rxiv-maker 1.16.3__py3-none-any.whl → 1.16.5__py3-none-any.whl

rxiv_maker/__version__.py

@@ -1,3 +1,3 @@
 """Version information."""
 
-__version__ = "1.16.3"
+__version__ = "1.16.5"

rxiv_maker/cli/commands/upgrade.py

@@ -1,7 +1,6 @@
 """Upgrade command for rxiv-maker CLI."""
 
-import shlex
-import subprocess
+import subprocess  # nosec B404 - needed for executing upgrade commands
 import sys
 
 import click
@@ -121,44 +120,34 @@ def upgrade(ctx: click.Context, yes: bool, check_only: bool) -> None:
             console.print("❌ Upgrade cancelled", style="yellow")
             sys.exit(0)
 
-    # Execute upgrade command
+    # Execute upgrade command directly
     console.print("\n🚀 Upgrading rxiv-maker...", style="blue")
     console.print(f"   Running: {upgrade_cmd}", style="dim")
 
     try:
-        # Split compound commands (with &&) and run sequentially
-        if " && " in upgrade_cmd:
-            commands = upgrade_cmd.split(" && ")
-            for cmd in commands:
-                result = subprocess.run(
-                    shlex.split(cmd),
-                    check=False,
-                    capture_output=False,  # Show output to user
-                )
-                if result.returncode != 0:
-                    console.print(
-                        f"\n⚠️  Command '{cmd}' exited with code {result.returncode}",
-                        style="yellow",
-                    )
-                    console.print("   You may need to run the command manually:", style="yellow")
-                    console.print(f"   {upgrade_cmd}", style="yellow")
-                    sys.exit(result.returncode)
-        else:
-            # Single command - use shlex.split to avoid shell injection
-            result = subprocess.run(
-                shlex.split(upgrade_cmd),
-                check=False,
-                capture_output=False,  # Show output to user
-            )
-            if result.returncode != 0:
-                console.print(
-                    f"\n⚠️  Upgrade command exited with code {result.returncode}",
-                    style="yellow",
-                )
-                console.print("   You may need to run the command manually:", style="yellow")
-                console.print(f"   {upgrade_cmd}", style="yellow")
-                sys.exit(result.returncode)
+        # 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")
         console.print("   Run 'rxiv --version' to verify the installation", style="blue")
 
@@ -169,12 +158,7 @@ def upgrade(ctx: click.Context, yes: bool, check_only: bool) -> None:
                 f"   View full changelog: https://github.com/henriqueslab/rxiv-maker/releases/tag/v{latest_version}",
                 style="blue",
             )
-
-    except subprocess.CalledProcessError as e:
-        console.print(f"\n❌ Upgrade failed: {e}", style="red")
-        console.print(f"   Try running manually: {upgrade_cmd}", style="yellow")
-        sys.exit(1)
-    except Exception as e:
-        console.print(f"\n❌ Unexpected error during upgrade: {e}", style="red")
+    else:
+        console.print(f"\n❌ Upgrade failed: {error}", style="red")
         console.print(f"   Try running manually: {upgrade_cmd}", style="yellow")
         sys.exit(1)

rxiv_maker/engines/operations/generate_docs.py

@@ -8,7 +8,7 @@ signatures.
 
 import os
 import shutil
-import subprocess
+import subprocess  # nosec B404
 from pathlib import Path
 
 
@@ -103,7 +103,10 @@ def generate_enhanced_index(docs_dir, successful_modules):
                 f.write(f"## {category.capitalize()} Modules\n\n")
                 for module in sorted(modules):
                     module_name = str(module).replace("/", ".")
-                    file_name = str(module).replace("/", "_") + ".md"
+                    # lazydocs generates files with just the basename + .md
+                    from pathlib import Path as ModPath
+
+                    file_name = ModPath(str(module)).name + ".md"
                     f.write(f"- [{module_name}]({file_name})\n")
                 f.write("\n")
 
@@ -216,7 +219,7 @@ def generate_api_docs(project_root: Path | None = None) -> bool:
                     "--no-watermark",
                     "--remove-package-prefix",
                     "--src-base-url",
-                    "https://github.com/henriqueslab/rxiv-maker/blob/main/src",
+                    "https://github.com/henriqueslab/rxiv-maker/blob/main",
                 ]
 
                 subprocess.run(

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-1.16.3.dist-info → rxiv_maker-1.16.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rxiv-maker
-Version: 1.16.3
+Version: 1.16.5
 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
@@ -27,7 +27,7 @@ Requires-Python: >=3.10
 Requires-Dist: click>=8.0.0
 Requires-Dist: crossref-commons>=0.0.7
 Requires-Dist: gitpython>=3.1.0
-Requires-Dist: henriqueslab-updater>=1.0.0
+Requires-Dist: henriqueslab-updater>=1.1.3
 Requires-Dist: latex2mathml>=3.78.0
 Requires-Dist: matplotlib>=3.7.0
 Requires-Dist: numpy>=1.24.0
@@ -85,76 +85,70 @@ Description-Content-Type: text/markdown
 
 **Write scientific preprints in Markdown. Generate publication-ready PDFs efficiently.**
 
+> **💡 Best Experience:** Use the [VS Code Extension](https://marketplace.visualstudio.com/items?itemName=HenriquesLab.rxiv-maker) for syntax highlighting and citations.
+
 Rxiv-Maker converts enhanced Markdown into professional PDFs with automated figure generation, citation management, and LaTeX typesetting. While LaTeX installation is required, users don't need to write LaTeX code directly.
 
 ## ✨ Why Rxiv-Maker?
 
-### 🎯 **For Researchers**
-- **Write in Markdown**: Focus on content, not formatting
-- **Automated Figures**: Python/R scripts become publication figures  
-- **Smart Citations**: BibTeX integration with cross-references
-- **Instant PDFs**: From Markdown to professional academic PDF
-
-### 🚀 **For Teams**  
+- **Write in Markdown**: Focus on content, not LaTeX formatting
+- **Automated Figures**: Python/R scripts become publication figures
+- **Smart Citations**: BibTeX integration with cross-references and DOI resolution
+- **Dual Output**: Generate both PDF and DOCX from the same source
 - **Git-Friendly**: Version control for manuscripts and figures
 - **Reproducible**: All figures generated from code
-- **Collaborative**: Standard tools, no vendor lock-in
-- **Multi-Platform**: Works everywhere with local installation
-
-### 📈 **For Publishing**
 - **arXiv Ready**: Generate submission packages automatically
 - **Track Changes**: Visual diff between manuscript versions
-- **Quality Assurance**: Built-in validation and error checking
 
 ## 🚀 Installation
 
-**⚠️ Choose ONE installation method below** (don't run all of them):
+<details>
+<summary>🍎 <strong>macOS</strong> (Recommended - includes LaTeX automatically)</summary>
 
-**🍎 macOS (Recommended):**
 ```bash
 brew tap henriqueslab/formulas
 brew install rxiv-maker
 rxiv check-installation
 ```
 
-**🐧 Linux / 🪟 Windows WSL (Recommended):**
+**Upgrade:**
+```bash
+brew upgrade rxiv-maker
+```
+
+> **📖 [Homebrew Formula](https://github.com/HenriquesLab/homebrew-formulas)** - Includes Python, LaTeX (MacTeX), and all dependencies
+
+</details>
+
+<details>
+<summary>🐧 <strong>Linux / Windows (WSL)</strong></summary>
+
+**Using pipx (recommended):**
 ```bash
 pipx install rxiv-maker
 rxiv check-installation
 ```
 
-**🔧 Alternative Methods:**
+**Using uv (faster alternative):**
 ```bash
-# Using pip (simpler, but may conflict with system packages)
-pip install rxiv-maker
-
-# Using uv (modern, fast package manager)
 uv tool install rxiv-maker
-
-# Verify any installation
 rxiv check-installation
 ```
 
-**📋 Requirements:**
-- **LaTeX Distribution**: Required for PDF generation
-  - **macOS**: MacTeX (recommended) or BasicTeX
-  - **Windows**: MiKTeX or TeX Live
-  - **Linux**: TeX Live (install via system package manager)
+**Requirements:**
 - **Python 3.11+**: For rxiv-maker CLI and figure generation
+- **LaTeX Distribution**: Install via system package manager
+  - **Ubuntu/Debian**: `sudo apt install texlive-latex-recommended`
+  - **Fedora/RHEL**: `sudo dnf install texlive-latex`
 
-**Upgrading:**
+**Upgrade:**
 ```bash
-# Automatic upgrade (detects your installation method)
-rxiv upgrade
-
-# Or use the same method you used to install:
-brew upgrade rxiv-maker              # If you installed with Homebrew
-pipx upgrade rxiv-maker              # If you installed with pipx
-pip install --upgrade rxiv-maker     # If you installed with pip
-uv tool upgrade rxiv-maker           # If you installed with uv
+pipx upgrade rxiv-maker  # or: uv tool upgrade rxiv-maker
 ```
 
-**Need help?** 📖 **[Installation Guide](docs/installation.md)**
+</details>
+
+> **📖 Need help?** See the [complete installation guide](https://rxiv-maker.henriqueslab.org/getting-started/installation/) for detailed platform-specific instructions.
 
 ## 🔥 Quick Start
 
@@ -180,7 +174,7 @@ cd manuscript-rxiv-maker/MANUSCRIPT
 rxiv pdf
 ```
 
-**🎯 [Getting Started Guide](docs/first-manuscript.md)**
+**🎯 [Getting Started Guide](https://rxiv-maker.henriqueslab.org/getting-started/first-manuscript/)**
 
 ## 🏆 Key Features
 
@@ -206,8 +200,7 @@ rxiv pdf
 - **Inline DOI resolution**: Paste DOIs directly in text `10.1038/...` and auto-convert to citations
 - CrossRef/DataCite DOI validation and metadata fetching
 
-
-> 📖 **Learn more**: [10-Minute Tutorial](https://rxiv-maker.henriqueslab.org/getting-started/citations-tutorial/) | [Complete Guide](https://rxiv-maker.henriqueslab.org/guides/citations-and-references/)
+> 📖 **Learn more**: [Quick Reference Cheat-Sheet](https://rxiv-maker.henriqueslab.org/getting-started/quick-reference/)
 
 ### 🔧 **Developer Experience**
 - Modern CLI with rich output and progress bars
@@ -225,32 +218,22 @@ rxiv pdf
 
 **Input Markdown:**
 ```markdown
-# Introduction
-
-{{py:exec
-import pandas as pd
-import numpy as np
-
-df = pd.read_csv("FIGURES/DATA/experimental_results.csv")
-
-# Calculate correlation between specific columns (safer than iloc)
-# Assuming the CSV has columns like 'treatment_effect' and 'baseline_score'
-correlation = df['treatment_effect'].corr(df['baseline_score'])
-sample_size = len(df)
-}}
+## Introduction
 
-Our analysis of {{py:get sample_size}} samples in Figure @fig:results shows 
-significant improvement over previous methods [@smith2023; @jones2024].
+Recent advances in microscopy have enabled new insights into
+cellular dynamics [@smith2023; @jones2024].
 
-![Research Results](https://github.com/HenriquesLab/manuscript-rxiv-maker/blob/main/MANUSCRIPT/FIGURES/SFigure__arxiv_growth.py)
+![Experimental Results](FIGURES/results_plot.py)
 {#fig:results}
 
-The correlation coefficient was r = {{py:get correlation:.2f}} (p < 0.001).
-
-## References
+Our analysis (Figure @fig:results) shows significant improvement
+over previous methods. Statistical analysis revealed p < 0.001.
 ```
 
-**Output:** Professional PDF with numbered figures, live data integration, citations, and LaTeX-quality typesetting.
+**Output:** Professional PDF with auto-numbered figures, formatted citations, and LaTeX typesetting.
+
+> **💡 See the complete working example:**
+> `rxiv get-rxiv-preprint` - clones [manuscript-rxiv-maker](https://github.com/HenriquesLab/manuscript-rxiv-maker) with advanced features including Python execution, DOI auto-resolution, and dynamic data integration.
 
 ## 📖 Documentation
 
@@ -264,12 +247,14 @@ Visit our **[official documentation website](https://rxiv-maker.henriqueslab.org
 
 ### For Developers
 - **[CONTRIBUTING.md](CONTRIBUTING.md)** - Contribution guidelines
-- **[CLAUDE.md](CLAUDE.md)** - AI assistant instructions & testing commands
 - **[CI-LOCAL-TESTING.md](CI-LOCAL-TESTING.md)** - Local CI workflow testing
 - **[Developer Docs](docs/)** - Technical documentation and API details
 
 ## 🎯 Use Cases
 
+<details>
+<summary>📄 <strong>Research Preprints, Reproducible Figures, and Collaborative Workflows</strong></summary>
+
 ### 📄 **Research Preprints**
 - arXiv preprints with automated submission packages
 - bioRxiv and other preprint servers with professional formatting
@@ -285,86 +270,66 @@ Visit our **[official documentation website](https://rxiv-maker.henriqueslab.org
 - **Collaborative preprint writing** with version control
 - **Supplementary materials** with automated generation
 
-## 🏃‍♀️ Ecosystem & Workflows
-
-**The rxiv-maker ecosystem consists of interconnected repositories:**
-
-### 📦 **Core Repositories**
-
-1. **[rxiv-maker](https://github.com/HenriquesLab/rxiv-maker)** (this repository)
-   - Main Python package and CLI tool
-   - Core processing engine
-   - Development and contribution hub
-
-2. **[website-rxiv-maker](https://github.com/HenriquesLab/website-rxiv-maker)**
-   - Official documentation website
-   - User guides and tutorials
-   - API reference and examples
-   - Visit: [rxiv-maker.henriqueslab.org](https://rxiv-maker.henriqueslab.org)
+</details>
 
-3. **[manuscript-rxiv-maker](https://github.com/HenriquesLab/manuscript-rxiv-maker)**
-   - Official example manuscript (published as arXiv:2508.00836)
-   - Complete working example with all features
-   - Clone with: `rxiv get-rxiv-preprint`
-
-### 🔧 **Development Tools**
-
-- **📝 [VS Code Extension](https://github.com/HenriquesLab/vscode-rxiv-maker)**
-  - Syntax highlighting and autocompletion
-  - Integrated build commands
-  - Real-time validation
-
-- **🐳 [Docker Support](https://github.com/HenriquesLab/docker-rxiv-maker)**
-  - Containerized execution environment with pre-installed rxiv-maker
-  - Pre-configured LaTeX, Python, R, and all dependencies
-  - Perfect for CI/CD and users without local LaTeX installation
-  - Separate repository for easier maintenance and faster image updates
+## 🏃‍♀️ Ecosystem & Workflows
 
-### 🚀 **Deployment Options**
+**Three ways to use rxiv-maker:**
+- 🖥️ **Local Installation**: Install directly on your system (recommended)
+- 🐳 **Docker**: Pre-configured container with all dependencies
+- ☁️ **Cloud**: GitHub Actions or Google Colab for browser-based editing
 
-- **⚡ Local Installation**: Native system setup (recommended for development)
-- **☁️ GitHub Actions**: Automated cloud builds and CI/CD
-- **🌐 Google Colab**: Browser-based editing without local installation
-- **🐳 Containers**: Docker for reproducible environments
+<details>
+<summary>🔗 <strong>Ecosystem</strong> - Related repositories and tools</summary>
 
-### 📦 **Simplified Architecture**
+### Ecosystem Overview
 
 ```mermaid
 graph LR
-    A[rxiv-maker<br/>Core Tool] --> B[PyPI]
+    A[rxiv-maker<br/>Core CLI] --> B[PyPI]
     A --> C[Homebrew]
     D[docker-rxiv-maker<br/>Container] --> E[Docker Hub]
-    D -.installs.-> A
-    F[vscode-rxiv-maker<br/>Extension] -.extends.-> A
-    G[website-rxiv-maker<br/>Docs] -.documents.-> A
-    H[manuscript-rxiv-maker<br/>Example] -.demonstrates.-> A
-
-    style A fill:#e1f5ff
-    style D fill:#fff4e6
-    style F fill:#fff4e6
-    style G fill:#e8f5e9
-    style H fill:#e8f5e9
+    D -.includes.-> A
+    F[vscode-rxiv-maker<br/>VS Code] -.enhances.-> A
+    G[manuscript-rxiv-maker<br/>Example] -.demonstrates.-> A
+
+    style A fill:#2563eb,stroke:#1e40af,stroke-width:3px,color:#fff
+    style D fill:#ea580c,stroke:#c2410c,stroke-width:2px,color:#fff
+    style F fill:#7c3aed,stroke:#6d28d9,stroke-width:2px,color:#fff
+    style G fill:#059669,stroke:#047857,stroke-width:2px,color:#fff
+    style B fill:#64748b,stroke:#475569,color:#fff
+    style C fill:#64748b,stroke:#475569,color:#fff
+    style E fill:#64748b,stroke:#475569,color:#fff
 ```
 
-> **Note**: As of v1.8.4, we've streamlined the ecosystem while maintaining multiple installation options (Homebrew, pip, pipx, uv) with optional Docker support for containerized workflows.
->
-> **📋 [Ecosystem Guide](docs/ECOSYSTEM.md)** - Complete architecture and integration patterns
-> **📋 [Migration Guide](docs/migration-v1.7.9.md)** - For users upgrading from previous versions
+### Related Repositories
+
+| Repository | Purpose | Access |
+|------------|---------|--------|
+| **[rxiv-maker](https://github.com/HenriquesLab/rxiv-maker)** | Main CLI tool and Python package | `brew install rxiv-maker` |
+| **[docker-rxiv-maker](https://github.com/HenriquesLab/docker-rxiv-maker)** | Pre-configured container with LaTeX + dependencies | `docker pull henriqueslab/rxiv-maker-base` |
+| **[manuscript-rxiv-maker](https://github.com/HenriquesLab/manuscript-rxiv-maker)** | Complete example (published as arXiv:2508.00836) | `rxiv get-rxiv-preprint` |
+| **[vscode-rxiv-maker](https://github.com/HenriquesLab/vscode-rxiv-maker)** | VS Code extension with syntax highlighting | VS Code Marketplace |
+| **[Documentation](https://rxiv-maker.henriqueslab.org)** | User guides, API reference, tutorials | Visit website |
+
+</details>
+
+## 🚀 Quick Commands
 
-### 🔗 **Repository Cross-Reference**
+**Essential commands to get started:**
 
-| Repository | Purpose | Install/Access | Dependencies |
-|------------|---------|----------------|--------------|
-| **rxiv-maker** (this repo) | Main CLI tool & Python package | `brew install` / `pipx install` | LaTeX |
-| **[docker-rxiv-maker](https://github.com/HenriquesLab/docker-rxiv-maker)** | Pre-built container with all deps | `docker pull henriqueslab/rxiv-maker-base` | Docker |
-| **[manuscript-rxiv-maker](https://github.com/HenriquesLab/manuscript-rxiv-maker)** | Official example (arXiv:2508.00836) | `rxiv get-rxiv-preprint` | rxiv-maker |
-| **[vscode-rxiv-maker](https://github.com/HenriquesLab/vscode-rxiv-maker)** | VS Code extension | VS Code Marketplace | rxiv-maker |
-| **[website-rxiv-maker](https://github.com/HenriquesLab/website-rxiv-maker)** | Documentation website | [rxiv-maker.henriqueslab.org](https://rxiv-maker.henriqueslab.org) | - |
+```bash
+rxiv init my-paper       # Create new manuscript
+rxiv pdf                 # Generate PDF
+rxiv validate           # Check manuscript quality
+rxiv upgrade            # Upgrade to latest version
+```
 
-## 🚀 Essential Commands
+<details>
+<summary>📋 <strong>Complete Command Reference</strong> - Repository management, export options, and advanced workflows</summary>
 
+### Core Commands
 ```bash
-# Core Commands
 rxiv init my-paper          # Create new manuscript
 rxiv get-rxiv-preprint     # Clone complete example manuscript
 rxiv pdf                    # Generate PDF
@@ -372,89 +337,55 @@ rxiv docx                   # Export to DOCX for collaborative review
 rxiv validate              # Check manuscript quality
 rxiv arxiv                 # Prepare arXiv submission
 rxiv track-changes v1 v2   # Visual version comparison
-
-# Repository Management
-rxiv create-repo           # Create new manuscript repository (with GitHub integration)
-rxiv repos                 # List all manuscript repositories
-rxiv repos-search          # Search and clone from GitHub
-rxiv config                # Interactive configuration menu
-
-# Maintenance
-rxiv upgrade               # Upgrade to latest version
-rxiv changelog             # View changelog and release notes
-rxiv changelog --recent 5  # View last 5 versions
 ```
 
-### 📂 Repository Management
-
-Manage multiple manuscript repositories with GitHub integration:
-
+### Repository Management
 ```bash
-# Initial setup (interactive)
-rxiv repo-init
+# Initial setup
+rxiv repo-init             # Interactive setup
+rxiv config                # Interactive configuration menu
+
+# Create and manage repositories
+rxiv create-repo my-paper  # Create new manuscript repository (with GitHub integration)
+rxiv repos                 # List all manuscript repositories
+rxiv repos-search          # Search and clone from GitHub
 
-# Or configure manually
+# Configuration
 rxiv config set-repo-parent-dir ~/manuscripts
 rxiv config set-repo-org YourGitHubOrg
-
-# Create new repository (manuscript-{name})
-rxiv create-repo my-paper
-
-# List all repositories with git status
-rxiv repos
-
-# Search and clone from GitHub
-rxiv repos-search my-paper
-
-# Interactive configuration
-rxiv config                 # Interactive menu
 rxiv config --non-interactive  # Show current settings
 ```
 
-> **💡 CI/Automation Note:** All interactive commands support non-interactive mode or configuration files for use in CI/CD pipelines and automated workflows. Use `--non-interactive` flag or configure via `~/.rxiv-maker/config` for non-TTY environments.
-
-### 📄 DOCX Export for Collaborative Review
-
-Share your manuscript with non-LaTeX collaborators by exporting to Microsoft Word format. The easiest way is to add the `--docx` flag when building your PDF:
-
+### Maintenance
 ```bash
-# Build PDF and also export to DOCX
-rxiv pdf --docx
+rxiv upgrade               # Upgrade to latest version
+rxiv changelog             # View changelog and release notes
+rxiv changelog --recent 5  # View last 5 versions
+```
 
-# With DOI resolution for missing entries
-rxiv pdf --docx --resolve-dois
+> **💡 CI/Automation Note:** All interactive commands support non-interactive mode or configuration files for use in CI/CD pipelines and automated workflows. Use `--non-interactive` flag or configure via `~/.rxiv-maker/config` for non-TTY environments.
 
-# Or use the standalone command
-rxiv docx                     # Just DOCX (without rebuilding PDF)
-rxiv docx --resolve-dois      # With DOI resolution
-rxiv docx --no-footnotes      # Without DOI footnotes
-```
+**📖 [Complete CLI Reference](https://rxiv-maker.henriqueslab.org/getting-started/quick-reference/)** - Full command documentation with examples and options.
+
+</details>
 
-**Output Location:**
-- Automatically saved to `MANUSCRIPT/YEAR__lastname_et_al__rxiv.docx`
-- Uses the same naming pattern as the PDF for easy identification
-- Saved directly in the manuscript directory
+## 📚 Publications Using Rxiv-Maker
 
-**Features:**
-- ✅ **Numbered Citations**: Converts `@cite` to superscript [1], [2], etc.
-- ✅ **References Section**: Complete bibliography with clickable DOI links
-- ✅ **Embedded Figures**: Automatically converts PDF figures to PNG and embeds them
-- ✅ **Figure Captions**: Properly formatted with labels
-- ✅ **Formatting Preserved**: Maintains bold, italic, and inline code
-- ✅ **Supplementary Info**: Automatically includes 02_SUPPLEMENTARY_INFO.md
-- ✅ **Missing DOI Resolution**: Attempts to fetch DOIs from CrossRef/DataCite
+| Publication | Authors | Venue | DOI |
+|-------------|---------|-------|-----|
+| Rxiv-Maker: an automated template engine for streamlined scientific publications | BM Saraiva et al. | arXiv (2025) | [10.48550/arXiv.2508.00836](https://doi.org/10.48550/arXiv.2508.00836) |
+| Customizable FDM-based zebrafish embryo mold for live imaging | MX Rivera Pineda et al. | bioRxiv (2025) | [10.1101/2025.11.24.689779](https://doi.org/10.1101/2025.11.24.689779) |
+| mAIcrobe: an open-source framework for high-throughput bacterial image analysis | AD Brito et al. | bioRxiv (2025) | [10.1101/2025.10.21.683709](https://doi.org/10.1101/2025.10.21.683709) |
+| Filopodome proteomics identifies CCT8 as a MYO10 interactor critical for filopodia functions | A Popović et al. | bioRxiv (2025) | [10.64898/2025.12.03.691809](https://doi.org/10.64898/2025.12.03.691809) |
 
-**Content Scope:**
-- Includes: Main manuscript (01_MAIN.md), supplementary information (02_SUPPLEMENTARY_INFO.md), and figures
-- Converts: PDF figures to embedded PNG images (150 DPI, max 6" width)
-- Excludes: YAML metadata headers
+**📸 [View Publication Previews](https://rxiv-maker.henriqueslab.org/examples/showcase/)** - See manuscript thumbnails and access preprints
 
-**[📖 CLI Reference](docs/cli-reference.md)**
+> **Using Rxiv-Maker for your research?** Submit your publication via [GitHub Issue](https://github.com/HenriquesLab/rxiv-maker/issues/new?template=publication_submission.yml)
 
 ## 🤝 Community
 
 - **💬 [GitHub Discussions](https://github.com/henriqueslab/rxiv-maker/discussions)** - Ask questions, share tips
-- **🐛 [Issues](https://github.com/henriqueslab/rxiv-maker/issues)** - Report bugs, request features  
+- **🐛 [Issues](https://github.com/henriqueslab/rxiv-maker/issues)** - Report bugs, request features
 - **📚 [Example Manuscript](https://github.com/HenriquesLab/manuscript-rxiv-maker)** - Clone instantly: `rxiv get-rxiv-preprint`
 - **🧪 [Google Colab](https://colab.research.google.com/github/HenriquesLab/rxiv-maker/blob/main/notebooks/rxiv_maker_colab.ipynb)** - Try without installing
 
@@ -502,6 +433,6 @@ MIT License - see [LICENSE](LICENSE) for details.
 
 *"Because science is hard enough without fighting with LaTeX."*
 
-**[🚀 Start Writing](docs/first-manuscript.md)** | **[📚 User Guide](docs/user_guide.md)** | **[⚙️ CLI Reference](docs/cli-reference.md)**
+**[🚀 Start Writing](https://rxiv-maker.henriqueslab.org/getting-started/first-manuscript/)** | **[📚 User Guide](https://rxiv-maker.henriqueslab.org/guides/)** | **[⚙️ CLI Reference](https://rxiv-maker.henriqueslab.org/getting-started/quick-reference/)**
 
 </div>

{rxiv_maker-1.16.3.dist-info → rxiv_maker-1.16.5.dist-info}/RECORD

@@ -1,5 +1,5 @@
 rxiv_maker/__init__.py,sha256=p04JYC5ZhP6dLXkoWVlKNyiRvsDE1a4C88f9q4xO3tA,3268
-rxiv_maker/__version__.py,sha256=Ee6U6W-eWQHTVnWV61WELv3p6G3PUDkO5Vt_RwLkSb0,51
+rxiv_maker/__version__.py,sha256=scH9t8S4Yy0pZ0rKdWKP1B1m1lQmPo9FwrixAZxLlR0,51
 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=5yA8Aa_zIwJ6PBE94NB_ZqRYhiQkawm-lc43u04NiYY,7301
+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
@@ -95,7 +95,7 @@ rxiv_maker/engines/operations/add_bibliography.py,sha256=eIYbZRmRFHPm09svhnrsgIj
 rxiv_maker/engines/operations/build_manager.py,sha256=TAX4-r8HjraAzzvQuIt0CNlvWLo5pF40I7BRuIxZZRc,45022
 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=f9IjZD2_nK-kD8RLRugRuXMslDgx4857f3AqLGRJFrY,11084
+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_preprint.py,sha256=wpKDAu2RLJ4amSdhX5GZ7hU-iTsTRt4etcEA7AZYp04,2662
 rxiv_maker/engines/operations/prepare_arxiv.py,sha256=cd0JN5IO-Wy9T8ab75eibyaA8_K8Gpwrz2F-95OMnx4,21551
@@ -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
@@ -187,8 +187,8 @@ rxiv_maker/validators/doi/metadata_comparator.py,sha256=euqHhKP5sHQAdZbdoAahUn6Y
 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-1.16.3.dist-info/METADATA,sha256=oM615ZOWCjw_f6jWA7K0rnaI9S19-C9mks2Afm9JLZ0,19818
-rxiv_maker-1.16.3.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-rxiv_maker-1.16.3.dist-info/entry_points.txt,sha256=ghCN0hI9A1GlG7QY5F6E-xYPflA8CyS4B6bTQ1YLop0,97
-rxiv_maker-1.16.3.dist-info/licenses/LICENSE,sha256=GSZFoPIhWDNJEtSHTQ5dnELN38zFwRiQO2antBezGQk,1093
-rxiv_maker-1.16.3.dist-info/RECORD,,
+rxiv_maker-1.16.5.dist-info/METADATA,sha256=2U4BcFzbnYaEhzXTOgtUCk13H5w_J_RyoCZ5lQQjaGE,17950
+rxiv_maker-1.16.5.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+rxiv_maker-1.16.5.dist-info/entry_points.txt,sha256=ghCN0hI9A1GlG7QY5F6E-xYPflA8CyS4B6bTQ1YLop0,97
+rxiv_maker-1.16.5.dist-info/licenses/LICENSE,sha256=GSZFoPIhWDNJEtSHTQ5dnELN38zFwRiQO2antBezGQk,1093
+rxiv_maker-1.16.5.dist-info/RECORD,,