docrev 0.11.1 → 0.11.3

package/dist/lib/templates.js

@@ -11,95 +11,95 @@ export const TEMPLATES = {
         name: 'Academic Paper',
         description: 'Standard paper with introduction, methods, results, discussion',
         files: {
-            'rev.yaml': `# Paper configuration
-title: "Your Paper Title"
-authors:
-  - name: First Author
-    affiliation: Institution
-    email: author@example.com
-
-# Section files in order
-sections:
-  - introduction.md
-  - methods.md
-  - results.md
-  - discussion.md
-
-# Bibliography (optional)
-bibliography: references.bib
-csl: null  # uses default CSL
-
-# Cross-reference settings
-crossref:
-  figureTitle: Figure
-  tableTitle: Table
-  figPrefix: [Fig., Figs.]
-  tblPrefix: [Table, Tables]
-  linkReferences: true
-
-# PDF output settings
-pdf:
-  documentclass: article
-  fontsize: 12pt
-  geometry: margin=1in
-  linestretch: 1.5
-  numbersections: false
-
-# Word output settings
-docx:
-  reference: null  # path to reference.docx template
-  keepComments: true
-`,
-            'introduction.md': `# Introduction
-
-Your introduction goes here. Use dynamic figure references like @fig:example.
-
-`,
-            'methods.md': `# Methods
-
-## Study Design
-
-Describe your methodology here.
-
-## Data Analysis
-
-Reference tables with @tbl:summary.
-
-`,
-            'results.md': `# Results
-
-Present your findings. See @fig:results for the main analysis.
-
-![Example figure caption](figures/placeholder.png){#fig:results}
-
-`,
-            'discussion.md': `# Discussion
-
-Interpret your results here.
-
-## Conclusions
-
-Summarize key findings.
-
-`,
-            'references.bib': `@article{example2024,
-  author = {Author, A. and Coauthor, B.},
-  title = {An Example Paper Title},
-  journal = {Journal Name},
-  year = {2024},
-  volume = {1},
-  pages = {1--10}
-}
-`,
-            '.gitignore': `# Build outputs
-*.pdf
-*.docx
-*.tex
-paper.md
-.paper-*.md
-
-# System
-.DS_Store
+            'rev.yaml': `# Paper configuration
+title: "Your Paper Title"
+authors:
+  - name: First Author
+    affiliation: Institution
+    email: author@example.com
+
+# Section files in order
+sections:
+  - introduction.md
+  - methods.md
+  - results.md
+  - discussion.md
+
+# Bibliography (optional)
+bibliography: references.bib
+csl: null  # uses default CSL
+
+# Cross-reference settings
+crossref:
+  figureTitle: Figure
+  tableTitle: Table
+  figPrefix: [Fig., Figs.]
+  tblPrefix: [Table, Tables]
+  linkReferences: true
+
+# PDF output settings
+pdf:
+  documentclass: article
+  fontsize: 12pt
+  geometry: margin=1in
+  linestretch: 1.5
+  numbersections: false
+
+# Word output settings
+docx:
+  reference: null  # path to reference.docx template
+  keepComments: true
+`,
+            'introduction.md': `# Introduction
+
+Your introduction goes here. Use dynamic figure references like @fig:example.
+
+`,
+            'methods.md': `# Methods
+
+## Study Design
+
+Describe your methodology here.
+
+## Data Analysis
+
+Reference tables with @tbl:summary.
+
+`,
+            'results.md': `# Results
+
+Present your findings. See @fig:results for the main analysis.
+
+![Example figure caption](figures/placeholder.png){#fig:results}
+
+`,
+            'discussion.md': `# Discussion
+
+Interpret your results here.
+
+## Conclusions
+
+Summarize key findings.
+
+`,
+            'references.bib': `@article{example2024,
+  author = {Author, A. and Coauthor, B.},
+  title = {An Example Paper Title},
+  journal = {Journal Name},
+  year = {2024},
+  volume = {1},
+  pages = {1--10}
+}
+`,
+            '.gitignore': `# Build outputs
+*.pdf
+*.docx
+*.tex
+paper.md
+.paper-*.md
+
+# System
+.DS_Store
 `,
         },
         directories: ['figures'],
@@ -111,15 +111,15 @@ paper.md
         name: 'Minimal',
         description: 'Single document with basic config',
         files: {
-            'rev.yaml': `title: "Document Title"
-authors: []
-sections:
-  - content.md
+            'rev.yaml': `title: "Document Title"
+authors: []
+sections:
+  - content.md
 `,
-            'content.md': `# Your Document
-
-Write your content here.
-
+            'content.md': `# Your Document
+
+Write your content here.
+
 `,
         },
         directories: [],
@@ -131,79 +131,79 @@ Write your content here.
         name: 'Thesis Chapter',
         description: 'Thesis-style with abstract, sections, appendix',
         files: {
-            'rev.yaml': `title: "Chapter Title"
-authors:
-  - name: Your Name
-    affiliation: University
-
-sections:
-  - abstract.md
-  - introduction.md
-  - literature.md
-  - methods.md
-  - results.md
-  - discussion.md
-  - conclusion.md
-  - appendix.md
-
-bibliography: references.bib
-
-pdf:
-  documentclass: report
-  fontsize: 11pt
-  geometry: "margin=1in"
-  linestretch: 2
-  numbersections: true
-`,
-            'abstract.md': `# Abstract
-
-Brief summary of the chapter (150-300 words).
-
-`,
-            'introduction.md': `# Introduction
-
-Background and research questions.
-
-`,
-            'literature.md': `# Literature Review
-
-Review of relevant prior work.
-
-`,
-            'methods.md': `# Materials and Methods
-
-Detailed methodology.
-
-`,
-            'results.md': `# Results
-
-Findings and analysis.
-
-`,
-            'discussion.md': `# Discussion
-
-Interpretation of results.
-
-`,
-            'conclusion.md': `# Conclusion
-
-Summary and implications.
-
-`,
-            'appendix.md': `# Appendix
-
-## Supplementary Materials
-
-Additional details here.
-
+            'rev.yaml': `title: "Chapter Title"
+authors:
+  - name: Your Name
+    affiliation: University
+
+sections:
+  - abstract.md
+  - introduction.md
+  - literature.md
+  - methods.md
+  - results.md
+  - discussion.md
+  - conclusion.md
+  - appendix.md
+
+bibliography: references.bib
+
+pdf:
+  documentclass: report
+  fontsize: 11pt
+  geometry: "margin=1in"
+  linestretch: 2
+  numbersections: true
+`,
+            'abstract.md': `# Abstract
+
+Brief summary of the chapter (150-300 words).
+
+`,
+            'introduction.md': `# Introduction
+
+Background and research questions.
+
+`,
+            'literature.md': `# Literature Review
+
+Review of relevant prior work.
+
+`,
+            'methods.md': `# Materials and Methods
+
+Detailed methodology.
+
+`,
+            'results.md': `# Results
+
+Findings and analysis.
+
+`,
+            'discussion.md': `# Discussion
+
+Interpretation of results.
+
+`,
+            'conclusion.md': `# Conclusion
+
+Summary and implications.
+
+`,
+            'appendix.md': `# Appendix
+
+## Supplementary Materials
+
+Additional details here.
+
 `,
             'references.bib': ``,
-            '.gitignore': `*.pdf
-*.docx
-*.tex
-paper.md
-.paper-*.md
-.DS_Store
+            '.gitignore': `*.pdf
+*.docx
+*.tex
+paper.md
+.paper-*.md
+.DS_Store
 `,
         },
         directories: ['figures', 'tables'],
@@ -215,123 +215,123 @@ paper.md
         name: 'LaTeX Project',
         description: 'LaTeX-native with journal template support',
         files: {
-            'rev.yaml': `# LaTeX Paper Configuration
-title: "Paper Title"
-authors:
-  - name: First Author
-    affiliation: University
-    email: author@example.edu
-    orcid: 0000-0000-0000-0000
-
-sections:
-  - introduction.md
-  - methods.md
-  - results.md
-  - discussion.md
-
-bibliography: references.bib
-csl: null
-
-# LaTeX-specific settings
-pdf:
-  documentclass: article
-  classoption: [11pt, a4paper]
-  fontsize: 11pt
-  geometry: "margin=2.5cm"
-  linestretch: 1.5
-  numbersections: true
-  header-includes: |
-    \\usepackage{amsmath}
-    \\usepackage{graphicx}
-    \\usepackage{booktabs}
-    \\usepackage{hyperref}
-    \\usepackage{natbib}
-
-# TEX output settings
-tex:
-  standalone: true
-  keep-tex: true
-`,
-            'introduction.md': `# Introduction
-
-Background and motivation.
-
-## Objectives
-
-State your research questions.
-
-`,
-            'methods.md': `# Materials and Methods
-
-## Study Area
-
-Describe the study area or data sources.
-
-## Statistical Analysis
-
-All analyses were performed in R [@R2024].
-
-`,
-            'results.md': `# Results
-
-Main findings presented here.
-
-![Caption for figure](figures/fig1.pdf){#fig:main width=100%}
-
-See @fig:main for the main results.
-
-| Variable | Value | SE |
-|----------|-------|------|
-| A | 1.23 | 0.05 |
-| B | 4.56 | 0.12 |
-
-: Summary statistics {#tbl:summary}
-
-`,
-            'discussion.md': `# Discussion
-
-Interpretation of findings.
-
-## Limitations
-
-Study limitations.
-
-## Conclusions
-
-Key takeaways.
-
-`,
-            'references.bib': `@Manual{R2024,
-  title = {R: A Language and Environment for Statistical Computing},
-  author = {{R Core Team}},
-  organization = {R Foundation for Statistical Computing},
-  address = {Vienna, Austria},
-  year = {2024},
-  url = {https://www.R-project.org/}
-}
-`,
-            '.gitignore': `# Build outputs
-*.pdf
-*.docx
-paper.md
-.paper-*.md
-
-# Keep .tex for version control
-# *.tex
-
-# LaTeX auxiliary files
-*.aux
-*.bbl
-*.blg
-*.log
-*.out
-*.toc
-*.fdb_latexmk
-*.fls
-*.synctex.gz
-
-# System
-.DS_Store
+            'rev.yaml': `# LaTeX Paper Configuration
+title: "Paper Title"
+authors:
+  - name: First Author
+    affiliation: University
+    email: author@example.edu
+    orcid: 0000-0000-0000-0000
+
+sections:
+  - introduction.md
+  - methods.md
+  - results.md
+  - discussion.md
+
+bibliography: references.bib
+csl: null
+
+# LaTeX-specific settings
+pdf:
+  documentclass: article
+  classoption: [11pt, a4paper]
+  fontsize: 11pt
+  geometry: "margin=2.5cm"
+  linestretch: 1.5
+  numbersections: true
+  header-includes: |
+    \\usepackage{amsmath}
+    \\usepackage{graphicx}
+    \\usepackage{booktabs}
+    \\usepackage{hyperref}
+    \\usepackage{natbib}
+
+# TEX output settings
+tex:
+  standalone: true
+  keep-tex: true
+`,
+            'introduction.md': `# Introduction
+
+Background and motivation.
+
+## Objectives
+
+State your research questions.
+
+`,
+            'methods.md': `# Materials and Methods
+
+## Study Area
+
+Describe the study area or data sources.
+
+## Statistical Analysis
+
+All analyses were performed in R [@R2024].
+
+`,
+            'results.md': `# Results
+
+Main findings presented here.
+
+![Caption for figure](figures/fig1.pdf){#fig:main width=100%}
+
+See @fig:main for the main results.
+
+| Variable | Value | SE |
+|----------|-------|------|
+| A | 1.23 | 0.05 |
+| B | 4.56 | 0.12 |
+
+: Summary statistics {#tbl:summary}
+
+`,
+            'discussion.md': `# Discussion
+
+Interpretation of findings.
+
+## Limitations
+
+Study limitations.
+
+## Conclusions
+
+Key takeaways.
+
+`,
+            'references.bib': `@Manual{R2024,
+  title = {R: A Language and Environment for Statistical Computing},
+  author = {{R Core Team}},
+  organization = {R Foundation for Statistical Computing},
+  address = {Vienna, Austria},
+  year = {2024},
+  url = {https://www.R-project.org/}
+}
+`,
+            '.gitignore': `# Build outputs
+*.pdf
+*.docx
+paper.md
+.paper-*.md
+
+# Keep .tex for version control
+# *.tex
+
+# LaTeX auxiliary files
+*.aux
+*.bbl
+*.blg
+*.log
+*.out
+*.toc
+*.fdb_latexmk
+*.fls
+*.synctex.gz
+
+# System
+.DS_Store
 `,
         },
         directories: ['figures', 'tables'],
@@ -343,64 +343,64 @@ paper.md
         name: 'Review Article',
         description: 'Literature review or synthesis paper',
         files: {
-            'rev.yaml': `title: "Review Title"
-authors:
-  - name: Author Name
-    affiliation: Institution
-
-sections:
-  - introduction.md
-  - section1.md
-  - section2.md
-  - section3.md
-  - synthesis.md
-  - conclusion.md
-
-bibliography: references.bib
-
-crossref:
-  figureTitle: Figure
-  tableTitle: Table
-  figPrefix: [Fig., Figs.]
-  tblPrefix: [Table, Tables]
-`,
-            'introduction.md': `# Introduction
-
-Scope and objectives of the review.
-
-`,
-            'section1.md': `# Theme One
-
-First major theme or topic.
-
-`,
-            'section2.md': `# Theme Two
-
-Second major theme.
-
-`,
-            'section3.md': `# Theme Three
-
-Third major theme.
-
-`,
-            'synthesis.md': `# Synthesis
-
-Integration of themes and emerging patterns.
-
-`,
-            'conclusion.md': `# Conclusion and Future Directions
-
-Key takeaways and research gaps.
-
+            'rev.yaml': `title: "Review Title"
+authors:
+  - name: Author Name
+    affiliation: Institution
+
+sections:
+  - introduction.md
+  - section1.md
+  - section2.md
+  - section3.md
+  - synthesis.md
+  - conclusion.md
+
+bibliography: references.bib
+
+crossref:
+  figureTitle: Figure
+  tableTitle: Table
+  figPrefix: [Fig., Figs.]
+  tblPrefix: [Table, Tables]
+`,
+            'introduction.md': `# Introduction
+
+Scope and objectives of the review.
+
+`,
+            'section1.md': `# Theme One
+
+First major theme or topic.
+
+`,
+            'section2.md': `# Theme Two
+
+Second major theme.
+
+`,
+            'section3.md': `# Theme Three
+
+Third major theme.
+
+`,
+            'synthesis.md': `# Synthesis
+
+Integration of themes and emerging patterns.
+
+`,
+            'conclusion.md': `# Conclusion and Future Directions
+
+Key takeaways and research gaps.
+
 `,
             'references.bib': ``,
-            '.gitignore': `*.pdf
-*.docx
-*.tex
-paper.md
-.paper-*.md
-.DS_Store
+            '.gitignore': `*.pdf
+*.docx
+*.tex
+paper.md
+.paper-*.md
+.DS_Store
 `,
         },
         directories: ['figures'],
@@ -439,60 +439,60 @@ export function generateCustomTemplate(sections, baseTemplate) {
     const files = {};
     // Generate rev.yaml with custom sections
     const sectionsList = sections.map((s) => `  - ${s}.md`).join('\n');
-    files['rev.yaml'] = `# Paper configuration
-title: "Your Paper Title"
-authors:
-  - name: First Author
-    affiliation: Institution
-    email: author@example.com
-
-# Section files in order
-sections:
-${sectionsList}
-
-# Bibliography (optional)
-bibliography: references.bib
-csl: null  # uses default CSL
-
-# Cross-reference settings
-crossref:
-  figureTitle: Figure
-  tableTitle: Table
-  figPrefix: [Fig., Figs.]
-  tblPrefix: [Table, Tables]
-  linkReferences: true
-
-# PDF output settings
-pdf:
-  documentclass: article
-  fontsize: 12pt
-  geometry: margin=1in
-  linestretch: 1.5
-  numbersections: false
-
-# Word output settings
-docx:
-  reference: null  # path to reference.docx template
-  keepComments: true
+    files['rev.yaml'] = `# Paper configuration
+title: "Your Paper Title"
+authors:
+  - name: First Author
+    affiliation: Institution
+    email: author@example.com
+
+# Section files in order
+sections:
+${sectionsList}
+
+# Bibliography (optional)
+bibliography: references.bib
+csl: null  # uses default CSL
+
+# Cross-reference settings
+crossref:
+  figureTitle: Figure
+  tableTitle: Table
+  figPrefix: [Fig., Figs.]
+  tblPrefix: [Table, Tables]
+  linkReferences: true
+
+# PDF output settings
+pdf:
+  documentclass: article
+  fontsize: 12pt
+  geometry: margin=1in
+  linestretch: 1.5
+  numbersections: false
+
+# Word output settings
+docx:
+  reference: null  # path to reference.docx template
+  keepComments: true
 `;
     // Generate section files
     for (const section of sections) {
         const header = titleCase(section);
-        files[`${section}.md`] = `# ${header}
-
+        files[`${section}.md`] = `# ${header}
+
 `;
     }
     // Add common files
     files['references.bib'] = base.files['references.bib'] || '';
-    files['.gitignore'] = base.files['.gitignore'] || `# Build outputs
-*.pdf
-*.docx
-*.tex
-paper.md
-.paper-*.md
-
-# System
-.DS_Store
+    files['.gitignore'] = base.files['.gitignore'] || `# Build outputs
+*.pdf
+*.docx
+*.tex
+paper.md
+.paper-*.md
+
+# System
+.DS_Store
 `;
     return {
         name: 'Custom',