rxiv-maker 1.16.4__py3-none-any.whl → 1.16.6__py3-none-any.whl

rxiv_maker/__version__.py

@@ -1,3 +1,3 @@
 """Version information."""
 
-__version__ = "1.16.4"
+__version__ = "1.16.6"

rxiv_maker/cli/commands/upgrade.py

@@ -1,9 +1,10 @@
 """Upgrade command for rxiv-maker CLI."""
 
+import subprocess  # nosec B404 - needed for executing upgrade commands
 import sys
 
 import click
-from henriqueslab_updater import execute_upgrade, force_update_check
+from henriqueslab_updater import force_update_check
 from rich.console import Console
 
 from ... import __version__
@@ -119,11 +120,32 @@ def upgrade(ctx: click.Context, yes: bool, check_only: bool) -> None:
             console.print("❌ Upgrade cancelled", style="yellow")
             sys.exit(0)
 
-    # Execute upgrade command using centralized executor
+    # Execute upgrade command directly
     console.print("\n🚀 Upgrading rxiv-maker...", style="blue")
     console.print(f"   Running: {upgrade_cmd}", style="dim")
 
-    success, error = execute_upgrade(upgrade_cmd, show_output=True, timeout=300)
+    try:
+        # Split command for safer execution without shell=True
+        import shlex
+
+        cmd_parts = shlex.split(upgrade_cmd)
+        result = subprocess.run(
+            cmd_parts,
+            check=True,
+            capture_output=False,
+            timeout=300,
+        )  # nosec B603 - upgrade_cmd comes from trusted install_detector module
+        success = result.returncode == 0
+        error = None
+    except subprocess.CalledProcessError as e:
+        success = False
+        error = f"Command failed with exit code {e.returncode}"
+    except subprocess.TimeoutExpired:
+        success = False
+        error = "Upgrade timed out after 5 minutes"
+    except Exception as e:
+        success = False
+        error = str(e)
 
     if success:
         console.print("\n✅ Upgrade completed successfully!", style="green")

rxiv_maker/cli/framework/utility_commands.py

@@ -187,13 +187,16 @@ class CheckInstallationCommand(BaseCommand):
         """Show next steps after dependency check."""
         if not missing_results:
             self.console.print("\n🚀 Next steps:", style="blue")
-            self.console.print("  • Test PDF generation: rxiv pdf ../manuscript-rxiv-maker/MANUSCRIPT")
+            self.console.print("  • Get example manuscript: rxiv get-rxiv-preprint")
+            self.console.print("  • Navigate to manuscript: cd manuscript-rxiv-maker/MANUSCRIPT")
+            self.console.print("  • Generate PDF: rxiv pdf")
             return
 
         self.console.print("\n🔧 Next steps:", style="blue")
         self.console.print("  • Install missing dependencies shown above")
         self.console.print("  • Re-run: rxiv check-installation")
-        self.console.print("  • Test PDF generation: rxiv pdf ../manuscript-rxiv-maker/MANUSCRIPT")
+        self.console.print("  • Get example manuscript: rxiv get-rxiv-preprint")
+        self.console.print("  • Generate PDF: cd manuscript-rxiv-maker/MANUSCRIPT && rxiv pdf")
 
     def _show_basic_results(self, results: dict) -> None:
         """Show basic installation results."""

rxiv_maker/engines/operations/generate_figures.py

@@ -250,31 +250,95 @@ class FigureGenerator:
                         response = get_with_retry(mermaid_url, max_attempts=5, timeout=30)
                     else:
                         response = requests.get(mermaid_url, timeout=30)
-                except Exception:
-                    # If retry fails, fall back to placeholder
-                    return self._create_fallback_mermaid_diagram(input_file, output_file)
+                except requests.Timeout:
+                    # Timeout - likely diagram too complex or service slow
+                    return self._create_fallback_mermaid_diagram(
+                        input_file, output_file, reason="timeout", details="30s timeout exceeded"
+                    )
+                except requests.HTTPError as e:
+                    # HTTP error (400, 503, etc.) - extract status code
+                    status_code = e.response.status_code if hasattr(e, "response") else "unknown"
+                    if status_code == 400:
+                        details = "syntax error or diagram too complex"
+                    elif status_code == 503:
+                        details = "service timeout (diagram too complex)"
+                    else:
+                        details = f"HTTP {status_code}"
+                    return self._create_fallback_mermaid_diagram(
+                        input_file, output_file, reason="http_error", details=details
+                    )
+                except Exception as e:
+                    # Network or other error during request
+                    error_msg = str(e)
+                    # Try to extract status code from error message if it's there
+                    if "400" in error_msg:
+                        details = "syntax error or diagram too complex"
+                    elif "503" in error_msg:
+                        details = "service timeout (diagram too complex)"
+                    elif "429" in error_msg:
+                        details = "rate limit exceeded"
+                    else:
+                        details = "connection error"
+                    return self._create_fallback_mermaid_diagram(
+                        input_file, output_file, reason="network_error", details=details
+                    )
 
                 if response.status_code == 200:
                     with open(output_file, "wb") as f:
                         f.write(response.content)
                     return True
                 else:
-                    print(f"mermaid.ink service returned status {response.status_code}")
-                    print(
-                        "💡 Tip: If this is a syntax error, check your Mermaid diagram at https://www.mermaidchart.com/"
+                    # Determine failure reason from status code
+                    if response.status_code == 400:
+                        reason_msg = "syntax error or diagram too complex"
+                    elif response.status_code == 429:
+                        reason_msg = "rate limit exceeded"
+                    elif response.status_code == 503:
+                        reason_msg = "service timeout (diagram too complex)"
+                    elif response.status_code >= 500:
+                        reason_msg = "service unavailable"
+                    else:
+                        reason_msg = f"HTTP {response.status_code}"
+
+                    return self._create_fallback_mermaid_diagram(
+                        input_file, output_file, reason="http_error", details=reason_msg
                     )
-                    return self._create_fallback_mermaid_diagram(input_file, output_file)
             else:
-                print("requests library not available for Mermaid generation")
-                return self._create_fallback_mermaid_diagram(input_file, output_file)
+                return self._create_fallback_mermaid_diagram(
+                    input_file, output_file, reason="no_requests_lib", details="requests library not available"
+                )
 
         except Exception as e:
-            print(f"mermaid.ink service error: {e}")
-            print("💡 Tip: Check your Mermaid diagram syntax at https://www.mermaidchart.com/")
-            return self._create_fallback_mermaid_diagram(input_file, output_file)
+            return self._create_fallback_mermaid_diagram(
+                input_file, output_file, reason="unexpected_error", details=str(e)
+            )
+
+    def _create_fallback_mermaid_diagram(
+        self, input_file: Path, output_file: Path, reason: str = "unknown", details: str = "service unavailable"
+    ) -> bool:
+        """Create a fallback placeholder diagram when Mermaid service is unavailable.
+
+        Args:
+            input_file: Source mermaid file
+            output_file: Output file path
+            reason: Failure reason category (timeout, http_error, network_error, etc.)
+            details: Detailed error message
+
+        Returns:
+            True if placeholder was created successfully
+        """
+        # Generate user-friendly warning message based on failure reason
+        if reason == "timeout":
+            warning_msg = f"diagram rendering timed out ({details})"
+        elif reason == "http_error":
+            warning_msg = f"{details}"
+        elif reason == "network_error":
+            warning_msg = f"network error: {details}"
+        elif reason == "no_requests_lib":
+            warning_msg = "requests library not available"
+        else:
+            warning_msg = f"{details}"
 
-    def _create_fallback_mermaid_diagram(self, input_file: Path, output_file: Path) -> bool:
-        """Create a fallback placeholder diagram when Mermaid service is unavailable."""
         try:
             if self.output_format.lower() == "svg":
                 # Create SVG placeholder
@@ -294,6 +358,7 @@ class FigureGenerator:
 </svg>"""
                 with open(output_file, "w", encoding="utf-8") as f:
                     f.write(svg_content)
+                print(f"⚠️  Created placeholder SVG for {input_file.name} ({warning_msg})")
                 return True
             elif self.output_format.lower() == "png":
                 # Create minimal PNG placeholder (1x1 white pixel)
@@ -303,7 +368,7 @@ class FigureGenerator:
                 )
                 with open(output_file, "wb") as f:
                     f.write(png_data)
-                print(f"⚠️  Created placeholder PNG for {input_file.name} (mermaid.ink unavailable)")
+                print(f"⚠️  Created placeholder PNG for {input_file.name} ({warning_msg})")
                 return True
             elif self.output_format.lower() == "pdf":
                 # Create minimal PDF placeholder
@@ -374,20 +439,83 @@ startxref
 """
                 with open(output_file, "w", encoding="utf-8") as f:
                     f.write(pdf_content)
-                print(f"⚠️  Created placeholder PDF for {input_file.name} (mermaid.ink unavailable)")
+                print(f"⚠️  Created placeholder PDF for {input_file.name} ({warning_msg})")
                 return True
             else:
                 # Fallback for other formats - create text file with warning
                 with open(output_file.with_suffix(".txt"), "w", encoding="utf-8") as f:
                     f.write(f"Mermaid diagram placeholder for {input_file.name}\n")
-                    f.write("mermaid.ink service unavailable - diagram generation failed\n")
+                    f.write(f"Reason: {warning_msg}\n")
                     f.write("\n💡 Tip: Check your Mermaid diagram syntax at https://www.mermaidchart.com/\n")
-                print(f"⚠️  Created text placeholder for {input_file.name} (mermaid.ink unavailable)")
+                print(f"⚠️  Created text placeholder for {input_file.name} ({warning_msg})")
                 return True
         except Exception as e:
             print(f"Failed to create fallback diagram: {e}")
             return False
 
+    def validate_mermaid_diagram(self, mmd_file: Path) -> tuple[bool, str, dict]:
+        """Validate a Mermaid diagram for mermaid.ink compatibility.
+
+        Args:
+            mmd_file: Path to .mmd file
+
+        Returns:
+            Tuple of (is_valid, message, details_dict)
+            - is_valid: True if diagram will render successfully
+            - message: Human-readable validation result
+            - details_dict: Dict with complexity metrics and suggestions
+        """
+        if not requests:
+            return False, "requests library not available for validation", {}
+
+        try:
+            # Read and analyze the diagram
+            with open(mmd_file, "r", encoding="utf-8") as f:
+                content = f.read().strip()
+
+            # Analyze complexity
+            details = {
+                "file_size": len(content),
+                "line_count": content.count("\n") + 1,
+                "subgraph_count": content.count("subgraph"),
+                "node_count": len(re.findall(r"\w+\[", content)),
+                "class_def_count": content.count("classDef"),
+            }
+
+            # Check for known problematic patterns
+            warnings = []
+            if details["file_size"] > 2500:
+                warnings.append(f"Large diagram ({details['file_size']} chars, limit ~2500)")
+            if details["subgraph_count"] > 5:
+                warnings.append(f"Many subgraphs ({details['subgraph_count']}, limit ~5)")
+            if details["class_def_count"] > 6:
+                warnings.append(f"Heavy styling ({details['class_def_count']} classes, limit ~6)")
+
+            # Test with mermaid.ink
+            encoded = base64.b64encode(content.encode("utf-8")).decode("ascii")
+            test_url = f"https://mermaid.ink/svg/{encoded}"  # Use SVG for faster testing
+
+            try:
+                response = requests.get(test_url, timeout=10)
+                if response.status_code == 200:
+                    if warnings:
+                        msg = f"✓ Valid (but complex: {', '.join(warnings)})"
+                        return True, msg, details
+                    return True, "✓ Valid and will render successfully", details
+                elif response.status_code == 400:
+                    return False, "✗ Syntax error or too complex for mermaid.ink", details
+                elif response.status_code == 503:
+                    return False, "✗ Diagram too complex (service timeout)", details
+                else:
+                    return False, f"✗ HTTP {response.status_code}", details
+            except requests.Timeout:
+                return False, "✗ Validation timeout (diagram likely too complex)", details
+            except Exception as e:
+                return False, f"✗ Network error: {str(e)[:50]}", details
+
+        except Exception as e:
+            return False, f"✗ Error reading diagram: {str(e)[:50]}", {}
+
     def _execute_python_files(self, progress=None, task_id=None, use_rich: bool = True):
         """Execute Python scripts to generate figures using local Python."""
         py_files = list(self.figures_dir.glob("*.py"))

rxiv_maker/templates/registry.py

@@ -163,38 +163,36 @@ citation_style: "numbered"
         """Get default main manuscript template."""
         return """## Abstract
 
-Your manuscript abstract goes here. Provide a comprehensive summary of your work,
-key findings, and significance to the field.
+Your manuscript abstract goes here. Provide a comprehensive summary of your work, including the main problem you are addressing, your approach, key findings, and the significance of your results to the field. The abstract should be self-contained and provide readers with a clear understanding of your contribution. Aim for 150-300 words that capture the essence of your research.
 
 ## Introduction
 
-Introduce your topic, provide background, and state your objectives.
+Introduce your research topic by providing essential background context and motivation. Start with the broader significance of your field, then narrow down to the specific problem your work addresses. Clearly state your research objectives and how your approach differs from or builds upon existing work in the literature [@smith2023]. Explain why this research is important and what gap in knowledge it fills.
 
 ## Methods
 
-Describe your methods, approaches, and techniques.
-(For reviews, you can remove this section or describe your literature search strategy)
+Describe your experimental design, data collection procedures, and analytical techniques in sufficient detail to allow replication of your work. For computational studies, specify software versions, parameters, and algorithms used. For experimental work, detail protocols, sample preparation, and measurement procedures [@johnson2022]. Include information about statistical methods and data validation approaches. If you are writing a review article, you may remove this section or describe your literature search and selection strategy.
 
 ## Results
 
-Present your findings with supporting figures and tables.
-(For reviews, you can remove this section or rename it to organize your discussion)
+Present your findings in a logical sequence, using figures and tables to support your narrative. Start with an overview of the key results, then provide detailed analyses.
 
-![](FIGURES/Figure__example.mmd)
-{{#fig:example}} **Example Figure.** This is an example Mermaid diagram that will be automatically converted to PDF during build.
+![A flowchart showing the progression from data input through processing to results output](FIGURES/Figure__example.mmd)
+{{#fig:example}} **Example workflow diagram.** This Mermaid diagram illustrates a typical data processing pipeline, automatically converted to PDF during manuscript compilation. The diagram shows three stages: data input (gray), processing and analysis (red), and results output (green).
+
+Our analysis demonstrates that the methodology produces consistent results across different datasets. The workflow presented in @fig:example provides a schematic overview of the processing pipeline. These findings build upon previous work [@smith2023; @johnson2022] while introducing novel approaches to data analysis.
 
 ## Discussion
 
-Interpret your findings, discuss implications, and acknowledge limitations.
+Interpret your results in the context of existing literature and theory. Discuss how your findings support or challenge current understanding in the field. Address the implications of your work for theory, practice, or policy. Acknowledge limitations of your study, such as sample size constraints, methodological limitations, or scope boundaries. Suggest directions for future research that build upon your findings.
 
 ## Conclusions
 
-Summarize your key conclusions and broader impact.
+Summarize your key findings and their significance. Reinforce the main contributions of your work and their broader impact on the field. Keep this section concise but impactful, leaving readers with a clear understanding of what your research has accomplished and why it matters.
 
 ## References
 
-Citations will be automatically formatted. Add entries to 03_REFERENCES.bib and
-reference them in your text: [@smith2023; @johnson2022]
+Citations are automatically formatted from 03_REFERENCES.bib. Reference works using citation keys like [@smith2023] for single citations or [@smith2023; @johnson2022] for multiple citations.
 """
 
     def _get_default_supplementary_template(self) -> str:
@@ -225,34 +223,60 @@ Information about code repositories, data availability, and reproducibility reso
     def _get_default_bibliography_template(self) -> str:
         """Get default bibliography template."""
         return """@article{{smith2023,
-    title = {{Example Research Article}},
-    author = {{Smith, John and Doe, Jane}},
-    journal = {{Nature}},
-    volume = {{123}},
-    pages = {{456-789}},
+    title = {{Advances in computational biology: methods and applications}},
+    author = {{Smith, John A. and Doe, Jane M. and Williams, Robert L.}},
+    journal = {{Nature Methods}},
+    volume = {{20}},
+    number = {{8}},
+    pages = {{1234--1245}},
     year = {{2023}},
-    doi = {{10.1038/nature12345}}
+    publisher = {{Springer Nature}},
+    doi = {{10.1038/s41592-023-01234-5}}
 }}
 
 @article{{johnson2022,
-    title = {{Another Important Study}},
-    author = {{Johnson, Alice and Brown, Bob}},
+    title = {{Machine learning approaches for biological data analysis}},
+    author = {{Johnson, Alice B. and Brown, Robert C. and Davis, Sarah K.}},
     journal = {{Cell}},
     volume = {{185}},
-    pages = {{1234-1245}},
+    number = {{12}},
+    pages = {{2156--2170}},
     year = {{2022}},
-    doi = {{10.1016/j.cell.2022.01.001}}
+    publisher = {{Elsevier}},
+    doi = {{10.1016/j.cell.2022.05.015}}
+}}
+
+@article{{wilson2024,
+    title = {{Reproducible research practices in modern science}},
+    author = {{Wilson, Greg and Jones, Emily R.}},
+    journal = {{PLOS Computational Biology}},
+    volume = {{20}},
+    number = {{3}},
+    pages = {{e1011234}},
+    year = {{2024}},
+    publisher = {{Public Library of Science}},
+    doi = {{10.1371/journal.pcbi.1011234}}
 }}
 """
 
     def _get_default_figure_template(self) -> str:
         """Get default figure template (Mermaid diagram)."""
-        return """graph TD
-    A[Start] --> B{{Decision}}
-    B -->|Yes| C[Process 1]
-    B -->|No| D[Process 2]
-    C --> E[End]
-    D --> E
+        return """---
+config:
+  look: neo
+  theme: neo
+---
+flowchart LR
+    A["<b>DATA</b><br/>Input"] --> B["<b>PROCESSING</b><br/>Analysis"]
+    B --> C["<b>RESULTS</b><br/>Output"]
+
+    classDef inputStyle fill:#1f2937,stroke:#374151,stroke-width:3px,color:#ffffff
+    classDef processStyle fill:#dc2626,stroke:#991b1b,stroke-width:3px,color:#ffffff
+    classDef outputStyle fill:#059669,stroke:#047857,stroke-width:3px,color:#ffffff
+
+    class A inputStyle
+    class B processStyle
+    class C outputStyle
 """
 
     def _get_default_gitignore_template(self) -> str:

rxiv_maker/validators/syntax_validator.py

@@ -854,8 +854,17 @@ class SyntaxValidator(BaseValidator):
         heading_texts = {}
         previous_level = 0
 
-        for line_num, line in enumerate(lines, 1):
-            match = heading_pattern.match(line)
+        # Protect code blocks (including {{py:exec}}) from being treated as headings
+        content = "\n".join(lines)
+        protected_content = self._protect_validation_sensitive_content(content)
+        protected_lines = protected_content.split("\n")
+
+        for line_num, (original_line, protected_line) in enumerate(zip(lines, protected_lines, strict=False), 1):
+            # Skip protected code blocks (they might contain # comments)
+            if "XXPROTECTEDCODEXX" in protected_line:
+                continue
+
+            match = heading_pattern.match(protected_line)
             if match:
                 hashes = match.group(1)
                 heading_text = match.group(2).strip()
@@ -904,7 +913,7 @@ class SyntaxValidator(BaseValidator):
                             f"Heading hierarchy skips levels: {previous_level} → {level}",
                             file_path=file_path,
                             line_number=line_num,
-                            context=line.strip(),
+                            context=original_line.strip(),
                             suggestion=(
                                 f"Consider using {'#' * (previous_level + 1)} instead of {'#' * level}.\n"
                                 f"   Skipping heading levels (e.g., ## to ####) makes document structure unclear."
@@ -927,7 +936,7 @@ class SyntaxValidator(BaseValidator):
                                 f"Standard section '{heading_text}' using level 1 heading (#)",
                                 file_path=file_path,
                                 line_number=line_num,
-                                context=line.strip(),
+                                context=original_line.strip(),
                                 suggestion=(
                                     f"Change to level 2 heading: ## {heading_text}\n"
                                     f"   Level 1 (#) should only be used for the document title.\n"

{rxiv_maker-1.16.4.dist-info → rxiv_maker-1.16.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rxiv-maker
-Version: 1.16.4
+Version: 1.16.6
 Summary: Write scientific preprints in Markdown. Generate publication-ready PDFs efficiently.
 Project-URL: Homepage, https://github.com/HenriquesLab/rxiv-maker
 Project-URL: Documentation, https://github.com/HenriquesLab/rxiv-maker#readme

{rxiv_maker-1.16.4.dist-info → rxiv_maker-1.16.6.dist-info}/RECORD

@@ -1,5 +1,5 @@
 rxiv_maker/__init__.py,sha256=p04JYC5ZhP6dLXkoWVlKNyiRvsDE1a4C88f9q4xO3tA,3268
-rxiv_maker/__version__.py,sha256=9jjbeowk49aKHUW-4TiyTbFpmPEuycMrStL-jO4XzP8,51
+rxiv_maker/__version__.py,sha256=qf0GMhAIH5L_wI59eHcfpHtgoZxaqziVuvj0M1daj0g,51
 rxiv_maker/rxiv_maker_cli.py,sha256=9Lu_mhFPXwx5jzAR6StCNxwCm_fkmP5qiOYdNuh_AwI,120
 rxiv_maker/validate.py,sha256=AIzgP59KbCQJqC9WIGfUdVv0xI6ud9g1fFznQkaGz5Q,9373
 rxiv_maker/cli/__init__.py,sha256=Jw0DTFUSofN-02xpVrt1UUzRcgH5NNd-GPNidhmNwpU,77
@@ -29,7 +29,7 @@ rxiv_maker/cli/commands/repos.py,sha256=SQ9nuhSkyHKFPYn_TrOxyQoGdDRI-OBOgUSGJpRu
 rxiv_maker/cli/commands/repos_search.py,sha256=6sUMvyHlHEX1p88hPtu0_Hf8z6JpOinJ53l9ZI-rirc,7743
 rxiv_maker/cli/commands/setup.py,sha256=9ue4bDETpSPGVkWFDfpuTDsysax5-QKGxmt42Gb7oeU,2294
 rxiv_maker/cli/commands/track_changes.py,sha256=omf_77A7htRSa8naUEPTTtUTxrSwMpzHFOuU0j1xAJw,1163
-rxiv_maker/cli/commands/upgrade.py,sha256=Cn2559onuCPLjqSnNDaWzS_40sPwpnRU_RLEZW5Xk4Y,5649
+rxiv_maker/cli/commands/upgrade.py,sha256=VJ1snYyLGrb5-snF4olfsMwfQsuKkAbXEr8aQ88WYYE,6349
 rxiv_maker/cli/commands/validate.py,sha256=3JghFQevJvQDQII4p_QWbQXMEUyDpM-t9-WxtaT4edo,1629
 rxiv_maker/cli/commands/version.py,sha256=VMlfSxxsrZH02d24MXLUDZfHBW39yZRpWxUpMhQ-X0Y,2737
 rxiv_maker/cli/framework/__init__.py,sha256=4FPXdP8J6v4eeEn46mwY0VtnwxjR1jnW_kTrXykQlQs,2704
@@ -38,7 +38,7 @@ rxiv_maker/cli/framework/cache_commands.py,sha256=J91UYLTsLTRoNdzuhAbNL2bJJovYYf
 rxiv_maker/cli/framework/config_commands.py,sha256=a1uOQkCCw3d4qlro3OwHIorcoNg03T_R4-HbfVb-hmQ,19336
 rxiv_maker/cli/framework/content_commands.py,sha256=RilxKeG2c1m2fu0CtWAvP3cGh11DGx9P-nh2kIewAg4,22596
 rxiv_maker/cli/framework/decorators.py,sha256=fh085e3k1CaLSMoZevt8hvgnEuejrf-mcNS-dwXoY_A,10365
-rxiv_maker/cli/framework/utility_commands.py,sha256=_P_KwjlyiNS-vVboU-DqkHynGPqzXyoZRWGmLMLTnOs,26214
+rxiv_maker/cli/framework/utility_commands.py,sha256=drIAc1TAYpne76gj7SZeZhPozVAY5uL9GFPVT_Ez0-E,26437
 rxiv_maker/cli/framework/workflow_commands.py,sha256=CFa3c5oJMmy9cUZxTAU97eKC6YrOljzerSAMrywjbKw,29684
 rxiv_maker/config/defaults.py,sha256=vHyLGVxe5-z9TLxu5f6NhquPvqQkER_KZv_j1I4_dHQ,3055
 rxiv_maker/config/validator.py,sha256=9XDPfo_YgasGt6NLkl6HIhaGh1fr6XsFNiXU2DSsivw,38299
@@ -96,7 +96,7 @@ rxiv_maker/engines/operations/build_manager.py,sha256=TAX4-r8HjraAzzvQuIt0CNlvWL
 rxiv_maker/engines/operations/cleanup.py,sha256=RfbXif0neEVMlprFIHWyvQh6kwghalcesY3t-69Iwsw,18095
 rxiv_maker/engines/operations/fix_bibliography.py,sha256=ZD8uO4YCxDCMWH4WtBSDc4TOMgM383fcLgsCCW0yK60,22428
 rxiv_maker/engines/operations/generate_docs.py,sha256=8d_oVYUuRRqTuYN1KnJKqM5Ydp4_yt52ntBv8gUoRVk,11223
-rxiv_maker/engines/operations/generate_figures.py,sha256=3oIuS0wryO9WpPZ3UD2qm0YscNidTOEiO4_Jd6r3SmY,32842
+rxiv_maker/engines/operations/generate_figures.py,sha256=YeKzH6qVsuPGjtCsvWugLJoys6y73xTyO7Y5g30KM20,38730
 rxiv_maker/engines/operations/generate_preprint.py,sha256=wpKDAu2RLJ4amSdhX5GZ7hU-iTsTRt4etcEA7AZYp04,2662
 rxiv_maker/engines/operations/prepare_arxiv.py,sha256=cd0JN5IO-Wy9T8ab75eibyaA8_K8Gpwrz2F-95OMnx4,21551
 rxiv_maker/engines/operations/setup_environment.py,sha256=gERuThHTldH0YqgXn85995deHBP6csY1ZhCNgU6-vFg,12691
@@ -141,7 +141,7 @@ rxiv_maker/services/publication_service.py,sha256=0p8yQ1jrY3RHwCkzTEl_sAbWYTafRk
 rxiv_maker/services/validation_service.py,sha256=eWg14NqJu6LzyJBgeXkTaVZAlX4wYFX8ZEvSR5hMx7U,14619
 rxiv_maker/templates/__init__.py,sha256=UTet1pYPkPdgvrLw-wwaY-PAgdjGJasAi_hdyIh0J8s,562
 rxiv_maker/templates/manager.py,sha256=HlI7Qb52866Okf4k1aRh0fUy9heOSNGjMQJtrCdL3Xk,6131
-rxiv_maker/templates/registry.py,sha256=L8M7M9Yhf2P0SQEghmCXufWfsGQhaW1TYjdkUw-wvDw,12993
+rxiv_maker/templates/registry.py,sha256=mRKUhuNg1VWzryEV-l6tD2pmdQG6b_JDh3_jtrR_K48,16200
 rxiv_maker/tex/python_execution_section.tex,sha256=pHz6NGfZN4ViBo6rInUO5FAuk81sV_Ppqszrvl00w_4,2218
 rxiv_maker/utils/__init__.py,sha256=4ya5VR8jqRqUChlnUeMeeetOuWV-gIvjPwcE1u_1OnI,1540
 rxiv_maker/utils/author_name_formatter.py,sha256=UjvarbyQm89EUIYqckygx3g37o-EcNyvipBtY8GJDxs,10222
@@ -180,15 +180,15 @@ rxiv_maker/validators/latex_error_parser.py,sha256=crk3NAniLBp2iABP4lxts7gvCEg6K
 rxiv_maker/validators/math_validator.py,sha256=LcRIGAv47OsPfOg4E48l2vKN1Q7lHAeduNN5MFMLQGE,27669
 rxiv_maker/validators/pdf_validator.py,sha256=YU4WRPeTEOtvBlquFEtZrG9p_WjlN5nnCByTSRAvWyw,21530
 rxiv_maker/validators/reference_validator.py,sha256=UqvsEa3kVOBkbGMo24fXpFVUtpN1feIf9MfDQIraQZs,15868
-rxiv_maker/validators/syntax_validator.py,sha256=H7JK3H116nI9f_3uzAS_RlIsbcbgajhpoU5T2aGh46w,43098
+rxiv_maker/validators/syntax_validator.py,sha256=hHpKVKky3UiA1ZylA6jJVP3DN47LgaSSJCK2PPA-8BA,43599
 rxiv_maker/validators/doi/__init__.py,sha256=NqATXseuS0zVNns56RvFe8TdqgvueY0Rbw2Pjozlajc,494
 rxiv_maker/validators/doi/api_clients.py,sha256=tqdYUq8LFgRIO0tWfcenwmy2uO-IB1-GMvBfF3lP7-0,21763
 rxiv_maker/validators/doi/metadata_comparator.py,sha256=euqHhKP5sHQAdZbdoAahUn6YqJqOfXIOobNgAqFHlN8,11533
 rxiv_maker/tex/template.tex,sha256=zrJ3aFfu8j9zkg1l375eE9w-j42P3rz16wMD3dSgi1I,1354
 rxiv_maker/tex/style/rxiv_maker_style.bst,sha256=jbVqrJgAm6F88cow5vtZuPBwwmlcYykclTm8RvZIo6Y,24281
 rxiv_maker/tex/style/rxiv_maker_style.cls,sha256=F2qtnS9mI6SwOIaVH76egXZkB2_GzbH4gCTG_ZcfCDQ,24253
-rxiv_maker-1.16.4.dist-info/METADATA,sha256=aEslQxuVrwfw0lXsEVzJTwxA_4vfAm6OrADsnYMhdAU,17950
-rxiv_maker-1.16.4.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-rxiv_maker-1.16.4.dist-info/entry_points.txt,sha256=ghCN0hI9A1GlG7QY5F6E-xYPflA8CyS4B6bTQ1YLop0,97
-rxiv_maker-1.16.4.dist-info/licenses/LICENSE,sha256=GSZFoPIhWDNJEtSHTQ5dnELN38zFwRiQO2antBezGQk,1093
-rxiv_maker-1.16.4.dist-info/RECORD,,
+rxiv_maker-1.16.6.dist-info/METADATA,sha256=7_r-ZEzlmKCVaCu_a-Z8tg8pr4kzfI3tDbvfCbc1dCw,17950
+rxiv_maker-1.16.6.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+rxiv_maker-1.16.6.dist-info/entry_points.txt,sha256=ghCN0hI9A1GlG7QY5F6E-xYPflA8CyS4B6bTQ1YLop0,97
+rxiv_maker-1.16.6.dist-info/licenses/LICENSE,sha256=GSZFoPIhWDNJEtSHTQ5dnELN38zFwRiQO2antBezGQk,1093
+rxiv_maker-1.16.6.dist-info/RECORD,,