Merge branch 'main' of https://git.mbeck.cologne/mischbeck/ScientificManuscriptTemplate

Manuscript/Taskfile.yml

@@ -4,6 +4,7 @@ vars:
   PROJECT_NAME: Manuscript
   PYTHON: '{{if eq OS "windows"}}python{{else}}python3{{end}}'
   UTILS: "../resources/scripts/task_utils.py"
+  OUTPUT_DIR: "_output"
 
 tasks:
   default:
@@ -12,43 +13,43 @@ tasks:
 
   render:
     desc: "Render with the default (non-anonymized) profile, all formats"
-    cmd: quarto render --profile=default --output-dir _output/default
+    cmd: quarto render --profile=default --output-dir {{.OUTPUT_DIR}}/default
 
   render:anonymized:
     desc: "Render with the anonymized profile, all formats"
-    cmd: quarto render --profile=anonymized --output-dir _output/anonymized
+    cmd: quarto render --profile=anonymized --output-dir {{.OUTPUT_DIR}}/anonymized
 
   render:html:
     desc: "Render to HTML only (default profile)"
-    cmd: quarto render --profile=default --to html --output-dir _output/default
+    cmd: quarto render --profile=default --to html --output-dir {{.OUTPUT_DIR}}/default
 
   render:docx:
     desc: "Render to docx only (default profile)"
-    cmd: quarto render --profile=default --to docx --output-dir _output/default
+    cmd: quarto render --profile=default --to docx --output-dir {{.OUTPUT_DIR}}/default
 
   render:jats:
     desc: "Render to JATS XML only (default profile)"
-    cmd: quarto render --profile=default --to jats --output-dir _output/default
+    cmd: quarto render --profile=default --to jats --output-dir {{.OUTPUT_DIR}}/default
 
   render:pdf:
     desc: "Render to PDF only (default profile) - requires pdf format configured in _quarto.yml"
-    cmd: quarto render --profile=default --to pdf --output-dir _output/default
+    cmd: quarto render --profile=default --to pdf --output-dir {{.OUTPUT_DIR}}/default
 
   package:
     desc: "Zip the default-profile rendered output into Manuscript-default.zip"
     deps: [render]
-    cmd: "{{.PYTHON}} {{.UTILS}} zip _output/default {{.PROJECT_NAME}}-default.zip"
+    cmd: "{{.PYTHON}} {{.UTILS}} zip {{.OUTPUT_DIR}}/default {{.PROJECT_NAME}}-default.zip"
     sources:
-      - _output/default/**/*
+      - "{{.OUTPUT_DIR}}/default/**/*"
     generates:
       - "{{.PROJECT_NAME}}-default.zip"
 
   package:anonymized:
     desc: "Zip the anonymized-profile rendered output into Manuscript-anonymized.zip"
     deps: [render:anonymized]
-    cmd: "{{.PYTHON}} {{.UTILS}} zip _output/anonymized {{.PROJECT_NAME}}-anonymized.zip"
+    cmd: "{{.PYTHON}} {{.UTILS}} zip {{.OUTPUT_DIR}}/anonymized {{.PROJECT_NAME}}-anonymized.zip"
     sources:
-      - _output/anonymized/**/*
+      - "{{.OUTPUT_DIR}}/anonymized/**/*"
     generates:
       - "{{.PROJECT_NAME}}-anonymized.zip"
 
@@ -61,5 +62,5 @@ tasks:
       - data.zip
 
   clean:
-    desc: "Remove _output, .quarto, and stray *_files/*_cache folders"
+    desc: "Remove {{.OUTPUT_DIR}}, .quarto, and stray *_files/*_cache folders"
     cmd: "{{.PYTHON}} {{.UTILS}} clean-project ."

Manuscript/_quarto.yml

@@ -14,7 +14,16 @@ format:
     fig-dpi: 300
     reference-doc: ../resources/custom-reference-doc.docx
   jats: default
-  pdf: default
+  pdf:
+    header-includes: |
+      \usepackage{pdfpages}
+      \pagenumbering{gobble}
+      \usepackage{booktabs}
+      \usepackage{caption}
+      \DeclareCaptionLabelSeparator{period-newline}{.\par}
+      \usepackage{setspace}
+      \usepackage{float}      % enables [H]
+      \usepackage[section]{placeins} % <- add [section]
 
 profile:
   default: default
@@ -46,14 +55,4 @@ keywords:
   - Replication
 
 abstract: |
-  Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet.
+  Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet.
-
-header-includes: |
-  \usepackage{pdfpages}
-  \pagenumbering{gobble}
-  \usepackage{booktabs}
-  \usepackage{caption}
-  \DeclareCaptionLabelSeparator{period-newline}{.\par}
-  \usepackage{setspace}
-  \usepackage{float}      % enables [H]
-  \usepackage[section]{placeins} % <- add [section]

README.md

@@ -25,6 +25,13 @@ In any arch-based Linux distro, run `go-task finalize` instead.
 
 More on how to include more detail in the front matter can be found in the official [quarto manual](https://quarto.org/docs/authoring/front-matter.html). Their quick introduction into [Markdown Basics](https://quarto.org/docs/authoring/markdown-basics.html) is also worth reading. 
 
+If you want to know, which command is being run by `task`, use the `--dry` parameter: 
+
+```bash
+> task manuscript:render:html --dry
+task: [manuscript:render:html] quarto render --profile=default --to html --output-dir _output/default
+```
+
 ## Project layout
 
 Each of `Manuscript/`, `ResearchReport/`, and `Supplements/` contains a Quarto project with its own `_quarto.yml`, `index.qmd`, `data/`, and `figures/` folders.

ResearchReport/Taskfile.yml

@@ -4,6 +4,7 @@ vars:
   PROJECT_NAME: ResearchReport
   PYTHON: '{{if eq OS "windows"}}python{{else}}python3{{end}}'
   UTILS: "../resources/scripts/task_utils.py"
+  OUTPUT_DIR: "_output"
 
 tasks:
   default:
@@ -12,39 +13,39 @@ tasks:
 
   render:
     desc: "Render with the default (non-anonymized) profile, all formats"
-    cmd: quarto render --profile=default --output-dir _output/default
+    cmd: quarto render --profile=default --output-dir {{.OUTPUT_DIR}}/default
 
   render:anonymized:
     desc: "Render with the anonymized profile, all formats"
-    cmd: quarto render --profile=anonymized --output-dir _output/anonymized
+    cmd: quarto render --profile=anonymized --output-dir {{.OUTPUT_DIR}}/anonymized
 
   render:html:
     desc: "Render to HTML only (default profile)"
-    cmd: quarto render --profile=default --to html --output-dir _output/default
+    cmd: quarto render --profile=default --to html --output-dir {{.OUTPUT_DIR}}/default
 
   render:docx:
     desc: "Render to docx only (default profile)"
-    cmd: quarto render --profile=default --to docx --output-dir _output/default
+    cmd: quarto render --profile=default --to docx --output-dir {{.OUTPUT_DIR}}/default
 
   render:pdf:
     desc: "Render to PDF only (default profile) - requires pdf format configured in _quarto.yml"
-    cmd: quarto render --profile=default --to pdf --output-dir _output/default
+    cmd: quarto render --profile=default --to pdf --output-dir {{.OUTPUT_DIR}}/default
 
   package:
     desc: "Zip the default-profile rendered output into ResearchReport-default.zip"
     deps: [render]
-    cmd: "{{.PYTHON}} {{.UTILS}} zip _output/default {{.PROJECT_NAME}}-default.zip"
+    cmd: "{{.PYTHON}} {{.UTILS}} zip {{.OUTPUT_DIR}}/default {{.PROJECT_NAME}}-default.zip"
     sources:
-      - _output/default/**/*
+      - "{{.OUTPUT_DIR}}/default/**/*"
     generates:
       - "{{.PROJECT_NAME}}-default.zip"
 
   package:anonymized:
     desc: "Zip the anonymized-profile rendered output into ResearchReport-anonymized.zip"
     deps: [render:anonymized]
-    cmd: "{{.PYTHON}} {{.UTILS}} zip _output/anonymized {{.PROJECT_NAME}}-anonymized.zip"
+    cmd: "{{.PYTHON}} {{.UTILS}} zip {{.OUTPUT_DIR}}/anonymized {{.PROJECT_NAME}}-anonymized.zip"
     sources:
-      - _output/anonymized/**/*
+      - "{{.OUTPUT_DIR}}/anonymized/**/*"
     generates:
       - "{{.PROJECT_NAME}}-anonymized.zip"
 
@@ -57,5 +58,5 @@ tasks:
       - data.zip
 
   clean:
-    desc: "Remove _output, .quarto, and stray *_files/*_cache folders"
+    desc: "Remove {{.OUTPUT_DIR}}, .quarto, and stray *_files/*_cache folders"
     cmd: "{{.PYTHON}} {{.UTILS}} clean-project ."

Supplements/Taskfile.yml

@@ -1,10 +1,10 @@
-# Supplements/Taskfile.yml
 version: "3"
 
 vars:
   PROJECT_NAME: Supplements
   PYTHON: '{{if eq OS "windows"}}python{{else}}python3{{end}}'
   UTILS: "../resources/scripts/task_utils.py"
+  OUTPUT_DIR: "_output"
 
 tasks:
   default:
@@ -13,39 +13,39 @@ tasks:
 
   render:
     desc: "Render with the default (non-anonymized) profile, all formats"
-    cmd: quarto render --profile=default --output-dir _output/default
+    cmd: quarto render --profile=default --output-dir {{.OUTPUT_DIR}}/default
 
   render:anonymized:
     desc: "Render with the anonymized profile, all formats"
-    cmd: quarto render --profile=anonymized --output-dir _output/anonymized
+    cmd: quarto render --profile=anonymized --output-dir {{.OUTPUT_DIR}}/anonymized
 
   render:html:
     desc: "Render to HTML only (default profile)"
-    cmd: quarto render --profile=default --to html --output-dir _output/default
+    cmd: quarto render --profile=default --to html --output-dir {{.OUTPUT_DIR}}/default
 
   render:docx:
     desc: "Render to docx only (default profile)"
-    cmd: quarto render --profile=default --to docx --output-dir _output/default
+    cmd: quarto render --profile=default --to docx --output-dir {{.OUTPUT_DIR}}/default
 
   render:pdf:
     desc: "Render to PDF only (default profile) - requires pdf format configured in _quarto.yml"
-    cmd: quarto render --profile=default --to pdf --output-dir _output/default
+    cmd: quarto render --profile=default --to pdf --output-dir {{.OUTPUT_DIR}}/default
 
   package:
     desc: "Zip the default-profile rendered output into Supplements-default.zip"
     deps: [render]
-    cmd: "{{.PYTHON}} {{.UTILS}} zip _output/default {{.PROJECT_NAME}}-default.zip"
+    cmd: "{{.PYTHON}} {{.UTILS}} zip {{.OUTPUT_DIR}}/default {{.PROJECT_NAME}}-default.zip"
     sources:
-      - _output/default/**/*
+      - "{{.OUTPUT_DIR}}/default/**/*"
     generates:
       - "{{.PROJECT_NAME}}-default.zip"
 
   package:anonymized:
     desc: "Zip the anonymized-profile rendered output into Supplements-anonymized.zip"
     deps: [render:anonymized]
-    cmd: "{{.PYTHON}} {{.UTILS}} zip _output/anonymized {{.PROJECT_NAME}}-anonymized.zip"
+    cmd: "{{.PYTHON}} {{.UTILS}} zip {{.OUTPUT_DIR}}/anonymized {{.PROJECT_NAME}}-anonymized.zip"
     sources:
-      - _output/anonymized/**/*
+      - "{{.OUTPUT_DIR}}/anonymized/**/*"
     generates:
       - "{{.PROJECT_NAME}}-anonymized.zip"
 
@@ -58,5 +58,5 @@ tasks:
       - data.zip
 
   clean:
-    desc: "Remove _output, .quarto, and stray *_files/*_cache folders"
+    desc: "Remove {{.OUTPUT_DIR}}, .quarto, and stray *_files/*_cache folders"
     cmd: "{{.PYTHON}} {{.UTILS}} clean-project ."

Supplements/_quarto.yml

@@ -11,6 +11,16 @@ format:
       hypothesis: true
   docx: default
   jats: default
+  pdf:
+    header-includes: |
+      \usepackage{pdfpages}
+      \pagenumbering{gobble}
+      \usepackage{booktabs}
+      \usepackage{caption}
+      \DeclareCaptionLabelSeparator{period-newline}{.\par}
+      \usepackage{setspace}
+      \usepackage{float}      % enables [H]
+      \usepackage[section]{placeins} % <- add [section]
 
   # (other formats)
   # pdf: default