MyST Markdown Refactor

.github/workflows/build-myst.yml

@@ -0,0 +1,99 @@
+name: MyST Documents, Source Code
+
+on:
+  push:
+    branches: [ main, myst ]
+  pull_request:
+    branches: [ main, myst ]
+  workflow_dispatch:
+
+jobs:
+  build-myst:
+    runs-on: ubuntu-24.04
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v5
+
+    - name: Setup Pixi
+      uses: prefix-dev/setup-pixi@v0.9.0
+      with:
+        pixi-version: latest
+
+    - name: Install dependencies
+      run: pixi install
+
+    - name: Build HTML
+      run: pixi run build-html
+
+    - name: Build PDF
+      run: pixi run build-pdf
+
+    - name: Build MECA
+      run: pixi run build-meca
+
+    - name: Upload build artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: myst-outputs
+        path: |
+          _build/
+          exports/
+        retention-days: 30
+
+  build-source:
+    runs-on: ubuntu-24.04
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v5
+
+    - name: Setup Pixi
+      uses: prefix-dev/setup-pixi@v0.9.0
+      with:
+        pixi-version: latest
+
+    - name: Install dependencies
+      run: pixi install
+
+    - name: Build source code
+      run: pixi run build-src
+
+    - name: Run tests
+      run: pixi run test-src
+
+    - name: Upload test results
+      uses: actions/upload-artifact@v4
+      if: always()
+      with:
+        name: test-results
+        path: |
+          build/Testing/
+        retention-days: 30
+
+  deploy:
+    runs-on: ubuntu-latest
+    needs: [build-myst, build-source]
+    if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/myst'
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v5
+
+    - name: Setup Pixi
+      uses: prefix-dev/setup-pixi@v0.9.0
+      with:
+        pixi-version: latest
+
+    - name: Install dependencies
+      run: pixi install
+
+    - name: Build for deployment
+      run: pixi run build-html
+
+    - name: Deploy to GitHub Pages
+      uses: peaceiris/actions-gh-pages@v3
+      if: github.ref == 'refs/heads/main'
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./_build/html

.github/workflows/build-test-latex.yml

@@ -1,22 +1,31 @@
-name: Build LaTeX document
+name: Build LaTeX Document
 
 on: [push,pull_request]
 
 jobs:
-  build_latex:
-    runs-on: ubuntu-latest
+  build-latex:
+    runs-on: ubuntu-24.04
     steps:
       - name: Set up Git repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v5
+
       - name: Set up LaTeX packages
         run: |
           sudo apt-get update
           sudo apt-get install texlive texlive-publishers texlive-science latexmk
-      - name: Compile LaTeX document
-        run: |
-          cd Document/LaTeX
-          make
-      - name: Check pdf files
-        run: |
-          set -e
-          file Document/LaTeX/ArticleExample.pdf | grep -q ' PDF '
+
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.9.0
+        with:
+          pixi-version: latest
+
+      - name: Build PDF
+        run: pixi run build-arxiv
+
+      - name: Upload build artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: arxiv-pdf-outputs
+          path: |
+            exports/
+          retention-days: 30

.gitignore

@@ -1,3 +1,4 @@
+# LaTeX build artifacts
 *.aux
 *.bbl
 *.blg
@@ -9,3 +10,49 @@
 *.ps
 *.toc
 _minted-*/
+
+# MyST Markdown build outputs
+_build/
+site/
+.myst/
+*.epub
+*.meca
+
+# Pixi environment and cache
+.pixi/
+pixi.lock
+__pycache__/
+*.pyc
+
+# IDE and editor files
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+
+# OS files
+.DS_Store
+Thumbs.db
+
+# Build directories
+build/
+dist/
+CMakeCache.txt
+CMakeFiles/
+cmake_install.cmake
+Makefile
+
+# Node.js (if using MyST plugins)
+node_modules/
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+
+# Python virtual environments
+venv/
+env/
+.env
+
+exports/
+data/img1.png.base.png

CITATION.cff

@@ -0,0 +1,32 @@
+cff-version: 1.2.0
+message: Please cite the following works when using this project.
+title: Insight Journal MyST Template
+authors:
+  - family-names: Galilei
+    given-names: Galileo
+    affiliation: Pisa University
+    address: Tower Drive, Pisa, Italy
+    orcid: 0000-0000-0000-0001
+    email: galileo@pisa.university
+  - family-names: Bruno
+    given-names: Giordano
+    affiliation: Rome University
+    address: Inquisition Street, Rome, Italy
+    orcid: 0000-0000-0000-0002
+    email: giordano@rome.university
+  - family-names: Leeuwenhoek
+    given-names: Anthony
+    affiliation: Netherlands Pragmatic University
+    address: Port Street, Netherlands
+    orcid: 0000-0000-0000-0003
+    email: anthony@netherlands.university
+contact:
+  - family-names: Galilei
+    given-names: Galileo
+    affiliation: Pisa University
+    address: Tower Drive, Pisa, Italy
+    orcid: 0000-0000-0000-0001
+    email: galileo@pisa.university
+license: CC-BY-4.0
+license-url: https://creativecommons.org/licenses/by/4.0/
+repository: https://github.com/InsightSoftwareConsortium/InsightJournalTemplate