Merge branch 'release/v0.9.0' [ci skip]

Author: abhi18av

.gitignore

@@ -48,8 +48,6 @@ Temporary Items
 .clerk
 
 
-# AnW template
-template/analysis/pbin
 
 # OCaml
 template/analysis/_build/
@@ -62,12 +60,16 @@ bazel-template
 bazel-testlogs
 
 MODULE.bazel.lock
-template/writeup/presentation/_extensions/
-template/writeup/manuscript/pollen/compiled
 
 template/.idea
 template/template.iml
 
+
+# DOCUMENTATION BUILDS
+template/analysis/pbin
+template/writeup/presentation/_extensions/
+template/writeup/manuscript/pollen/compiled
+
 docs/presentations/academic-template/output/src/template-presentation_files
 docs/presentations/academic-template/output/template-presentation_files
 template-presentation_files

copier.yml

@@ -64,13 +64,13 @@ include_writeup:
 include_infrastructure:
   type: bool
   help: Include infrastructure folder (Docker, cloud deployment, CI/CD)
-  default: false
+  default: true
   when: "{{ project_type == 'Custom (choose components manually)' }}"
 
 include_misc:
   type: bool
   help: Include misc folder (utilities, legacy code, experimental features)
-  default: false
+  default: true
   when: "{{ project_type == 'Custom (choose components manually)' }}"
 
 # Project Configuration
@@ -208,12 +208,7 @@ include_testing:
 include_packages:
   type: bool
   help: Include local package development structure
-  default: >
-    {%- if project_type == "Package Development (software/library)" -%}
-    true
-    {%- else -%}
-    false
-    {%- endif -%}
+
   when: "{{ include_analysis }}"
 
 # === SUBCOMPONENT SELECTION FOR WRITEUP ===
@@ -232,23 +227,13 @@ include_presentations:
 include_grants:
   type: bool
   help: Include grant application management
-  default: >
-    {%- if project_type in ["Full Academic Project (analysis + writeup)", "Manuscript Only (writing and publications)"] -%}
-    true
-    {%- else -%}
-    false
-    {%- endif -%}
+
   when: "{{ include_writeup }}"
 
 include_abstracts:
   type: bool
   help: Include abstract submission management
-  default: >
-    {%- if project_type in ["Full Academic Project (analysis + writeup)", "Manuscript Only (writing and publications)"] -%}
-    true
-    {%- else -%}
-    false
-    {%- endif -%}
+
   when: "{{ include_writeup }}"
 
 include_posters:
@@ -266,7 +251,7 @@ include_reports:
 include_blog:
   type: bool
   help: Include blog post templates for informal writing
-  default: false
+
   when: "{{ include_writeup }}"
 
 # === INFRASTRUCTURE SUBCOMPONENTS ===
@@ -279,13 +264,13 @@ include_docker:
 include_cloud_deployment:
   type: bool
   help: Include cloud deployment templates (AWS, GCP, Azure)
-  default: false
+
   when: "{{ include_infrastructure }}"
 
 include_virtualization:
   type: bool
   help: Include VM and container orchestration
-  default: false
+
   when: "{{ include_infrastructure }}"
 
 include_automation:
@@ -298,15 +283,15 @@ include_automation:
 include_jujutsu:
   type: bool
   help: Include Jujutsu (jj) version control with Git backend for enhanced academic workflows
-  default: false
+
 
 include_fossil:
   type: bool
   help: Include Fossil SCM for self-contained archives and manuscript versioning
-  default: false
+
 
 use_hybrid_vcs:
   type: bool
   help: Use hybrid version control (Jujutsu + Fossil) for comprehensive research management
-  default: false
+
   when: "{{ include_jujutsu and include_fossil }}"

docs/assets/.gitkeep

@@ -0,0 +1,13 @@
+# Assets Directory
+
+This directory contains supporting assets for the presentation:
+
+- `logo.png` - Organization logo
+- `template.pptx` - PowerPoint template for PPTX output
+- Additional images and graphics as needed
+
+To use the presentation:
+
+1. Add your organization's logo as `logo.png`
+2. Customize the PowerPoint template as needed
+3. Run `quarto render template-presentation.qmd` to generate outputs

docs/custom.scss

@@ -0,0 +1,239 @@
+/*-- scss:defaults --*/
+
+// Color scheme for academic presentation
+$primary-color: #2563eb;
+$secondary-color: #059669;
+$accent-color: #dc2626;
+$text-color: #1f2937;
+$background-color: #ffffff;
+$code-bg-color: #f8fafc;
+
+// Typography
+$font-family-sans-serif: 'Inter', 'Segoe UI', 'Roboto', sans-serif !default;
+$font-family-monospace: 'JetBrains Mono', 'Fira Code', 'Monaco', monospace !default;
+
+/*-- scss:rules --*/
+
+// Base styling
+.reveal {
+  font-family: $font-family-sans-serif;
+  color: $text-color;
+}
+
+// Title slide styling
+.reveal .slides section.title {
+  text-align: center;
+  
+  h1 {
+    color: $primary-color;
+    font-weight: 700;
+    font-size: 2.5em;
+    margin-bottom: 0.5em;
+  }
+  
+  h2 {
+    color: $secondary-color;
+    font-weight: 400;
+    font-size: 1.2em;
+    margin-bottom: 1em;
+  }
+  
+  .author, .date {
+    color: #6b7280;
+    font-size: 1em;
+  }
+}
+
+// Section headers with colored backgrounds
+.reveal .slides section[data-background-color] {
+  h1, h2 {
+    color: white;
+    text-shadow: 2px 2px 4px rgba(0,0,0,0.3);
+  }
+}
+
+// Code blocks
+.reveal pre code {
+  background-color: $code-bg-color;
+  border: 1px solid #e5e7eb;
+  border-radius: 8px;
+  padding: 1em;
+  font-family: $font-family-monospace;
+  font-size: 0.8em;
+  line-height: 1.4;
+  overflow-x: auto;
+}
+
+// Inline code
+.reveal code {
+  background-color: $code-bg-color;
+  color: $primary-color;
+  padding: 0.2em 0.4em;
+  border-radius: 4px;
+  font-family: $font-family-monospace;
+  font-size: 0.9em;
+}
+
+// Lists
+.reveal ul, .reveal ol {
+  margin-left: 1em;
+  
+  li {
+    margin-bottom: 0.5em;
+    line-height: 1.4;
+  }
+}
+
+// Emphasized text
+.reveal strong {
+  color: $primary-color;
+  font-weight: 600;
+}
+
+// Columns layout improvements
+.reveal .columns {
+  display: flex;
+  align-items: flex-start;
+  justify-content: space-between;
+  gap: 2em;
+  
+  .column {
+    flex: 1;
+  }
+}
+
+// Callout boxes
+.reveal .callout {
+  border-left: 4px solid $primary-color;
+  background-color: #f8fafc;
+  padding: 1em;
+  margin: 1em 0;
+  border-radius: 0 8px 8px 0;
+}
+
+.reveal .callout.success {
+  border-left-color: $secondary-color;
+  background-color: #ecfdf5;
+}
+
+.reveal .callout.warning {
+  border-left-color: #f59e0b;
+  background-color: #fffbeb;
+}
+
+.reveal .callout.error {
+  border-left-color: $accent-color;
+  background-color: #fef2f2;
+}
+
+// Tables
+.reveal table {
+  border-collapse: collapse;
+  width: 100%;
+  margin: 1em 0;
+  
+  th, td {
+    border: 1px solid #e5e7eb;
+    padding: 0.75em;
+    text-align: left;
+  }
+  
+  th {
+    background-color: $primary-color;
+    color: white;
+    font-weight: 600;
+  }
+  
+  tr:nth-child(even) {
+    background-color: #f9fafb;
+  }
+}
+
+// Buttons and interactive elements
+.reveal .button {
+  background-color: $primary-color;
+  color: white;
+  padding: 0.75em 1.5em;
+  border: none;
+  border-radius: 6px;
+  font-weight: 500;
+  text-decoration: none;
+  display: inline-block;
+  transition: background-color 0.2s;
+  
+  &:hover {
+    background-color: darken($primary-color, 10%);
+  }
+}
+
+// Mermaid diagrams
+.reveal .mermaid {
+  text-align: center;
+  
+  svg {
+    max-width: 100%;
+    height: auto;
+  }
+}
+
+// Footer customization
+.reveal .footer {
+  font-size: 0.6em;
+  color: #6b7280;
+}
+
+// Progress bar
+.reveal .progress {
+  color: $primary-color;
+}
+
+// Slide numbers
+.reveal .slide-number {
+  color: $primary-color;
+  background-color: rgba(255, 255, 255, 0.8);
+  padding: 0.3em 0.6em;
+  border-radius: 4px;
+}
+
+// Notes styling
+.reveal .notes {
+  font-style: italic;
+  color: #6b7280;
+  font-size: 0.9em;
+  margin-top: 1em;
+  padding: 1em;
+  background-color: #f9fafb;
+  border-radius: 6px;
+}
+
+// Responsive design
+@media (max-width: 768px) {
+  .reveal .columns {
+    flex-direction: column;
+    gap: 1em;
+  }
+  
+  .reveal h1 {
+    font-size: 2em;
+  }
+  
+  .reveal h2 {
+    font-size: 1.5em;
+  }
+  
+  .reveal pre code {
+    font-size: 0.7em;
+  }
+}
+
+// Print styles
+@media print {
+  .reveal {
+    background: white;
+    color: black;
+  }
+  
+  .reveal .slides section {
+    page-break-after: always;
+  }
+}