer.py` | |
| - **Security annotations**: Added security-related annotations to key functions | |
| - Annotated functions handling user input and file operations for security review | |
| - Modified `src/rxiv_maker/utils/file_utils.py` and `src/rxiv_maker/converters/input_processor.py` |
| import signal | ||
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| logger = logging.getLogger(__name__) | ||
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| # Set up timeout handler | ||
| class DOIValidationTimeout(Exception): | ||
| pass | ||
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| def timeout_handler(signum, frame): | ||
| raise DOIValidationTimeout("DOI validation timed out") | ||
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| # Run DOI validation with 30-second timeout | ||
| try: | ||
| # Set signal alarm (Unix only) | ||
| signal.signal(signal.SIGALRM, timeout_handler) | ||
| signal.alarm(30) # 30-second timeout | ||
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| doi_validator = DOIValidator( | ||
| self.manuscript_path, | ||
| enable_online_validation=self.enable_doi_validation, | ||
| ignore_ci_environment=True, # Allow validation in CI for consistent test behavior | ||
| ) | ||
| doi_result = doi_validator.validate() | ||
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| # Cancel the alarm | ||
| signal.alarm(0) | ||
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| # Merge DOI validation results | ||
| errors.extend(doi_result.errors) | ||
| metadata["doi_validation"] = doi_result.metadata | ||
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| except DOIValidationTimeout: | ||
| # Cancel the alarm | ||
| signal.alarm(0) |
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The use of signal.SIGALRM and signal.alarm() is Unix-specific and will fail on Windows systems. This breaks cross-platform compatibility. Consider using threading.Timer or concurrent.futures.TimeoutError with the executor's timeout parameter instead, which work across all platforms.
| import signal | |
| logger = logging.getLogger(__name__) | |
| # Set up timeout handler | |
| class DOIValidationTimeout(Exception): | |
| pass | |
| def timeout_handler(signum, frame): | |
| raise DOIValidationTimeout("DOI validation timed out") | |
| # Run DOI validation with 30-second timeout | |
| try: | |
| # Set signal alarm (Unix only) | |
| signal.signal(signal.SIGALRM, timeout_handler) | |
| signal.alarm(30) # 30-second timeout | |
| doi_validator = DOIValidator( | |
| self.manuscript_path, | |
| enable_online_validation=self.enable_doi_validation, | |
| ignore_ci_environment=True, # Allow validation in CI for consistent test behavior | |
| ) | |
| doi_result = doi_validator.validate() | |
| # Cancel the alarm | |
| signal.alarm(0) | |
| # Merge DOI validation results | |
| errors.extend(doi_result.errors) | |
| metadata["doi_validation"] = doi_result.metadata | |
| except DOIValidationTimeout: | |
| # Cancel the alarm | |
| signal.alarm(0) | |
| import concurrent.futures | |
| logger = logging.getLogger(__name__) | |
| # Run DOI validation with 30-second timeout using ThreadPoolExecutor | |
| try: | |
| with concurrent.futures.ThreadPoolExecutor(max_workers=1) as executor: | |
| future = executor.submit( | |
| DOIValidator( | |
| self.manuscript_path, | |
| enable_online_validation=self.enable_doi_validation, | |
| ignore_ci_environment=True, # Allow validation in CI for consistent test behavior | |
| ).validate | |
| ) | |
| doi_result = future.result(timeout=30) | |
| # Merge DOI validation results | |
| errors.extend(doi_result.errors) | |
| metadata["doi_validation"] = doi_result.metadata | |
| except concurrent.futures.TimeoutError: |
| # Use the same aggressive timeout and retry settings for fallback APIs | ||
| if self.enable_fallback_apis: | ||
| self.openalex_client = OpenAlexClient(timeout=self.fallback_timeout) if self.enable_openalex else None | ||
| self.openalex_client = ( | ||
| OpenAlexClient(timeout=client_timeout, max_retries=client_retries) if self.enable_openalex else None | ||
| ) |
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The comment states "Use the same aggressive timeout and retry settings for fallback APIs" but the code ignores the self.fallback_timeout attribute that was previously used. This creates inconsistency where the fallback_timeout parameter passed to the constructor is now unused, which could confuse users who set this parameter expecting it to work.
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Closing old release PR - superseded by v1.16.3 |
Summary
Fixes unused variable warning in title sync tests for cleaner CI runs.
Changes
result =to_ =in test_title_sync.pyFiles Modified
tests/unit/test_title_sync.py: Fixed unused variable warningsrc/rxiv_maker/__version__.py: Bumped version to 1.14.2CHANGELOG.md: Added v1.14.2 release notesRelease Notes
This is a patch release addressing test linting issues.