ENH: Update builds for other export formats

Author: thewtex

.gitignore

@@ -53,3 +53,5 @@ yarn-error.log*
 venv/
 env/
 .env
+
+exports/

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: [email protected]
+  - family-names: Bruno
+    given-names: Giordano
+    affiliation: Rome University
+    address: Inquisition Street, Rome, Italy
+    orcid: 0000-0000-0000-0002
+    email: [email protected]
+  - family-names: Leeuwenhoek
+    given-names: Anthony
+    affiliation: Netherlands Pragmatic University
+    address: Port Street, Netherlands
+    orcid: 0000-0000-0000-0003
+    email: [email protected]
+contact:
+  - family-names: Galilei
+    given-names: Galileo
+    affiliation: Pisa University
+    address: Tower Drive, Pisa, Italy
+    orcid: 0000-0000-0000-0001
+    email: [email protected]
+license: CC-BY-4.0
+license-url: https://creativecommons.org/licenses/by/4.0/
+repository: https://github.com/InsightSoftwareConsortium/InsightJournalTemplate

docs/index.md

@@ -1,6 +1,15 @@
 ---
 title: The Importance of Open Access in Scientific Publications
 subtitle: A Template for MyST Markdown Articles in the Insight Journal
+abstract: |
+  This document describes a new algorithm implemented using the Insight Toolkit
+  ITK (www.itk.org). The code of the algorithm is written following the
+  ITK CodingStyle as described in the directory ITK/Documentation/Style.pdf.
+
+  This paper is accompanied with the source code, input data, parameters and
+  output data that the authors used for validating the algorithm described in
+  this paper. This adheres to the fundamental principle that scientific
+  publications must facilitate reproducibility of the reported results.
 authors:
   - name: Galileo Galilei
     email: [email protected]
@@ -24,40 +33,29 @@ affiliations:
   - id: Netherlands Pragmatic University
     name: Netherlands Pragmatic University
     address: Port Street, Netherlands
-date: 2024-07-14
+
+# License and access
+license:
+  code: Apache-2.0
+  content: CC-BY-4.0
+open_access: true
+
+# Repository links
+github: InsightSoftwareConsortium/InsightJournalTemplate
+
+# Keywords for indexing
 keywords:
   - open science
   - reproducible research
   - image processing
   - ITK
   - scientific computing
-license: CC-BY-4.0
-open_access: true
-subject: Computer Science
-venue:
-  title: Insight Journal
-  url: https://insight-journal.org
-github: InsightSoftwareConsortium/InsightJournalTemplate
-doi: 10.5281/zenodo.1234567
-abstract: |
-  This document describes a new algorithm implemented using the Insight Toolkit
-  ITK (www.itk.org). The code of the algorithm is written following the
-  ITK CodingStyle as described in the directory ITK/Documentation/Style.pdf.
+  - MyST markdown
 
-  This paper is accompanied with the source code, input data, parameters and
-  output data that the authors used for validating the algorithm described in
-  this paper. This adheres to the fundamental principle that scientific
-  publications must facilitate reproducibility of the reported results.
-exports:
-  - format: pdf
-    template: arxiv_two_column
-    article_type: research-article
-  - format: pdf
-    template: plain_latex_book
-  - format: meca
-  - format: tex
-bibliography:
-  - references.bib
+abbreviations:
+  FAIR: Findable, Accessible, Interoperable, and Reusable
+  ITK: Insight Toolkit
+  WASM: WebAssembly
 ---
 
 Using filters from the Insight Toolkit, we develop an algorithm for detecting

myst.yml

@@ -4,12 +4,12 @@ project:
   id: insight-journal-000
   title: Insight Journal MyST Template
   description: A template for open science article submissions to the Insight Journal using MyST Markdown
+
   authors:
     - name: Galileo Galilei
       email: [email protected]
       affiliation: Pisa University
       orcid: 0000-0000-0000-0001
-      corresponding: true
     - name: Giordano Bruno
       email: [email protected]
       affiliation: Rome University
@@ -18,6 +18,16 @@ project:
       email: [email protected]
       affiliation: Netherlands Pragmatic University
       orcid: 0000-0000-0000-0003
+  affiliations:
+    - id: Pisa University
+      name: Pisa University
+      address: Tower Drive, Pisa, Italy
+    - id: Rome University
+      name: Rome University
+      address: Inquisition Street, Rome, Italy
+    - id: Netherlands Pragmatic University
+      name: Netherlands Pragmatic University
+      address: Port Street, Netherlands
 
   # License and access
   license:
@@ -28,45 +38,28 @@ project:
   # Repository links
   github: InsightSoftwareConsortium/InsightJournalTemplate
 
-  # Keywords for indexing
-  keywords:
-    - open science
-    - reproducible research
-    - image processing
-    - ITK
-    - scientific computing
-    - MyST markdown
-
-  abbreviations:
-    FAIR: Findable, Accessible, Interoperable, and Reusable
-    ITK: Insight Toolkit
-    WASM: WebAssembly
-
   # Publication venue
   venue:
     title: Insight Journal
     url: https://insight-journal.org
 
-  # Bibliography
-  bibliography:
-    - docs/references.bib
-
   # Export configurations
   exports:
-    - format: pdf
-      template: arxiv_two_column
-      article_type: research-article
+    - format: typst
+      template: lapreprint-typst
       output: exports/manuscript.pdf
     - format: pdf
-      template: plain_latex_book
-      output: exports/manuscript_book.pdf
-    - format: meca
-      output: exports/manuscript.meca.zip
+      template: arxiv_nips
+      article_type: research-article
+      output: exports/arxiv.pdf
     - format: tex
-      template: arxiv_two_column
+      template: arxiv_nips
       output: exports/manuscript.tex
     - format: docx
       output: exports/manuscript.docx
+    - format: cff
+    - format: meca
+      output: exports/manuscript.meca.zip
 
   toc:
     - file: docs/index.md
@@ -76,6 +69,10 @@ project:
     - src/
     - data/
 
+  # Bibliography
+  bibliography:
+    - docs/references.bib
+
   # Requirements for reproducibility
   requirements:
     - pixi.toml

pixi.toml

@@ -1,13 +1,8 @@
 [project]
 name = "insight-journal-template"
 description = "A template for open science article submissions to the Insight Journal using MyST Markdown"
-authors = [
-    "Galileo Galilei <[email protected]>",
-    "Giordano Bruno <[email protected]>",
-    "Anthony Leeuwenhoek <[email protected]>"
-]
 channels = ["conda-forge"]
-platforms = ["linux-64", "osx-64", "osx-arm64", "win-64"]
+platforms = ["linux-64", "osx-arm64", "win-64"]
 
 [dependencies]
 # MyST ecosystem
@@ -20,39 +15,33 @@ numpy = "*"
 matplotlib = "*"
 scipy = "*"
 
-# Document processing
-pandoc = "*"
-tectonic = "*"
-
 # Development tools
 jupyterlab = "*"
 
 # Optional: for notebook execution
 ipykernel = "*"
+typst = ">=0.13.1,<0.14"
 
 [pypi-dependencies]
 # Image processing (ITK ecosystem)
 itk = "*"
 simpleitk = "*"
 
 [tasks]
-# Build MyST documentation
 build-html = "myst build --html"
-build-pdf = "myst build --pdf"
-build-all = "myst build"
+build-pdf = "myst build --typst"
+build-arxiv = "myst build --pdf"
+build-tex = "myst build --tex"
+build-docx = "myst build --docx"
+build-cff = "myst build --cff"
+build-meca = "myst build --meca"
 
 # Start development server
 serve = "myst start"
 
 # Clean build artifacts
 clean = "myst clean"
 
-# Export formats
-export-pdf = "myst build --pdf --template arxiv_two_column"
-export-arxiv = "myst build --pdf --template arxiv_two_column --output exports/arxiv.pdf"
-export-docx = "myst build --docx"
-export-meca = "myst build --meca"
-
 # Development and testing
 dev = { depends-on = ["serve"] }
 lint = "myst check"
@@ -62,8 +51,9 @@ build-src = { cmd = "mkdir -p build && cd build && cmake ../src && make", cwd =
 test-src = { cmd = "cd build && ctest", cwd = ".", depends-on = ["build-src"] }
 
 # Combined tasks
-build-paper = { depends-on = ["build-html", "export-pdf", "export-arxiv"] }
-build-complete = { depends-on = ["build-paper", "export-docx", "export-meca"] }
+build = { depends-on = ["build-html", "build-pdf", "build-tex", "build-docx", "build-cff", "build-meca"] }
+build-paper = { depends-on = ["build-html", "build-pdf", "build-arxiv"] }
+build-complete = { depends-on = ["build-paper", "build-tex", "build-docx", "build-cff", "build-meca"] }
 
 [feature.cmake.dependencies]
 cmake = "*"
@@ -78,7 +68,3 @@ test-cmake = "cd build && ctest"
 [environments]
 default = { features = [], solve-group = "default" }
 dev = { features = ["cmake"], solve-group = "default" }
-
-# Platform-specific dependencies
-[target.linux-64.dependencies]
-texlive-core = "*"