├── .gitattributes
├── .gitignore
├── .luacheckrc
├── .vscode
    ├── launch.json
    ├── settings.json
    └── tasks.json
├── LICENSE
├── README.md
├── addpackages.sty
├── blank.txt
├── by-nc-sa.png
├── cite-abbr.json
├── csl
    ├── annual-reviews-author-date.csl
    ├── apa-ian-injournal.csl
    ├── apa-ian.csl
    ├── apa-numeric-superscript.csl
    ├── apa.csl
    ├── apa6.csl
    ├── bmc-neuroscience.csl
    ├── bmc-psychology.csl
    ├── cell-doi.csl
    ├── cell.csl
    ├── cell2022.csl
    ├── cell2024-ian.csl
    ├── cerebral-cortex.csl
    ├── chicago-author-date.csl
    ├── chicago17-note.csl
    ├── copeia.csl
    ├── current-opinion.csl
    ├── elife.csl
    ├── elsevier-harvard.csl
    ├── eneuro.csl
    ├── european-journal-of-neuroscience.csl
    ├── frontiers.csl
    ├── ieee-with-url.csl
    ├── ieee.csl
    ├── nature-neuroscience.csl
    ├── nature-reviews-neuroscience.csl
    ├── nature.csl
    ├── neuron.csl
    ├── pnas.csl
    ├── science.csl
    ├── scientific-reports.csl
    ├── the-journal-of-neuroscience.csl
    ├── trends-in-neurosciences.csl
    ├── trends-journals.csl
    └── vancouver.csl
├── custom
    ├── README.md
    ├── lapreprint.cls
    ├── lapreprint.typ
    ├── tufte-book.cls
    ├── tufte-common.def
    ├── tufte-handout.cls
    └── tufte.bst
├── defaults
    ├── convert-docx.yaml
    ├── convert-odt.yaml
    ├── crossref.yaml
    ├── debug.yaml
    ├── docs.yaml
    ├── docx-crossref.yaml
    ├── docx-refs.yaml
    ├── docx-zotero-live.yaml
    ├── docx.yaml
    ├── eisvogel-logo.yaml
    ├── eisvogel-refs.yaml
    ├── eisvogel.yaml
    ├── html-refs.yaml
    ├── html.yaml
    ├── jats.yaml
    ├── lapreprint.yaml
    ├── latex-crossref.yaml
    ├── latex-refs.yaml
    ├── latex.yaml
    ├── leaflet.yaml
    ├── letter-latex.yaml
    ├── letter.yaml
    ├── odt-crossref.yaml
    ├── odt-refs-index.yaml
    ├── odt-refs.yaml
    ├── odt-zotero-live.yaml
    ├── odt.yaml
    ├── pdf-crossref.yaml
    ├── pdf-eisvogel.yaml
    ├── pdf-lualatex-default.yaml
    ├── pdf-lualatex.yaml
    ├── pdf-prince-default.yaml
    ├── pdf-prince-refs.yaml
    ├── pdf-prince.yaml
    ├── pdf-refs.yaml
    ├── pdf-xelatex-default.yaml
    ├── pdf-xelatex.yaml
    ├── plain-refs.yaml
    ├── plain.yaml
    ├── readme.md
    ├── refs-biblatex.yaml
    ├── refs-natbib.yaml
    ├── refs.yaml
    ├── text-refs.yaml
    ├── tufte-book.yaml
    ├── typst-crossref.yaml
    ├── typst-full.yaml
    ├── typst-index.yaml
    ├── typst-refs-native.yaml
    ├── typst-refs.yaml
    ├── typst-secnums.yaml
    ├── typst-titlepage.yaml
    ├── typst.yaml
    └── zotero-live.yaml
├── filters
    ├── LuaPanda.lua
    ├── README.md
    ├── abstract-section.lua
    ├── addToday.lua
    ├── addToday.rb
    ├── alerts.lua
    ├── annotate.rb
    ├── assimilateMetadata.rb
    ├── author-info-blocks.lua
    ├── capitaliseHeading.rb
    ├── citation-backlinks.lua
    ├── citation-key.lua
    ├── convertIndex.lua
    ├── customParaStyle.lua
    ├── enstyle-list.lua
    ├── firstParagraph.rb
    ├── highlight-text.lua
    ├── include-files.lua
    ├── insertCode.rb
    ├── latex-div.lua
    ├── list-table.lua
    ├── logging.lua
    ├── lua-debug.lua
    ├── lua-log.lua
    ├── modifyHeadings.lua
    ├── noop.rb
    ├── numbering-depth.lua
    ├── pagebreak.lua
    ├── paruVersion.rb
    ├── prependAbstract.rb
    ├── prependAll.rb
    ├── prependAuthor.rb
    ├── prependComments.rb
    ├── prependInstitute.rb
    ├── prependKeywords.rb
    ├── pretty-urls.lua
    ├── querverweis.lua
    ├── removeDimensions.lua
    ├── removeEmphasis.lua
    ├── removeHR.rb
    ├── removeSpacesBeforeCitations.lua
    ├── replaceUnitlessDimensions.lua
    ├── scholarly-metadata.lua
    ├── shared.lua
    ├── simplifyMetadata.rb
    ├── testErrorFilter.rb
    ├── testFilter.rb
    ├── testFilterByebug.rb
    ├── text-crossrefs.lua
    ├── typstFix.lua
    ├── wordcount.lua
    └── zotero.lua
├── metadata
    ├── typst-includes.yaml
    └── typst-plain.yaml
├── pandocomatic.yaml
├── postprocessors
    ├── fixHTML.rb
    ├── fixLaTeX.rb
    └── typst2pdf
├── preprocessors
    ├── convertEndnoteRefs.rb
    ├── criticmarkup-accept.py
    ├── criticmarkup-reject.py
    ├── criticmarkup.rb
    ├── criticmarkup.sh
    ├── fixCrossref.rb
    ├── removeAffiliations.rb
    ├── removeImageDimensions.rb
    └── setupKaobook.sh
├── scripts
    ├── copy-resources.elv
    └── test.elv
├── templates
    ├── TufteTemplate.typst
    ├── after-header-includes.latex
    ├── background1.pdf
    ├── background1.svg
    ├── background2.pdf
    ├── background2.svg
    ├── background3.pdf
    ├── background3.svg
    ├── background4.pdf
    ├── background4.svg
    ├── background5.pdf
    ├── background5.svg
    ├── background6.pdf
    ├── background6.svg
    ├── background7.pdf
    ├── background7.svg
    ├── baseline.css
    ├── bootstrap.html5
    ├── common.latex
    ├── cover.jpg
    ├── custom-JNS.docx
    ├── custom-blue.docx
    ├── custom-calibri.docx
    ├── custom-calibri.odt
    ├── custom-cambria.docx
    ├── custom-embed.docx
    ├── custom-greta.docx
    ├── custom-memoir.latex
    ├── custom-nsfc.docx
    ├── custom.css
    ├── custom.docx
    ├── custom.html
    ├── custom.icml
    ├── custom.latex
    ├── custom.odt
    ├── custom.opendocument
    ├── custom.openxml
    ├── custom.plain
    ├── custom.typst
    ├── eisvogel.latex
    ├── elsarticle.latex
    ├── fonts.latex
    ├── hypersetup.latex
    ├── ieee.latex
    ├── interface.css
    ├── lapreprint.latex
    ├── lapreprint.typst
    ├── layout.css
    ├── leaflet.latex
    ├── letter-pro-v3.0.0.typ
    ├── letter-simple.typst
    ├── letter.latex
    ├── materialize.html5
    ├── minbook.typ
    ├── minbook.typst
    ├── mytemplate.typst
    ├── pagedjs.html
    ├── pandoc-scholar.css
    ├── pandoc-scholar.html
    ├── pandoc-scholar.latex
    ├── passoptions.latex
    ├── print.css
    ├── recto-verso.css
    ├── revealjs.html
    ├── styles.citations.html
    ├── styles.html
    ├── template.markdown
    ├── tufte-book.latex
    ├── tufte.css
    ├── tufte.html5
    └── tuftepandoc.css
├── test-tufte.md
├── test.bib
├── test.md
├── test_elsarticle.md
├── writers
    └── bbcode.lua
└── xkcd.png


/.gitattributes:
--------------------------------------------------------------------------------
 1 | .gitattributes text eol=lf
 2 | .gitignore text eol=lf
 3 | .doxyfile text eol=lf
 4 | *.build text eol=lf
 5 | *.c text eol=lf
 6 | *.cmake text eol=lf
 7 | *.cpp text eol=lf
 8 | *.csv text eol=lf
 9 | *.h text eol=lf
10 | *.m text eol=lf
11 | *.md text eol=lf
12 | *.lua text eol=lf
13 | *.py text eol=lf
14 | *.rb text eol=lf
15 | *.rst text eol=lf
16 | *.sh text eol=lf
17 | *.txt text eol=lf
18 | *.yml text eol=lf
19 | *.frag text eol=lf
20 | *.vert text eol=lf
21 | *.ino text eol=lf
22 | *.mat binary
23 | *.mexa64 binary
24 | *.mexmaci64 binary
25 | *.mexw64 binary
26 | *.zip binary


--------------------------------------------------------------------------------
/.gitignore:
--------------------------------------------------------------------------------
 1 | .DS_Store
 2 | *~
 3 | .ruby-version
 4 | CoreTest.bib
 5 | Core.bib
 6 | Core.json
 7 | CoreFast.json
 8 | pandoclog.json
 9 | *.spl
10 | *.log
11 | *.bbl
12 | *.aux
13 | *.fls
14 | *.xdv
15 | *.blg
16 | *.out
17 | .pixi
18 | /.luarc.json
19 | custom/lapreprint.pdf
20 | 


--------------------------------------------------------------------------------
/.luacheckrc:
--------------------------------------------------------------------------------
 1 | stds.pandoc = {
 2 |     read_globals = {
 3 |         'FORMAT',
 4 |         'PANDOC_READER_OPTIONS',
 5 |         'PANDOC_WRITER_OPTIONS',
 6 |         'PANDOC_VERSION',
 7 |         'PANDOC_API_VERSION',
 8 |         'PANDOC_SCRIPT_FILE',
 9 |         'PANDOC_STATE',
10 |         'pandoc',
11 |         'lpeg',
12 |         're'
13 |     },
14 | 
15 |     globals = {
16 |         'traverse',
17 |         'BlockQuote',
18 |         'Blocks',
19 |         'BulletList',
20 |         'Cite',
21 |         'Code',
22 |         'CodeBlock',
23 |         'DefinitionList',
24 |         'Div',
25 |         'Emph',
26 |         'Figure',
27 |         'Header',
28 |         'HorizontalRule',
29 |         'Image',
30 |         'Inlines',
31 |         'LineBlock',
32 |         'LineBreak',
33 |         'Link',
34 |         'Math',
35 |         'Meta',
36 |         'Note',
37 |         'OrderedList',
38 |         'Pandoc',
39 |         'Para',
40 |         'Plain',
41 |         'Quote',
42 |         'RawBlock',
43 |         'RawInline',
44 |         'SmallCaps',
45 |         'SoftBreak',
46 |         'Space',
47 |         'Span',
48 |         'Str',
49 |         'Strikeout',
50 |         'Strong',
51 |         'Subscript',
52 |         'Superscript',
53 |         'Underline',
54 |         'Table'
55 |     }
56 | }
57 | 
58 | std = 'lua54+pandoc'
59 | 


--------------------------------------------------------------------------------
/.vscode/launch.json:
--------------------------------------------------------------------------------
 1 | {
 2 | 	// Use IntelliSense to learn about possible attributes.
 3 | 	// Hover to view descriptions of existing attributes.
 4 | 	// For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
 5 | 	"version": "0.2.0",
 6 | 	"configurations": [	
 7 | 		
 8 | 		{
 9 | 			"type": "emmylua_new",
10 | 			"request": "launch",
11 | 			"name": "EmmyLua New Debug",
12 | 			"host": "localhost",
13 | 			"port": 9966,
14 | 			"ext": [
15 | 				".lua",
16 | 				".lua.txt",
17 | 				".lua.bytes"
18 | 			],
19 | 			"ideConnectDebugger": true
20 | 		},
21 | 		{
22 | 			"type": "emmylua_launch",
23 | 			"request": "launch",
24 | 			"name": "Attach by launch program",
25 | 			"program": "/opt/homebrew/bin/lua",
26 | 			"workingDir": "",
27 | 			"arguments": [],
28 | 			"newWindow": false
29 | 		},
30 | 		{
31 | 			"name": "Lua MobDebug: Current File",
32 | 			"type": "luaMobDebug",
33 | 			"request": "launch",
34 | 			"workingDirectory": "${workspaceFolder}",
35 | 			"sourceBasePath": "${workspaceFolder}",
36 | 			"listenPort": 8172,
37 | 			"stopOnEntry": true,
38 | 			"sourceEncoding": "UTF-8",
39 | 			"interpreter": "lua",
40 | 			"arguments": [
41 | 				"${relativeFile}"
42 | 			]
43 | 		},
44 | 		{
45 | 			"name": "Lua MobDebug: Listen",
46 | 			"type": "luaMobDebug",
47 | 			"request": "attach",
48 | 			"workingDirectory": "${workspaceFolder}",
49 | 			"sourceBasePath": "${workspaceFolder}",
50 | 			"listenPublicly": false,
51 | 			"listenPort": 8172,
52 | 			"stopOnEntry": true,
53 | 			"sourceEncoding": "UTF-8"
54 | 		},
55 | 		{ // Name: VSCode rdbg Ruby Debugger https://marketplace.visualstudio.com/items?itemName=KoichiSasada.vscode-rdbg
56 | 			"type": "rdbg",
57 | 			"name": "Debug current file with rdbg",
58 | 			"request": "launch",
59 | 			"script": "${file}",
60 | 			"args": [],
61 | 			"askParameters": true,
62 | 			"rdbgPath": "~/.pixi/bin/rdbg"
63 | 		},
64 | 		{ // Name: VSCode rdbg Ruby Debugger https://marketplace.visualstudio.com/items?itemName=KoichiSasada.vscode-rdbg
65 | 				"type": "rdbg",
66 | 				"name": "Attach with Ruby Debug rdbg",
67 | 				"request": "attach",
68 | 				"rdbgPath": "~/.pixi/bin/rdbg"
69 | 		},
70 | 		{
71 | 			"name": "Debug < MD",
72 | 			"type": "rdbg",
73 | 			"request": "launch",
74 | 			"program": "${file}",
75 | 			"args": [" < ${workspaceROOT}/test.md"]
76 | 		},
77 | 		{
78 | 			"name": "Debug < JSON",
79 | 			"type": "rdbg",
80 | 			"request": "launch",
81 | 			"program": "${file}",
82 | 			"args": [" < ${workspaceROOT}/test.json"]
83 | 		},
84 | 	]
85 | }


--------------------------------------------------------------------------------
/.vscode/settings.json:
--------------------------------------------------------------------------------
 1 | {
 2 | 	"files.exclude": {
 3 | 		"**/.classpath": true,
 4 | 		"**/.project": true,
 5 | 		"**/.settings": true,
 6 | 		"**/.factorypath": true
 7 | 	},
 8 | 	"yaml.schemas": {
 9 | 		"none": "*.yaml",
10 | 		"https://json.schemastore.org/prettierrc.json": [
11 | 			"file:///Users/ian/Code/dotpandoc/defaults/refs.yaml",
12 | 			"file:///Users/ian/Code/dotpandoc/defaults/typst.yaml"
13 | 		],
14 | 		"https://json.schemastore.org/sourcehut-build-0.65.0.json": "file:///Users/ian/Code/dotpandoc/defaults/typst-refs-native.yaml"
15 | 	}
16 | }


--------------------------------------------------------------------------------
/.vscode/tasks.json:
--------------------------------------------------------------------------------
 1 | {
 2 | 	// See https://go.microsoft.com/fwlink/?LinkId=733558
 3 | 	// for the documentation about the tasks.json format
 4 | 	"version": "2.0.0",
 5 | 	"tasks": [
 6 | 		{
 7 | 			"label": "Scrivomatic",
 8 | 			"type": "shell",
 9 | 			"options": {
10 | 				"cwd": "${fileDirname}"
11 | 			},
12 | 			"command": "scrivomatic",
13 | 			"args": [
14 | 				"-v",
15 | 				"${file}"
16 | 			],
17 | 			"group": "build",
18 | 			"presentation": {
19 | 				"reveal": "always",
20 | 				"panel": "new"
21 | 			},
22 | 			"problemMatcher": []
23 | 		},
24 | 		{
25 | 			"label": "Pandoc Tufte",
26 | 			"type": "shell",
27 | 			"options": {
28 | 				"cwd": "${fileDirname}"
29 | 			},
30 | 			"command": "pandoc",
31 | 			"args": [
32 | 				"-d tufte-book",
33 | 				"-o tuftebook.tex",
34 | 				"${file}"
35 | 			],
36 | 			"group": {
37 | 				"kind": "build",
38 | 				"isDefault": true
39 | 			},
40 | 			"presentation": {
41 | 				"reveal": "always",
42 | 				"panel": "new"
43 | 			},
44 | 			"problemMatcher": []
45 | 		},
46 | 		{
47 | 			"label": "Scrivomatic+Build",
48 | 			"type": "shell",
49 | 			"options": {
50 | 				"cwd": "${fileDirname}"
51 | 			},
52 | 			"command": "scrivomatic",
53 | 			"args": [
54 | 				"-v",
55 | 				"-b",
56 | 				"${file}"
57 | 			],
58 | 			"group": "build",
59 | 			"presentation": {
60 | 				"reveal": "always",
61 | 				"panel": "new"
62 | 			},
63 | 			"problemMatcher": []
64 | 		}
65 | 	]
66 | }


--------------------------------------------------------------------------------
/LICENSE:
--------------------------------------------------------------------------------
 1 | MIT License
 2 | 
 3 | Copyright (c) 2017 Ian
 4 | 
 5 | Permission is hereby granted, free of charge, to any person obtaining a copy
 6 | of this software and associated documentation files (the "Software"), to deal
 7 | in the Software without restriction, including without limitation the rights
 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 9 | copies of the Software, and to permit persons to whom the Software is
10 | furnished to do so, subject to the following conditions:
11 | 
12 | The above copyright notice and this permission notice shall be included in all
13 | copies or substantial portions of the Software.
14 | 
15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21 | SOFTWARE.
22 | 


--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
1 | # Pandoc Configuration Files #
2 | This is my "live" Pandoc data directory contents (default location: `$HOME/.local/share/pandoc/` on macOS and Linux). I usually use [`pandocomatic`](https://github.com/htdebeer/pandocomatic) to manage Pandoc via my [`pandocomatic.yaml`](https://github.com/iandol/dotpandoc/blob/master/pandocomatic.yaml) configuration file. Pandocomatic automates all Pandoc settings, so you simply assign one or more "recipes" in your document metadata (docx-refs, latex-letter etc.) and the correct Pandoc settings are used for you. Pandocomatic can also run pre– and post–processing scripts to help with tweaks Pandoc may not be able to implement directly. Some of my pandocomatic recipes are also available as [defaults files](https://pandoc.org/MANUAL.html#defaults-files) callable directly using `pandoc -d`.
3 | 
4 | Most of my writing is academic in nature. I generally use my pandocomatic recipes triggered automagically via Scrivener's post-processing compile feature; see [Scrivomatic](https://github.com/iandol/scrivomatic) for more details of the workflow. My templates and filters are customised: I've collected and modified several [Pandoc templates](https://github.com/iandol/dotpandoc/tree/master/templates) and use a [set of filters to transform Academic metadata](https://github.com/iandol/dotpandoc/tree/master/filters) to multiple outputs; my filters are written in Ruby using [https://github.com/htdebeer/paru](Paru). 
5 | 
6 | I have my own personal choice of fonts, you should change the font metadata to those you have on your computer.
7 | 


--------------------------------------------------------------------------------
/addpackages.sty:
--------------------------------------------------------------------------------
 1 | %% File   : addstyles.sty
 2 | %% Purpose: To include project specific packages without the need to insert
 3 | %%          multiplpe `header-includes:` statements in the 
 4 | %%          pandocomatic.yaml configuration file. 
 5 | %%          Although there is no functional difference between both approaches,
 6 | %%          for me this file seems to provide me with a more simple overview
 7 | %%          about which packages and their whereabouts. 
 8 | %%          Note that for this approach to work, you need to insert the name
 9 | %%          of this file in the `header-includes:` statement.     
10 | %% Author : Paul Brandt, date Nov. 11, 2021
11 | %%%%%%%%%%%
12 | %
13 | % Add your .sty files below
14 | %
15 | %   One can make a differentiation in where to store specific addons to your
16 | %   LaTeX environment:
17 | %   - Generics, i.e., re-usable ones, are maintained in folders below your TeX  
18 | %     home directory. Use `kpsewhich -var-value=TEXMFHOME` at the command prompt 
19 | %     to find your TeX Home. But respect the TeX Directory Structure (TDS) from
20 | %     TeX Home downwards.
21 | %   - Project specific stuff can be maintained in the same folder as your 
22 | %     document for this project. 
23 | %   No particular assumptions are made by the elsarticle templates with regard to 
24 | %   locations of files.
25 | %
26 | %%%%%%%%%%%
27 | 
28 | %\usepackage{myBrilliantlyGenericStyleFile}
29 | 
30 | \usepackage{cleveref}		% sourced from http://tug.ctan.org/macros/latex/contrib/cleveref/cleveref.pdf 
31 |                             % Makes varioref clever, and reuses its work to improve its own workings. 
32 | 							% The cleveref package must be loaded after all other packages that 
33 |                             % don’t specifically support it. Therefore, to be safe, we declare it as last 
34 |                             % in the document's preamble.
35 | 							% Also note that all \newtheorem definitions must be placed after the 
36 |                             % cleveref package is loaded.
37 | 
38 | %%%%%%%%%%%
39 | %% End of File: addstyles.sty
40 | %%%%%%%%%%%
41 | 


--------------------------------------------------------------------------------
/blank.txt:
--------------------------------------------------------------------------------
1 | % this is a fix for crossref


--------------------------------------------------------------------------------
/by-nc-sa.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/iandol/dotpandoc/01ca3fc68697022506ad376810bb2c4d90b386df/by-nc-sa.png


--------------------------------------------------------------------------------
/cite-abbr.json:
--------------------------------------------------------------------------------
 1 | {
 2 |   "default": {
 3 |     "container-title": {
 4 |       "Annual Review of Neuroscience": "Annu. Rev. Neurosci.",
 5 |       "Annual Review of Visual Science": "Annu. Rev. Vis. Sci.",
 6 |       "Behavioural and Brain Sciences": "Beh. Brain Sci.",
 7 |       "Cerebral Cortex": "Cereb. Cortex",
 8 |       "Current Biology": "Curr. Biol.",
 9 |       "Current Opinion in Neurobiology": "Curr. Opin. Neurobiol.",
10 |       "Experimental Brain Research": "Exp. Br. Res.",
11 |       "Journal of Cognitive Neuroscience": "J. Cog. Neurosci.",
12 |       "Journal of Comparative Neurology": "J. Comp. Neurol.",
13 |       "Journal of Neuroscience Methods": "J. Neurosci. Methods",
14 |       "Journal of Neuroscience": "J. Neurosci.",
15 |       "Journal of Neurophysiology": "J. Neurophysiol.",
16 |       "Journal of Physiology": "J. Physiol.",
17 |       "Journal of the Optical Society of America A": "J. Opt. Soc. Am. A",
18 |       "Journal of Vision": "J. Vis.",
19 |       "Nature Communications": "Nat. Comm.",
20 |       "Nature Reviews Neuroscience": "Nat. Rev. Neurosci.",
21 |       "Nature Neuroscience": "Nat. Neurosci.",
22 |       "Philosophical Transactions of the Royal Society B": "Phil. Trans. R. Soc. B",
23 |       "Proceedings of the Royal Society of London B: Biological Sciences": "Proc. R. Soc. Lond. B",
24 |       "Proceedings of the Royal Society of London": "Proc. R. Soc. Lond.",
25 |       "Proceedings of the National Academy of Sciences USA": "PNAS",
26 |       "Proceedings of the National Academy of Sciences United States of America": "PNAS",
27 |       "Scientific Reports": "Sci. Rep.",
28 |       "Trends in Cognitive Sciences": "Trends Cog. Sci.",
29 |       "Trends in Neuroscience": "Trends Neurosci.",
30 |       "Vision Research": "Vis. Res."
31 |     }
32 |   }
33 | }


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12 |     <eissn>2045-2322</eissn>
13 |     <updated>2014-06-16T12:00:00+00:00</updated>
14 |     <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
15 |   </info>
16 | </style>
17 | 


--------------------------------------------------------------------------------
/csl/trends-in-neurosciences.csl:
--------------------------------------------------------------------------------
 1 | <?xml version="1.0" encoding="utf-8"?>
 2 | <style xmlns="http://purl.org/net/xbiblio/csl" version="1.0" default-locale="en-US">
 3 |   <!-- Generated with https://github.com/citation-style-language/utilities/tree/master/generate_dependent_styles/data/cell-press-trends -->
 4 |   <info>
 5 |     <title>Trends in Neurosciences</title>
 6 |     <id>http://www.zotero.org/styles/trends-in-neurosciences</id>
 7 |     <link href="http://www.zotero.org/styles/trends-in-neurosciences" rel="self"/>
 8 |     <link href="http://www.zotero.org/styles/trends-journals" rel="independent-parent"/>
 9 |     <link href="http://www.cell.com/trends/neurosciences" rel="documentation"/>
10 |     <category citation-format="numeric"/>
11 |     <category field="medicine"/>
12 |     <issn>0166-2236</issn>
13 |     <eissn>1878-108X</eissn>
14 |     <updated>2014-05-17T16:25:19+00:00</updated>
15 |     <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
16 |   </info>
17 | </style>
18 | 


--------------------------------------------------------------------------------
/custom/README.md:
--------------------------------------------------------------------------------
1 | # Custom files
2 | 
3 | This includes some custom or updated templates for LaTeX and Typst. They would usually be copied to the folder where the markdown document is being processed.
4 | 
5 | * https://github.com/chriskgrant/tufte-latex/tree/modernize
6 | * https://github.com/LaPreprint/typst
7 | * https://github.com/LaPreprint/LaPreprint
8 | 
9 | 


--------------------------------------------------------------------------------
/custom/tufte-book.cls:
--------------------------------------------------------------------------------
 1 | \NeedsTeXFormat{LaTeX2e}[1994/06/01]
 2 | \ProvidesClass{tufte-book}
 3 |   [2023/03/20 v3.6.0 Tufte-book class]
 4 | 
 5 | %%
 6 | % Declare we're tufte-book
 7 | % The base LaTeX class (defaults to the book style)
 8 | \newcommand{\@tufte@class}{book}
 9 | % The name of the package (defaults to tufte-handout)
10 | \newcommand{\@tufte@pkgname}{tufte-book}
11 | 
12 | %%
13 | % Load the common style elements
14 | \input{tufte-common.def}
15 | 
16 | %%
17 | % Set up any book-specific stuff now
18 | 
19 | %%
20 | % The front matter in Tufte's /Beautiful Evidence/ contains everything up
21 | % to the opening page of Chapter 1.  The running heads, when they appear,
22 | % contain only the (arabic) page number in the outside corner.
23 | %\newif\if@mainmatter \@mainmattertrue
24 | \renewcommand\frontmatter{%
25 |   \if@openright%
26 |     \cleardoublepage%
27 |   \else%
28 |     \clearpage%
29 |   \fi%
30 |   \@mainmatterfalse%
31 |   \pagenumbering{arabic}%
32 |   %\pagestyle{plain}%
33 |   \fancyhf{}%
34 |   \ifthenelse{\boolean{@tufte@twoside}}{%
35 |     \fancyhead[LE,RO]{\thepage}
36 |   }{%
37 |     \fancyhead[RE,RO]{\thepage}
38 |   }%
39 | }
40 | 
41 | %%
42 | % The main matter in Tufte's /Beautiful Evidence/ doesn't restart the page
43 | % numbering---it continues where it left off in the front matter.
44 | \renewcommand\mainmatter{%
45 |   \if@openright%
46 |     \cleardoublepage%
47 |   \else%
48 |     \clearpage%
49 |   \fi%
50 |   \@mainmattertrue%
51 |   \fancyhf{}%
52 |   \ifthenelse{\boolean{@tufte@twoside}}{%
53 |     % Two-side
54 |     \renewcommand{\chaptermark}[1]{\markboth{##1}{}}%
55 |     % Book title
56 |     \fancyhead[LE]{\thepage\quad\smallcaps{\newlinetospace{\plaintitle}}}%
57 |     % Chapter title
58 |     \fancyhead[RO]{\smallcaps{\newlinetospace{\leftmark}}\quad\thepage}%
59 |   }{%
60 |     % One-side
61 |     %  Book title
62 |     \fancyhead[RE,RO]{\smallcaps{\newlinetospace{\plaintitle}}\quad\thepage}%
63 |   }%
64 | }
65 | 
66 | %%
67 | % The back matter contains appendices, indices, glossaries, endnotes,
68 | % bibliographies, list of contributors, illustration credits, etc.
69 | \renewcommand\backmatter{%
70 |   \if@openright%
71 |     \cleardoublepage%
72 |   \else%
73 |     \clearpage%
74 |   \fi%
75 |   \@mainmatterfalse%
76 | }
77 | 
78 | %%
79 | % Only show the chapter titles in the table of contents
80 | \setcounter{tocdepth}{0}
81 | 
82 | %%
83 | % If there is a `tufte-book-local.sty' file, load it.
84 | \IfFileExists{tufte-book-local.tex}{%
85 |   \@tufte@info@noline{Loading tufte-book-local.tex}%
86 |   \input{tufte-book-local}%
87 | }{}
88 | 
89 | %%
90 | % End of file
91 | \endinput
92 | 


--------------------------------------------------------------------------------
/custom/tufte-handout.cls:
--------------------------------------------------------------------------------
 1 | \NeedsTeXFormat{LaTeX2e}[1994/06/01]
 2 | \ProvidesClass{tufte-handout}
 3 |   [2023/03/20 v3.6.0 Tufte-handout class]
 4 | 
 5 | %%
 6 | % Declare we're tufte-handout
 7 | % The base LaTeX class (defaults to the article/handout style)
 8 | \newcommand{\@tufte@class}{article}
 9 | % The name of the package (defaults to tufte-handout)
10 | \newcommand{\@tufte@pkgname}{tufte-handout}
11 | 
12 | %%
13 | % Load the common style elements
14 | \input{tufte-common.def}
15 | 
16 | %%
17 | % Set up any handout-specific stuff now
18 | 
19 | %%
20 | % Abstract
21 | % TODO The abstract should be printed on its own page of the `titlepage'
22 | % option was specified.
23 | \renewenvironment{abstract}{%
24 |   \begin{quotation}
25 |     \if@tufte@sfsidenotes
26 |       \begin{sffamily}
27 |     \fi
28 | }{%
29 |     \if@tufte@sfsidenotes
30 |       \end{sffamily}
31 |     \fi
32 |   \end{quotation}
33 | }
34 | 
35 | %%
36 | % If there is a `tufte-handout-local.tex' file, load it.
37 | \IfFileExists{tufte-handout-local.tex}{%
38 |   \input{tufte-handout-local}%
39 |   \@tufte@info@noline{Loading tufte-handout-local.tex}%
40 | }{}
41 | 
42 | %%
43 | % End of file
44 | \endinput
45 | 


--------------------------------------------------------------------------------
/defaults/convert-docx.yaml:
--------------------------------------------------------------------------------
1 | standalone: true
2 | verbosity: INFO
3 | from: docx+citations
4 | to: markdown
5 | extract-media: ./
6 | output-file: Out.md
7 | filters:
8 |   - citation-key.lua


--------------------------------------------------------------------------------
/defaults/convert-odt.yaml:
--------------------------------------------------------------------------------
1 | standalone: true
2 | verbosity: INFO
3 | from: odt
4 | to: markdown
5 | extract-media: ./
6 | output-file: Out.md
7 | filters:
8 |   - citation-key.lua


--------------------------------------------------------------------------------
/defaults/crossref.yaml:
--------------------------------------------------------------------------------
1 | verbosity: INFO # verbose by default
2 | top-level-division: chapter
3 | filters: 
4 |   - pandoc-crossref # process cross-references
5 | metadata:
6 |   linkReferences: true
7 | 


--------------------------------------------------------------------------------
/defaults/debug.yaml:
--------------------------------------------------------------------------------
1 | verbosity: INFO # verbose by default
2 | standalone: true
3 | from: markdown
4 | to: native
5 | filters:
6 |   - lua-debug.lua


--------------------------------------------------------------------------------
/defaults/docs.yaml:
--------------------------------------------------------------------------------
 1 | verbosity: INFO
 2 | standalone: true
 3 | from: markdown
 4 | to: html5
 5 | number-sections: true
 6 | section-divs: true
 7 | filters: [include-files.lua]
 8 | table-of-contents: true
 9 | toc-depth: 3
10 | metadata:
11 |   lang: 'en-GB'
12 |   toc-title: "Table of Contents"
13 | variables:
14 |   document-css: true
15 |   header-includes:
16 |       - |
17 |         <style>
18 |             html {font-family: Avenir Next,Avenir,Gill Sans,Helvetica,sans-serif;}
19 |             body {padding: 0px 50px;}
20 |             p {text-align: justify;}
21 |             a {text-decoration: underline solid #888888;}
22 |             pre {font-family: consolas, menlo, monospace; line-height: 0.6em !important; background-color: #F0F0F0}
23 |             pre code {font-size: 0.6em !important; white-space: pre}
24 |             kbd, .caja {font-size: 0.8em;margin: 0px 0.1em;padding: 0.1em 0.1em;border-radius: 3px;border: 1px solid rgb(204, 204, 204);display: inline-block;box-shadow: 0px 1px 0px rgba(0,0,0,0.2), inset 0px 0px 0px 2px #ffffff;background-color: rgb(247, 247, 247);text-shadow: 0 1px 0 #fff}
25 |         </style>


--------------------------------------------------------------------------------
/defaults/docx-crossref.yaml:
--------------------------------------------------------------------------------
1 | defaults:
2 | - crossref
3 | - refs
4 | - docx


--------------------------------------------------------------------------------
/defaults/docx-refs.yaml:
--------------------------------------------------------------------------------
1 | defaults:
2 |   - refs
3 |   - docx


--------------------------------------------------------------------------------
/defaults/docx-zotero-live.yaml:
--------------------------------------------------------------------------------
1 | defaults:
2 |   - zotero-live
3 |   - docx


--------------------------------------------------------------------------------
/defaults/docx.yaml:
--------------------------------------------------------------------------------
 1 | standalone: true
 2 | from: markdown
 3 | to: docx
 4 | output-file: Out.docx
 5 | filters:
 6 |   - prependAll.rb # prepends institute:, comments: and keywords: metadata into the text
 7 |   - simplifyMetadata.rb #collapse down metadata "author: [name: affiliation:]" to author:
 8 |   - pretty-urls.lua
 9 |   - convertIndex.lua
10 |   - pagebreak.lua
11 | reference-doc: ${USERDATA}/templates/custom.docx


--------------------------------------------------------------------------------
/defaults/eisvogel-logo.yaml:
--------------------------------------------------------------------------------
 1 | defaults: [refs]
 2 | from: markdown
 3 | to: latex
 4 | standalone: true
 5 | filters: 
 6 |   - assimilateMetadata.rb # handle academic matadata
 7 | template: eisvogel.latex
 8 | toc: true
 9 | metadata:
10 |   #titlepage-logo: "${HOME}/Library/CloudStorage/Dropbox/Images/Logos/Platform-CEBSIT-Banner-White.png"
11 |   #logo-width: 350
12 |   titlepage-background: /Users/ian/Dropbox/Images/Logos/backgroundlogo.pdf
13 |   titlepage-text-color: 555555
14 |   titlepage-rule-color: 555555
15 |   titlepage: true
16 |   titlepage-rule-height: 10
17 |   caption-justification: justified
18 |   toc-own-page: true
19 |   listings-disable-line-numbers: false
20 |   float-placement-figure: H
21 |   mainfont: 'Greta Sans Pro'
22 |   mainfontoptions: 'Numbers=OldStyle,Numbers=Proportional'
23 |   sansfont: 'Graublau Slab'
24 |   sansfontoptions: 'Numbers=OldStyle,Numbers=Proportional'
25 |   monofont: 'Fira Code'
26 |   mathfont: 'Cambria Math'
27 |   mathfontoptions: 'math-style=ISO,bold-style=ISO'
28 |   #CJKmainfont: 'PingFang SC'
29 |   #CJKsansfont: 'PingFang SC'
30 |   fontsize: '12pt'
31 |   linestretch: '1.5'
32 |   colorlinks: true
33 |   linkcolor: Mahogany
34 |   citecolor: Sepia
35 |   urlcolor: BrickRed
36 |   nonumberfigures: true
37 |   lang: 'en-GB'
38 |   disable-header-and-footer: false
39 |   header-right:
40 |   header-left:
41 |   header-center:
42 |   footer-right:
43 |   footer-left: 
44 |   footer-center:
45 |   footnotes_pretty: true
46 |   footnotes-disable-backlinks: false


--------------------------------------------------------------------------------
/defaults/eisvogel-refs.yaml:
--------------------------------------------------------------------------------
1 | defaults: [refs, eisvogel]
2 | to: latex
3 | 


--------------------------------------------------------------------------------
/defaults/eisvogel.yaml:
--------------------------------------------------------------------------------
 1 | defaults: [refs]
 2 | to: latex
 3 | from: markdown
 4 | standalone: true
 5 | filters: 
 6 |   - assimilateMetadata.rb # handle academic matadata
 7 |   - pagebreak.lua # use \newpage{} also for HTML, DOCX, ODT & EPUB
 8 |   - list-table.lua
 9 |   - abstract-section.lua
10 |   - pretty-urls.lua
11 | template: eisvogel.latex
12 | toc: true
13 | shift-heading-level-by: 0
14 | metadata: 
15 |   titlepage: true
16 |   titlepage-color: BB4433
17 |   titlepage-text-color: FFFFFF
18 |   titlepage-rule-color: FFFFFF
19 |   titlepage-rule-height: 10
20 |   caption-justification: justified
21 |   toc-own-page: true
22 |   listings-disable-line-numbers: false
23 |   float-placement-figure: H
24 |   mainfont: 'Greta Sans Pro'
25 |   mainfontoptions: 'Numbers=OldStyle,Numbers=Proportional'
26 |   sansfont: 'Graublau Slab'
27 |   sansfontoptions: 'Numbers=OldStyle,Numbers=Proportional'
28 |   monofont: 'Fira Code'
29 |   mathfont: 'Cambria Math'
30 |   mathfontoptions: 'math-style=ISO,bold-style=ISO'
31 |   #CJKmainfont: 'PingFang SC'
32 |   #CJKsansfont: 'PingFang SC'
33 |   fontsize: '12pt'
34 |   linestretch: '1.5'
35 |   colorlinks: true
36 |   linkcolor: Mahogany
37 |   citecolor: Sepia
38 |   urlcolor: BrickRed
39 |   nonumberfigures: true
40 |   lang: 'en-GB'
41 |   disable-header-and-footer: false
42 |   header-right:
43 |   header-left:
44 |   header-center:
45 |   footer-right:
46 |   footer-left: 
47 |   footer-center:
48 |   footnotes_pretty: true
49 |   footnotes-disable-backlinks: false


--------------------------------------------------------------------------------
/defaults/html-refs.yaml:
--------------------------------------------------------------------------------
1 | defaults:
2 | - refs
3 | - html


--------------------------------------------------------------------------------
/defaults/html.yaml:
--------------------------------------------------------------------------------
 1 | standalone: true
 2 | from: markdown
 3 | to: html5
 4 | fail-if-warnings: false
 5 | number-sections: false
 6 | section-divs: true
 7 | template: custom.html
 8 | css: ${USERDATA}/templates/custom.css
 9 | eol: lf
10 | html-math-method:
11 |   method: mathjax
12 |   #url: "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"
13 | filters: 
14 |   - pagebreak.lua
15 |   - assimilateMetadata.rb #regularise metadata
16 | table-of-contents: true
17 | toc-depth: 3
18 | shift-heading-level-by: 0
19 | metadata:
20 |   lang: 'en-GB'
21 |   toc-title: "Table of Contents"


--------------------------------------------------------------------------------
/defaults/jats.yaml:
--------------------------------------------------------------------------------
1 | defaults:
2 | - refs
3 | standalone: true
4 | from: markdown
5 | to: jats


--------------------------------------------------------------------------------
/defaults/lapreprint.yaml:
--------------------------------------------------------------------------------
 1 | verbosity: INFO
 2 | standalone: true
 3 | from: markdown
 4 | to: typst
 5 | citeproc: false
 6 | #bibliography: Core.bib
 7 | #csl: nature.csl
 8 | template: lapreprint.typst
 9 | wrap: none
10 | filters:
11 |   - typstFix.lua
12 |   - pagebreak.lua
13 |   - abstract-section.lua
14 |   - pretty-urls.lua
15 | 
16 | 


--------------------------------------------------------------------------------
/defaults/latex-crossref.yaml:
--------------------------------------------------------------------------------
1 | defaults:
2 | - crossref
3 | - refs
4 | - latex


--------------------------------------------------------------------------------
/defaults/latex-refs.yaml:
--------------------------------------------------------------------------------
1 | defaults:
2 | - refs
3 | - latex


--------------------------------------------------------------------------------
/defaults/latex.yaml:
--------------------------------------------------------------------------------
 1 | from: markdown
 2 | to: latex
 3 | standalone: true
 4 | shift-heading-level-by: 0 # reader option
 5 | top-level-division: default # part | chapter | section |default
 6 | number-sections: false
 7 | listings: false
 8 | filters:
 9 |   - assimilateMetadata.rb # handle academic metadata
10 |   - convertIndex.lua
11 |   - pretty-urls.lua
12 |   - abstract-section.lua
13 | template: custom.latex
14 | metadata:
15 |   documentclass: 'scrarticle'
16 |   classoption: twoside
17 |   pagestyle: plain # control \pagestyle{}: the default article class supports plain (default), empty (no running heads or page numbers), and headings (section titles in running heads)
18 |   fontsize: '12pt'
19 |   linestretch: '1.5'
20 |   geometry: ['inner=2.2cm','outer=1.8cm','bottom=2.5cm','twoside']
21 |   mainfont: 'Alegreya'
22 |   mainfontoptions: 'Numbers=OldStyle,Numbers=Proportional'
23 |   mainfontfallback: ['Cambria Math','Apple Color Emoji','Noto Color Emoji']
24 |   sansfont: 'Alegreya Sans'
25 |   sansfontoptions: 'Numbers=OldStyle,Numbers=Proportional'
26 |   sansfontfallback: ['Arial Unicode MS','Apple Color Emoji','Noto Color Emoji']
27 |   monofont: 'Rec Mono Duotone'
28 |   mathfont: 'STIX Two Math'
29 |   mathfontoptions: 'math-style=ISO,bold-style=ISO'
30 |   #CJKmainfont: 'PingFang SC'
31 |   #CJKsansfont: 'PingFang SC'
32 |   colorlinks: true
33 |   linkcolor: Mahogany
34 |   citecolor: Sepia
35 |   urlcolor: BrickRed
36 |   lang: 'en-GB'
37 |   nonumberfigures: true # I use Scrivener autonumbering, so disable for LaTeX
38 |   doindex: true # add index commands
39 | 


--------------------------------------------------------------------------------
/defaults/leaflet.yaml:
--------------------------------------------------------------------------------
1 | #currently we cannot run our ruby script to fix references in styled captions, this is one reason I still prefer pandocomatic
2 | standalone: true
3 | verbosity: INFO # verbose by default
4 | to: latex
5 | pdf-engine: xelatex
6 | template: leaflet.latex


--------------------------------------------------------------------------------
/defaults/letter-latex.yaml:
--------------------------------------------------------------------------------
 1 | from: markdown
 2 | to: latex
 3 | pdf-engine: xelatex
 4 | standalone: true
 5 | template: letter.latex
 6 | metadata:
 7 |   papersize: a4
 8 |   return-address: 
 9 |     - Cognition \& Behaviour Platform
10 |     - Institute of Neuroscience, CAS
11 |     - Room 307, Systems Building
12 |     - 320 Yueyang Rd, Shanghai 200031, CHINA
13 |     - ✉ <i.andolina@ion.ac.cn>
14 |     - ✆ +86 021 54921747
15 |   author: 'Ian Max Andolina Ph.D.\newline Director, Cognition \& Behaviour Platform'
16 |   opening: To whom it may concern,
17 |   closing: Sincerely yours,
18 |   mainfont: 'Graublau Sans'
19 |   mainfontoptions: 'Numbers=OldStyle,Numbers=Proportional'
20 |   monofont: 'Fira Code'
21 |   mathfont: 'Cambria Math'
22 |   mathfontoptions: 'math-style=ISO,bold-style=ISO'
23 |   #CJKmainfont: 'PingFang SC'
24 |   fontsize: '11pt'
25 |   linestretch: '1.2'
26 |   letterhead: "${HOME}/Dropbox/Work/ION-Letterhead.pdf"
27 |   signature: "${HOME}/Dropbox/Work/Ian-Signature.png"
28 |   signature-width: 45mm
29 |   signature-before: -11ex
30 |   signature-after: -1.5ex
31 |   closing-indentation: 12pt
32 |   links-as-notes: false
33 |   colorlinks: true
34 |   linkcolor: Mahogany
35 |   citecolor: Sepia
36 |   urlcolor: BrickRed
37 |   lang: 'en-GB'
38 |   geometry: ['margin=1.5cm','top=2.1cm']
39 | 


--------------------------------------------------------------------------------
/defaults/letter.yaml:
--------------------------------------------------------------------------------
 1 | standalone: true
 2 | verbosity: INFO
 3 | from: markdown
 4 | to: typst
 5 | template: letter-simple.typst
 6 | wrap: preserve
 7 | pdf-engine-opt: '--pdf-standard=a-3b'
 8 | filters:
 9 |   - typstFix.lua
10 |   - pagebreak.lua
11 |   - pretty-urls.lua
12 | metadata:
13 |   #subject: 'Letter to the Editor'
14 |   #address: "Cognition & Behaviour Platform, Institute of Neuroscience CAS, Room 307 Systems Building, 320 Yueyang Rd Shanghai 200031, CHINA, ✉ i.andolina@ion.ac.cn, ✆ +86 021 54921747"
15 |   #return-address: "..."
16 |   #signature: "Ian-Signature.png"
17 |   #signature-name: 'Ian Max Andolina Ph.D.'
18 |   address: none
19 |   mainfont: 'Alegreya'
20 |   linestretch: '1.2'
21 |   lang: 'en-GB'
22 | 


--------------------------------------------------------------------------------
/defaults/odt-crossref.yaml:
--------------------------------------------------------------------------------
1 | defaults:
2 | - crossref
3 | - refs
4 | - odt
5 | 


--------------------------------------------------------------------------------
/defaults/odt-refs-index.yaml:
--------------------------------------------------------------------------------
1 | defaults:
2 | - odt-refs
3 | metadata:
4 |   doindex: true


--------------------------------------------------------------------------------
/defaults/odt-refs.yaml:
--------------------------------------------------------------------------------
1 | defaults:
2 | - refs
3 | - odt


--------------------------------------------------------------------------------
/defaults/odt-zotero-live.yaml:
--------------------------------------------------------------------------------
1 | defaults:
2 | - zotero-live
3 | - odt


--------------------------------------------------------------------------------
/defaults/odt.yaml:
--------------------------------------------------------------------------------
 1 | standalone: true
 2 | from: markdown
 3 | to: odt
 4 | output-file: Out.odt
 5 | filters:
 6 |   - prependAll.rb # prepends institute:, comments: and keywords: metadata into the text
 7 |   - simplifyMetadata.rb #collapse down metadata "author: [name: affiliation:]" to author:
 8 |   - pretty-urls.lua
 9 |   - convertIndex.lua
10 |   - pagebreak.lua
11 | reference-doc: ${USERDATA}/templates/custom.odt
12 | template: ${USERDATA}/templates/custom.opendocument


--------------------------------------------------------------------------------
/defaults/pdf-crossref.yaml:
--------------------------------------------------------------------------------
1 | defaults: [crossref, refs, latex]
2 | to: pdf
3 | pdf-engine: xelatex
4 | output-file: Out.pdf


--------------------------------------------------------------------------------
/defaults/pdf-eisvogel.yaml:
--------------------------------------------------------------------------------
1 | defaults: [refs, eisvogel]
2 | to: pdf
3 | pdf-engine: xelatex


--------------------------------------------------------------------------------
/defaults/pdf-lualatex-default.yaml:
--------------------------------------------------------------------------------
1 | to: pdf
2 | pdf-engine: lualatex


--------------------------------------------------------------------------------
/defaults/pdf-lualatex.yaml:
--------------------------------------------------------------------------------
1 | defaults: [refs, latex]
2 | to: pdf
3 | pdf-engine: lualatex


--------------------------------------------------------------------------------
/defaults/pdf-prince-default.yaml:
--------------------------------------------------------------------------------
1 | output-file: Out.pdf
2 | to: pdf
3 | pdf-engine: prince
4 | pdf-engine-opt: ['--page-size=A4']


--------------------------------------------------------------------------------
/defaults/pdf-prince-refs.yaml:
--------------------------------------------------------------------------------
1 | defaults:
2 | - refs
3 | - pdf-prince


--------------------------------------------------------------------------------
/defaults/pdf-prince.yaml:
--------------------------------------------------------------------------------
 1 | standalone: true
 2 | from: markdown
 3 | to: pdf
 4 | output-file: Prince.pdf
 5 | pdf-engine: prince
 6 | pdf-engine-opt: ['--page-size=A4']
 7 | fail-if-warnings: false
 8 | number-sections: false
 9 | section-divs: true
10 | template: custom.html
11 | css:
12 |   - ${USERDATA}/templates/custom.css
13 |   - ${USERDATA}/templates/print.css
14 | eol: lf
15 | html-math-method:
16 |   method: mathjax
17 |   #url: "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"
18 | filters:
19 |   - pretty-urls.lua
20 |   - pagebreak.lua
21 |   - list-table.lua
22 | table-of-contents: true
23 | toc-depth: 3
24 | shift-heading-level-by: 0
25 | metadata:
26 |   lang: 'en-GB'
27 |   toc-title: "Table of Contents"


--------------------------------------------------------------------------------
/defaults/pdf-refs.yaml:
--------------------------------------------------------------------------------
1 | defaults: [refs, latex]
2 | to: pdf
3 | pdf-engine: xelatex


--------------------------------------------------------------------------------
/defaults/pdf-xelatex-default.yaml:
--------------------------------------------------------------------------------
1 | to: pdf
2 | pdf-engine: xelatex


--------------------------------------------------------------------------------
/defaults/pdf-xelatex.yaml:
--------------------------------------------------------------------------------
1 | defaults: [refs, latex]
2 | to: pdf
3 | pdf-engine: xelatex


--------------------------------------------------------------------------------
/defaults/plain-refs.yaml:
--------------------------------------------------------------------------------
1 | defaults:
2 |   - refs
3 |   - plain


--------------------------------------------------------------------------------
/defaults/plain.yaml:
--------------------------------------------------------------------------------
 1 | verbosity: INFO
 2 | from: markdown
 3 | to: plain
 4 | template: custom.plain
 5 | standalone: true
 6 | wrap: preserve
 7 | columns: 120
 8 | tab-stop: 4
 9 | eol: lf
10 | preserve-tabs: true
11 | filters:
12 |   - prependAll.rb #prepends institute:, comments: and keywords: metadata into the text
13 |   - prependAuthor.rb #prepends authors
14 | #  - prependAbstract
15 |   - modifyHeadings.lua


--------------------------------------------------------------------------------
/defaults/readme.md:
--------------------------------------------------------------------------------
 1 | # Pandoc Defaults
 2 | 
 3 | Since V2.8, Pandoc allows one to pass in sets of default.yaml settings, using the `--defaults | -d` option. This option uses a folder (this one) containing yaml files. You can call them directly from pandoc (no need for pandocomatic and ruby at all) like so:
 4 | 
 5 | ```shell
 6 | pandoc -d refs -d latex test.md -o test.tex
 7 | ```
 8 | 
 9 | Notice how you can combine sets together, so for example `-d refs -d html -d pdf-prince` will make a PDF using [princeXML](https://www.princexml.com) from HTML outputs with full CSL academic references. Since Pandoc V2.11 default files can even call other default files, for example see [latex-refs.yaml](https://github.com/iandol/dotpandoc/blob/master/defaults/latex-refs.yaml), so now the combination is specified by the defaults file and you only need to call `-d latex-refs`.
10 | 
11 | Since Pandoc V2.12 we can now use relative or other paths, using `${VARIABLE}`; for example to refer to the home directory use `${HOME}`. There are two magic env variables:
12 | 
13 | * `${USERDATA}` — points to the Pandoc data directory (default is `~/.local/share/pandoc/`).
14 | * `${.}` — points to the same folder the defaults file is found, allowing to package up resources in a portable folder.
15 | 
16 | Documentation is here: https://pandoc.org/MANUAL.html#default-files 
17 | 
18 | ## Defaults and Scrivener
19 | 
20 | While I still prefer to use pandocomatic, the defaults files do simplify the setup for people who may prefer a single install requirement (only Pandoc is needed, not Ruby). Currently you cannot call pandoc defaults from Scrivener's project metadata file (though see [issue #5870](https://github.com/jgm/pandoc/issues/5870)), what this means is that you can't use the metadata edited *in* Scrivener to customise your compile. **BUT** you can create *different Compile formats* in Scriveners Compile manager, each with a different set of pandoc defaults options, i.e. to output citeproc references to docx:
21 | 
22 | ![](https://raw.githubusercontent.com/iandol/scrivomatic/master/images/defaults.png)
23 | _ _ _ _ _ _
24 | _Figure 1 — Compile post-processing pane in Scrivener to call the default files to generate a docx with references processed with citeproc…_
25 | _ _ _ _ _ _
26 | 
27 | You make different Compile formats for different combinations of `defaults` options. 
28 | 
29 | ## Why I still prefer pandocomatic?
30 | 
31 | This is because of pandocomatic's ability to call pre/post processing scripts in a single recipe. For example, by default pandoc-crossref cannot recognise crossrefs in styled caption, so I made a [small script to fix this in the source markdown file](https://github.com/iandol/dotpandoc/blob/master/pandocomatic.yaml#L18). Pandocomatic enables me to easily call this before pandoc is run, without any other fiddling or manual intervention. This is not possible with pandoc directly, you would need to write a wrapper script to call your modifier processors first then run pandoc, and, well, I already have pandocomatic to do that elegantly for me!
32 | 
33 | As I mentioned above, I also prefer to edit frontmatter metadata in Scrivener's editor (https://github.com/iandol/scrivomatic#compiling-your-project see Fig. 3) -- it means I can quickly change outputs with edits to a text file I manage **directly** in Scrivener's binder, no need to go to the command line, or fiddle with compile formats etc.
34 | 
35 | 


--------------------------------------------------------------------------------
/defaults/refs-biblatex.yaml:
--------------------------------------------------------------------------------
1 | verbosity: INFO # verbose by default
2 | cite-method: biblatex
3 | bibliography: ${USERDATA}/Core.bib
4 | metadata:
5 |   biblio-style: authoryear #verbose for tufte
6 |   biblatexoptions:
7 |     - backend=biber
8 | 


--------------------------------------------------------------------------------
/defaults/refs-natbib.yaml:
--------------------------------------------------------------------------------
1 | verbosity: INFO # verbose by default
2 | cite-method: natbib
3 | bibliography: ${USERDATA}/Core.bib
4 | metadata:
5 |   biblio-style: plainnat
6 | 
7 | 


--------------------------------------------------------------------------------
/defaults/refs.yaml:
--------------------------------------------------------------------------------
 1 | verbosity: INFO # verbose by default
 2 | citeproc: true
 3 | cite-method: citeproc
 4 | bibliography: ${USERDATA}/CoreFast.json #JSON faster than BIB, symlinked into Pandoc data dir
 5 | csl: ${USERDATA}/csl/apa.csl
 6 | citation-abbreviations: ${USERDATA}/cite-abbr.json # my journal abbreviations
 7 | metadata:
 8 |   reference-section-title: Bibliography
 9 |   notes-after-punctuation: false
10 |   link-citations: true
11 |   link-bibliography: true
12 | 
13 | 


--------------------------------------------------------------------------------
/defaults/text-refs.yaml:
--------------------------------------------------------------------------------
 1 | defaults:
 2 |   - refs
 3 | verbosity: INFO
 4 | from: markdown
 5 | to: plain
 6 | template: custom.plain
 7 | standalone: true
 8 | wrap: preserve
 9 | columns: 120
10 | tab-stop: 4
11 | eol: lf
12 | preserve-tabs: true
13 | filters:
14 |   - modifyHeadings.lua


--------------------------------------------------------------------------------
/defaults/tufte-book.yaml:
--------------------------------------------------------------------------------
 1 | verbosity: INFO # verbose by default
 2 | from: markdown
 3 | to: latex
 4 | pdf-engine: xelatex
 5 | standalone: true
 6 | template: tufte-book.latex
 7 | top-level-division: chapter # part | chapter | section |default
 8 | number-sections: false
 9 | toc: true
10 | toc-depth: 4
11 | wrap: none
12 | cite-method: biblatex
13 | bibliography: ${USERDATA}/Core.bib
14 | filters:
15 |   - latex-div.lua
16 |   - pretty-urls.lua
17 | metadata:
18 |   documentclass: 'tufte-book' # also: tufte-handout
19 |   lang: 'en-GB'
20 |   papersize: a4
21 |   #linestretch: 1.4
22 |   classoption:
23 |     #- debug
24 |     #- nobib # !!! needed with V3.5.2 & biblatex
25 |     #- notoc # disbles Tufte TOC style
26 |     #- nofonts #do not auto-specify fonts
27 |     #- symmetric # note this is buggy...
28 |     - sfsidenotes # sans-serif side notes
29 |     - british
30 |     - justified
31 |   symmetric: false # set to true if you use symmetric margins
32 |   publisher: Octopoda Publishing • Shanghai • China
33 |   epigraph:
34 |     - author: Anaïs Nin
35 |       text: "“We don’t see things as they are, we see them as we are.”"
36 |     - author: Michael Shermer
37 |       text: "“Humans are pattern-seeking story-telling animals, and we are quite adept at telling stories about patterns, whether they exist or not.”"
38 |   dedication: |
39 |     This book is was written to honour all the myriad cephalopods in the deep blue sea…
40 |   copyright-link: https://creativecommons.org/licenses/by-nc-sa/4.0/
41 |   copyright-image: /Users/ian/Code/dotpandoc/by-nc-sa.png
42 |   copyright: |
43 |     © Creative Commons CC BY-NC-SA 4.0 — This license enables reusers to distribute, remix, adapt, and build upon the material in any medium or format for noncommercial purposes only, and only so long as attribution is given to the creator. If you remix, adapt, or build upon the material, you must license the modified material under identical terms. CC BY-NC-SA includes the following elements:  BY: credit must be given to the creator.  NC: Only noncommercial uses of the work are permitted.  SA: Adaptations must be shared under the same terms.
44 |   biblatexoptions:
45 |     - autocite=footnote
46 |   mainfont: 'Alegreya'
47 |   mainfontoptions: 'Numbers=OldStyle,Numbers=Proportional'
48 |   sansfont: 'Alegreya Sans'
49 |   sansfontoptions: 'Numbers=OldStyle,Numbers=Proportional'
50 |   monofont: 'Fantasque Sans Mono'
51 |   mathfont: 'STIX Two Math'
52 |   mathfontoptions: 'math-style=ISO,bold-style=ISO'
53 |   colorlinks: true
54 |   linkcolor: Mahogany
55 |   citecolor: Sepia
56 |   urlcolor: BrickRed
57 |   listings: false
58 | 


--------------------------------------------------------------------------------
/defaults/typst-crossref.yaml:
--------------------------------------------------------------------------------
1 | defaults: [crossref, refs, typst]
2 | metadata:
3 |   doindex: true


--------------------------------------------------------------------------------
/defaults/typst-full.yaml:
--------------------------------------------------------------------------------
 1 | standalone: true
 2 | from: markdown
 3 | to: typst-citations
 4 | metadata-file: typst-includes.yaml
 5 | verbosity: INFO
 6 | template: custom.typst
 7 | filters:
 8 |   - typstFix.lua
 9 |   - convertIndex.lua
10 |   - citeproc
11 |   - list-table.lua
12 |   - pagebreak.lua
13 |   - abstract-section.lua
14 |   - pretty-urls.lua
15 | table-of-contents: true
16 | cite-method: citeproc
17 | bibliography: ${USERDATA}/CoreFast.json #JSON faster than BIB, symlinked into Pandoc data dir
18 | csl: ${USERDATA}/csl/cell-doi.csl
19 | citation-abbreviations: ${USERDATA}/cite-abbr.json # my journal abbreviations
20 | metadata:
21 |   doindex: true
22 |   reference-section-title: Bibliography
23 |   notes-after-punctuation: false
24 |   link-citations: true
25 |   link-bibliography: true


--------------------------------------------------------------------------------
/defaults/typst-index.yaml:
--------------------------------------------------------------------------------
1 | defaults: [typst-refs]
2 | filters:
3 |   - convertIndex.lua
4 | metadata:
5 |   doindex: true


--------------------------------------------------------------------------------
/defaults/typst-refs-native.yaml:
--------------------------------------------------------------------------------
1 | defaults: typst
2 | to: typst
3 | bibliography: ${USERDATA}/Core.bib
4 | 


--------------------------------------------------------------------------------
/defaults/typst-refs.yaml:
--------------------------------------------------------------------------------
 1 | standalone: true
 2 | verbosity: INFO
 3 | from: markdown
 4 | to: typst-citations
 5 | metadata-file: typst-includes.yaml
 6 | template: custom.typst
 7 | wrap: preserve
 8 | filters:
 9 |   - assimilateMetadata.rb
10 |   - typstFix.lua
11 |   - citeproc
12 |   - pagebreak.lua
13 |   - removeDimensions.lua
14 |   - convertIndex.lua
15 |   - list-table.lua
16 |   - abstract-section.lua
17 |   - pretty-urls.lua
18 | table-of-contents: true
19 | cite-method: citeproc
20 | bibliography: ${USERDATA}/CoreFast.json #JSON faster than BIB, symlinked into Pandoc data dir
21 | csl: ${USERDATA}/csl/cell-doi.csl
22 | citation-abbreviations: ${USERDATA}/cite-abbr.json # my journal abbreviations
23 | metadata:
24 |   reference-section-title: Bibliography
25 |   notes-after-punctuation: false
26 |   link-citations: true
27 |   link-bibliography: true


--------------------------------------------------------------------------------
/defaults/typst-secnums.yaml:
--------------------------------------------------------------------------------
1 | defaults: typst
2 | metadata:
3 |   section-numbering: "1.1.1"
4 | 


--------------------------------------------------------------------------------
/defaults/typst-titlepage.yaml:
--------------------------------------------------------------------------------
1 | defaults: typst-refs
2 | metadata:
3 |   titlepage: true
4 |   titlepage-background: background.svg # WARNING: must be relative to compile folder
5 | 


--------------------------------------------------------------------------------
/defaults/typst.yaml:
--------------------------------------------------------------------------------
 1 | standalone: true
 2 | verbosity: INFO
 3 | from: markdown
 4 | to: typst
 5 | metadata-file: typst-includes.yaml
 6 | template: custom.typst
 7 | wrap: preserve
 8 | pdf-engine-opt: '--pdf-standard=a-2b'
 9 | filters:
10 |   - assimilateMetadata.rb
11 |   - typstFix.lua
12 |   - pagebreak.lua
13 |   #- removeDimensions.lua
14 |   - convertIndex.lua
15 |   - list-table.lua
16 |   - abstract-section.lua
17 |   - pretty-urls.lua
18 | table-of-contents: true
19 | metadata:
20 |   nonumberfigures: true


--------------------------------------------------------------------------------
/defaults/zotero-live.yaml:
--------------------------------------------------------------------------------
1 | verbosity: INFO # verbose by default
2 | filters:
3 |   - zotero.lua
4 | metadata:
5 |   reference-section-title: Bibliography
6 |   zotero_csl_style: 'cell'
7 |   zotero_client: 'zotero'


--------------------------------------------------------------------------------
/filters/README.md:
--------------------------------------------------------------------------------
 1 | # My Filters #
 2 | Most of the filters here are really aimed to handle academic paper workflows. For scientific papers we normally have multiple authors, each with an affiliation to an Institution and optionally an address for correspondence. Pandoc offers templates that allow us to convert metadata into this structured content, and for HTML and LaTeX I use this mechanism. Word and LibreOffice do not allow such flexibility, and so we must use filters to transform the metadata to add the correct information to the document body itself.
 3 | 
 4 | My YAML metadata normally looks something like this (<$ … > are Scrivener placeholders):
 5 | 
 6 | ```yaml
 7 | title: "<$projecttitle>"
 8 | author:
 9 |   - name: Joanna Doe
10 |     affiliation: [1, 2]
11 |     equal_contributor: true
12 |     correspondence: joanna@doe.org
13 |   - name: John Doe
14 |     affiliation: 2
15 |     equal_contributor: true
16 | institute:
17 |   - 1: University of X
18 |   - 2: Institute of Y
19 | keywords:
20 |   - example
21 |   - metadata
22 | created: "<$createdDate>"
23 | compiled: "<$fulldate> @ <$fulltime>"
24 | wordcount: <$wc>
25 | pandocomatic_:
26 |   use-template: [docx-refs, html-refs-pdf]
27 |   pandoc:
28 |     bibliography: CoreFast.json 
29 |     csl: csl/apa.csl
30 | ```
31 | 
32 | The [assimilateMetadata](https://github.com/iandol/dotpandoc/blob/master/filters/assimilateMetadata) filter is the main filter that makes sure the author and institute fields are converted into the correct formats, adding a new field `correspondence_list` and `equal_contributions` for Pandoc templates to use.
33 | 
34 | The [simplifyMetadata](https://github.com/iandol/dotpandoc/blob/master/filters/authorSimplifyMetadata) filter takes the author fields and modifies them to work with Word/LibreOffice, collapsing `affiliation`, `correspondence` and `equal_contributor` to superscripts after the name, and adding the `correspondence` information as a paragraph directly into the document body:
35 | 
36 | ```
37 | ---
38 | author:
39 |   - Joanna Doe ^12*†^
40 |   - John Doe ^2†^
41 | ---
42 | † equal contribution
43 | * Correspondence: joanna@doe.org
44 | ```
45 | 
46 | 
47 | Likewise, my [prependInstitute](https://github.com/iandol/dotpandoc/blob/master/filters/prependInstitute) filter takes the `institute` metadata and prepends a paragraph into the document body:
48 | 
49 | ```
50 | Affiliations: ^1^ — University of X & ^2^ — Institute of Y
51 | ```
52 | 
53 | As I also prepend comments and keywords, I've created a filter that prepends a "list of metadata entries", which is a bit faster than running separate prependXXX filters for each item to prepend: [prependAll](https://github.com/iandol/dotpandoc/blob/master/filters/prependAll). [prependAuthor](https://github.com/iandol/dotpandoc/blob/master/filters/prependAuthor) is used to get author information into plain-text outputs.
54 | 
55 | Other filters here are from other sources or for testing purposes. I do use `pagebreak.lua`, `addToday` and `removeHR` regularly.
56 | 
57 | As an alternative to my academic metadata filter, you could use Pandoc-Scholar's Lua filter: https://github.com/pandoc-scholar/pandoc-scholar/tree/master/lua-filters/scholarly-metadata  
58 | 
59 | 
60 | 


--------------------------------------------------------------------------------
/filters/abstract-section.lua:
--------------------------------------------------------------------------------
 1 | --[[
 2 | abstract-section – move an "abstract" section into document metadata
 3 | 
 4 | Copyright: © 2017–2023 Albert Krewinkel
 5 | License:   MIT – see LICENSE file for details
 6 | ]]
 7 | local stringify = (require 'pandoc.utils').stringify
 8 | local section_identifiers = {
 9 |   abstract = true,
10 | }
11 | local collected = {}
12 | --- The level of the highest heading that was seen so far. Abstracts
13 | --- must be at or above this level to prevent nested sections from being
14 | --- treated as metadata. Only top-level sections should become metadata.
15 | local toplevel = 6
16 | 
17 | --- Extract abstract from a list of blocks.
18 | local function abstract_from_blocklist (blocks)
19 |   local body_blocks = {}
20 |   local looking_at_section = false
21 | 
22 |   for _, block in ipairs(blocks) do
23 |     if block.t == 'Header' and block.level <= toplevel then
24 |       toplevel = block.level
25 |       if section_identifiers[block.identifier] then
26 |         looking_at_section = block.identifier
27 |         collected[looking_at_section] = {}
28 |       else
29 |         looking_at_section = false
30 |         body_blocks[#body_blocks + 1] = block
31 |       end
32 |     elseif looking_at_section then
33 |       if block.t == 'HorizontalRule' then
34 |         looking_at_section = false
35 |       else
36 |         local collect = collected[looking_at_section]
37 |         collect[#collect + 1] = block
38 |       end
39 |     else
40 |       body_blocks[#body_blocks + 1] = block
41 |     end
42 |   end
43 | 
44 |   return body_blocks
45 | end
46 | 
47 | Pandoc = function (doc)
48 |   local meta = doc.meta
49 | 
50 |   -- configure
51 |   section_identifiers_list =
52 |     (doc.meta['abstract-section'] or {})['section-identifiers']
53 |   if section_identifiers_list and #section_identifiers_list > 0 then
54 |     section_identifiers = {}
55 |     for i, ident in ipairs(section_identifiers_list) do
56 |       section_identifiers[stringify(ident)] = true
57 |     end
58 |   end
59 |   -- unset config in meta
60 |   doc.meta['abstract-section'] = nil
61 | 
62 |   local blocks = {}
63 |   if PANDOC_VERSION >= {2,17} then
64 |     -- Walk all block lists by default
65 |     blocks = doc.blocks:walk{Blocks = abstract_from_blocklist}
66 |   elseif PANDOC_VERSION >= {2,9,2} then
67 |     -- Do the same with pandoc versions that don't have walk methods but the
68 |     -- `walk_block` function.
69 |     blocks = pandoc.utils.walk_block(
70 |       pandoc.Div(doc.blocks),
71 |       {Blocks = abstract_from_blocklist}
72 |     ).content
73 |   else
74 |     -- otherwise, just check the top-level block-list
75 |     blocks = abstract_from_blocklist(doc.blocks)
76 |   end
77 |   for metakey in pairs(section_identifiers) do
78 |     metakey = stringify(metakey)
79 |     local abstract = collected[metakey]
80 |     if not meta[metakey] and abstract and #abstract > 0 then
81 |       meta[metakey] = pandoc.MetaBlocks(abstract)
82 |     end
83 |   end
84 |   return pandoc.Pandoc(blocks, meta)
85 | end
86 | 


--------------------------------------------------------------------------------
/filters/addToday.lua:
--------------------------------------------------------------------------------
1 | function Meta(m)
2 |   m.date = os.date("%B %e, %Y")
3 |   return m
4 | end
5 | 


--------------------------------------------------------------------------------
/filters/addToday.rb:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env ruby
 2 | # add today's date to metadata
 3 | 
 4 | require 'paru/filter'
 5 | require 'date'
 6 | 
 7 | Paru::Filter.run do 
 8 |   metadata["date"] = "#{Date.today.to_s}"
 9 |   stop!
10 | end
11 | 


--------------------------------------------------------------------------------
/filters/annotate.rb:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env ruby
 2 | # Annotate custom blocks: example blocks and important blocks
 3 | require "paru/filter"
 4 | 
 5 | example_count = 0
 6 | 
 7 | Paru::Filter.run do
 8 |   
 9 |   with "Div.example > Header" do |header|
10 |     if header.level == 3 
11 |         example_count += 1
12 |         header.inner_markdown = "Example #{example_count}: #{header.inner_markdown}"
13 |     end
14 |   end
15 | 
16 |   with "Div.important" do |d|
17 |     d.inner_markdown = d.inner_markdown + "\n\n*(important)*"
18 |   end
19 | end
20 | 


--------------------------------------------------------------------------------
/filters/assimilateMetadata.rb:
--------------------------------------------------------------------------------
  1 | #!/usr/bin/env ruby
  2 | # This regularises author:, affiliation: and institute: metadata fields
  3 | # into a standardised structure that is better parsed by a Pandoc template.
  4 | # It generates correspondence_list and equal_contribution fields if present in
  5 | # the author list.
  6 | # ---
  7 | # author:
  8 | #   - name: Joanna Doe
  9 | #     afilliation: [1,2]
 10 | #     correspondence: jdoe@example.ac.cn
 11 | #     equal_contributor: true
 12 | #   - name: John Doe
 13 | #     affiliation: 2
 14 | #     equal_contributor: true
 15 | # institute:
 16 | #   - 1: Institute of Cool
 17 | #   - 2: Centre for Assimilation
 18 | # ...
 19 | #
 20 | # You should be able to use several different input styles, including strings
 21 | # like 'Joanna Doe^1,2^' and lists without specifying the name: subfield
 22 | #
 23 | # VERSION: 1.0.3
 24 | 
 25 | require 'paru/filter'
 26 | 
 27 | def authorSuperscript(input)
 28 | 	cp = input.match(/\s?\^([\w\d\s\,§‡¶†\*]+)\^/)
 29 | 	if cp.nil?
 30 | 		Hash['name' => input]
 31 | 	else
 32 | 		Hash['name' => cp.pre_match, 'affiliation' => [cp[1]]]
 33 | 	end
 34 | end
 35 | 
 36 | def instituteSuperscript(inst, index = 1)
 37 | 	cp = inst.match(/^\s?\^([\w\d]+)\^\s?/)
 38 | 	if cp.nil?
 39 | 		Hash['name' => inst]
 40 | 	else
 41 | 		Hash['index' => cp[1], 'name' => cp.post_match.strip]
 42 | 	end
 43 | end
 44 | 
 45 | def fixName(author)
 46 | 	author = Hash['name' => author] if author.is_a?(String)
 47 | 	unless author.key?('name') # convert first key id to name: key
 48 | 		if author.values[0].is_a?(Hash)
 49 | 			values = author.values[0]
 50 | 			values['id'] = author.keys[0]
 51 | 			values['name'] = values['id']
 52 | 			author = values
 53 | 		else
 54 | 			author['name'] = 'Unknown'
 55 | 		end
 56 | 	end
 57 | 	author
 58 | end
 59 | 
 60 | def fixAffiliations(author)
 61 | 	return author unless author.key?('affiliation')
 62 | 	if author['affiliation'].is_a?(String)
 63 | 		list = author['affiliation'].chomp.split(',')
 64 | 		newList = Array.new(list.length, String)
 65 | 		list.each_with_index do |item, i|
 66 | 			newList[i] = item
 67 | 		end
 68 | 	elsif author['affiliation'].is_a?(Integer)
 69 | 		newList = [author['affiliation']]
 70 | 	elsif author['affiliation'].is_a?(Array)
 71 | 		newList = author['affiliation']
 72 | 	end
 73 | 	author['affiliation'] = newList
 74 | 	return author
 75 | end
 76 | 
 77 | Paru::Filter.run do
 78 | 	stop! unless metadata.key?('author') || metadata.key?('institute')
 79 | 	newAuthor = nil
 80 | 	newInst = nil
 81 | 	correspondenceList = []
 82 | 	emailList = []
 83 | 	equalContributors = false
 84 | 	#============Standardise author fields
 85 | 	authors = metadata['author']
 86 | 	authors = [Hash['name' => authors]] if authors.is_a?(String)
 87 | 	if authors.is_a?(Array)
 88 | 		newAuthor = Array.new(authors.length, {})
 89 | 		authors.each_with_index do |au, i|
 90 | 			if au.is_a?(String) # just an array of strings, turn to array of hashes
 91 | 				au = authorSuperscript(au)
 92 | 				newAuthor[i] = fixName(au)
 93 | 			elsif au.is_a?(Hash)
 94 | 				newAuthor[i] = fixName(au)
 95 | 			end
 96 | 
 97 | 			newAuthor[i] = fixAffiliations(newAuthor[i])
 98 | 			
 99 | 			#newAuthor[i]['email'] = newAuthor[i]['correspondence'] if newAuthor[i].key?('correspondence')
100 | 			if newAuthor[i].key?('correspondence')
101 | 				correspondenceList.push(newAuthor[i]['name'] + ' <' + newAuthor[i]['correspondence'] + '>')
102 | 			end
103 | 			if newAuthor[i].key?('email')
104 | 				emailList.push(newAuthor[i]['name'] + ' <' + newAuthor[i]['email'] + '>')
105 | 			end
106 | 
107 | 			if newAuthor[i].key?('equal_contributor')
108 | 				equalContributors = true
109 | 			end
110 | 		end
111 | 	end
112 | 	#============Standardise institute fields
113 | 	inst = metadata['institute']
114 | 	inst = [Hash['index' => 1, 'name' => inst]] if inst.is_a?(String)
115 | 	if inst.is_a?(Array)
116 | 		inst.each_with_index do |mi, i|
117 | 			if mi.is_a?(String)
118 | 				inst[i] = instituteSuperscript(mi, i)
119 | 			elsif mi.is_a?(Array) && mi.length == 2
120 | 				inst[i] = Hash('index' => mi[0].to_s, 'name' => mi[1].to_s)
121 | 			elsif mi.is_a?(Hash) && mi.keys.length == 1
122 | 				inst[i] = Hash('index' => mi.keys[0].to_s, 'name' => mi.values[0].to_s)
123 | 			end
124 | 		end
125 | 		newInst = inst
126 | 	end
127 | 	#============Write our new fields
128 | 	metadata['author'] = newAuthor unless newAuthor.nil?
129 | 	metadata['institute'] = newInst unless newInst.nil?
130 | 	metadata['correspondence_list'] = correspondenceList unless correspondenceList.empty?
131 | 	metadata['email_list'] = emailList unless emailList.empty?
132 | 	metadata['equal_contributors'] = true if equalContributors == true
133 | 	# just in case a template uses tags instead of keywords
134 | 	metadata['tags'] = metadata['keywords'] if metadata['keywords']
135 | 	# tell paru no more processing needed!
136 | 	stop!
137 | end
138 | 


--------------------------------------------------------------------------------
/filters/capitaliseHeading.rb:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env ruby
 2 | 
 3 | require "paru/filter"
 4 | 
 5 | END_CAPITAL = 10
 6 | Paru::Filter.run do 
 7 |   with "Header" do |h|
 8 |     text = h.inner_markdown
 9 |     first_line = text.slice(0, END_CAPITAL).upcase
10 |     rest = text.slice(END_CAPITAL, text.size)
11 |     h.inner_markdown = first_line + rest
12 |   end
13 | end
14 | 


--------------------------------------------------------------------------------
/filters/citation-backlinks.lua:
--------------------------------------------------------------------------------
 1 | --- citation-backlinks.lua – adds citation backlinks to the bibliography
 2 | ---
 3 | --- Copyright: © 2022 John MacFarlane and Albert Krewinkel
 4 | --- License: MIT – see LICENSE for details
 5 | 
 6 | -- Makes sure users know if their pandoc version is too old for this
 7 | -- filter.
 8 | PANDOC_VERSION:must_be_at_least '2.17'
 9 | 
10 | -- cites is a table mapping citation item identifiers
11 | -- to an array of cite identifiers
12 | local cites = {}
13 | 
14 | -- counter for cite identifiers
15 | local cite_number = 1
16 | 
17 | local function with_latex_label(s, el)
18 |   if FORMAT == "latex" then
19 |     return {pandoc.RawInline("latex", "\\label{" .. s .. "}"), el}
20 |   else
21 |     return {el}
22 |   end
23 | end
24 | 
25 | function Cite(el)
26 |   local cite_id = "cite_" .. cite_number
27 |   cite_number = cite_number + 1
28 |   for _,citation in ipairs(el.citations) do
29 |     if cites[citation.id] then
30 |       table.insert(cites[citation.id], cite_id)
31 |     else
32 |       cites[citation.id] = {cite_id}
33 |     end
34 |   end
35 |   return pandoc.Span(with_latex_label(cite_id, el), pandoc.Attr(cite_id))
36 | end
37 | 
38 | function append_inline(blocks, inlines)
39 |   local last = blocks[#blocks]
40 |   if last.t == 'Para' or last.t == 'Plain' then
41 |     -- append to last block
42 |     last.content:extend(inlines)
43 |   else
44 |     -- append as additional block
45 |     blocks[#blocks + 1] = pandoc.Plain(inlines)
46 |   end
47 |   return blocks
48 | end
49 | 
50 | function Div(el)
51 |   local citation_id = el.identifier:match("ref%-(.+)")
52 |   if citation_id then
53 |     local backlinks = pandoc.Inlines{pandoc.Str("Cited:"),pandoc.Space()}
54 |     for i,cite_id in ipairs(cites[citation_id] or {}) do
55 |       local marker = pandoc.Str(i)
56 |       if FORMAT == "latex" then
57 |         marker = pandoc.RawInline("latex", "\\pageref{" .. cite_id .. "}")
58 |       end
59 |       if #backlinks > 2 then
60 |         table.insert(backlinks, pandoc.Str(","))
61 |         table.insert(backlinks, pandoc.Space())
62 |       end
63 |       table.insert(backlinks, pandoc.Link(marker, "#"..cite_id))
64 |     end
65 |     if #backlinks > 2 then
66 |       append_inline(el.content, {pandoc.Space()} .. backlinks)
67 |     end
68 |     return el
69 |   end
70 | end
71 | 


--------------------------------------------------------------------------------
/filters/citation-key.lua:
--------------------------------------------------------------------------------
 1 | --[[
 2 | When converting from DOCX with embedded Zotero refs, BetterBibTeX keys are
 3 | never used for the id of the reference. This filter checks if a citation-key
 4 | is present and if so replaces the id in the references YAML metadata and
 5 | also the citation key used in the text. If there is no citation-key, because
 6 | Zotero IDs are not legible for humans, it generates one based on the
 7 | author+year plus first four digits of the Zotero ID
 8 | Verison: 0.1
 9 | Copyright: (c) 2024 Ian Max Andolina License=MIT, see LICENSE for details
10 | ]]
11 | 
12 | local ids = {} -- map of Zotero IDs to citation key
13 | 
14 | function Cite(c)
15 | 	for i,v in ipairs(c.citations) do
16 | 		id = v["id"]
17 | 		if ids[id] ~= nil then
18 | 			c.citations[i]["id"] = ids[id]
19 | 		end
20 | 	end
21 | 	return c
22 | end
23 | 
24 | function Meta(m)
25 | 	if m.references then
26 | 		for i,ref in ipairs(m.references) do
27 | 			if ref["author"][1].family ~= nil then
28 | 				author = ref["author"][1].family
29 | 			elseif ref["author"][1].literal ~= nil then
30 | 				author = ref["author"][1].literal
31 | 			else
32 | 				author = ""
33 | 			end
34 | 			author = author:gsub(" ", ""):lower()
35 | 			if ref["issued"] ~= nil then
36 | 				year = ref["issued"]:match("^%d%d%d%d")
37 | 			else
38 | 				year = ""
39 | 			end
40 | 			id = ref["id"]
41 | 			key = ref["citation-key"]
42 | 			ids[id] = id
43 | 			if key ~= nil then
44 | 				ids[id] = pandoc.utils.stringify(key)
45 | 				m.references[i]["id"] = ids[id]
46 | 			else
47 | 				key = author:lower() .. year .. ":" ..id:sub(1,4)
48 | 				ids[id] = pandoc.utils.stringify(key)
49 | 				m.references[i]["id"] = ids[id]
50 | 				m.references[i]["citation-key"] = ids[id]
51 | 			end
52 | 		end
53 | 	end
54 | 	return m
55 | end
56 | 
57 | return { 
58 | 	{ Meta = Meta }, 
59 | 	{ Cite = Cite } 
60 | }
61 | 


--------------------------------------------------------------------------------
/filters/customParaStyle.lua:
--------------------------------------------------------------------------------
1 | --takes all paragraphs and wraps them in a styled div
2 | function Para(blk)
3 |    local attr = pandoc.Attr()
4 |    attr.attributes["custom-style"] = "My Style"
5 |    return pandoc.Div({blk}, attr)
6 | end


--------------------------------------------------------------------------------
/filters/enstyle-list.lua:
--------------------------------------------------------------------------------
 1 | --[[
 2 | 	The purpose of this filter is to take ordered and bulleted lists and add 
 3 | 	custom-styles to the first and subsequent items…
 4 | 	Version:   1.00
 5 | 	Copyright: (c) 2024 Ian Max Andolina License=MIT, see LICENSE for details
 6 | ]]
 7 | 
 8 | local olfirst	= "Numbered 1"
 9 | local olrest	= "Numbered"
10 | local blfirst	= "Bulleted 1"
11 | local blrest	= "Bulleted"
12 | 
13 | function OrderedList(ol)
14 | 	local i = 0
15 | 	return ol:walk {
16 | 		Plain = function (p)
17 | 			i = i + 1
18 | 			if i == 1 then styleName = olfirst else styleName = olrest end
19 | 			return pandoc.Div(pandoc.Para(p.content), {['custom-style'] = styleName})
20 | 		end 
21 | 	}
22 | end
23 | 
24 | function BulletList(bl)
25 | 	local i = 0
26 | 	return bl:walk {
27 | 		Plain = function (p)
28 | 			i = i + 1
29 | 			if i == 1 then styleName = blfirst else styleName = blrest end
30 | 			return pandoc.Div(pandoc.Para(p.content), {['custom-style'] = styleName})
31 | 		end 
32 | 	}
33 | end
34 | 


--------------------------------------------------------------------------------
/filters/firstParagraph.rb:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env ruby
 2 | # Capitalize the first N characters of a paragraph
 3 | require "paru/filter"
 4 | 
 5 | END_CAPITAL = 10
 6 | Paru::Filter.run do 
 7 |   with "Header +1 Para" do |p|
 8 |     text = p.inner_markdown
 9 |     first_line = text.slice(0, END_CAPITAL).upcase
10 |     rest = text.slice(END_CAPITAL, text.size)
11 |     p.inner_markdown = first_line + rest
12 |   end
13 | end
14 | 


--------------------------------------------------------------------------------
/filters/include-files.lua:
--------------------------------------------------------------------------------
  1 | --- include-files.lua – filter to include Markdown files
  2 | ---
  3 | --- Copyright: © 2019–2021 Albert Krewinkel
  4 | --- License:   MIT – see LICENSE file for details
  5 | 
  6 | -- Module pandoc.path is required and was added in version 2.12
  7 | PANDOC_VERSION:must_be_at_least '2.12'
  8 | 
  9 | local List = require 'pandoc.List'
 10 | local path = require 'pandoc.path'
 11 | local system = require 'pandoc.system'
 12 | 
 13 | --- Get include auto mode
 14 | local include_auto = false
 15 | function get_vars (meta)
 16 |   if meta['include-auto'] then
 17 |     include_auto = true
 18 |   end
 19 | end
 20 | 
 21 | --- Keep last heading level found
 22 | local last_heading_level = 0
 23 | function update_last_level(header)
 24 |   last_heading_level = header.level
 25 | end
 26 | 
 27 | --- Update contents of included file
 28 | local function update_contents(blocks, shift_by, include_path)
 29 |   local update_contents_filter = {
 30 |     -- Shift headings in block list by given number
 31 |     Header = function (header)
 32 |       if shift_by then
 33 |         header.level = header.level + shift_by
 34 |       end
 35 |       return header
 36 |     end,
 37 |     -- If image paths are relative then prepend include file path
 38 |     Image = function (image)
 39 |       if path.is_relative(image.src) then
 40 |         image.src = path.normalize(path.join({include_path, image.src}))
 41 |       end
 42 |       return image
 43 |     end,
 44 |     -- Update path for include-code-files.lua filter style CodeBlocks
 45 |     CodeBlock = function (cb)
 46 |       if cb.attributes.include and path.is_relative(cb.attributes.include) then
 47 |         cb.attributes.include =
 48 |           path.normalize(path.join({include_path, cb.attributes.include}))
 49 |         end
 50 |       return cb
 51 |     end
 52 |   }
 53 | 
 54 |   return pandoc.walk_block(pandoc.Div(blocks), update_contents_filter).content
 55 | end
 56 | 
 57 | --- Filter function for code blocks
 58 | local transclude
 59 | function transclude (cb)
 60 |   -- ignore code blocks which are not of class "include".
 61 |   if not cb.classes:includes 'include' then
 62 |     return
 63 |   end
 64 | 
 65 |   -- Markdown is used if this is nil.
 66 |   local format = cb.attributes['format']
 67 | 
 68 |   -- Attributes shift headings
 69 |   local shift_heading_level_by = 0
 70 |   local shift_input = cb.attributes['shift-heading-level-by']
 71 |   if shift_input then
 72 |     shift_heading_level_by = tonumber(shift_input)
 73 |   else
 74 |     if include_auto then
 75 |       -- Auto shift headings
 76 |       shift_heading_level_by = last_heading_level
 77 |     end
 78 |   end
 79 | 
 80 |   --- keep track of level before recusion
 81 |   local buffer_last_heading_level = last_heading_level
 82 | 
 83 |   local blocks = List:new()
 84 |   for line in cb.text:gmatch('[^\n]+') do
 85 |     if line:sub(1,2) ~= '//' then
 86 |       local fh = io.open(line)
 87 |       if not fh then
 88 |         io.stderr:write("Cannot open file " .. line .. " | Skipping includes\n")
 89 |       else
 90 |         -- read file as the given format with global reader options
 91 |         local contents = pandoc.read(
 92 |           fh:read '*a',
 93 |           format,
 94 |           PANDOC_READER_OPTIONS
 95 |         ).blocks
 96 |         last_heading_level = 0
 97 |         -- recursive transclusion
 98 |         contents = system.with_working_directory(
 99 |             path.directory(line),
100 |             function ()
101 |               return pandoc.walk_block(
102 |                 pandoc.Div(contents),
103 |                 { Header = update_last_level, CodeBlock = transclude }
104 |               )
105 |             end).content
106 |         --- reset to level before recursion
107 |         last_heading_level = buffer_last_heading_level
108 |         blocks:extend(update_contents(contents, shift_heading_level_by,
109 |                                       path.directory(line)))
110 |         fh:close()
111 |       end
112 |     end
113 |   end
114 |   return blocks
115 | end
116 | 
117 | return {
118 |   { Meta = get_vars },
119 |   { Header = update_last_level, CodeBlock = transclude }
120 | }
121 | 


--------------------------------------------------------------------------------
/filters/insertCode.rb:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env ruby
 2 | require "paru/filter"
 3 | 
 4 | Paru::Filter.run do 
 5 |   with "CodeBlock" do |code_block|
 6 |     command, path, *classes = code_block.string.strip.split " "
 7 |     if command == "::paru::insert"
 8 |       code_block.string = File.read path.gsub(/\\_/, "_")
 9 |       classes.each {|c| code_block.attr.classes.push c}
10 |     end
11 |   end
12 | end
13 | 


--------------------------------------------------------------------------------
/filters/latex-div.lua:
--------------------------------------------------------------------------------
 1 | --[[
 2 |      A Pandoc 2 Lua filter converting Pandoc native divs to LaTeX environments
 3 |      Author: Romain Lesur, Christophe Dervieux, Atsushi Yasumoto and Yihui Xie
 4 |      License: Public domain
 5 |      https://github.com/rstudio/rmarkdown/tree/main/inst/rmarkdown/lua
 6 | --]]
 7 | 
 8 | --md = require("mobdebug")
 9 | --md.start()
10 | 
11 | --[[
12 | -- REQUIREMENTS: Load shared lua filter - see `shared.lua` for more details.
13 | -- dofile(os.getenv 'RMARKDOWN_LUA_SHARED')
14 | -- require('./filters/shared')
15 |   About the requirement:
16 |   * PANDOC_VERSION -> 2.1
17 | if (not pandocAvailable {2,1}) then
18 |     io.stderr:write("[WARNING] (latex-div.lua) requires at least Pandoc 2.1. Lua Filter skipped.\n")
19 |     return {}
20 | end
21 | ]]
22 | 
23 | -- START OF THE FILTER'S FUNCTIONS --
24 | 
25 | text = require 'text'
26 | 
27 | Div = function (div)
28 |   --md.pause() --breakpoint
29 |   -- look for 'latex' or 'data-latex' and at least 1 class
30 |   local options = div.attributes['latex']
31 |   if not options then
32 |     options = div.attributes['data-latex']
33 |   end
34 |   if not options or #div.attr.classes == 0 then
35 |     return nil
36 |   end
37 | 
38 |   -- if the output format is not latex, remove the attr and return
39 |   if FORMAT ~= 'latex' and FORMAT ~= 'beamer' then
40 |     if div.attributes['latex'] then div.attributes['latex'] = nil end
41 |     if div.attributes['data-latex'] then div.attributes['data-latex'] = nil end
42 |     return div
43 |   end
44 | 
45 |   -- if it's "1" or "true" then just set it to empty string
46 |   if options == "1" or text.lower(options) == "true" then
47 |     options = ""
48 |   end
49 | 
50 |   -- environment begin/end
51 |   local env = div.classes[1]
52 |   local beginEnv = '\\begin' .. '{' .. env .. '}' .. options
53 |   local endEnv = '\n\\end{' .. env .. '}'
54 | 
55 |   -- if the first and last div blocks are paragraphs then we can
56 |   -- bring the environment begin/end closer to the content
57 |   if div.content[1].t == "Para" and div.content[#div.content].t == "Para" then
58 |     table.insert(div.content[1].content, 1, pandoc.RawInline('tex', beginEnv .. "\n"))
59 |     table.insert(div.content[#div.content].content, pandoc.RawInline('tex', "\n" .. endEnv))
60 |   else
61 |     table.insert(div.content, 1, pandoc.RawBlock('tex', beginEnv))
62 |     table.insert(div.content, pandoc.RawBlock('tex', endEnv))
63 |   end
64 |   return div
65 | end
66 | 


--------------------------------------------------------------------------------
/filters/lua-debug.lua:
--------------------------------------------------------------------------------
  1 | --[[
  2 | # Lua Filter REPL Test
  3 | 
  4 | You can remote debug Pandoc Lua filters using [Zerobrane
  5 | Studio](https://studio.zerobrane.com) The debugger requires luasocket and
  6 | mobdebug, both are bundled in Zerobrane, or you can use your Lua installed
  7 | versions. 
  8 | 
  9 | ## Without Lua Installed:
 10 | If you don't have Lua installed on your system, should update the
 11 | environment search path to use mobdebug.lua and luasocket from Zerobrane's
 12 | install location. See
 13 | [documentation](https://studio.zerobrane.com/doc-remote-debugging) for
 14 | details. For e.g. macOS this would be for zsh:
 15 | 
 16 |     export ZBS=/Applications/ZeroBraneStudio.app/Contents/ZeroBraneStudio 
 17 |     export LUA_PATH="./?.lua;$ZBS/lualibs/?/?.lua;$ZBS/lualibs/?.lua"  
 18 |     export LUA_CPATH="$ZBS/bin/?.dylib;$ZBS/bin/clibs53/?.dylib;$ZBS/bin/clibs53/?/?.dylib"
 19 | 
 20 | Elvish: 
 21 | 
 22 |     set-env ZBS /Applications/ZeroBraneStudio.app/Contents/ZeroBraneStudio
 23 |     set-env LUA_PATH "./?.lua;"$E:ZBS"/lualibs/?/?.lua;"$E:ZBS"/lualibs/?.lua"
 24 |     set-env LUA_CPATH $E:ZBS"/bin/?.dylib;"$E:ZBS"/bin/clibs54/?.dylib;"$E:ZBS"/bin/clibs54/?/?.dylib"
 25 | 
 26 | ## With Lua installed:
 27 | If you have installed Lua v5.4 and added mobdebug + luasocket using luarocks
 28 | then they should be available in the default path locations (at least for
 29 | POSIX systems), and you shouldn't need to set any path variables.
 30 | 
 31 | ## How to Trigger the Debugger:
 32 | 
 33 | 1) Ensure the filter.lua file is opened in the Zerobrane editor; Project >
 34 | Start Debugger Server is turned ON; and editor.autoactivate = true is
 35 | enabled in your user.lua settings file.
 36 | 
 37 | 2) Then run pandoc from terminal with the filter that is open in the editor:
 38 | 
 39 |     > pandoc --lua-filter luatest.lua Here is a *test* for **REPL**
 40 |     debugging. [ctrl]+[d]
 41 | 
 42 | 3) Zerobrane's debugger will activate. Use the Stack window and Remote
 43 | console to examine the environment and execute Lua commands while stepping
 44 | through the code.
 45 | 
 46 | ## Commandline Use:
 47 | With mobdebug and luasocket installed, you can also debug from your teminal
 48 | without running an IDE:
 49 | 
 50 | > pandoc-lua -e "require('mobdebug').listen()"
 51 | 
 52 | But Zerobrane offers richer functionality…
 53 | 
 54 | ## VS Code Alterative:
 55 | 
 56 | https://github.com/EmmyLua/VSCode-EmmyLua -- it injects a precompiled
 57 | library. Inject the library loading code using command palette, then use
 58 | dbg.waitIDE() to pause, and dbg.breakHere() to break. Run code BEFORE debugger.
 59 | 
 60 | https://github.com/moteus/vscode-mobdebug -- need to use `luarocks install
 61 | vscode-mobdebug` and then `require("vscode-mobdebug")`, you may need to
 62 | `luarocks remove --force mobdebug`
 63 | 
 64 | LuaPanda is another option https://github.com/Tencent/LuaHelper 
 65 | 
 66 | ]]
 67 | 
 68 | lg = require("logging")
 69 | md = require("mobdebug")
 70 | md.logging = true
 71 | 
 72 | --package.cpath = package.cpath .. ";/Users/ian/.vscode/extensions/tangzx.emmylua-0.8.20-darwin-arm64/debugger/emmy/mac/arm64/emmy_core.dylib"
 73 | --local dbg = require("emmy_core")
 74 | --dbg.tcpListen("localhost", 9966)
 75 | --dbg.waitIDE()
 76 | 
 77 | function OrderedList(l)
 78 | 	md.start() --breakpoint
 79 | 	--dbg.breakHere()
 80 | 	i = 0
 81 | 	ll = l:walk {
 82 | 		Plain = function (p)
 83 | 			i = i + 1
 84 | 			if i == 1 then
 85 | 				d = pandoc.Div(p, {['custom-style'] = 'Numbered 1'})
 86 | 			else
 87 | 				d = pandoc.Div(p, {['custom-style'] = 'Numbered'})
 88 | 			end
 89 | 			return d
 90 | 		end 
 91 | 	}
 92 | 	return ll
 93 | end
 94 | 
 95 | function Div(d)
 96 | 	--md.start()
 97 | 	dbg.breakHere()
 98 | 	return d
 99 | end
100 | 
101 | function Meta(m)
102 | 	md.start() --breakpoint
103 | 	--dbg.breakHere()
104 | 	return m
105 | end
106 | 
107 | function Cite(elem)
108 | 	md.start() --breakpoint
109 | 	--dbg.breakHere()
110 | 	return elem
111 | end
112 | 
113 | function Emph(elem)
114 | 	md.start() --breakpoint
115 | 	--dbg.breakHere()
116 | 	return elem.content
117 | end
118 | 
119 | function Strong(elem)
120 | 	md.start() --breakpoint
121 | 	--dbg.breakHere()
122 | 	return pandoc.SmallCaps(elem.content)
123 | end
124 | 
125 | function Note(elem)
126 | 	md.start() --breakpoint
127 | 	--dbg.breakHere()
128 | 	return elem
129 | end


--------------------------------------------------------------------------------
/filters/lua-log.lua:
--------------------------------------------------------------------------------
 1 | --	need to set path for logging.lua to be found: 
 2 | --	set-env LUA-PATH $E:HOME"/.local/share/pandoc/filters/?.lua;;"
 3 | 
 4 | local logging = require 'logging'
 5 | 
 6 | function Pandoc(pandoc)
 7 | 	logging.temp('PANDOC', pandoc)
 8 | 	logging.temp('READ',PANDOC_READER_OPTIONS)
 9 | 	logging.temp('WRITE',PANDOC_WRITER_OPTIONS)
10 | end


--------------------------------------------------------------------------------
/filters/modifyHeadings.lua:
--------------------------------------------------------------------------------
 1 | -- for plain text make Headings stand out a bit
 2 | 
 3 | function Header(el)
 4 | 	if el.level == 1 then
 5 | 		Strs = pandoc.walk_block(el, {
 6 | 			Str = function(el)
 7 | 				 return pandoc.SmallCaps(el.text)
 8 | 			end })
 9 | 		Strs.content:extend{pandoc.Str('\n===============')}
10 | 		return Strs
11 | 	elseif el.level == 2 then
12 | 		el.content:extend{pandoc.Str('\n---------------')}
13 | 		return el
14 | 	else
15 | 		el.content:extend{pandoc.Str('\n- - - - - - - -')}
16 | 		return el
17 | 	end
18 | end
19 | 
20 | function Strong(elem)
21 | 	return pandoc.SmallCaps(elem.content)
22 | end


--------------------------------------------------------------------------------
/filters/noop.rb:
--------------------------------------------------------------------------------
1 | #!/usr/bin/env ruby
2 | 
3 | require 'paru/filter'
4 | 
5 | Paru::Filter.run do
6 |   stop!
7 | end
8 | 


--------------------------------------------------------------------------------
/filters/numbering-depth.lua:
--------------------------------------------------------------------------------
1 | -- adjust as needed
2 | local max_numbering_level = 3
3 | 
4 | function Header (h)
5 |   if h.level > max_numbering_level then 
6 |     h.classes:insert 'unnumbered'
7 |   end
8 |   return h
9 | end


--------------------------------------------------------------------------------
/filters/paruVersion.rb:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env ruby
 2 | # A filter to insert paru's version. All occurrences of 
 3 | # '::paru::version' are replaced by paru's version.
 4 | #
 5 | # VERSION: 1.0.0
 6 | 
 7 | require "paru"
 8 | require "paru/filter"
 9 | 
10 | def version(str)
11 |   str.gsub "::paru::version", Paru::VERSION.join(".")
12 | end
13 | 
14 | Paru::Filter.run do 
15 |   
16 |   with "Str" do |str|
17 |     str.string = version(str.string)
18 |   end
19 | 
20 |   with "CodeBlock" do |code|
21 |     code.string = version(code.string)
22 |   end
23 | 
24 |   with "Link" do |link|
25 |     link.target.url = version(link.target.url)
26 |     link.target.title = version(link.target.title)
27 |   end
28 | 
29 | end
30 | 


--------------------------------------------------------------------------------
/filters/prependAbstract.rb:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env ruby
 2 | # If we have abstract: metadata, convert it to an
 3 | # "Abstract: " paragraph at the start of the document
 4 | # This is because some templates / plain text cannot handle this natively
 5 | #
 6 | # VERSION: 1.0.0
 7 | 
 8 | require 'paru/filter'
 9 | 
10 | Paru::Filter.run do
11 |   stop! unless metadata.key?('abstract')
12 |   text = ''
13 |   ab = metadata['abstract']
14 |   if ab.is_a?(String)
15 |     text += ab
16 |   elsif ab.is_a?(Array)
17 |     ab.each_index { |i| text += ab[i].to_s + '. ' }
18 |     text = text[0..-3]
19 |   end
20 |   stop! if text.length == 0
21 |   text = '**Abstract**: ' + text
22 |   p = Paru::PandocFilter::Para.new([])
23 |   p.inner_markdown = text
24 |   document.prepend(p)
25 |   stop!
26 | end


--------------------------------------------------------------------------------
/filters/prependAll.rb:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env ruby
 2 | # If we have particular metadata, prepend it to a
 3 | # paragraph at the start of the document;
 4 | # as Word/ODT templates cannot handle this natively
 5 | #
 6 | # VERSION: 1.0.2
 7 | 
 8 | require 'paru/filter'
 9 | 
10 | # here is our list of metadata to convert
11 | 	prepend_list = {
12 | 		:comments => "Comments", 
13 | 		:wordcount => "Wordcount", 
14 | 		:conflicts => "Conflict of interest statement", 
15 | 		:acknowledgements => "Acknowledgements", 
16 | 		:contributions => "Author contributions",
17 | 		:institute => "Affiliations",
18 | 		:keywords => "Keywords"
19 | 	}
20 | 
21 | Paru::Filter.run do
22 | 	prepend_list.each do |key,val|
23 | 		next unless metadata.key?(key.to_s)
24 | 		text = ''
25 | 		kw = metadata[key.to_s]
26 | 		if kw.is_a?(String)
27 | 			text += kw
28 | 		elsif kw.is_a?(Array)
29 | 			kw.each do |x|
30 | 				if x.is_a?(Hash)
31 | 					text += '^' + x.keys[0].to_s + '^ ' + x.values[0].to_s + '; '
32 | 				else
33 | 					text += x.to_s + '; '
34 | 				end
35 | 			end
36 | 			text = text[0..-3]
37 | 		else
38 | 			text = ''
39 | 		end
40 | 		next if text.empty?
41 | 
42 | 		text = '**' + val + '**: ' + text
43 | 		p = Paru::PandocFilter::Para.new([])
44 | 		p.inner_markdown = text
45 | 		document.prepend(p)
46 | 	end
47 | 	stop!
48 | end


--------------------------------------------------------------------------------
/filters/prependAuthor.rb:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env ruby
 2 | # If we have author: metadata, convert it to an
 3 | # "Authors" and Affiliations" paragraph at the start of the document
 4 | # This is because plain text template etc. cannot handle this natively
 5 | #
 6 | # VERSION: 1.0.0
 7 | 
 8 | require 'paru/filter'
 9 | 
10 | def fixName(author)
11 |   author = Hash['name' => author] if author.is_a?(String)
12 |   unless author.key?('name') # convert first key id to name: key
13 |     if author.values[0].is_a?(Hash)
14 |       values = author.values[0]
15 |       values['id'] = author.keys[0]
16 |       values['name'] = values['id']
17 |       author = values
18 |     else
19 |       author['name'] = 'Unknown'
20 |     end
21 |   end
22 |   author
23 | end
24 | 
25 | Paru::Filter.run do
26 |   stop! unless metadata.key?('author')
27 |   authors = metadata['author']
28 |   authors = [Hash['name' => authors]] if authors.is_a?(String)
29 |   text = '**Authors**: '
30 |   addContribution = false
31 |   if authors.is_a?(Array)
32 |     authors.each_with_index do |au,i|
33 |       au = fixName(au)
34 |       text += au['name'].to_s
35 |       #--------------------parse affiliation
36 |       if au.key?('affiliation')
37 |         if au['affiliation'].is_a?(String) || au['affiliation'].is_a?(Integer)
38 |           aff = au['affiliation'].to_s
39 |           frag = ''
40 |           a = aff.split(',') # comma seperated values
41 |           a.each do |af|
42 |             if af.match(/^\d+$/)
43 |               frag += '^' + af + '^ '
44 |             else
45 |               frag += af + ''
46 |             end
47 |             text += frag + ' '
48 |           end
49 |         elsif au['affiliation'].is_a?(Array)
50 |           frag = ''
51 |           au['affiliation'].each do |af|
52 |             if af.to_s.match(/^\d+$/)
53 |               frag += '^' + af.to_s + '^ '
54 |             else
55 |               frag += af.to_s
56 |             end
57 |           end
58 |           text += frag[0..-2]
59 |         end
60 |       end
61 |       #----------------parse correspondence
62 |       if au.key?('correspondence') || au.key?('email')
63 |         if au.key?('email')
64 |           text += ' <' + au['email'].to_s + '>'
65 |         else
66 |           text += ' <' + au['correspondence'].to_s + '>'
67 |         end
68 |       end
69 |       #-----------------parse contributions
70 |       if au.key?('equal_contributor')
71 |         text += '†'
72 |         addContribution = true
73 |       end
74 |       text += '  &  '
75 |     end
76 |     text = text[0..-6]
77 |   end
78 |   stop! if text.length < 14
79 | 
80 |   if addContribution
81 |     p = Paru::PandocFilter::Para.new([])
82 |     p.inner_markdown = "† equal contribution"
83 |     document.prepend(p)
84 |   end
85 |   p = Paru::PandocFilter::Para.new([])
86 |   p.inner_markdown = text
87 |   document.prepend(p)
88 | 
89 |   stop!
90 | end
91 | 


--------------------------------------------------------------------------------
/filters/prependComments.rb:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env ruby
 2 | # If we have comments: metadata, convert it to an
 3 | # "Comments" paragraph at the start of the document
 4 | # This is because Word template cannot handle this natively
 5 | 
 6 | require 'paru/filter'
 7 | 
 8 | Paru::Filter.run do
 9 |   stop! unless metadata.key?('comments')
10 |   kw = metadata['comments']
11 |   text = '**Comments**: '
12 |   if kw.is_a?(String)
13 |     text += kw
14 |   elsif kw.is_a?(Array)
15 |     kw.each_index do |i|
16 |       text += kw[i].to_s + ', '
17 |     end
18 |     text = text[0..-3]
19 |   elsif kw[0].is_a?(Hash)
20 |     text = 'HASH TODO'
21 |   end
22 |   p = Paru::PandocFilter::Para.new([])
23 |   p.inner_markdown = text
24 |   document.prepend(p)
25 |   stop!
26 | end


--------------------------------------------------------------------------------
/filters/prependInstitute.rb:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env ruby
 2 | # If we have institute: metadata, convert it to an
 3 | # "Affiliations" paragraph at the start of the document
 4 | # This is because Word template cannot handle this natively
 5 | #
 6 | # VERSION: 1.0.0
 7 | 
 8 | require 'paru/filter'
 9 | 
10 | Paru::Filter.run do
11 |   stop! unless metadata.key?('institute')
12 |   inst = metadata['institute']
13 |   text = '**Affiliations**: '
14 |   if inst.is_a?(String)
15 |     text += inst
16 |   elsif inst.is_a?(Array)
17 |     inst.each_with_index do |x,i| 
18 |         if x.is_a?(Hash)
19 |           text += x.keys[0].to_s + ': ' + x.values[0].to_s + ' & ' 
20 |         else
21 |           text += x.to_s + ' & ' 
22 |         end
23 |       end
24 |       text = text[0..-4]
25 |     end
26 |   elsif inst[0].is_a?(Hash)
27 |     text = 'HASH TODO'
28 |   end
29 |   stop! if text.length < 19
30 |   p = Paru::PandocFilter::Para.new([])
31 |   p.inner_markdown = text
32 |   document.prepend(p)
33 |   stop!
34 | end
35 | 


--------------------------------------------------------------------------------
/filters/prependKeywords.rb:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env ruby
 2 | # If we have keywords: metadata, convert it to an
 3 | # "Keywords" paragraph at the start of the document
 4 | # This is because Word template cannot handle this natively
 5 | #
 6 | # VERSION: 1.0.0
 7 | 
 8 | require 'paru/filter'
 9 | 
10 | Paru::Filter.run do
11 |   stop! unless metadata.key?('keywords')
12 |   kw = metadata['keywords']
13 |   text = '**Keywords**: '
14 |   if kw.is_a?(String)
15 |     text += kw
16 |   elsif kw.is_a?(Array)
17 |     kw.each_index do |i|
18 |       text += kw[i].to_s + ', '
19 |     end
20 |     text = text[0..-3]
21 |   elsif kw[0].is_a?(Hash)
22 |     text = 'HASH TODO'
23 |   end
24 |   p = Paru::PandocFilter::Para.new([])
25 |   p.inner_markdown = text
26 |   document.prepend(p)
27 |   stop!
28 | end


--------------------------------------------------------------------------------
/filters/pretty-urls.lua:
--------------------------------------------------------------------------------
 1 | --- pretty-urls.lua – let URLs look a little nicer
 2 | ---
 3 | --- Copyright: © 2022 Albert Krewinkel
 4 | --- License: MIT – see LICENSE for details
 5 | -- Ensure a recent enough pandoc version.
 6 | PANDOC_VERSION:must_be_at_least '2.7'
 7 | 
 8 | local stringify = pandoc.utils.stringify
 9 | 
10 | local function prettify_url (link)
11 |   -- Do not change the link if the description does not match the
12 |   -- target and it is not an autolink (marked by the 'uri' class).
13 |   if stringify(link.content) ~= link.target and
14 |      not link.classes:includes 'uri' then
15 |     return nil
16 |   end
17 | 
18 |   -- Remove http and https protocol prefix
19 |   local is_unsafe_protocol = link.target:match '^http%:%/%/' ~= nil
20 |   link_text = link.target
21 |     :gsub('^https?%:%/%/', '')
22 |     :gsub('^(d?x?%.?)doi%.org%/', 'doi:') --prettify DOIs
23 | 
24 |   if is_unsafe_protocol then
25 |     link_text = link_text .. ' 🔓'
26 |   end
27 |   link.content = {pandoc.Str(link_text)}
28 | 
29 |   -- fix DOI links
30 |   link.target = link.target:gsub('^doi%:', 'https://doi.org/')
31 | 
32 |   return link
33 | end
34 | 
35 | return {{Link = prettify_url}}
36 | 


--------------------------------------------------------------------------------
/filters/removeDimensions.lua:
--------------------------------------------------------------------------------
 1 | -- if has image dimensions remove them
 2 | 
 3 | function Image(im)
 4 | 	if im.attributes.width then
 5 | 		im.attributes.width = nil
 6 | 	end
 7 | 	if im.attributes.height then
 8 | 		im.attributes.height = nil
 9 | 	end
10 | 	return im
11 | end


--------------------------------------------------------------------------------
/filters/removeEmphasis.lua:
--------------------------------------------------------------------------------
 1 | -- for plain text output remove emph that gets turned to _word_ otherwise, 
 2 | -- and make strong become smallcap/uppercase
 3 | 
 4 | function Emph(elem)
 5 | 	return elem.content
 6 | end
 7 | 
 8 | function Strong(elem)
 9 | 	return pandoc.SmallCaps(elem.content)
10 | end


--------------------------------------------------------------------------------
/filters/removeHR.rb:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env ruby
 2 | # remove horizontal rules
 3 | 
 4 | require "paru/filter"
 5 | 
 6 | Paru::Filter.run do
 7 |   with "HorizontalRule" do |rule|
 8 |     if rule.has_parent? then
 9 |       rule.parent.delete(rule)
10 |     end
11 |   end
12 | end
13 | 


--------------------------------------------------------------------------------
/filters/removeSpacesBeforeCitations.lua:
--------------------------------------------------------------------------------
 1 | -- see https://github.com/jgm/pandoc/blob/master/doc/lua-filters.md#remove-spaces-before-citations
 2 | --➜ pandoc -t native
 3 | --This is a test [@jdoe2008] and @jdoe2008 said this.
 4 | --[Para [Str "This",Space,Str "is",Space,Str "a",Space,Str "test",Space,Cite [Citation {citationId = "jdoe2008", citationPrefix = [], citationSuffix = [], citationMode = NormalCitation, citationNoteNum = 0, citationHash = 0}] [Str "[@jdoe2008]"],Space,Str "and",Space,Cite [Citation {citationId = "jdoe2008", citationPrefix = [], citationSuffix = [], citationMode = AuthorInText, citationNoteNum = 0, citationHash = 0}] [Str "@jdoe2008"],Space,Str "said",Space,Str "this."]]
 5 | 
 6 | local function is_space_before_author_in_text(spc, cite)
 7 |   return spc and spc.t == 'Space'
 8 |   and cite and cite.t == 'Cite'
 9 |   -- there must be only a single citation, and it must have
10 |   -- mode 'AuthorInText'
11 |   --and #cite.citations == 1
12 |   --and cite.citations[1].mode == 'NormalCitation'
13 | end
14 |   
15 | function Inlines (inlines)
16 |   -- Go from end to start to avoid problems with shifting indices.
17 |   require("mobdebug").start()
18 |   for i = #inlines-1, 1, -1 do
19 |     if is_space_before_author_in_text(inlines[i], inlines[i+1]) then
20 |       inlines:remove(i)
21 |     end
22 |   end
23 |   return inlines
24 | end


--------------------------------------------------------------------------------
/filters/replaceUnitlessDimensions.lua:
--------------------------------------------------------------------------------
 1 | -- if image dimensions without any units, assume points
 2 | 
 3 | function Image(im)
 4 | 	if im.attributes.width then
 5 | 		if im.attributes.width:match "^%d+$" then
 6 | 			im.attributes.width = '' .. im.attributes.width .. 'pt'
 7 | 		end
 8 | 	end
 9 | 	if im.attributes.height then
10 | 		if im.attributes.height:match "^%d+$" then
11 | 			im.attributes.height = '' .. im.attributes.height .. 'pt'
12 | 		end
13 | 	end
14 | 	return im
15 | end


--------------------------------------------------------------------------------
/filters/shared.lua:
--------------------------------------------------------------------------------
 1 | --[[
 2 |   SHARED LUA FILTER
 3 |     This filter contains utility functions that are useful in several filters.
 4 | 
 5 |   USAGE
 6 |     This script is loaded in other script by an RMARKDOW_LUA_SHARED environment variable
 7 |     set inside rmarkdown R package by `render()`.
 8 | 
 9 |     Use this line in other script to use this function
10 |       dofile(os.getenv 'RMARKDOWN_LUA_SHARED')
11 | 
12 |     To use this script directly, use `dofile(<path-to-script>)`
13 | 
14 |   NOTE
15 |     USAGE could change if Pandoc 2.1.2+ is supported only as PANDOC_SCRIPT_FILE is
16 |     available from other Lua Filters. In this case, path to `shared.lua` could be
17 |     determined from other filters relatively and loaded with `dofile()`
18 | 
19 |     See https://gist.github.com/cderv/ca24d2681b0a1c4b6f91e0b49d725f36 for an example
20 |     of `import("shared.lua")`
21 | 
22 |   LICENSE
23 |     MIT License
24 | ]]
25 | 
26 | 
27 | --[[
28 |   This function tests the pandoc version againt a target version.
29 | 
30 |   USAGE
31 |     pandocAvailable {2,1}
32 |   NOTE
33 |     For Pandoc 2.7.3, PANDOC_VERSION >= "2.8" would be enough but before 2.7.3
34 |     it is a table object
35 | ]]
36 | function pandocAvailable(target)
37 |   -- this function only work for Pandoc 2.1 and above. It returns false is not
38 |   if not PANDOC_VERSION then return false end
39 |   assert(target, "No target version specified in pandocAvailable.")
40 |   -- checking each version number
41 |   -- EPOCH.MAJOR.MINOR.PATCH (https://pvp.haskell.org)
42 |   for i = 1,4 do
43 |     -- some versions do not have all numbers
44 |     if not PANDOC_VERSION[i] or not target[i] then break end
45 |     if PANDOC_VERSION[i] < target[i] then return false end
46 |     if PANDOC_VERSION[i] > target[i] then return true end
47 |   end
48 |   return true
49 | end
50 | 
51 | -- for debuging purpose
52 | function print_debug(label,obj,iter)
53 |   local debug_mode = os.getenv("DEBUG_PANDOC_LUA") == "TRUE"
54 |   obj = obj or nil
55 |   iter = iter or pairs
56 |   label = label or ""
57 |   label = "DEBUG (from custom-environment.lua): "..label
58 |   if (debug_mode) then
59 |       if not obj then
60 |           print(label.." nil")
61 |       elseif (type(obj) == "string") then
62 |           print(label.." "..obj)
63 |       elseif type(obj) == "table" then
64 |           for k,v in iter(obj) do
65 |               print(label.."id:"..k.. " val:"..v)
66 |           end
67 |       end
68 |   end
69 |   return nil
70 | end
71 | 
72 | 
73 | --- Returns the type of a metadata value.
74 | --  Author: Albert Krewinkel
75 | --  Source: https://github.com/pandoc/lua-filters/commit/3057acc52d1d6cfb7134c934a5039ce170bf78fa
76 | --
77 | --  Backward compatible function as retrieving type on Metadata has changed.
78 | --  `pandoc.utils.type()` not available before Pandoc 2.17
79 | --
80 | -- @param v a metadata value
81 | -- @treturn string one of `Blocks`, `Inlines`, `List`, `Map`, `string`, `boolean`
82 | function pandoc_type (v)
83 |   if pandoc.utils.type == nil then
84 |     local metatag = type(v) == 'table' and v.t and v.t:gsub('^Meta', '')
85 |     return metatag and metatag ~= 'Map' and metatag or type(v)
86 |   end
87 |   return pandoc.utils.type(v)
88 | end
89 | 
90 | 


--------------------------------------------------------------------------------
/filters/simplifyMetadata.rb:
--------------------------------------------------------------------------------
  1 | #!/usr/bin/env ruby
  2 | # this converts an author metadata field
  3 | # author:  [name: ..., affiliation:..., correspondence:...]) into a format
  4 | # author: Name^affiliation,correspondence,contribution^ that the Word/ODT templates can handle.
  5 | # This is because the Word/ODT templates do not have the flexibility
  6 | # the other pandoc output formats do...
  7 | #
  8 | # VERSION: 1.0.2
  9 | 
 10 | 
 11 | require 'paru/filter'
 12 | def fixName(author)
 13 | 	author = Hash['name' => author] if author.is_a?(String)
 14 | 	unless author.key?('name') # convert first key id to name: key
 15 | 	if author.values[0].is_a?(Hash)
 16 | 		values = author.values[0]
 17 | 		values['id'] = author.keys[0]
 18 | 		values['name'] = values['id']
 19 | 		author = values
 20 | 	else
 21 | 		author['name'] = 'Unknown'
 22 | 	end
 23 |   end
 24 |   author
 25 | end
 26 | 
 27 | testKey = 'author'
 28 | pKey = 'pandocomatic-fileinfo'
 29 | nameKey = 'name'
 30 | affKey = 'affiliation'
 31 | corrKey = 'correspondence'
 32 | corrMarker = '\*' # which marker to use, if asterisk you must escape it.
 33 | contributionKey = 'equal_contributor'
 34 | conMarker = '†'
 35 | 
 36 | Paru::Filter.run do
 37 | 	
 38 | 	stop! unless metadata.key?(testKey)
 39 | 	stop! if metadata.key?(pKey) && !metadata[pKey]['to'].match(/docx|odt/)
 40 | 	newAuthor = nil
 41 | 	correspondence = nil
 42 | 	contribution = nil
 43 | 	text = ''
 44 | 	authors = metadata[testKey]
 45 | 	authors = [Hash['name' => authors]] if authors.is_a?(String)
 46 | 	if authors.is_a?(Array)
 47 | 		newAuthor = Array.new(authors.length)
 48 | 		authors.each_with_index do |aut, i|
 49 | 			aut = fixName(aut)
 50 | 			if aut.key?(nameKey)
 51 | 				newAuthor[i] = aut[nameKey].to_s
 52 | 				if aut.key?(affKey)
 53 | 					if aut[affKey].is_a?(String) || aut[affKey].is_a?(Integer)
 54 | 						aff = aut[affKey].to_s
 55 | 						frag = ''
 56 | 						a = aff.split(',') # comma seperated values
 57 | 						a.each do |af|
 58 | 							if af.match(/^\d+$/)
 59 | 								frag += '^' + af + '^'
 60 | 							else
 61 | 								frag += af + ''
 62 | 							end
 63 | 							newAuthor[i] += frag + ' '
 64 | 						end
 65 | 					elsif aut['affiliation'].is_a?(Array)
 66 | 						newAuthor[i] += '^'
 67 | 						aut[affKey].each { |aff| newAuthor[i] += aff.to_s + ',' }
 68 | 						newAuthor[i] = newAuthor[i][0..-2] + '^'
 69 | 					end
 70 | 				end
 71 | 				if aut.key?(corrKey)
 72 | 					if newAuthor[i] =~ /\^$/
 73 | 						newAuthor[i] = newAuthor[i][0..-2] + corrMarker + '^'
 74 | 					else
 75 | 						newAuthor[i] += '^' + corrMarker + '^'
 76 | 					end
 77 | 					if aut.key?('email')
 78 | 						email = aut['email']
 79 | 					else
 80 | 						email = aut[corrKey]
 81 | 					end
 82 | 					if correspondence.nil?
 83 | 						correspondence = "[#{email}](#{email})"
 84 | 					else
 85 | 						correspondence += ' & ' + "[#{email}](#{email})"
 86 | 					end
 87 | 				end
 88 | 				if aut.key?(contributionKey)
 89 | 					if newAuthor[i] =~ /\^$/
 90 | 						newAuthor[i] = newAuthor[i][0..-2] + conMarker + '^'
 91 | 					else
 92 | 						newAuthor[i] += '^' + conMarker + '^'
 93 | 					end
 94 | 					contribution = '† equal contribution'
 95 | 				end
 96 | 			end
 97 | 		end
 98 | 	elsif authors.is_a?(Hash) # single name: John Doe author
 99 | 		newAuthor = Array.new(authors.length)
100 | 		newAuthor[0] = authors[nameKey]
101 | 	end
102 | 
103 | 	metadata[testKey] = newAuthor unless newAuthor.nil?
104 | 
105 | 	unless contribution.nil?
106 | 		p = Paru::PandocFilter::Para.new([])
107 | 		p.inner_markdown = contribution
108 | 		document.prepend(p)
109 | 	end
110 | 	unless correspondence.nil?
111 | 		correspondence = '**' + corrMarker + ' Correspondence**: ' + correspondence + '  \n'
112 | 		p = Paru::PandocFilter::Para.new([])
113 | 		p.inner_markdown = correspondence
114 | 		document.prepend(p)
115 | 	end
116 | 
117 | 	stop!
118 | end
119 | 


--------------------------------------------------------------------------------
/filters/testErrorFilter.rb:
--------------------------------------------------------------------------------
1 | #!/usr/bin/env ruby
2 | # this is designed fail and cause a pandoc error, useful for testing only
3 | require "paru/filter"
4 | Paru::Filter.run do 
5 |     with "Emph" do |e|
6 |         e.append(Paru::PandocFilter::Para.new([]))
7 |     end
8 | end


--------------------------------------------------------------------------------
/filters/testFilter.rb:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env ruby
 2 | # testing filter, uses new debug gem to remote debug.
 3 | #
 4 | # > gem install debug
 5 | #
 6 | # In VSCode: https://marketplace.visualstudio.com/items?itemName=KoichiSasada.vscode-rdbg
 7 | 
 8 | # DEBUG BLOCK START
 9 | require 'debug/open_nonstop' 
10 | require 'paru/filter'
11 | 
12 | testKey = 'author'
13 | pmaticKey = 'pandocomatic-fileinfo'
14 | insertKey = 'testname'
15 | 
16 | Paru::Filter.run do
17 |   binding.break # we will halt here, connect with `rdbg -A` or use VS Code extension
18 |   if metadata.key?(testKey) 
19 |     if metadata.key?(pmaticKey) && (metadata[pmaticKey]['to'].match(/docx|odt/))
20 |       stop!
21 |     end
22 |     au = metadata[testKey]
23 |     if au.is_a?(String)
24 |       nau = [ Hash[ insertKey => au ] ]
25 |     elsif au.is_a?(Array)
26 |       if au[0].is_a?(String)
27 |         nau = Array.new(au.length) {Hash.new}
28 |         au.each_index { |i| 
29 |           cp = au[i].match(/\^[\d\s\,§†\*]+\^/)
30 |           if cp.nil?
31 |             nau[i] = Hash[ insertKey => au[i] ] 
32 |           else
33 |             nau[i] = Hash[ insertKey => cp.pre_match, 'affiliation' => cp.to_s ] 
34 |           end
35 |         }
36 |       elsif au[0].is_a?(Hash)
37 |         nau = [ Hash[ insertKey => au[0]['name'] ] ]
38 |       end
39 |     end
40 |     if not nau.nil?
41 |       metadata['testFilterOutput'] = nau
42 |     end
43 |   end
44 |   if metadata['keywords']
45 |     metadata['tags'] = metadata['keywords']
46 |   end
47 |   stop!
48 | end
49 | 


--------------------------------------------------------------------------------
/filters/testFilterByebug.rb:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env ruby
 2 | # testing filter, uses byebug to remote debug
 3 | 
 4 | # DEBUG BLOCK START
 5 | require 'byebug/core'
 6 | require 'byebug'
 7 | PORT = 1234
 8 | warn "\n!!!DEBUG Server started: localhost:#{PORT} @ " + Time.now.to_s + "\n\n"
 9 | Byebug.wait_connection = true
10 | Byebug.start_server('127.0.0.1', PORT)
11 | # DEBUG BLOCK END
12 | 
13 | byebug
14 | 
15 | require 'paru/filter'
16 | 
17 | testKey = 'author'
18 | pmaticKey = 'pandocomatic-fileinfo'
19 | insertKey = 'testname'
20 | 
21 | Paru::Filter.run do
22 |   byebug
23 |   if metadata.key?(testKey) 
24 |     if metadata.key?(pmaticKey) && (metadata[pmaticKey]['to'].match(/docx|odt/))
25 |       stop!
26 |     end
27 |     au = metadata[testKey]
28 |     if au.is_a?(String)
29 |       nau = [ Hash[ insertKey => au ] ]
30 |     elsif au.is_a?(Array)
31 |       if au[0].is_a?(String)
32 |         nau = Array.new(au.length) {Hash.new}
33 |         au.each_index { |i| 
34 |           cp = au[i].match(/\^[\d\s\,§†\*]+\^/)
35 |           if cp.nil?
36 |             nau[i] = Hash[ insertKey => au[i] ] 
37 |           else
38 |             nau[i] = Hash[ insertKey => cp.pre_match, 'affiliation' => cp.to_s ] 
39 |           end
40 |         }
41 |       elsif au[0].is_a?(Hash)
42 |         nau = [ Hash[ insertKey => au[0]['name'] ] ]
43 |       end
44 |     end
45 |     if not nau.nil?
46 |       metadata['testFilterOutput'] = nau
47 |     end
48 |   end
49 |   if metadata['keywords']
50 |     metadata['tags'] = metadata['keywords']
51 |   end
52 |   stop!
53 | end
54 | 


--------------------------------------------------------------------------------
/filters/typstFix.lua:
--------------------------------------------------------------------------------
 1 | --[[
 2 | 	typstFix.lua: typst fix filter for pandoc 
 3 | 	Version:   1.05
 4 | 	Copyright: (c) 2024 Ian Max Andolina License=MIT, see LICENSE for details
 5 | 
 6 | 	Usage: Solves some problems for Typst output from Pandoc:
 7 | 	(1) Typst uses <label> syntax for #ids, which is not compatible with the
 8 | 	Raw HTML extension. We take advantage of Raw HTML extension to convert
 9 | 	<...> to a typst RawInline. (2) The second problem is that Typst uses @fig-
10 | 	and @tbl- to refer to figures and tables, which is not compatible with
11 | 	the use of @ for Pandoc citations. So we check if the ref starts with
12 | 	fig- or tbl- and convert it to a typst RawInline. (3) [this is now fixed] 
13 | 	Finally, Pandoc injects a physical width into Images, causing them to 
14 | 	overflow the page margins, if no width has been set, we set it to 100%.
15 | ]]
16 | 
17 | -- convert raw html to raw typst as typst uses <label> for #IDs
18 | function RawInline(r)
19 | 	if not FORMAT:match('typst') then return end
20 | 	if string.match(r.format, "html") then
21 | 		return pandoc.RawInline("typst", r.text)
22 | 	end
23 | end
24 | 
25 | -- convert Typst crossreferences like @fig-one to RawInlines
26 | -- everything else stays a bibliographic citation
27 | function Cite(cite)
28 | 	if not FORMAT:match('typst') then return end
29 | 	local c = cite.citations[1].id
30 | 	if string.match(c, "^fig%-") or
31 | 	string.match(c, "^tbl%-") or
32 | 	string.match(c, "^eq%-") or
33 | 	string.match(c, "^lst%-") or 
34 | 	string.match(c, "^sec%-") then
35 | 		c = "@" .. c
36 | 		return pandoc.RawInline("typst", c)
37 | 	end
38 | end
39 | 
40 | -- make sure images without width attribute have a 100% width
41 | -- see https://github.com/jgm/pandoc/issues/9236
42 | -- now fixed V0.11.0 of Typst + Pandoc v3.1.12.3, so not needed
43 | -- function Image(im)
44 | -- 	local env = pandoc.system.environment()
45 | -- 	local var = env["FIGWIDTH"] -- possible override with ENV
46 | -- 	if not var or var == "" then
47 | -- 		newwidth = "100%"
48 | -- 	else
49 | -- 		newwidth = var
50 | -- 	end
51 | -- 	if not im.attributes.width then
52 | -- 		im.attributes.width = newwidth
53 | -- 		return im
54 | -- 	end
55 | -- end
56 | 
57 | 


--------------------------------------------------------------------------------
/filters/wordcount.lua:
--------------------------------------------------------------------------------
 1 | -- counts words in a document 
 2 | -- use it as: pandoc --lua-filter wordcount.lua input.md
 3 | 
 4 | words = 0 
 5 | 
 6 | wordcount = { 
 7 |   Str = function(el) 
 8 |     -- we don't count a word if it's entirely punctuation: 
 9 |     if el.text:match("%P") then 
10 |         words = words + 1 
11 |     end 
12 |   end, 
13 | 
14 |   Code = function(el) 
15 |     _,n = el.text:gsub("%S+","") 
16 |     words = words + n 
17 |   end, 
18 | 
19 |   CodeBlock = function(el) 
20 |     _,n = el.text:gsub("%S+","") 
21 |     words = words + n 
22 |   end 
23 | } 
24 | 
25 | function Pandoc(el) 
26 |     -- skip metadata, just count body: 
27 |     pandoc.walk_block(pandoc.Div(el.blocks), wordcount) 
28 |     print("There were " .. words .. " words in body") 
29 |     os.exit(0) 
30 | end 


--------------------------------------------------------------------------------
/metadata/typst-includes.yaml:
--------------------------------------------------------------------------------
 1 | header-includes: |
 2 |   ```{=typst}
 3 |   // header-includes
 4 |   #set text(ligatures: true, discretionary-ligatures: false, number-type: "old-style")
 5 |   ```
 6 | fontsize: 12pt
 7 | linestretch: 1.75
 8 | mainfont: "Dolly Pro"
 9 | headerfont: "Alegreya Sans SC"
10 | sansfont: "Alegreya Sans"
11 | monofont: "Rec Mono Casual"
12 | papersize: a4
13 | margin: {x: 1.75cm, y: 2cm}
14 | columns: 1
15 | lang: "en-GB"
16 | toc-title: "Contents"
17 | doindex: false


--------------------------------------------------------------------------------
/metadata/typst-plain.yaml:
--------------------------------------------------------------------------------
1 | mainfont: "Alegreya Sans"
2 | fontsize: 12pt
3 | monofont: "Rec Mono Casual"
4 | papersize: a4
5 | margin: {x: 1.75cm, y: 2cm}
6 | columns: 1
7 | lang: "en-GB"
8 | toc-title: "Table of Contents"
9 | doindex: false


--------------------------------------------------------------------------------
/postprocessors/fixHTML.rb:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env ruby
 2 | #encoding: utf-8
 3 | # This fixes several problems with HTML output
 4 | 
 5 | Encoding.default_external = Encoding::UTF_8
 6 | Encoding.default_internal = Encoding::UTF_8
 7 | 
 8 | output = $stdin.read
 9 | # remove these divs if they are empty!
10 | output.gsub!(%r{<div class="correspondence">\s+</div>}, '')
11 | output.gsub!(%r{<div class="author_affiliations">\s+</div>}, '')
12 | 
13 | puts output
14 | 


--------------------------------------------------------------------------------
/postprocessors/fixLaTeX.rb:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env ruby
 2 | #encoding: utf-8
 3 | 
 4 | # This tweaks several parts of the Pandoc LaTeX output
 5 | # VERSION: 1.0.3
 6 | 
 7 | Encoding.default_external = Encoding::UTF_8
 8 | Encoding.default_internal = Encoding::UTF_8
 9 | 
10 | output = $stdin.read
11 | 
12 | # make sure we perform font substitutions for characters that may not have a font entry
13 | # fixfont uses Cambria Math with a huge glyph range
14 | list = %w[⌘ ⬄ ↔ ⇔ ⇄ ⇨ ⇦ → ← ⇳ Δ ⟳ ⟲ ‐ ⌲ ⌖ ⌽ ⌀ ⎆ ⎅ ⎌ ⎊ ⏎ ⌨︎]
15 | list.each do |ch|
16 |   output.gsub!(/(?<!fixfont\{)(#{ch})(?!\})/, "\\fixfont\{#{ch}\}")
17 | end
18 | 
19 | # make sure we perform font substitutions for characters that may not have a font entry
20 | # fixfontB uses Arial Unicode MS with a huge glyph range
21 | list = %w[⌦ ⌫ ✉ ☢︎ ✆ ☠︎ ✎ ♂︎ ♀︎ ☍ ☤ ☁︎]
22 | list.each do |ch|
23 |   output.gsub!(/(?<!fixfontB\{)(#{ch})(?!\})/, "\\fixfontB\{#{ch}\}")
24 | end
25 | 
26 | # ensure correct titlecase for Neuroscience terms
27 | list = %w[MT MST TEO TRN GABA GABAergic LGN dLGN V1 V2 V3 V4 V5 fMRI EEG MEG tDCS]
28 | list.each do |phrase|
29 |   output.gsub!(/\b#{phrase}\b/i, phrase)
30 | end
31 | 
32 | # make quotes italicised
33 | output.gsub!(/\\begin\{quote\}/, '\begin{quote}\emph{')
34 | output.gsub!(/\\end\{quote\}/, '}\end{quote}')
35 | 
36 | # make isolated figures centered
37 | output.gsub!(/^\\includegraphics{/, '\\includegraphics[center]{')
38 | #output.gsub!(/^\\includegraphics\[([^\]]*)\]/, '\\includegraphics[\1,center]')
39 | 
40 | # make sure reference typography is small and sans-font
41 | output.gsub!(/\\label{(.*(references|bibliography))}/, '\\label{\1}\\sffamily\\small')
42 | 
43 | # simplify DOI links
44 | output.gsub!(/\\url{https:\/\/doi.org\/([^\}]+)}/,'\\href{https://doi.org/\1}{doi:\1}')
45 | 
46 | puts output
47 | 


--------------------------------------------------------------------------------
/postprocessors/typst2pdf:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env elvish
 2 | # Finds all *.typ files and compiles them if they've been modified 
 3 | # in the last 120 seconds.
 4 | # VERSION: 0.1.2
 5 | 
 6 | var @files = *[nomatch-ok][type:regular].{typ typst}
 7 | var now = (date +%s); # current time in seconds
 8 | 
 9 | each {|f|
10 | 	var mod = (stat -f %c $f) # file modified time in seconds
11 | 	if ( < (- $now $mod) 120 ) { 
12 | 		try { typst compile --pdf-standard a-2b $f $f".pdf" 2>&1 } catch { } 
13 | 	}
14 | } $files


--------------------------------------------------------------------------------
/preprocessors/convertEndnoteRefs.rb:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env ruby
 2 | #encoding: utf-8
 3 | 
 4 | Encoding.default_external = Encoding::UTF_8
 5 | Encoding.default_internal = Encoding::UTF_8
 6 | 
 7 | # the job of this preproceccer is to convert endnote citations to pandoc citations.
 8 | # It assumes your BibTeX keys are authorYear and will not be able to handle collisions
 9 | # as endnote uses unique IDs which cannot be used in the bib file easily.
10 | input = $stdin.read
11 | # this regex matches {Letter ... Number} should get endnote refs but not overmatch, replace with brackets
12 | output = input.gsub(/(?:\{)([\p{Alpha}][^\}]+?)(?:(?<=[0-9])\})/, '[\1]')
13 | #this converts to @authorYear pandoc format
14 | output.gsub!(/([\p{Alpha}][\p{Alnum}\s-]+)(?:,\s)(\d{4})(?:\s#\d+)/) { | str | str = "@" + $1.tr(' ', '').downcase + $2 }
15 | #this combines adjacent pandoc refs together
16 | output.gsub!(/\]\[@(?=\p{Alpha})/) { | str | str = "; @" }
17 | 
18 | puts output
19 | 


--------------------------------------------------------------------------------
/preprocessors/criticmarkup-accept.py:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env python
 2 | 
 3 | import re
 4 | import sys
 5 | 
 6 | 
 7 | selected_string = sys.argv[1]
 8 | 
 9 | add_edit = re.compile(r'(?s)\{\+\+(.*?)\+\+[ \t]*(\[(.*?)\])?[ \t]*\}')
10 | del_edit = re.compile(r'(?s)\{\-\-(.*?)\-\-[ \t]*(\[(.*?)\])?[ \t]*\}')
11 | sub_edit = re.compile(r'''(?s)\{\~\~(?P<original>(?:[^\~\>]|(?:\~(?!\>)))+)\~\>(?P<new>(?:[^\~\~]|(?:\~(?!\~\})))+)\~\~\}''')
12 | 
13 | if len(selected_string) > 0:
14 |     a = add_edit.sub(r'\1', selected_string)
15 |     d = del_edit.sub(r'', a)
16 |     s = sub_edit.sub(r'\2', d)
17 |     print s
18 | else:
19 | 	print selected_string


--------------------------------------------------------------------------------
/preprocessors/criticmarkup-reject.py:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env python
 2 | 
 3 | import re
 4 | import sys
 5 | 
 6 | 
 7 | selected_string = sys.argv[1]
 8 | 
 9 | add_edit = re.compile(r'(?s)\{\+\+(.*?)\+\+[ \t]*(\[(.*?)\])?[ \t]*\}')
10 | del_edit = re.compile(r'(?s)\{\-\-(.*?)\-\-[ \t]*(\[(.*?)\])?[ \t]*\}')
11 | sub_edit = re.compile(r'''(?s)\{\~\~(?P<original>(?:[^\~\>]|(?:\~(?!\>)))+)\~\>(?P<new>(?:[^\~\~]|(?:\~(?!\~\})))+)\~\~\}''')
12 | 
13 | if len(selected_string) > 0:
14 |     a = add_edit.sub(r'', selected_string)
15 |     d = del_edit.sub(r'\1', a)
16 |     s = sub_edit.sub(r'\1', d)
17 |     print s
18 | else:
19 | 	print selected_string


--------------------------------------------------------------------------------
/preprocessors/criticmarkup.rb:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env ruby
 2 | #encoding: utf-8
 3 | 
 4 | Encoding.default_external = Encoding::UTF_8
 5 | Encoding.default_internal = Encoding::UTF_8
 6 | 
 7 | # the job of this preproceccer is to convert criticmarkup to HTML
 8 | # which pandoc can parse to e.g. Word output
 9 | input = $stdin.read
10 | output = input.gsub(/{~~/, '<del>')
11 | output.gsub!(/~~}/, '</ins>')
12 | output.gsub!(/(?<=\S)~>(?=\S)/, '</del><ins>')
13 | output.gsub!(/\{\+\+/, '<ins>')
14 | output.gsub!(/\+\+\}/, '</ins>')
15 | output.gsub!(/\{--/,   '<del>')
16 | output.gsub!(/--\}/,   '</del>')
17 | output.gsub!(/\{\=\=/, '<mark>')
18 | output.gsub!(/\=\=\}/, '</mark>')
19 | output.gsub!(/\{\>\>/, '<span class="comment" title="')
20 | output.gsub!(/\<\<\}/, '">†</span>')
21 | puts output
22 | 


--------------------------------------------------------------------------------
/preprocessors/criticmarkup.sh:
--------------------------------------------------------------------------------
  1 | #!/bin/bash
  2 | cd "$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
  3 | 
  4 | # getopts
  5 | 
  6 | ## reset getopts
  7 | OPTIND=1
  8 | 
  9 | ## Initialize parameters
 10 | accept=false
 11 | reject=false
 12 | permanent=false
 13 | output_EXT=''
 14 | 
 15 | ## get the options
 16 | while getopts "arpd:" opt; do
 17 | 	case "$opt" in
 18 | 	a)  accept=true
 19 | 		;;
 20 | 	r)  reject=true
 21 | 		;;
 22 | 	p)  permanent=true
 23 | 		;;
 24 | 	d)  output_EXT=$OPTARG
 25 | 		;;
 26 | 	esac
 27 | done
 28 | 
 29 | shift $((OPTIND-1))
 30 | 
 31 | [ "$1" = "--" ] && shift
 32 | 
 33 | ## check output_EXT
 34 | if [ "$output_EXT" != '' ] && [ "$output_EXT" != "html" ] && [ "$output_EXT" != "tex" ] && [ "$output_EXT" != "pdf" ]; then
 35 | 	echo "Output format should be either html or tex/pdf."
 36 | 	exit 1
 37 | fi
 38 | 
 39 | # preparation
 40 | 
 41 | ## get the content of the file
 42 | if [ $# -ge 1 -a -f "$1" ]; then
 43 | 	CONTENT=$(<"$@")
 44 | else
 45 | 	CONTENT=$(<"/dev/stdin")
 46 | fi
 47 | 
 48 | # cooking the result
 49 | 
 50 | ## if d then show diff (CriticMarkup)
 51 | if [ "$output_EXT" = "html" ] || [ "$output_EXT" = "tex" ] || [ "$output_EXT" = "pdf" ]; then
 52 | ### if html then show CriticMarkup in html (sub, del, ins, mark, comment)
 53 | 	if [ "$output_EXT" = "html" ]; then
 54 | 		CONTENT=$(echo "$CONTENT" | sed \
 55 | 			-e s/'~~}'/'<\/ins>'/g \
 56 | 			-e s/'{~~'/'<del>'/g \
 57 | 			-e s/'~>'/'<\/del><ins>'/g \
 58 | 			-e s/'{--'/'<del>'/g \
 59 | 			-e s/'--}'/'<\/del>'/g \
 60 | 			-e s/'{++'/'<ins>'/g \
 61 | 			-e s/'++}'/'<\/ins>'/g \
 62 | 			-e s/'{=='/'<mark>'/g \
 63 | 			-e s/'==}'/'<\/mark>'/g \
 64 | 			-e s/'{>>'/'<aside>'/g \
 65 | 			-e s/'<<}'/'<\/aside>'/g)
 66 | ### else (tex/pdf) then show CriticMarkup in tex (sub, del, ins, mark, comment)
 67 | 	else
 68 | 		CONTENT=$(echo "$CONTENT" | sed \
 69 | 			-e s/'~~}'/'}'/g \
 70 | 			-e s/'{~~'/'\\st{'/g \
 71 | 			-e s/'~>'/'}\\underline{'/g \
 72 | 			-e s/'{--'/'\\st{'/g \
 73 | 			-e s/'--}'/'}'/g \
 74 | 			-e s/'{++'/'\\underline{'/g \
 75 | 			-e s/'++}'/'}'/g \
 76 | 			-e s/'{=='/'\\hl{'/g \
 77 | 			-e s/'==}'/'}'/g \
 78 | 			-e s/'{>>'/'\\marginpar{'/g \
 79 | 			-e s/'<<}'/'}'/g)
 80 | ## else (not d, not showing CriticMarkup)
 81 | 	fi
 82 | else
 83 | ### if r or a then remove highlights and archive comments
 84 | 	if [ $reject = true ] || [ $accept = true ]; then
 85 | 		CONTENT=$(echo "$CONTENT" | sed \
 86 | 			-e s/'{=='/''/g \
 87 | 			-e s/'==}'/''/g \
 88 | 			-e s/'{>>'/'<\!-- '/g \
 89 | 			-e s/'<<}'/' -->'/g)
 90 | #### if r then reject sub, del, ins
 91 | 		if [ $reject = true ]; then
 92 | 			CONTENT=$(./criticmarkup-reject.py "$CONTENT")
 93 | #### else (a then accept sub, del, ins)
 94 | 		else
 95 | 			CONTENT=$(./criticmarkup-accept.py "$CONTENT")
 96 | 		fi
 97 | 	fi
 98 | fi
 99 | 
100 | # output
101 | if [ $permanent = false ]; then
102 | 	echo "$CONTENT"
103 | else
104 | 	echo "$CONTENT" > "$@"
105 | fi


--------------------------------------------------------------------------------
/preprocessors/fixCrossref.rb:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env ruby
 2 | #encoding: utf-8
 3 | 
 4 | # This script is used to move pandoc-crossref labels from inside markup,
 5 | # which is what Scrivener would generate from it style system, moving the
 6 | # labels to the correct places so that pandoc-crossref can find them.
 7 | # https://lierdakil.github.io/pandoc-crossref/#image-labels
 8 | # This script only corrects figures and equations.
 9 | 
10 | Encoding.default_external = Encoding::UTF_8
11 | Encoding.default_internal = Encoding::UTF_8
12 | 
13 | text = $stdin.read
14 | text = text.split(/\n/)
15 | labels = []
16 | tags = []
17 | text.each {|line|
18 | 	next if line.empty?
19 | 	m = line.match(/^!\[(#fig:[^ ]+).+\]\[(.+)\]/)
20 | 	if !m.nil?
21 | 		labels = labels.push(m[1])
22 | 		tags = tags.push(m[2])
23 | 		line.gsub!(/#{m[1]}/,'')
24 | 	end
25 | 	# fix equations
26 | 	line.gsub!(/(\{#eq:.+\})(\s+\$\$)\s*$/, '  $$  \1')
27 | }
28 | 
29 | text = text.join("\n")
30 | 
31 | labels.each_index {|idx|
32 | 	tR = '(\[' + tags[idx] + '\]:.+)\{(.+)\}'
33 | 	text.gsub!(/#{tR}/, '\1 {' + labels[idx] + ' \2}')
34 | }
35 | 
36 | text.gsub!(/\n!\[\s+/, "\n![")
37 | 
38 | puts text
39 | 


--------------------------------------------------------------------------------
/preprocessors/removeAffiliations.rb:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env ruby
 2 | #encoding: utf-8
 3 | Encoding.default_external = Encoding::UTF_8
 4 | Encoding.default_internal = Encoding::UTF_8
 5 | 
 6 | # This removes an affiliation paragraph if present, 
 7 | # as LaTeX will generate this from the metadata
 8 | input = $stdin.read
 9 | output = input.gsub(/(^[\*]?Affiliations[^\n]+)/, "\n")
10 | 
11 | puts output
12 | 


--------------------------------------------------------------------------------
/preprocessors/removeImageDimensions.rb:
--------------------------------------------------------------------------------
 1 | #!/usr/bin/env ruby
 2 | #encoding: utf-8
 3 | Encoding.default_external = Encoding::UTF_8
 4 | Encoding.default_internal = Encoding::UTF_8
 5 | 
 6 | # Scrivener adds image dimensions for 300DPI images, 
 7 | # and doesn't use units
 8 | # this makes images too small in LaTeX, and
 9 | # typst fails with unitless values
10 | input = $stdin.read
11 | output = input.gsub(/((width|height)=\d+\s*)/, "")
12 | puts output
13 | 


--------------------------------------------------------------------------------
/preprocessors/setupKaobook.sh:
--------------------------------------------------------------------------------
1 | #!/bin/zsh
2 | 
3 | texmf=`kpsewhich -var-value=TEXMFHOME`
4 | if [[ ! -d $texmf/tex/latex/kaobook]]; then
5 | 	mkdir -p $texmf/tex/latex
6 | 	cd $texmf/tex/latex
7 | 	git clone https://github.com/fmarotta/kaobook.git kaobook
8 | fi
9 | 


--------------------------------------------------------------------------------
/scripts/copy-resources.elv:
--------------------------------------------------------------------------------
1 | #!/usr/bin/env elvish
2 | 
3 | var curdir = (pwd)
4 | var pd = $E:HOME/.local/share/pandoc
5 | cp $pd/custom/* $curdir
6 | cp $pd/templates/*.svg $curdir
7 | echo (styled "Copied Pandoc support files to current folder" bold italic yellow)


--------------------------------------------------------------------------------
/scripts/test.elv:
--------------------------------------------------------------------------------
1 | #!/usr/bin/env elvish
2 | 
3 | echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
4 | print "\n\n"
5 | put $paths
6 | env|sort
7 | print "\n\n"
8 | echo "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"


--------------------------------------------------------------------------------
/templates/after-header-includes.latex:
--------------------------------------------------------------------------------
 1 | \usepackage{bookmark}
 2 | \IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
 3 | \urlstyle{$if(urlstyle)$$urlstyle$$else$same$endif$}
 4 | $if(links-as-notes)$
 5 | % Make links footnotes instead of hotlinks:
 6 | \DeclareRobustCommand{\href}[2]{#2\footnote{\url{#1}}}
 7 | $endif$
 8 | $if(verbatim-in-note)$
 9 | \VerbatimFootnotes % allow verbatim text in footnotes
10 | $endif$
11 | 


--------------------------------------------------------------------------------
/templates/background1.pdf:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/iandol/dotpandoc/01ca3fc68697022506ad376810bb2c4d90b386df/templates/background1.pdf


--------------------------------------------------------------------------------
/templates/background1.svg:
--------------------------------------------------------------------------------
 1 | <?xml version="1.0" encoding="UTF-8"?>
 2 | <!-- Created with Inkscape (http://www.inkscape.org/) -->
 3 | <svg width="210mm" height="297mm" version="1.1" viewBox="0 0 793.7 1122.5" xmlns="http://www.w3.org/2000/svg">
 4 |  <defs>
 5 |   <clipPath id="clipPath2">
 6 |    <path transform="translate(-595.28 87.214)" d="m0 460.76h595.28v-547.98h-595.28z"/>
 7 |   </clipPath>
 8 |   <clipPath id="clipPath4">
 9 |    <path transform="matrix(1.3333 0 0 -1.3333 0 1122.5)" d="M 0,841.89 H 595.276 V 0 H 0 Z"/>
10 |   </clipPath>
11 |   <clipPath id="clipPath5">
12 |    <path transform="translate(0 -201.73)" d="m0 201.73h412.11v-288.94h-412.11z"/>
13 |   </clipPath>
14 |   <clipPath id="clipPath7">
15 |    <path transform="matrix(1.3333 0 0 -1.3333 0 1122.5)" d="M 0,841.89 H 595.276 V 0 H 0 Z"/>
16 |   </clipPath>
17 |  </defs>
18 |  <g transform="matrix(1 0 0 .9167 1.1125 93.506)" clip-path="url(#clipPath4)" opacity=".4">
19 |   <path transform="matrix(1.3333 0 0 -1.3333 793.7 1238.8)" d="m0 0v547.98l-595.28-547.98z" clip-path="url(#clipPath2)" fill="#f5b000"/>
20 |  </g>
21 |  <g clip-path="url(#clipPath7)" opacity=".6">
22 |   <path transform="matrix(1.3333 0 0 -1.3333 0 853.54)" d="m0 0 412.11-288.94h-412.11z" clip-path="url(#clipPath5)" fill="#f24900"/>
23 |  </g>
24 | </svg>
25 | 


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/templates/background2.pdf:
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https://raw.githubusercontent.com/iandol/dotpandoc/01ca3fc68697022506ad376810bb2c4d90b386df/templates/background2.pdf


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/templates/background2.svg:
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 1 | <?xml version="1.0" encoding="UTF-8"?>
 2 | <!-- Created with Inkscape (http://www.inkscape.org/) -->
 3 | <svg width="210mm" height="297mm" version="1.1" viewBox="0 0 793.7 1122.5" xmlns="http://www.w3.org/2000/svg">
 4 |  <g>
 5 |   <path transform="matrix(1.3333 0 0 -1.3333 0 1122.5)" d="m595.28 487.98-530.1-487.98h530.1z" fill="#01a4ad"/>
 6 |   <path transform="matrix(1.3333 0 0 -1.3333 0 1122.5)" d="m0 228.94v-228.94h326.54z" fill="#7fd800"/>
 7 |   <path transform="matrix(1.3333 0 0 -1.3333 0 1122.5)" d="m260.74 180.02-195.56-180.02h452.32z" fill="#117298"/>
 8 |   <path transform="matrix(1.3333 0 0 -1.3333 0 1122.5)" d="m178.18 104.02-113-104.02h261.36z" fill="#004857"/>
 9 |  </g>
10 | </svg>
11 | 


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/templates/background3.pdf:
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https://raw.githubusercontent.com/iandol/dotpandoc/01ca3fc68697022506ad376810bb2c4d90b386df/templates/background3.pdf


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/templates/background3.svg:
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 1 | <?xml version="1.0" encoding="UTF-8"?>
 2 | <!-- Created with Inkscape (http://www.inkscape.org/) -->
 3 | <svg width="793.7" height="1122.5" version="1.1" viewBox="0 0 793.7 1122.5" xmlns="http://www.w3.org/2000/svg">
 4 |  <g>
 5 |   <path transform="matrix(1.3333 0 0 -1.3333 0 1122.5)" d="m595.28-1e-3v547.98l-595.28-547.98z" fill="#00c8d8" opacity=".56014"/>
 6 |   <path transform="matrix(1.3333 0 0 -1.3333 0 1122.5)" d="m0 288.94 412.11-288.94h-412.11z" fill="#009292" opacity=".61856"/>
 7 |   <path transform="matrix(1.3333 0 0 -1.3333 0 1122.5)" d="m178.18 164.02-178.18-164.02h412.11z" fill="#00737c"/>
 8 |  </g>
 9 | </svg>
10 | 


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/templates/background4.pdf:
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https://raw.githubusercontent.com/iandol/dotpandoc/01ca3fc68697022506ad376810bb2c4d90b386df/templates/background4.pdf


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/templates/background4.svg:
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 1 | <?xml version="1.0" encoding="UTF-8"?>
 2 | <!-- Created with Inkscape (http://www.inkscape.org/) -->
 3 | <svg width="793.7" height="1122.5" version="1.1" viewBox="0 0 793.7 1122.5" xmlns="http://www.w3.org/2000/svg">
 4 |  <g>
 5 |   <path transform="matrix(1.3333 0 0 -1.3333 0 1122.5)" d="m595.28-60.001v547.98l-595.28-547.98z" fill="#ffcc01" opacity=".69759"/>
 6 |   <path transform="matrix(1.3333 0 0 -1.3333 0 1122.5)" d="m0 228.94 412.11-288.94h-412.11z" fill="#05386e" opacity=".76632"/>
 7 |   <path transform="matrix(1.3333 0 0 -1.3333 0 1122.5)" d="m178.18 104.02-178.18-164.02h412.11z" fill="#fe771e"/>
 8 |  </g>
 9 | </svg>
10 | 


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/templates/background5.pdf:
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https://raw.githubusercontent.com/iandol/dotpandoc/01ca3fc68697022506ad376810bb2c4d90b386df/templates/background5.pdf


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/templates/background5.svg:
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 1 | <?xml version="1.0" encoding="UTF-8"?>
 2 | <!-- Created with Inkscape (http://www.inkscape.org/) -->
 3 | <svg width="793.7" height="1122.5" version="1.1" viewBox="0 0 793.7 1122.5" xmlns="http://www.w3.org/2000/svg">
 4 |  <g>
 5 |   <path transform="matrix(1.3333 0 0 -1.3333 0 1122.5)" d="m595.28 487.98-530.1-487.98h530.1z" fill="#205a6d" opacity=".72165"/>
 6 |   <path transform="matrix(1.3333 0 0 -1.3333 0 1122.5)" d="m0 228.94v-228.94h326.54z" fill="#d8e3de" opacity=".80069"/>
 7 |   <path transform="matrix(1.3333 0 0 -1.3333 0 1122.5)" d="m178.18 104.02-113-104.02h261.36z" fill="#93c7a3" opacity=".80412"/>
 8 |  </g>
 9 | </svg>
10 | 


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/templates/background6.pdf:
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https://raw.githubusercontent.com/iandol/dotpandoc/01ca3fc68697022506ad376810bb2c4d90b386df/templates/background6.pdf


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/templates/background6.svg:
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 1 | <?xml version="1.0" encoding="UTF-8"?>
 2 | <!-- Created with Inkscape (http://www.inkscape.org/) -->
 3 | <svg width="793.7" height="1122.5" version="1.1" viewBox="0 0 793.7 1122.5" xmlns="http://www.w3.org/2000/svg">
 4 |  <g>
 5 |   <path transform="matrix(1.3333 0 0 -1.3333 0 1122.5)" d="m595.28 487.98-530.1-487.98h530.1z" fill="#95043e" opacity=".71134"/>
 6 |   <path transform="matrix(1.3333 0 0 -1.3333 0 1122.5)" d="m0 228.94v-228.94h326.54z" fill="#aaa" opacity=".6323"/>
 7 |   <path transform="matrix(1.3333 0 0 -1.3333 0 1122.5)" d="m178.18 104.02-113-104.02h261.36z" fill="#5b1647" opacity=".47766"/>
 8 |  </g>
 9 | </svg>
10 | 


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/templates/background7.pdf:
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https://raw.githubusercontent.com/iandol/dotpandoc/01ca3fc68697022506ad376810bb2c4d90b386df/templates/background7.pdf


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/templates/background7.svg:
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 1 | <?xml version="1.0" encoding="UTF-8"?>
 2 | <!-- Created with Inkscape (http://www.inkscape.org/) -->
 3 | <svg width="793.7" height="1122.5" version="1.1" viewBox="0 0 793.7 1122.5" xmlns="http://www.w3.org/2000/svg">
 4 |  <g>
 5 |   <path transform="matrix(1.3333 0 0 -1.3333 0 1122.5)" d="m595.28 487.98-530.1-487.98h530.1z" fill="#fcc02e" opacity=".7732"/>
 6 |   <path transform="matrix(1.3333 0 0 -1.3333 0 1122.5)" d="m0 228.94v-228.94h326.54z" fill="#36474f" opacity=".47079"/>
 7 |   <path transform="matrix(1.3333 0 0 -1.3333 0 1122.5)" d="m595.28 251.1-272.78-251.1h272.78z" fill="#ff9f01" opacity=".72165"/>
 8 |   <path transform="matrix(1.3333 0 0 -1.3333 0 1122.5)" d="m178.18 104.02-113-104.02h261.36z" fill="#546f7a" opacity=".46735"/>
 9 |  </g>
10 | </svg>
11 | 


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/templates/baseline.css:
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 1 | 
 2 | 
 3 | @media screen {
 4 | 
 5 |     .pagedjs_pagebox{
 6 |         --pagedjs-baseline: 12px;
 7 |         --pagedjs-baseline-position: 1px;
 8 |         --pagedjs-baseline-color: cyan;
 9 |         background: linear-gradient( var(--color-paper) 0%, var(--color-paper) calc(var(--pagedjs-baseline) - 1px), var(--pagedjs-baseline-color) calc(var(--pagedjs-baseline) - 1px),  var(--pagedjs-baseline-color) var(--pagedjs-baseline)), transparent;
10 |         background-size: 100% var(--pagedjs-baseline);
11 |         background-repeat: repeat-y;
12 |         background-position-y: var(--pagedjs-baseline-position);
13 |     }
14 | 
15 | 
16 | }


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/templates/bootstrap.html5:
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 1 | <!DOCTYPE html>
 2 | <html$if(lang)$ lang="$lang$"$endif$$if(dir)$ dir="$dir$"$endif$>
 3 | <head>
 4 |   <meta charset="utf-8">
 5 |   <meta name="generator" content="pandoc">
 6 |   <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 7 | $for(author-meta)$
 8 |   <meta name="author" content="$author-meta$">
 9 | $endfor$
10 | $if(date-meta)$
11 |   <meta name="dcterms.date" content="$date-meta$">
12 | $endif$
13 | $if(keywords)$
14 |   <meta name="keywords" content="$for(keywords)$$keywords$$sep$, $endfor$">
15 | $endif$
16 |   <title>$if(title-prefix)$$title-prefix$ – $endif$$pagetitle$</title>
17 |   <style type="text/css">code{white-space: pre;}</style>
18 | $if(quotes)$
19 |   <style type="text/css">q { quotes: "“" "”" "‘" "’"; }</style>
20 | $endif$
21 | $if(highlighting-css)$
22 |   <style type="text/css">
23 | $highlighting-css$
24 |   </style>
25 | $endif$
26 | $for(css)$
27 |   <link rel="stylesheet" href="$css$">
28 | $endfor$
29 | <style type="text/css">
30 |   .markdown-body { max-width: 960px; margin: 0 auto; padding: 32px; }
31 | </style>
32 | $if(math)$
33 |   $math$
34 | $endif$
35 |   <!--[if lt IE 9]>
36 |     <script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv-printshiv.min.js"></script>
37 |   <![endif]-->
38 | $for(header-includes)$
39 |   $header-includes$
40 | $endfor$
41 | <link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet">
42 | </head>
43 | <body>
44 | <div class="markdown-body">
45 |   $for(include-before)$
46 |   $include-before$
47 |   $endfor$
48 |   $if(title)$
49 |   <header>
50 |   <h1 class="title">$title$</h1>
51 |   $if(subtitle)$
52 |   <p class="subtitle">$subtitle$</p>
53 |   $endif$
54 |   $for(author)$
55 |   <p class="author">$author$</p>
56 |   $endfor$
57 |   $if(date)$
58 |   <p class="date">$date$</p>
59 |   $endif$
60 |   </header>
61 |   $endif$
62 |   $if(toc)$
63 |   <nav id="$idprefix$TOC">
64 |   $toc$
65 |   </nav>
66 |   $endif$
67 |   $body$
68 |   $for(include-after)$
69 |   $include-after$
70 |   $endfor$
71 | </div>
72 | <script type="text/javascript" src="https://code.jquery.com/jquery-1.12.4.min.js"></script>
73 | <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js"></script>
74 | </body>
75 | </html>
76 | 


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/templates/cover.jpg:
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https://raw.githubusercontent.com/iandol/dotpandoc/01ca3fc68697022506ad376810bb2c4d90b386df/templates/cover.jpg


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/templates/custom-JNS.docx:
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/templates/custom-blue.docx:
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https://raw.githubusercontent.com/iandol/dotpandoc/01ca3fc68697022506ad376810bb2c4d90b386df/templates/custom-blue.docx


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/templates/custom-calibri.docx:
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https://raw.githubusercontent.com/iandol/dotpandoc/01ca3fc68697022506ad376810bb2c4d90b386df/templates/custom-calibri.docx


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/templates/custom-calibri.odt:
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/templates/custom-cambria.docx:
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https://raw.githubusercontent.com/iandol/dotpandoc/01ca3fc68697022506ad376810bb2c4d90b386df/templates/custom-cambria.docx


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/templates/custom-embed.docx:
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/templates/custom-greta.docx:
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https://raw.githubusercontent.com/iandol/dotpandoc/01ca3fc68697022506ad376810bb2c4d90b386df/templates/custom-greta.docx


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/templates/custom-nsfc.docx:
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https://raw.githubusercontent.com/iandol/dotpandoc/01ca3fc68697022506ad376810bb2c4d90b386df/templates/custom-nsfc.docx


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/templates/custom.docx:
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https://raw.githubusercontent.com/iandol/dotpandoc/01ca3fc68697022506ad376810bb2c4d90b386df/templates/custom.docx


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/templates/custom.html:
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  1 | <!DOCTYPE html>
  2 | <html xmlns="http://www.w3.org/1999/xhtml" lang="$lang$" xml:lang="$lang$"$if(dir)$ dir="$dir$"$endif$>
  3 | <head>
  4 |   <meta charset="utf-8" />
  5 |   <meta name="generator" content="pandoc & pandocomatic" />
  6 |   <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
  7 | $if(title)$
  8 |   <meta name="title" content="$title$" />
  9 |   <meta name="citation_title" content="$title$" /> 
 10 | $endif$
 11 | $if(author)$
 12 | $for(author)$
 13 |   <meta name="author" content="$author.name$" />
 14 |   <meta name="citation_author" content="$author.name$" />
 15 | $endfor$
 16 | $endif$
 17 | $if(date-meta)$
 18 |   <meta name="dcterms.date" content="$date-meta$" />
 19 | $endif$
 20 | $if(keywords)$
 21 |   <meta name="keywords" content="$for(keywords)$$keywords$$sep$, $endfor$" />
 22 | $endif$
 23 | $if(description-meta)$
 24 |   <meta name="description" content="$description-meta$" />
 25 | $endif$
 26 |   <title>$if(title-prefix)$$title-prefix$ – $endif$$pagetitle$</title>
 27 |   <style>
 28 |     $styles.html()$
 29 |   </style>
 30 | $for(css)$
 31 |   <link rel="stylesheet" href="$css$" />
 32 | $endfor$
 33 | $if(math)$
 34 |   $math$
 35 | $endif$
 36 | $for(header-includes)$
 37 |   $header-includes$
 38 | $endfor$
 39 | </head>
 40 | <body>
 41 | $for(include-before)$
 42 | $include-before$
 43 | $endfor$
 44 | $if(title)$
 45 | <header id="title-block-header">
 46 | <h1 class="title">$title$</h1>
 47 | $if(subtitle)$
 48 | <p class="subtitle">$subtitle$</p>
 49 | $endif$
 50 | 
 51 | $if(author)$
 52 | <p class="author-list">
 53 | $for(author)$
 54 |   $if(author.last)$ and $endif$<span class="author" property="author" typeof="Person">$author.name$</span><sup>$if(author.affiliation)$$for(author.affiliation)$$author.affiliation$$sep$,$endfor$$endif$$if(author.equal_contributor)$†$endif$$if(author.correspondence)$<a class="email-svg" href="mailto:$author.correspondence$"></a>$endif$$if(author.orcid)$<span class="orcid-svg"></span>$endif$</sup>$sep$, 
 55 | $endfor$
 56 | </p>
 57 | $endif$
 58 | 
 59 | $if(equal_contributors)$
 60 | <p class="author_contributions"><sup>†</sup> Authors contributed equally to this work.</p>
 61 | $endif$
 62 | 
 63 | $if(institute)$
 64 | <div class="author_affiliations">
 65 | $for(institute)$
 66 |   <div class="affiliation-item"><sup>$institute.index$</sup> $institute.name$$if(institute.address)$, $institute.address$$endif$</div>    
 67 | $endfor$
 68 | </div>
 69 | $endif$
 70 | 
 71 | $if(correspondence_list)$
 72 | <div class="correspondence">
 73 |   $for(correspondence_list)$<span class="correspondence-item">$correspondence_list$</span>$sep$ | $endfor$
 74 | </div>
 75 | $endif$
 76 | $if(email_list)$
 77 | <div class="emails">
 78 |   $for(email_list)$<span class="email-item">$email_list$</span>$sep$ | $endfor$
 79 | </div>
 80 | $endif$
 81 | $if(abstract)$<p class="abstract" property="description">$abstract$</p>$endif$
 82 | $if(doi)$<p><a href="https://doi.org/$doi$">doi: $doi$</a></p>$endif$
 83 | 
 84 | $if(date)$
 85 | <p class="date">$date$</p>
 86 | $endif$
 87 | </header>
 88 | $endif$
 89 | 
 90 | $if(toc)$
 91 | <nav id="$idprefix$TOC" role="doc-toc">
 92 | $if(toc-title)$
 93 | <h2 id="$idprefix$toc-title">$toc-title$</h2>
 94 | $endif$
 95 | $table-of-contents$
 96 | </nav>
 97 | $endif$
 98 | 
 99 | $body$
100 | $for(include-after)$
101 | $include-after$
102 | $endfor$
103 | </body>
104 | </html>
105 | 


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/templates/custom.icml:
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 1 | <?xml version="1.0" encoding="UTF-8" standalone="yes"?>
 2 | <?aid style="50" type="snippet" readerVersion="6.0" featureSet="513" product="8.0(370)" ?>
 3 | <?aid SnippetType="InCopyInterchange"?>
 4 | <!--  comment here -->
 5 | <Document DOMVersion="8.0" Self="pandoc_doc">
 6 |     <RootCharacterStyleGroup Self="pandoc_character_styles">
 7 |       <CharacterStyle Self="$$ID/NormalCharacterStyle" Name="Default" />
 8 |       $charStyles$
 9 |     </RootCharacterStyleGroup>
10 |     <RootParagraphStyleGroup Self="pandoc_paragraph_styles">
11 |       <ParagraphStyle Self="$$ID/NormalParagraphStyle" Name="$$ID/NormalParagraphStyle"
12 |           SpaceBefore="6" SpaceAfter="6"> <!-- paragraph spacing -->
13 |         <Properties>
14 |           <TabList type="list">
15 |             <ListItem type="record">
16 |               <Alignment type="enumeration">LeftAlign</Alignment>
17 |               <AlignmentCharacter type="string">.</AlignmentCharacter>
18 |               <Leader type="string"></Leader>
19 |               <Position type="unit">10</Position> <!-- first tab stop -->
20 |             </ListItem>
21 |           </TabList>
22 |         </Properties>
23 |       </ParagraphStyle>
24 |       $parStyles$
25 |     </RootParagraphStyleGroup>
26 |     <RootTableStyleGroup Self="pandoc_table_styles">
27 |       <TableStyle Self="TableStyle/Table" Name="Table" />
28 |     </RootTableStyleGroup>
29 |     <RootCellStyleGroup Self="pandoc_cell_styles">
30 |       <CellStyle Self="CellStyle/Cell" AppliedParagraphStyle="ParagraphStyle/$$ID/[No paragraph style]" Name="Cell" />
31 |     </RootCellStyleGroup>
32 |   <Story Self="pandoc_story"
33 |       TrackChanges="false"
34 |       StoryTitle="$if(title-prefix)$$title-prefix$ – $endif$$pagetitle$"
35 |       AppliedTOCStyle="n"
36 |       AppliedNamedGrid="n" >
37 |     <StoryPreference OpticalMarginAlignment="true" OpticalMarginSize="12" />
38 | <!-- body needs to be non-indented, otherwise code blocks are indented too far -->
39 | $body$
40 | 
41 |   </Story>
42 |   $hyperlinks$
43 | </Document>
44 | 


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/templates/custom.odt:
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https://raw.githubusercontent.com/iandol/dotpandoc/01ca3fc68697022506ad376810bb2c4d90b386df/templates/custom.odt


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/templates/custom.openxml:
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 1 | <?xml version="1.0" encoding="UTF-8"?>
 2 | <w:document xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" xmlns:m="http://schemas.openxmlformats.org/officeDocument/2006/math" xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:v="urn:schemas-microsoft-com:vml" xmlns:w10="urn:schemas-microsoft-com:office:word" xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" xmlns:pic="http://schemas.openxmlformats.org/drawingml/2006/picture" xmlns:wp="http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing">
 3 | <w:body>
 4 | $if(title)$
 5 |     <w:p>
 6 |       <w:pPr>
 7 |         <w:pStyle w:val="Title" />
 8 |       </w:pPr>
 9 |       $title$
10 |     </w:p>
11 | $endif$
12 | $if(subtitle)$
13 |     <w:p>
14 |       <w:pPr>
15 |         <w:pStyle w:val="Subtitle" />
16 |       </w:pPr>
17 |       $subtitle$
18 |     </w:p>
19 | $endif$
20 | $for(author)$
21 |     <w:p>
22 |       <w:pPr>
23 |         <w:pStyle w:val="Author" />
24 |       </w:pPr>
25 |       $author$
26 |     </w:p>
27 | $endfor$
28 | $if(date)$
29 |     <w:p>
30 |       <w:pPr>
31 |         <w:pStyle w:val="Date" />
32 |       </w:pPr>
33 |       $date$
34 |     </w:p>
35 | $endif$
36 | $if(abstract)$
37 | $if(abstract-title)$
38 |     <w:p>
39 |       <w:pPr>
40 |         <w:pStyle w:val="AbstractTitle" />
41 |       </w:pPr>
42 |       <w:r><w:t xml:space="preserve">$abstract-title$</w:t></w:r>
43 |     </w:p>
44 | $endif$
45 |     $abstract$
46 | $endif$
47 | $for(include-before)$
48 |     $include-before$
49 | $endfor$
50 | $if(toc)$
51 |     $toc$
52 | $endif$
53 |     $body$
54 | $for(include-after)$
55 |     $include-after$
56 | $endfor$
57 | $-- sectpr will be set to the last sectpr in a reference.docx, if present
58 | $if(sectpr)$
59 |     $sectpr$
60 | $else$
61 |     <w:sectPr />
62 | $endif$
63 |   </w:body>
64 | </w:document>
65 | 


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/templates/custom.plain:
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 1 | $if(titleblock)$
 2 | $titleblock$
 3 | 
 4 | $endif$
 5 | $for(header-includes)$
 6 | $header-includes$
 7 | 
 8 | $endfor$
 9 | $for(include-before)$
10 | $include-before$
11 | 
12 | $endfor$
13 | $if(toc)$
14 | Contents
15 | ========
16 | $table-of-contents$
17 | $endif$
18 | $body$
19 | $for(include-after)$
20 | 
21 | $include-after$
22 | $endfor$


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/templates/custom.typst:
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  1 | $if(doindex)$
  2 | // https://typst.app/universe/package/in-dexter
  3 | #import "@preview/in-dexter:0.5.3": *
  4 | $endif$
  5 | // https://typst.app/universe/package/gentle-clues/
  6 | #import "@preview/gentle-clues:1.0.0": *
  7 | 
  8 | #show terms: it => {
  9 | 	it.children
 10 | 		.map(child => [
 11 | 			#strong[#child.term]
 12 | 			#block(inset: (left: 1.5em, top: -0.4em))[#child.description]
 13 | 			])
 14 | 		.join()
 15 | }
 16 | 
 17 | #let horizontalrule = [
 18 | 	#line(start: (5%,0%), end: (95%,0%), stroke: (paint: gray, thickness: 4pt, cap: "round"))
 19 | ]
 20 | 
 21 | $if(mainfont)$
 22 | #let main-font = ("$mainfont$")
 23 | $else$
 24 | #let main-font = ("Dolly Pro","Alegreya","Libertinus Serif", "Source Serif 4")
 25 | $endif$
 26 | $if(headerfont)$
 27 | #let heading-font = ("$headerfont$")
 28 | $elseif(sansfont)$
 29 | #let heading-font = ("$sansfont$")
 30 | $else$
 31 | #let heading-font = ("Alegreya Sans SC","Graublau Slab","Source Sans 3")
 32 | $endif$
 33 | $if(sansfont)$
 34 | #let sans-font = ("$sansfont$")
 35 | $else$
 36 | #let sans-font = ("Alegreya Sans","Graublau Slab","Source Sans 3")
 37 | $endif$
 38 | $if(monofont)$
 39 | #let mono-font = ("$monofont$")
 40 | $else$
 41 | #let mono-font = ("Rec Mono Casual","Cascadia Code","Menlo")
 42 | $endif$
 43 | 
 44 | #set table(inset: 6pt)
 45 | #set text(font: main-font, ligatures: true, discretionary-ligatures: false, number-type: "old-style")
 46 | #set par(leading: 0.85em, justify: true)
 47 | #set quote(block: true)
 48 | #show quote: set align(center)
 49 | #show quote: set text(style: "italic")
 50 | #show quote: set pad(x: 5em, y: 1.75em)
 51 | #show heading: set text(weight: "extrabold", font: heading-font, fill: luma(30%))
 52 | #show heading: set block(below: 1.5em)
 53 | #show raw: set text(font: mono-font)
 54 | #show link: set text(fill: rgb(65%, 25%, 0%))
 55 | #show table: set par(justify: false)
 56 | #show ref: strong
 57 | 
 58 | $if(linestretch)$
 59 | #set par(justify: true, spacing: 2em, leading: $linestretch$em)
 60 | $else$
 61 | #set par(justify: true, spacing: 2em, leading: 1.5em)
 62 | $endif$
 63 | $if(nonumberfigures)$
 64 | #set figure(numbering: none)
 65 | #show figure.caption: it => [
 66 | 	#set align(left)
 67 | 	#set par(justify: true, leading: 1em)
 68 | 	#set text(font: sans-font, size: 11pt, discretionary-ligatures: false, number-type: "lining")
 69 | 	#emph[#it.body]
 70 | ]
 71 | $else$
 72 | #show figure.caption: it => [
 73 | 	#set align(left)
 74 | 	#set par(justify: true, leading: 1em)
 75 | 	#set text(font: sans-font, size: 11pt, discretionary-ligatures: false, number-type: "lining")
 76 | 	#emph[#it.supplement~#context(it.counter.display(it.numbering)) — #it.body]
 77 | ]
 78 | $endif$
 79 | #show <refs>: set par(leading: 0.9em, spacing: 1.75em)
 80 | #show <refs>: set text(size: 11pt, font: sans-font)
 81 | 
 82 | $for(header-includes)$
 83 | $header-includes$
 84 | 
 85 | $endfor$
 86 | 
 87 | $if(mytemplate)$
 88 | #import "$mytemplate$": conf
 89 | $else$
 90 | $mytemplate.typst()$
 91 | $endif$
 92 | 
 93 | #show: doc => conf(
 94 | $if(title)$
 95 | 	title: [$title$],
 96 | $endif$
 97 | $if(running-head)$
 98 | 	running-head: [$running-head$],
 99 | $endif$
100 | $if(subtitle)$
101 |   subtitle: [$subtitle$],
102 | $endif$
103 | $if(author)$
104 | 	authors: (
105 | $for(author)$
106 | $if(it.name)$
107 | 		(name: [$it.name$],
108 | $if(it.affiliation)$
109 | 			affiliation: [$it.affiliation$],
110 | $endif$
111 | $if(equal_contributor)$
112 | 			equal_contributor: true,
113 | $endif$
114 | $if(it.correspondence)$
115 | 			correspondence: [$it.correspondence$],
116 | $endif$
117 | $if(it.email)$
118 | 			email: [$it.email$],
119 | $endif$
120 | $if(it.orcid)$
121 | 			orcid: [$it.orcid$],
122 | $endif$
123 | 		),
124 | $else$
125 | 		(name: [$it$],
126 | 			affiliation: (),
127 | 			orcid: (),
128 | 			equal_contributor: false,
129 | 			correspondence: (),
130 | 			email: (),
131 | 		),
132 | $endif$
133 | $endfor$
134 | 	),
135 | $endif$
136 | $if(institute)$
137 | 	affiliations: (
138 | $for(institute)$
139 | 		(id: "$institute.index$", name: "$institute.name$"),
140 | $endfor$
141 | 	),
142 | $endif$
143 | $if(keywords)$
144 | 	keywords: ($for(keywords)$"$it$"$sep$, $endfor$),
145 | $endif$
146 | $if(date)$
147 | 	date: [$date$],
148 | $endif$
149 | $if(toc)$
150 | 	toc: true,
151 | $endif$
152 | $if(lang)$
153 | 	lang: "$lang$",
154 | $endif$
155 | $if(region)$
156 | 	region: "$region$",
157 | $endif$
158 | $if(abstract)$
159 | 	abstract: [$abstract$],
160 | $endif$
161 | $if(titlepage-background)$
162 | 	titlepage-background: "$titlepage-background$",
163 | $endif$
164 | $if(margin)$
165 | 	margin: ($for(margin/pairs)$$margin.key$: $margin.value$,$endfor$),
166 | $endif$
167 | $if(papersize)$
168 | 	paper: "$papersize$",
169 | $endif$
170 | 	font: main-font,
171 | $if(fontsize)$
172 | 	fontsize: $fontsize$,
173 | $endif$
174 | 	numbering: $if(page-numbering)$"$page-numbering$"$else$none$endif$,
175 | $if(section-numbering)$
176 | 	sectionnumbering: "$section-numbering$",
177 | $endif$
178 | 	cols: $if(columns)$$columns$$else$1$endif$,
179 | 	doc,
180 | )
181 | 
182 | $for(include-before)$
183 | $include-before$
184 | 
185 | $endfor$
186 | 
187 | $body$
188 | 
189 | $if(citations)$
190 | $if(csl)$
191 | 
192 | #set bibliography(style: "$csl$")
193 | $elseif(bibliographystyle)$
194 | 
195 | #set bibliography(style: "$bibliographystyle$")
196 | $endif$
197 | $if(bibliography)$
198 | 
199 | #bibliography($for(bibliography)$"$bibliography$"$sep$,$endfor$)
200 | $endif$
201 | $endif$
202 | 
203 | $if(doindex)$
204 | #pagebreak()
205 | = Index
206 | #columns(2)[
207 |   #make-index(title: none)
208 | ]
209 | 
210 | $endif$
211 | $for(include-after)$
212 | 
213 | $include-after$
214 | $endfor$
215 | 


--------------------------------------------------------------------------------
/templates/fonts.latex:
--------------------------------------------------------------------------------
  1 | \usepackage{iftex}
  2 | \ifPDFTeX
  3 |   \usepackage[$if(fontenc)$$fontenc$$else$T1$endif$]{fontenc}
  4 |   \usepackage[utf8]{inputenc}
  5 |   \usepackage{textcomp} % provide euro and other symbols
  6 | \else % if luatex or xetex
  7 | $if(mathspec)$
  8 |   \ifXeTeX
  9 |     \usepackage{mathspec} % this also loads fontspec
 10 |   \else
 11 |     \usepackage{unicode-math} % this also loads fontspec
 12 |   \fi
 13 | $else$
 14 |   \usepackage{unicode-math} % this also loads fontspec
 15 | $endif$
 16 |   \defaultfontfeatures{Scale=MatchLowercase}$-- must come before Beamer theme
 17 |   \defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1}
 18 | \fi
 19 | $if(fontfamily)$
 20 | $else$
 21 | $-- Set default font before Beamer theme so the theme can override it
 22 | \usepackage{lmodern}
 23 | $endif$
 24 | $-- User font settings (must come after default font and Beamer theme)
 25 | $if(fontfamily)$
 26 | \usepackage[$for(fontfamilyoptions)$$fontfamilyoptions$$sep$,$endfor$]{$fontfamily$}
 27 | $endif$
 28 | \ifPDFTeX\else
 29 |   % xetex/luatex font selection
 30 | $if(mainfont)$
 31 |   $if(mainfontfallback)$
 32 |     \ifLuaTeX
 33 |       \usepackage{luaotfload}
 34 |       \directlua{luaotfload.add_fallback("mainfontfallback",{
 35 |         $for(mainfontfallback)$"$mainfontfallback$"$sep$,$endfor$
 36 |       })}
 37 |     \fi
 38 |   $endif$
 39 |   \setmainfont[$for(mainfontoptions)$$mainfontoptions$$sep$,$endfor$$if(mainfontfallback)$,RawFeature={fallback=mainfontfallback}$endif$]{$mainfont$}
 40 | $endif$
 41 | $if(sansfont)$
 42 |   $if(sansfontfallback)$
 43 |     \ifLuaTeX
 44 |       \usepackage{luaotfload}
 45 |       \directlua{luaotfload.add_fallback("sansfontfallback",{
 46 |         $for(sansfontfallback)$"$sansfontfallback$"$sep$,$endfor$
 47 |       })}
 48 |     \fi
 49 |   $endif$
 50 |   \setsansfont[$for(sansfontoptions)$$sansfontoptions$$sep$,$endfor$$if(sansfontfallback)$,RawFeature={fallback=sansfontfallback}$endif$]{$sansfont$}
 51 | $endif$
 52 | $if(monofont)$
 53 |   $if(monofontfallback)$
 54 |     \ifLuaTeX
 55 |       \usepackage{luaotfload}
 56 |       \directlua{luaotfload.add_fallback("monofontfallback",{
 57 |         $for(monofontfallback)$"$monofontfallback$"$sep$,$endfor$
 58 |       })}
 59 |     \fi
 60 |   $endif$
 61 |   \setmonofont[$for(monofontoptions)$$monofontoptions$$sep$,$endfor$$if(monofontfallback)$,RawFeature={fallback=monofontfallback}$endif$]{$monofont$}
 62 | $endif$
 63 | $for(fontfamilies)$
 64 |   \newfontfamily{$fontfamilies.name$}[$for(fontfamilies.options)$$fontfamilies.options$$sep$,$endfor$]{$fontfamilies.font$}
 65 | $endfor$
 66 | $if(mathfont)$
 67 | $if(mathspec)$
 68 |   \ifXeTeX
 69 |     \setmathfont(Digits,Latin,Greek)[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$}
 70 |   \else
 71 |     \setmathfont[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$}
 72 |   \fi
 73 | $else$
 74 |   \setmathfont[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$}
 75 | $endif$
 76 | $endif$
 77 | $if(CJKmainfont)$
 78 |   \ifXeTeX
 79 |   \IfFileExists{xecjk.sty}{
 80 |     \usepackage{xeCJK}
 81 |     \setCJKmainfont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKmainfont$}
 82 |     $if(CJKsansfont)$
 83 |       \setCJKsansfont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKsansfont$}
 84 |     $endif$
 85 |     $if(CJKmonofont)$
 86 |       \setCJKmonofont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKmonofont$}
 87 |     $endif$
 88 |   }
 89 |   \fi
 90 | $endif$
 91 | $if(luatexjapresetoptions)$
 92 |   \ifLuaTeX
 93 |     \usepackage[$for(luatexjapresetoptions)$$luatexjapresetoptions$$sep$,$endfor$]{luatexja-preset}
 94 |   \fi
 95 | $endif$
 96 | $if(CJKmainfont)$
 97 |   \ifLuaTeX
 98 |     \usepackage[$for(luatexjafontspecoptions)$$luatexjafontspecoptions$$sep$,$endfor$]{luatexja-fontspec}
 99 |     \setmainjfont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKmainfont$}
100 |   \fi
101 | $endif$
102 | \fi
103 | $if(zero-width-non-joiner)$
104 | %% Support for zero-width non-joiner characters.
105 | \makeatletter
106 | \def\zerowidthnonjoiner{%
107 |   % Prevent ligatures and adjust kerning, but still support hyphenating.
108 |   \texorpdfstring{%
109 |     \TextOrMath{\nobreak\discretionary{-}{}{\kern.03em}%
110 |       \ifvmode\else\nobreak\hskip\z@skip\fi}{}%
111 |   }{}%
112 | }
113 | \makeatother
114 | \ifPDFTeX
115 |   \DeclareUnicodeCharacter{200C}{\zerowidthnonjoiner}
116 | \else
117 |   \catcode`^^^^200c=\active
118 |   \protected\def ^^^^200c{\zerowidthnonjoiner}
119 | \fi
120 | %% End of ZWNJ support
121 | $endif$
122 | % Use upquote if available, for straight quotes in verbatim environments
123 | \IfFileExists{upquote.sty}{\usepackage{upquote}}{}
124 | \IfFileExists{microtype.sty}{% use microtype if available
125 |   \usepackage[$for(microtypeoptions)$$microtypeoptions$$sep$,$endfor$]{microtype}
126 |   \UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
127 | }{}
128 | 
129 | 


--------------------------------------------------------------------------------
/templates/hypersetup.latex:
--------------------------------------------------------------------------------
 1 | \hypersetup{
 2 | $if(title-meta)$
 3 |   pdftitle={$title-meta$},
 4 | $endif$
 5 | $if(author)$
 6 |   pdfauthor={${ for(author) }${ it.name }${ sep }, ${ endfor }},
 7 | $endif$
 8 | $if(lang)$
 9 |   pdflang={$lang$},
10 | $endif$
11 | $if(subject)$
12 |   pdfsubject={$subject$},
13 | $endif$
14 | $if(keywords)$
15 |   pdfkeywords={$for(keywords)$$keywords$$sep$, $endfor$},
16 | $endif$
17 | $if(colorlinks)$
18 |   colorlinks=true,
19 |   linkcolor={$if(linkcolor)$$linkcolor$$else$Mahogany$endif$},
20 |   filecolor={$if(filecolor)$$filecolor$$else$Mahogany$endif$},
21 |   citecolor={$if(citecolor)$$citecolor$$else$Sepia$endif$},
22 |   urlcolor={$if(urlcolor)$$urlcolor$$else$BrickRed$endif$},
23 | $else$
24 | $if(boxlinks)$
25 | $else$
26 |   hidelinks,
27 | $endif$
28 | $endif$
29 |   pdfcreator={Scrivomatic, Pandoc and LaTeX}}
30 | 
31 | 


--------------------------------------------------------------------------------
/templates/interface.css:
--------------------------------------------------------------------------------
 1 | /* CSS for Paged.js interface – v0.2 */
 2 | 
 3 | /* Change the look */
 4 | :root {
 5 |   --color-background: whitesmoke;
 6 |   --color-pageSheet: #cfcfcf;
 7 |   --color-pageBox: violet;
 8 |   --color-paper: white;
 9 |   --color-marginBox: transparent;
10 |   --pagedjs-crop-color: #000;
11 |   --pagedjs-crop-stroke: 1px;
12 | }
13 | 
14 | .pagedjs_marks-crop{
15 |   z-index: 999999999999;
16 | }
17 | 
18 | /* To define how the book look on the screen: */
19 | @media screen {
20 |   body {
21 |       background-color: var(--color-background);
22 |   }
23 | 
24 |   .pagedjs_pages {
25 |       display: flex;
26 |       width: calc(var(--pagedjs-width) * 2);
27 |       flex: 0;
28 |       flex-wrap: wrap;
29 |       margin: 0 auto;
30 |   }
31 | 
32 |   .pagedjs_page {
33 |       background-color: var(--color-paper);
34 |       box-shadow: 0 0 0 1px var(--color-pageSheet);
35 |       margin: 0;
36 |       flex-shrink: 0;
37 |       flex-grow: 0;
38 |       margin-top: 10mm;
39 |   }
40 | 
41 |   .pagedjs_first_page {
42 |       margin-left: var(--pagedjs-width);
43 |   }
44 | 
45 |   .pagedjs_page:last-of-type {
46 |       margin-bottom: 10mm;
47 |   }
48 | 
49 |   .pagedjs_pagebox{
50 |       box-shadow: 0 0 0 1px var(--color-pageBox);
51 |   }
52 | 
53 |   .pagedjs_left_page{
54 |       z-index: 20;
55 |       width: calc(var(--pagedjs-bleed-left) + var(--pagedjs-pagebox-width))!important;
56 |   }
57 | 
58 |   .pagedjs_left_page .pagedjs_bleed-right .pagedjs_marks-crop {
59 |       border-color: transparent;
60 |   }
61 |   
62 |   .pagedjs_left_page .pagedjs_bleed-right .pagedjs_marks-middle{
63 |       width: 0;
64 |   } 
65 | 
66 |   .pagedjs_right_page{
67 |       z-index: 10;
68 |       position: relative;
69 |       left: calc(var(--pagedjs-bleed-left)*-1);
70 |   }
71 | 
72 |   /* show the margin-box */
73 | 
74 |   .pagedjs_margin-top-left-corner-holder,
75 |   .pagedjs_margin-top,
76 |   .pagedjs_margin-top-left,
77 |   .pagedjs_margin-top-center,
78 |   .pagedjs_margin-top-right,
79 |   .pagedjs_margin-top-right-corner-holder,
80 |   .pagedjs_margin-bottom-left-corner-holder,
81 |   .pagedjs_margin-bottom,
82 |   .pagedjs_margin-bottom-left,
83 |   .pagedjs_margin-bottom-center,
84 |   .pagedjs_margin-bottom-right,
85 |   .pagedjs_margin-bottom-right-corner-holder,
86 |   .pagedjs_margin-right,
87 |   .pagedjs_margin-right-top,
88 |   .pagedjs_margin-right-middle,
89 |   .pagedjs_margin-right-bottom,
90 |   .pagedjs_margin-left,
91 |   .pagedjs_margin-left-top,
92 |   .pagedjs_margin-left-middle,
93 |   .pagedjs_margin-left-bottom {
94 |       box-shadow: 0 0 0 1px inset var(--color-marginBox);
95 |   }
96 | 
97 | }
98 | 


--------------------------------------------------------------------------------
/templates/lapreprint.typst:
--------------------------------------------------------------------------------
  1 | // Update this import to where you put the `lapreprint.typ` file
  2 | // It should probably be in the same folder
  3 | #import "./lapreprint.typ": template
  4 | 
  5 | //mail icon
  6 | #let mailSvg = ```<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 199.2 199.3" xmlns:v="https://vecta.io/nano"><path d="M99.6 199.3c54.5 0 99.6-45.1 99.6-99.6C199.2 45.3 154 .1 99.5.1 45.1.1 0 45.3 0 99.7c0 54.5 45.2 99.6 99.6 99.6z" opacity=".49" fill="#404040" fill-opacity=".25"/><path d="M99.6 105c-1.5 0-3.1-.6-4.6-2L45.4 59.3c2.7-1.7 5.7-2.3 9.9-2.3H144c4 0 7 .8 9.9 2.4L104.2 103c-1.5 1.4-3 2-4.6 2zM41 134.4c-.9-2-1.4-4.1-1.4-7.2V72.3c0-3.2.7-5.8 1.2-6.8l36.6 32.3L41 134.4zm12.8 8.1c-3.5 0-6.2-.8-8.2-2.1l37.7-37.6 7.1 6.3c2.8 2.5 6.1 3.8 9.2 3.8s6.3-1.3 9.3-3.8l7-6.3 37.7 37.6c-2 1.2-4.7 2.1-8.2 2.1H53.8zm104.5-8.1l-36.6-36.6 36.7-32.2c.5 1 1.1 3.5 1.1 6.7v54.9c0 3-.4 5.2-1.2 7.2z" fill="#7e8c7b"/></svg>```.text
  7 | 
  8 | $definitions.typst()$
  9 | 
 10 | #show: template.with(
 11 | $if(title)$
 12 |   title: "$title$",
 13 | $endif$
 14 | $if(subtitle)$
 15 |   subtitle: "$subtitle$",
 16 | $endif$
 17 | $if(short-title)$
 18 |   short-title: "$short-title$",
 19 | $endif$
 20 |   open-access: true,
 21 |   kind: "Original Research",
 22 | $if(theme)$
 23 |   theme: $theme$,
 24 | $else$
 25 |   theme: red.darken(50%),
 26 | $endif$
 27 | $if(venue)$
 28 |   venue: [$venue$],
 29 | $else$
 30 |   venue: [bio#text(fill: red.darken(20%))[R]χiv],
 31 | $endif$
 32 | $if(logo)$
 33 |   logo: "$logo$",
 34 | $endif$
 35 | $if(doi)$
 36 |   doi: "$doi$",
 37 | $endif$
 38 | $if(date)$
 39 | $if(date.year)$
 40 |   date: $for(date)$ (title: $it.title$, date: (year: $it.year$, month: $it.month$, day: $it.day$),$endfor$
 41 | $else$
 42 |   date: $date$,
 43 | $endif$
 44 | $endif$
 45 | $if(papersize)$
 46 |   paper-size: "$papersize$",
 47 | $endif$
 48 | $if(mainfont)$
 49 |   font-face: "$mainfont$",
 50 | $endif$
 51 | $if(bibliography)$
 52 |   bibliography-file: "$bibliography$",
 53 | $endif$
 54 | $if(csl)$
 55 |   bibliography-style: "$csl$",
 56 | $elseif(bibliographystyle)$
 57 |   bibliography-style: "$bibliographystyle$",
 58 | $endif$
 59 | $if(author)$
 60 |   authors: (
 61 | $for(author)$
 62 | $if(author.name)$
 63 |     (
 64 |       name: "$author.name$",
 65 | $if(author.affiliation)$
 66 |       affiliations: "$author.affiliation$",
 67 | $endif$
 68 | $if(author.email)$
 69 |       email: "$author.email$",
 70 | $endif$
 71 | $if(author.orcid)$
 72 |       orcid: "$author.orcid$"
 73 | $endif$
 74 |     ),
 75 | $else$
 76 |     (
 77 |       name: "$author$"
 78 |     ),
 79 | $endif$
 80 | $endfor$
 81 |   ),
 82 | $endif$
 83 | $if(institute)$
 84 |   affiliations: (
 85 | $for(institute)$
 86 |     (id: "$it.index$", name: "$it.name$"),
 87 | $endfor$
 88 |   ),
 89 | $elseif(affiliations)$
 90 |   affiliations: (
 91 | $for(affiliations)$
 92 |     (id: "$it.index$", name: "$it.name$"),
 93 | $endfor$
 94 |   ),
 95 | $endif$
 96 | $if(abstract)$
 97 |   abstract: (
 98 |     (title: "Abstract", content: [$abstract$]),
 99 |   ),
100 | $endif$
101 | $if(keywords)$
102 |   keywords: ($for(keywords)$"$it$"$sep$,$endfor$),
103 | $endif$
104 |   margin: (
105 | $if(margin-keypoints)$
106 |     (
107 |       title: "Key Points",
108 |       content: [
109 | $for(margin-keypoints)$
110 |         - $it$
111 | $endfor$
112 |       ],
113 |     ),
114 | $endif$
115 | $if(margin-correspondence)$
116 |     (
117 |       title: [#box(height: 1.1em, baseline: 13.5%)[#image.decode(mailSvg)]Correspondence],
118 |       content: [
119 | $for(margin-correspondence)$
120 | #strong[#emph[$it$]]$sep$ & 
121 | $endfor$
122 |       ],
123 |     ),
124 | $endif$
125 | $if(margin-code)$
126 |     (
127 |       title: "Code Availability",
128 |       content: [
129 | $for(margin-code)$
130 |         $it$$sep$. 
131 | $endfor$
132 |       ],
133 |     ),
134 | $endif$
135 | $if(margin-funding)$
136 |     (
137 |       title: "Funding",
138 |       content: [
139 | $for(margin-funding)$
140 |         $it$$sep$. 
141 | $endfor$
142 |       ],
143 |     ),
144 | $endif$
145 |     (
146 |       title: "Competing Interests",
147 |       content: [
148 |         The authors declare no competing interests.
149 |       ],
150 |     ),
151 |   ),
152 | )
153 | 
154 | $for(header-includes)$
155 | $header-includes$
156 | 
157 | $endfor$
158 | $for(include-before)$
159 | $include-before$
160 | 
161 | $endfor$
162 | $if(toc)$
163 | #outline(
164 |   title: auto,
165 |   depth: none
166 | );
167 | $endif$
168 | 
169 | $if(linestretch)$
170 | #set par(leading: $linestretch$em)
171 | $endif$
172 | #set par(justify: true)
173 | #show table: set par(justify: false)
174 | #show ref: strong
175 | 
176 | $body$
177 | 
178 | $for(include-after)$
179 | 
180 | $include-after$
181 | $endfor$
182 | 


--------------------------------------------------------------------------------
/templates/layout.css:
--------------------------------------------------------------------------------
  1 | body{
  2 |     --bleed: 6mm;
  3 | }
  4 | 
  5 | @media print {
  6 | 
  7 |     /* ALL PAGES ----------------------------------------------------------------------- */
  8 | 
  9 |     @page {
 10 |         size: 165mm 235mm;
 11 |         margin-top: 36px;
 12 |         margin-bottom: 76px;
 13 |         bleed: 6mm; 
 14 |         marks: crop;
 15 |     }
 16 |     
 17 | 
 18 |     /* LEFT PAGES ----------------------------------------------------------------------- */
 19 | 
 20 |     @page:left {
 21 |         margin-right: 36mm;
 22 |         margin-left: 14mm;
 23 |         @bottom-left {
 24 |             content: counter(page);
 25 |             text-align: left;
 26 |             font-family: var(--font-title);
 27 |             font-size: 20px;
 28 |             position: relative;
 29 |             top: 4px;
 30 |         }
 31 |     }
 32 |     
 33 | 
 34 |     /* RIGHT PAGES ----------------------------------------------------------------------- */
 35 |     
 36 |     @page:right {
 37 |         margin-left: 36mm;
 38 |         margin-right: 14mm;
 39 |         @bottom-right {
 40 |             content: counter(page);
 41 |             text-align: right;
 42 |             font-family: var(--font-title);
 43 |             font-size: 20px; 
 44 |             position: relative;
 45 |             top: 4px;
 46 |         }
 47 |         @bottom-center {
 48 |             /* content: string(title) */
 49 |         }
 50 |     }
 51 | 
 52 |     /* h2 {  string-set: title content(text) } */
 53 |     
 54 | 
 55 |     
 56 | 
 57 |     /* BREAKS ----------------------------------------------------------------------- */
 58 | 
 59 |     #copyright {  break-before: page; }
 60 |     #title-page { break-before: page; }
 61 |     #a-propos { break-before: right; }
 62 |     #toc { break-before: right; }
 63 | 
 64 |     #colophon {  break-before: right; }
 65 |     #citation {  break-before: page; }
 66 | 
 67 |     .page-title-part { break-before: right; }
 68 |     .partie-texte { break-before: right; }
 69 | 
 70 |     .refs-biblio { break-before: page; }
 71 |     #refs-biblio-03 { break-before: right; }
 72 | 
 73 |     .notice { break-before: page; }
 74 |     .notice figure { break-before: page; }
 75 | 
 76 | 
 77 |     #notice-ra178{ break-before: right; }
 78 |     #figure-ra52 { break-before: right!important; }
 79 |     #refs-biblio-04 { break-before: right!important; }
 80 |     #grid-2-01-right { break-before: right!important; }
 81 |     #grid-3-01-right{ break-before: right; }
 82 |     
 83 |     .notices-list{ break-before: right; }
 84 | 
 85 |     /* BLANK PAGES --------------------------------------------------------------------- */
 86 | 
 87 |      @page :blank {
 88 |         @bottom-left { content: none; }
 89 |         @bottom-center { content: none; }
 90 |         @bottom-right { content: none; }
 91 |     }
 92 | 
 93 | 
 94 | 
 95 |     /* NAMED PAGES --------------------------------------------------------------------- */
 96 | 
 97 |     #half-title, 
 98 |     #copyright, 
 99 |     #title-page, 
100 |     #a-propos, 
101 |     #toc { 
102 |         page: frontmatter; 
103 |     }
104 | 
105 |     @page frontmatter {
106 | 
107 |         /* background-color: moccasin; */
108 | 
109 |         @bottom-left { content: none; }
110 |         @bottom-center { content: none; }
111 |         @bottom-right { content: none; }
112 | 
113 |     }
114 | 
115 | 
116 |     /* SPECIFIC PAGES --------------------------------------------------------------------- */
117 | 
118 |     @page :nth(8) { 
119 |         @bottom-left { content: none; } 
120 |     }
121 |     
122 |     @page :nth(114) { 
123 |         @bottom-left { content: none; } 
124 |     }
125 | 
126 | 
127 | }
128 | 
129 | 


--------------------------------------------------------------------------------
/templates/letter-simple.typst:
--------------------------------------------------------------------------------
 1 | #import "letter-pro-v3.0.0.typ": letter-simple
 2 | 
 3 | #set text(lang: "en")
 4 | 
 5 | #show: letter-simple.with(
 6 | 	sender: (
 7 | $if(sender)$
 8 | 		name: [$sender$],
 9 | $elseif(author)$
10 | 		name: [$author$],
11 | $endif$
12 | $if(address)$
13 | 		address: [$address$],
14 | $endif$
15 | $if(return-address)$
16 | 		return-address: ["$return-address$"],
17 | $endif$
18 | 	),
19 | $if(date)$
20 | 	date: "$date$",
21 | $endif$
22 | $if(subject)$
23 | 	subject: "$subject$",
24 | $endif$
25 | )
26 | 
27 | $body$
28 | 
29 | $if(signature)$
30 | #box(image("$signature$",width: 4cm))
31 | $endif$
32 | 
33 | #v(1em)
34 | 
35 | $if(signature-name)$
36 | #emph[$signature-name$]
37 | $endif$
38 | 


--------------------------------------------------------------------------------
/templates/materialize.html5:
--------------------------------------------------------------------------------
 1 | <!DOCTYPE html>
 2 | <html$if(lang)$ lang="$lang$"$endif$$if(dir)$ dir="$dir$"$endif$>
 3 | <head>
 4 |   <meta charset="utf-8">
 5 |   <meta name="generator" content="pandoc">
 6 |   <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 7 | $for(author-meta)$
 8 |   <meta name="author" content="$author-meta$">
 9 | $endfor$
10 | $if(date-meta)$
11 |   <meta name="dcterms.date" content="$date-meta$">
12 | $endif$
13 | $if(keywords)$
14 |   <meta name="keywords" content="$for(keywords)$$keywords$$sep$, $endfor$">
15 | $endif$
16 |   <title>$if(title-prefix)$$title-prefix$ – $endif$$pagetitle$</title>
17 |   <style type="text/css">code{white-space: pre;}</style>
18 | $if(quotes)$
19 |   <style type="text/css">q { quotes: "“" "”" "‘" "’"; }</style>
20 | $endif$
21 | $if(highlighting-css)$
22 |   <style type="text/css">
23 | $highlighting-css$
24 |   </style>
25 | $endif$
26 | $for(css)$
27 |   <link rel="stylesheet" href="$css$">
28 | $endfor$
29 | <style type="text/css">
30 |   .markdown-body { max-width: 960px; margin: 0 auto; padding: 32px; }
31 | </style>
32 | $if(math)$
33 |   $math$
34 | $endif$
35 |   <!--[if lt IE 9]>
36 |     <script src="https://cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv-printshiv.min.js"></script>
37 |   <![endif]-->
38 | $for(header-includes)$
39 |   $header-includes$
40 | $endfor$
41 | <link href="http://fonts.googleapis.com/icon?family=Material+Icons" rel="stylesheet">
42 | <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/materialize/0.98.0/css/materialize.min.css">
43 | </head>
44 | <body>
45 | <div class="markdown-body">
46 |   $for(include-before)$
47 |   $include-before$
48 |   $endfor$
49 |   $if(title)$
50 |   <header>
51 |   <h1 class="title">$title$</h1>
52 |   $if(subtitle)$
53 |   <p class="subtitle">$subtitle$</p>
54 |   $endif$
55 |   $for(author)$
56 |   <p class="author">$author$</p>
57 |   $endfor$
58 |   $if(date)$
59 |   <p class="date">$date$</p>
60 |   $endif$
61 |   </header>
62 |   $endif$
63 |   $if(toc)$
64 |   <nav id="$idprefix$TOC">
65 |   $toc$
66 |   </nav>
67 |   $endif$
68 |   $body$
69 |   $for(include-after)$
70 |   $include-after$
71 |   $endfor$
72 | </div>
73 | <script type="text/javascript" src="https://code.jquery.com/jquery-2.1.1.min.js"></script>
74 | <script src="https://cdnjs.cloudflare.com/ajax/libs/materialize/0.98.0/js/materialize.min.js"></script>
75 | </body>
76 | </html>
77 | 


--------------------------------------------------------------------------------
/templates/minbook.typst:
--------------------------------------------------------------------------------
 1 | #import "minbook.typ": *
 2 | 
 3 | $for(header-includes)$
 4 | $header-includes$
 5 | 
 6 | $endfor$
 7 | 
 8 | #show: book.with(
 9 | 	title: [$title$],
10 | 	subtitle: [$subtitle$],
11 | 	authors: "$author$",
12 | 	titlepage: true,
13 | $if(cover)$
14 | 	cover: if "$cover$".ends-with(".jpg") or "$cover$".ends-with(".jpeg") or "$cover$".ends-with(".png") or "$cover$".ends-with(".svg") or "$cover$".ends-with(".pdf") {
15 |     image("$cover$", width: 100%, height: 100%, fit: "stretch")
16 |   } else if "$cover$" == "auto" {
17 |     auto
18 |   } else if "$cover$" == "none" {
19 |     none
20 |   } else {
21 |     auto
22 |   },
23 | $endif$
24 | 	paper: "$paper$",
25 | 	font: "$main-font$",
26 | 	font-math: "$math-font$",
27 | 	font-size: 11pt,
28 | 	part: none,
29 | 	chapter: none,
30 | 	numbering-style: none,
31 | 	toc: true,
32 | 	justify: true,
33 | 	line-space: 1.25em,
34 | )
35 | 
36 | $for(include-before)$
37 | $include-before$
38 | 
39 | $endfor$
40 | 
41 | $body$
42 | 
43 | $for(include-after)$
44 | 
45 | $include-after$
46 | $endfor$


--------------------------------------------------------------------------------
/templates/mytemplate.typst:
--------------------------------------------------------------------------------
  1 | #let content-to-string(content) = {
  2 | 	if content.has("text") {
  3 | 		content.text
  4 | 	} else if content.has("children") {
  5 | 		content.children.map(content-to-string).join("")
  6 | 	} else if content.has("body") {
  7 | 		content-to-string(content.body)
  8 | 	} else if content == [ ] {
  9 | 		" "
 10 | 	}
 11 | }
 12 | #let conf(
 13 | 	title: none,
 14 | 	subtitle: none,
 15 | 	running-head: none,
 16 | 	titlepage: false,
 17 | 	titlepage-background: none,
 18 | 	toc: none,
 19 | 	authors: (),
 20 | 	affiliations: (),
 21 | 	keywords: (),
 22 | 	date: none,
 23 | 	abstract: none,
 24 | 	cols: 1,
 25 | 	margin: (x: 1.75cm, y: 2cm),
 26 | 	paper: "a4",
 27 | 	lang: "en",
 28 | 	region: "GB",
 29 | 	font: (),
 30 | 	fontsize: 12pt,
 31 | 	sectionnumbering: none,
 32 | 	numbering: "1",
 33 | 	doc,
 34 | ) = {
 35 | 	if titlepage-background != none { titlepage = true} else { titlepage = false }
 36 | 	set document(
 37 | 		title: title,
 38 | 		author: authors.map(author => content-to-string(author.name)),
 39 | 		keywords: keywords,
 40 | 	)
 41 | 	set page(
 42 | 			paper: paper,
 43 | 			margin: margin,
 44 | 			numbering: numbering,
 45 | 			background: context {
 46 | 				if titlepage { image(titlepage-background, fit: "stretch") } else { none }
 47 | 			},
 48 | 			header: context {
 49 | 				if titlepage { none } else { align(right, text(size: 8pt, title)) }
 50 | 			},
 51 | 			footer: context {
 52 | 				if titlepage { none } else { grid(columns: (1fr, 1fr),align(left, text(style: "italic", font: sans-font, size: 8pt, running-head)),align(right, [#context counter(page).display()]))}
 53 | 			},
 54 | 	)
 55 | 	set par(justify: true)
 56 | 	set text(lang: lang,
 57 | 					 region: region,
 58 | 					 font: font,
 59 | 					 size: fontsize)
 60 | 	set heading(numbering: sectionnumbering)
 61 | 
 62 | 	if title != none {
 63 | 		align(center)[#block(inset: 2em)[
 64 | 			#text(fill: luma(30%), font: heading-font, weight: "extrabold", size: 2em)[#title]
 65 | 			#(if subtitle != none {
 66 | 				parbreak()
 67 | 				text(fill: luma(40%), font: heading-font, style: "italic", weight: "bold", size: 1.75em)[#subtitle]
 68 | 			})
 69 | 		]]
 70 | 	}
 71 | 
 72 | 	if authors != none and authors != [] {
 73 | 		let count = authors.len()
 74 | 		let ncols = calc.min(count, 3)
 75 | 		grid(
 76 | 			columns: (1fr,) * ncols,
 77 | 			row-gutter: 1.5em,
 78 | 			column-gutter: 1.25em,
 79 | 			..authors.map(author =>
 80 | 					align(center)[
 81 | 						#strong[#emph[#author.name]]
 82 | 						#if "affiliation" in author [#super[#author.affiliation]]
 83 | 						#if "email" in author [ \ 
 84 | 						#text(size: 0.7em)[📧 #underline[#author.email]]
 85 | 						]
 86 | 					]
 87 | 			)
 88 | 		)
 89 | 	}
 90 | 
 91 | 	if date != none {
 92 | 		align(center)[#block(inset: 1em)[
 93 | 			#date
 94 | 		]]
 95 | 	}
 96 | 
 97 | 	if affiliations.len() > 0 {
 98 | 		set text(size: 9pt)
 99 | 		block(width: 100%, stroke: none, inset: (top: 20pt, bottom: 20pt), {
100 | 			text(size: 1.2em, style: "italic", weight: "bold", "Affiliations: ")
101 | 			parbreak()
102 | 			affiliations.map(affiliation => {
103 | 				strong([#affiliation.id — ])
104 | 				affiliation.name 
105 | 				parbreak()
106 | 			}).join("")
107 | 		})
108 | 	}
109 | 
110 | 	if abstract != none {
111 | 		block(inset: (left: 2em, right: 2em))[
112 | 		#text(weight: "semibold")[Abstract] #h(1em) #abstract
113 | 		]
114 | 	}
115 | 
116 | 	if (keywords.len() > 0) {
117 | 		text(size: 9pt, {
118 | 			h(2em)
119 | 			text(weight: "semibold", "Keywords")
120 | 			h(8pt)
121 | 			keywords.join(", ")
122 | 		})
123 | 	}
124 | 	v(10pt)
125 | 
126 | 	if toc != none {
127 | 		outline(
128 | 			title: auto,
129 | 			depth: $toc-depth$
130 | 		)
131 | 	}
132 | 
133 | 	if titlepage { 
134 | 		set page(
135 | 		background: none,
136 | 		fill: none,
137 | 		header: align(right, text(style: "italic", font: sans-font, size: 8pt, title)),
138 | 		footer: grid(columns: (1fr, 1fr),align(left, text(style: "italic", font: sans-font, size: 8pt, running-head)),align(right, [#context counter(page).display()]))
139 | 		)
140 | 		if title != none or subtitle != none or authors != () or affiliations != () or keywords != () or toc != none { counter(page).update(1) }
141 | 		if cols == 1 {
142 | 			doc
143 | 		} else {
144 | 			columns(cols, doc)
145 | 		}
146 | 	} else {
147 | 		if cols == 1 {
148 | 			doc
149 | 		} else {
150 | 			columns(cols, doc)
151 | 		}
152 | 	}
153 | }
154 | 


--------------------------------------------------------------------------------
/templates/pagedjs.html:
--------------------------------------------------------------------------------
  1 | <!DOCTYPE html>
  2 | <html xmlns="http://www.w3.org/1999/xhtml" lang="$lang$" xml:lang="$lang$"$if(dir)$ dir="$dir$"$endif$>
  3 | <head>
  4 |   <meta charset="utf-8" />
  5 |   <meta name="generator" content="pandoc & pandocomatic" />
  6 |   <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
  7 | $if(title)$
  8 |   <meta name="title" content="$title$" />
  9 |   <meta name="citation_title" content="$title$" /> 
 10 | $endif$
 11 | $if(author)$
 12 | $for(author)$
 13 |   <meta name="author" content="$author.name$" />
 14 |   <meta name="citation_author" content="$author.name$" />
 15 | $endfor$
 16 | $endif$
 17 | $if(date-meta)$
 18 |   <meta name="dcterms.date" content="$date-meta$" />
 19 | $endif$
 20 | $if(keywords)$
 21 |   <meta name="keywords" content="$for(keywords)$$keywords$$sep$, $endfor$" />
 22 | $endif$
 23 | $if(description-meta)$
 24 |   <meta name="description" content="$description-meta$" />
 25 | $endif$
 26 |   <title>$if(title-prefix)$$title-prefix$ – $endif$$pagetitle$</title>
 27 |   <style>
 28 |     $styles.html()$
 29 |   </style>
 30 |   <script src="https://unpkg.com/pagedjs/dist/paged.polyfill.js"></script>
 31 | $for(css)$
 32 |   <link rel="stylesheet" href="$css$"/>
 33 | $endfor$
 34 | $if(math)$
 35 |   $math$
 36 | $endif$
 37 | $for(header-includes)$
 38 |   $header-includes$
 39 | $endfor$
 40 | </head>
 41 | <body>
 42 | $for(include-before)$
 43 | $include-before$
 44 | $endfor$
 45 | $if(title)$
 46 | <header id="title-block-header">
 47 | <h1 class="title">$title$</h1>
 48 | $if(subtitle)$
 49 | <p class="subtitle">$subtitle$</p>
 50 | $endif$
 51 | 
 52 | $if(author)$
 53 | <p class="author-list">
 54 | $for(author)$
 55 |   $if(author.last)$ and $endif$<span class="author" property="author" typeof="Person">$author.name$</span><sup>$if(author.affiliation)$$for(author.affiliation)$$author.affiliation$$sep$,$endfor$$endif$$if(author.correspondence)$<a href="mailto:$author.correspondence$">✉</a>$endif$$if(author.equal_contributor)$†$endif$</sup>$sep$, 
 56 | $endfor$
 57 | </p>
 58 | $endif$
 59 | 
 60 | $if(equal_contributors)$
 61 | <p class="author_contributions"><sup>†</sup> Authors contributed equally to this work.</p>
 62 | $endif$
 63 | 
 64 | $if(institute)$
 65 | <div class="author_affiliations">
 66 | $for(institute)$
 67 |   <div class="affiliation-item"><sup>$institute.index$</sup> $institute.name$$if(institute.address)$, $institute.address$$endif$</div>    
 68 | $endfor$
 69 | </div>
 70 | $endif$
 71 | 
 72 | $if(correspondence_list)$
 73 | <div class="correspondence">
 74 |   $for(correspondence_list)$<span class="correspondence-item">$correspondence_list$</span>$sep$ | $endfor$
 75 | </div>
 76 | $endif$
 77 | $if(email_list)$
 78 | <div class="email">
 79 |   $for(email_list)$<span class="email-item">$email_list$</span>$sep$ | $endfor$
 80 | </div>
 81 | $endif$
 82 | $if(abstract)$<p class="abstract" property="description">$abstract$</p>$endif$
 83 | $if(doi)$<p><a href="https://doi.org/$doi$">doi: $doi$</a></p>$endif$
 84 | 
 85 | $if(date)$
 86 | <p class="date">$date$</p>
 87 | $endif$
 88 | </header>
 89 | $endif$
 90 | 
 91 | $if(toc)$
 92 | <nav id="$idprefix$TOC" role="doc-toc">
 93 | $if(toc-title)$
 94 | <h2 id="$idprefix$toc-title">$toc-title$</h2>
 95 | $endif$
 96 | $table-of-contents$
 97 | </nav>
 98 | $endif$
 99 | 
100 | $body$
101 | $for(include-after)$
102 | $include-after$
103 | $endfor$
104 | </body>
105 | </html>
106 | 


--------------------------------------------------------------------------------
/templates/pandoc-scholar.html:
--------------------------------------------------------------------------------
  1 | <!doctype html>
  2 | <!--
  3 | Template created by Andrew G. York, based on this theme by Diana Mounter:
  4 | https://github.com/broccolini/dinky, which mentioned that
  5 | attribution is appreciated. Thanks, broccolini! -->
  6 | <html lang="en">
  7 | <head>
  8 |   <base target="_blank"/>
  9 |   <meta charset="utf-8"/>
 10 |   <meta http-equiv="X-UA-Compatible" content="IE=edge"/>
 11 |   <meta name="viewport" content="width=device-width, initial-scale=1, user-scalable=no"/>
 12 | $if(author)$
 13 | $for(author)$
 14 |   <meta name="author" content="$author.name$" />
 15 |   <meta name="citation_author" content="$author.name$" />
 16 | $endfor$
 17 | $endif$
 18 | $if(date-meta)$
 19 |   <meta name="dcterms.date" content="$date-meta$"/>
 20 | $endif$
 21 | $if(keywords)$
 22 |   <meta name="keywords" content="$for(keywords)$$keywords$$sep$, $endfor$"/>
 23 | $endif$
 24 |   <title>$if(title-prefix)$$title-prefix$ – $endif$$pagetitle$</title>
 25 |   <style type="text/css">code{white-space: pre;}</style>
 26 | $if(quotes)$
 27 |   <style type="text/css">q { quotes: "“" "”" "‘" "’"; }</style>
 28 | $endif$
 29 | $if(highlighting-css)$
 30 |   <style type="text/css">
 31 | $highlighting-css$
 32 |   </style>
 33 | $endif$
 34 | $for(css)$
 35 |   <link rel="stylesheet" href="$css$">
 36 | $endfor$
 37 | $if(math)$
 38 |   $math$
 39 | $endif$
 40 |   <!--[if lt IE 9]>
 41 |     <script src="//cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv-printshiv.min.js"></script>
 42 |   <![endif]-->
 43 | $for(header-includes)$
 44 |   $header-includes$
 45 | $endfor$
 46 | </head>
 47 | <body>
 48 | <div class="wrapper">
 49 | $if(project)$
 50 | <header class="page-header">
 51 |   <h1 class="header">$project.title$</h1>
 52 |   <ul>
 53 | $if(project.zip-url)$
 54 |     <li class="download"><a class="buttons" href="$project.zip-url$">Download ZIP</a></li>
 55 | $endif$
 56 | $if(project.github-url)$
 57 |     <li><a class="buttons github" href="$project.github-url$">View On GitHub</a></li>
 58 | $endif$
 59 | $if(project.pdf-url)$
 60 |     <li><a class="buttons pdf" href="$project.pdf-url$">Download PDF</a></li>
 61 | $endif$
 62 |   </ul>
 63 |   <p class="header">This project is maintained by $project.maintainer$</p>
 64 | </header>
 65 | $endif$
 66 | <article typeof="ScholarlyArticle" vocab="http://schema.org/">
 67 |     <!-- <header class="article-header"> -->
 68 | <h1 property="headline">$title$</h1>
 69 | $if(subtitle)$
 70 | <p property="alternativeHeadline" class="subtitle">$subtitle$</p>
 71 | $endif$
 72 | <!-- </header> -->
 73 | <p class="author-list">
 74 | $for(author)$
 75 |   $if(author.last)$and $endif$<span property="author" typeof="Person">
 76 |     $author.name$</span><sup>$for(author.affiliation)$$author.affiliation$$sep$,$endfor$
 77 |     $if(author.correspondence)$<a href="mailto:$author.correspondence$">✉</a>$endif$
 78 |     $if(author.equal_contributor)$†$endif$</sup>$sep$,
 79 | $endfor$
 80 | </p>
 81 | <div class="author_affiliations">
 82 | $for(institute)$
 83 |   <div class="affiliation"><sup>$institute.index$</sup>$institute.name$
 84 |   $if(institute.address)$, $institute.address$$endif$
 85 |   </div>
 86 | $endfor$
 87 | </div>
 88 | <div class="author-info">
 89 |     $if(equal_contributors)$
 90 |     <div class="author-contrib">
 91 |         <sup>$if(equal_contributor_symbol)$$equal_contributor_symbol$$else$†$endif$</sup>These authors contributed equally to this work
 92 |     </div>
 93 |     $endif$
 94 |     $if(correspondence_list)$
 95 |     <div class="author-correspondence">
 96 |       $for(correspondence_list)$<span class="correspondence-item">$correspondence_list$</span>$sep$    $endfor$
 97 |     </div>
 98 |     $endif$
 99 | </div>
100 | $if(abstract)$<p class="abstract" property="description">$abstract$</p>$endif$
101 | $if(doi)$<p><a href="https://doi.org/$doi$">doi: $doi$</a></p>$endif$
102 | 
103 | $for(include-before)$
104 | $include-before$
105 | 
106 | $endfor$
107 | 
108 | <div property="articleBody" class="article-body">
109 | $body$
110 | </div>
111 | </article>
112 | <footer>
113 |   <p><small>$title$</small></p>
114 | </footer>
115 | </div>
116 |  <!--[if !IE]><script>fixScale(document);</script><![endif]-->
117 | </body>
118 | </html>
119 | 


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/templates/passoptions.latex:
--------------------------------------------------------------------------------
 1 | % Options for packages loaded elsewhere
 2 | \PassOptionsToPackage{unicode$for(hyperrefoptions)$,$hyperrefoptions$$endfor$}{hyperref}
 3 | \PassOptionsToPackage{hyphens}{url}
 4 | $if(colorlinks)$
 5 | \PassOptionsToPackage{dvipsnames,svgnames,x11names}{xcolor}
 6 | $endif$
 7 | $if(CJKmainfont)$
 8 | \PassOptionsToPackage{space}{xeCJK}
 9 | $endif$
10 | 


--------------------------------------------------------------------------------
/templates/print.css:
--------------------------------------------------------------------------------
1 | @page { 
2 | 	size: A4;
3 | 	margin: 18mm;
4 | 	counter-increment: page;
5 | 	prince-bleed: 5mm;
6 | 	marks: crop cross;
7 | }


--------------------------------------------------------------------------------
/templates/recto-verso.css:
--------------------------------------------------------------------------------
 1 | @media screen {
 2 | 
 3 |   .pagedjs_pages {
 4 |       flex-direction: column;
 5 |       width: 100%;
 6 |   }
 7 | 
 8 |   .pagedjs_first_page {
 9 |       margin-left: 0;
10 |   }
11 | 
12 |   .pagedjs_page {
13 |       margin: 0 auto;
14 |       margin-top: 10mm;
15 |   } 
16 | 
17 |   .pagedjs_left_page{
18 |       width: calc(var(--pagedjs-bleed-left) + var(--pagedjs-pagebox-width) + var(--pagedjs-bleed-left))!important;
19 |   }
20 | 
21 |   .pagedjs_left_page .pagedjs_bleed-right .pagedjs_marks-crop{
22 |       border-color: var(--pagedjs-crop-color);
23 |   }
24 | 
25 |   .pagedjs_left_page .pagedjs_bleed-right .pagedjs_marks-middle{
26 |       width: var(--pagedjs-cross-size)!important;
27 |   } 
28 | 
29 |   .pagedjs_right_page{
30 |       left: 0; 
31 |   } 
32 |   
33 | }


--------------------------------------------------------------------------------
/templates/styles.citations.html:
--------------------------------------------------------------------------------
 1 | /* CSS for citations */
 2 | div.csl-bib-body { }
 3 | div.csl-entry {
 4 |   clear: both;
 5 | $if(csl-entry-spacing)$
 6 |   margin-bottom: $csl-entry-spacing$;
 7 | $endif$
 8 | }
 9 | .hanging-indent div.csl-entry {
10 |   margin-left:2em;
11 |   text-indent:-2em;
12 | }
13 | div.csl-left-margin {
14 |   min-width:2em;
15 |   float:left;
16 | }
17 | div.csl-right-inline {
18 |   margin-left:2em;
19 |   padding-left:1em;
20 | }
21 | div.csl-indent {
22 |   margin-left: 2em;
23 | }


--------------------------------------------------------------------------------
/templates/styles.html:
--------------------------------------------------------------------------------
  1 | $if(document-css)$
  2 | html {
  3 | $if(mainfont)$
  4 |   font-family: $mainfont$;
  5 | $endif$
  6 | $if(fontsize)$
  7 |   font-size: $fontsize$;
  8 | $endif$
  9 | $if(linestretch)$
 10 |   line-height: $linestretch$;
 11 | $endif$
 12 |   color: $if(fontcolor)$$fontcolor$$else$#1a1a1a$endif$;
 13 |   background-color: $if(backgroundcolor)$$backgroundcolor$$else$#fdfdfd$endif$;
 14 | }
 15 | body {
 16 |   margin: 0 auto;
 17 |   max-width: $if(maxwidth)$$maxwidth$$else$36em$endif$;
 18 |   padding-left: $if(margin-left)$$margin-left$$else$50px$endif$;
 19 |   padding-right: $if(margin-right)$$margin-right$$else$50px$endif$;
 20 |   padding-top: $if(margin-top)$$margin-top$$else$50px$endif$;
 21 |   padding-bottom: $if(margin-bottom)$$margin-bottom$$else$50px$endif$;
 22 |   hyphens: auto;
 23 |   overflow-wrap: break-word;
 24 |   text-rendering: optimizeLegibility;
 25 |   font-kerning: normal;
 26 | }
 27 | @media (max-width: 600px) {
 28 |   body {
 29 |     font-size: 0.9em;
 30 |     padding: 12px;
 31 |   }
 32 |   h1 {
 33 |     font-size: 1.8em;
 34 |   }
 35 | }
 36 | @media print {
 37 |   html {
 38 |     background-color: $if(backgroundcolor)$$backgroundcolor$$else$white$endif$;
 39 |   }
 40 |   body {
 41 |     background-color: transparent;
 42 |     color: black;
 43 |     font-size: 12pt;
 44 |   }
 45 |   p, h2, h3 {
 46 |     orphans: 3;
 47 |     widows: 3;
 48 |   }
 49 |   h2, h3, h4 {
 50 |     page-break-after: avoid;
 51 |   }
 52 | }
 53 | p {
 54 |   margin: 1em 0;
 55 | }
 56 | a {
 57 |   color: $if(linkcolor)$$linkcolor$$else$#1a1a1a$endif$;
 58 | }
 59 | a:visited {
 60 |   color: $if(linkcolor)$$linkcolor$$else$#1a1a1a$endif$;
 61 | }
 62 | img {
 63 |   max-width: 100%;
 64 | }
 65 | svg {
 66 |   height: auto;
 67 |   max-width: 100%;
 68 | }
 69 | h1, h2, h3, h4, h5, h6 {
 70 |   margin-top: 1.4em;
 71 | }
 72 | h5, h6 {
 73 |   font-size: 1em;
 74 |   font-style: italic;
 75 | }
 76 | h6 {
 77 |   font-weight: normal;
 78 | }
 79 | ol, ul {
 80 |   padding-left: 1.7em;
 81 |   margin-top: 1em;
 82 | }
 83 | li > ol, li > ul {
 84 |   margin-top: 0;
 85 | }
 86 | blockquote {
 87 |   margin: 1em 0 1em 1.7em;
 88 |   padding-left: 1em;
 89 |   border-left: 2px solid #e6e6e6;
 90 |   color: #606060;
 91 | }
 92 | $if(abstract)$
 93 | div.abstract {
 94 |   margin: 2em 2em 2em 2em;
 95 |   text-align: left;
 96 |   font-size: 85%;
 97 | }
 98 | div.abstract-title {
 99 |   font-weight: bold;
100 |   text-align: center;
101 |   padding: 0;
102 |   margin-bottom: 0.5em;
103 | }
104 | $endif$
105 | code {
106 |   font-family: $if(monofont)$$monofont$$else$Menlo, Monaco, Consolas, 'Lucida Console', monospace$endif$;
107 | $if(monobackgroundcolor)$
108 |   background-color: $monobackgroundcolor$;
109 |   padding: .2em .4em;
110 | $endif$
111 |   font-size: 85%;
112 |   margin: 0;
113 |   hyphens: manual;
114 | }
115 | pre {
116 |   margin: 1em 0;
117 | $if(monobackgroundcolor)$
118 |   background-color: $monobackgroundcolor$;
119 |   padding: 1em;
120 | $endif$
121 |   overflow: auto;
122 | }
123 | pre code {
124 |   padding: 0;
125 |   overflow: visible;
126 |   overflow-wrap: normal;
127 | }
128 | .sourceCode {
129 |  background-color: transparent;
130 |  overflow: visible;
131 | }
132 | hr {
133 |   background-color: #1a1a1a;
134 |   border: none;
135 |   height: 1px;
136 |   margin: 1em 0;
137 | }
138 | table {
139 |   margin: 1em 0;
140 |   border-collapse: collapse;
141 |   width: 100%;
142 |   overflow-x: auto;
143 |   display: block;
144 |   font-variant-numeric: lining-nums tabular-nums;
145 | }
146 | table caption {
147 |   margin-bottom: 0.75em;
148 | }
149 | tbody {
150 |   margin-top: 0.5em;
151 |   border-top: 1px solid $if(fontcolor)$$fontcolor$$else$#1a1a1a$endif$;
152 |   border-bottom: 1px solid $if(fontcolor)$$fontcolor$$else$#1a1a1a$endif$;
153 | }
154 | th {
155 |   border-top: 1px solid $if(fontcolor)$$fontcolor$$else$#1a1a1a$endif$;
156 |   padding: 0.25em 0.5em 0.25em 0.5em;
157 | }
158 | td {
159 |   padding: 0.125em 0.5em 0.25em 0.5em;
160 | }
161 | header {
162 |   margin-bottom: 4em;
163 |   text-align: center;
164 | }
165 | #TOC li {
166 |   list-style: none;
167 | }
168 | #TOC ul {
169 |   padding-left: 1.3em;
170 | }
171 | #TOC > ul {
172 |   padding-left: 0;
173 | }
174 | #TOC a:not(:hover) {
175 |   text-decoration: none;
176 | }
177 | $endif$
178 | code{white-space: pre-wrap;}
179 | span.smallcaps{font-variant: small-caps;}
180 | div.columns{display: flex; gap: min(4vw, 1.5em);}
181 | div.column{flex: auto; overflow-x: auto;}
182 | div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
183 | /* The extra [class] is a hack that increases specificity enough to
184 |    override a similar rule in reveal.js */
185 | ul.task-list[class]{list-style: none;}
186 | ul.task-list li input[type="checkbox"] {
187 |   font-size: inherit;
188 |   width: 0.8em;
189 |   margin: 0 0.8em 0.2em -1.6em;
190 |   vertical-align: middle;
191 | }
192 | $if(quotes)$
193 | q { quotes: "“" "”" "‘" "’"; }
194 | $endif$
195 | $if(displaymath-css)$
196 | .display.math{display: block; text-align: center; margin: 0.5rem auto;}
197 | $endif$
198 | $if(highlighting-css)$
199 | /* CSS for syntax highlighting */
200 | $highlighting-css$
201 | $endif$
202 | $if(csl-css)$
203 | $styles.citations.html()$
204 | $endif$


--------------------------------------------------------------------------------
/templates/template.markdown:
--------------------------------------------------------------------------------
 1 | $if(titleblock)$
 2 | $titleblock$
 3 | 
 4 | $endif$
 5 | $for(header-includes)$
 6 | $header-includes$
 7 | 
 8 | $endfor$
 9 | $for(include-before)$
10 | $include-before$
11 | 
12 | $endfor$
13 | $if(toc)$
14 | $toc$
15 | 
16 | $endif$
17 | $body$
18 | $for(include-after)$
19 | 
20 | $include-after$
21 | $endfor$
22 | 


--------------------------------------------------------------------------------
/templates/tufte.html5:
--------------------------------------------------------------------------------
  1 | <!DOCTYPE html>
  2 | <html$if(lang)$ lang="$lang$"$endif$$if(dir)$ dir="$dir$"$endif$>
  3 | <head>
  4 |   <meta charset="utf-8">
  5 |   <meta name="generator" content="pandoc">
  6 |   <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
  7 | $if(title)$
  8 |   <meta name="title" content="$title$" />
  9 |   <meta name="citation_title" content="$title$" /> 
 10 | $endif$
 11 | $if(author)$
 12 | $for(author)$
 13 |   <meta name="author" content="$author.name$" />
 14 |   <meta name="citation_author" content="$author.name$" />
 15 | $endfor$
 16 | $endif$
 17 | $if(date)$
 18 |   <meta name="citation_date" content="$date$" />
 19 | $endif$
 20 | $if(date-meta)$
 21 |   <meta name="dcterms.date" content="$date-meta$">
 22 | $endif$
 23 | $if(keywords)$
 24 |   <meta name="keywords" content="$for(keywords)$$keywords$$sep$, $endfor$">
 25 | $endif$
 26 |   <title>$if(title-prefix)$$title-prefix$ – $endif$$pagetitle$</title>
 27 |   <style type="text/css">code{white-space: pre;}</style>
 28 | $if(quotes)$
 29 |   <style type="text/css">q { quotes: "“" "”" "‘" "’"; }</style>
 30 | $endif$
 31 | $if(highlighting-css)$
 32 |   <style type="text/css">
 33 | $highlighting-css$
 34 |   </style>
 35 | $endif$
 36 | $for(css)$
 37 |   <link rel="stylesheet" href="$css$">
 38 | $endfor$
 39 | $if(math)$
 40 |   $math$
 41 | $endif$
 42 |   <!--[if lt IE 9]>
 43 |     <script src="//cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv-printshiv.min.js"></script>
 44 |   <![endif]-->
 45 | $for(header-includes)$
 46 |   $header-includes$
 47 | $endfor$
 48 | </head>
 49 | <body>
 50 | $for(include-before)$
 51 | $include-before$
 52 | $endfor$
 53 | <article>
 54 | $if(title)$
 55 | <header>
 56 | <h1 class="title">$title$</h1>
 57 | $if(subtitle)$
 58 | <p class="subtitle">$subtitle$</p>
 59 | $endif$
 60 | $if(author)$
 61 | <p class="author-list">
 62 | $for(author)$
 63 |   $if(author.last)$and $endif$<span property="author" typeof="Person">
 64 |     $author.name$</span><sup>$for(author.affiliation)$$author.affiliation$$sep$,$endfor$
 65 |     $if(author.correspondence)$<a href="mailto:$author.correspondence$">✉</a>$endif$
 66 |     $if(author.equal_contributor)$†$endif$</sup>$sep$,$endfor$
 67 | </p>
 68 | $endif$
 69 | $if(equal_contributors)$
 70 | <p class="author_contributions"><sup>†</sup> Authors contributed equally to this work.</p>
 71 | $endif$
 72 | 
 73 | $if(institute)$
 74 | <div class="author_affiliations">
 75 | $for(institute)$
 76 |   <span class="affiliation-item"><sup>$institute.index$</sup> $institute.name$$if(institute.address)$, $institute.address$$endif$</span>    
 77 | $endfor$
 78 | </div>
 79 | $endif$
 80 | 
 81 | $if(correspondence_list)$
 82 | <div class="correspondence">
 83 |   $for(correspondence_list)$<span class="correspondence-item">$correspondence_list$</span>$sep$    $endfor$
 84 | </div>
 85 | $endif$
 86 | $if(doi)$<p><a href="https://doi.org/$doi$">doi: $doi$</a></p>$endif$
 87 | $if(date)$
 88 | <p class="date">$date$</p>
 89 | $endif$
 90 | </header>
 91 | $endif$
 92 | $if(toc)$
 93 | <nav id="$idprefix$TOC">
 94 | $table-of-contents$
 95 | </nav>
 96 | $endif$
 97 | $body$
 98 | </article>
 99 | $for(include-after)$
100 | $include-after$
101 | $endfor$
102 | </body>
103 | </html>
104 | 


--------------------------------------------------------------------------------
/templates/tuftepandoc.css:
--------------------------------------------------------------------------------
  1 | 
  2 | /* For smart quotes */
  3 | q { quotes: "“" "”" "‘" "’"; }
  4 | 
  5 | /* Override section behavior.
  6 |  * We only want the top-level <section> to have padding.
  7 |  * This makes it easier to work with --section-divs. */
  8 | section {
  9 |   padding-top: initial;
 10 |   padding-bottom: initial;
 11 | }
 12 | article > section {
 13 |   padding-top: 1rem;
 14 |   padding-bottom: 1rem;
 15 | }
 16 | 
 17 | /* Make byline (date and/or author) small */
 18 | p.byline { font-size: 1.2rem; }
 19 | 
 20 | 
 21 | /* Simulate Pandoc's table output styles */
 22 | table {
 23 |   border-top: 2px solid black;
 24 |   border-bottom: 2px solid black;
 25 | }
 26 | th {
 27 |   border-bottom: 1px solid black;
 28 | }
 29 | td, th {
 30 |   font-size: 1.4rem;
 31 |   padding: 10px;
 32 |   text-align: left;
 33 | }
 34 | 
 35 | /* Allow tables to be full width
 36 |  * if they're wrapped in a figure.fullwidth
 37 |  * (Easier to insert from Pandoc than manually adding table) */
 38 | figure.fullwidth table {
 39 |   width: 90%;
 40 | }
 41 | 
 42 | @media (max-width: 760px) {
 43 |   figure.fullwidth table {
 44 |     width: 100%;
 45 |   }
 46 | }
 47 | 
 48 | /* Code blocks
 49 |  *
 50 |  * Code blocks with a language look like div.sourceCode > pre.sourceCode
 51 |  * Otherwise, it's just a pre (without .sourceCode) */
 52 | div.sourceCode,
 53 | pre:not(.sourceCode) {
 54 |   padding: 1.4rem;
 55 |   margin: -0.7rem -1.4rem;
 56 |   width: 55%;
 57 |   font-size: 0.9rem;
 58 |   overflow-x: auto;
 59 | }
 60 | 
 61 | div.sourceCode code,
 62 | pre:not(.sourceCode) code {
 63 |   font-size: 0.9rem;
 64 | }
 65 | 
 66 | .fullwidth div.sourceCode,
 67 | .fullwidth pre:not(.sourceCode) {
 68 |   width: 100%;
 69 | }
 70 | 
 71 | /* We've handled all the margin/padding on the outer-most div.sourceCode */
 72 | div.sourceCode pre {
 73 |   padding: 0;
 74 |   margin: 0;
 75 | }
 76 | 
 77 | @media (max-width: 760px) {
 78 |   div.sourceCode,
 79 |   pre:not(.sourceCode) {
 80 |     width: 100%;
 81 |   }
 82 | }
 83 | 
 84 | /* Pandoc-generated line numbers need the same stylings as normal <code> */
 85 | .lineNumbers pre {
 86 |   line-height: 1.42;
 87 |   font-size: 0.9rem;
 88 | }
 89 | 
 90 | /* The default x-height for code is slightly too large in side notes */
 91 | .marginnote code, .sidenote code { font-size: 0.9rem; }
 92 | 
 93 | 
 94 | div.sourceCode, pre:not(.sourceCode) { background: #FDF6E3; }
 95 | pre code { color: #657B83; }
 96 | code > span.kw { color: #859900; font-weight: bold;   font-style: normal; } /* Keyword */
 97 | code > span.dt { color: #B58900; font-weight: normal; font-style: normal; } /* DataType */
 98 | code > span.dv { color: #2AA198; font-weight: normal; font-style: normal; } /* DecVal */
 99 | code > span.bn { color: #2AA198; font-weight: normal; font-style: normal; } /* BaseN */
100 | code > span.fl { color: #2AA198; font-weight: normal; font-style: normal; } /* Float */
101 | code > span.ch { color: #2AA198; font-weight: normal; font-style: normal; } /* Char */
102 | code > span.st { color: #2AA198; font-weight: normal; font-style: normal; } /* String */
103 | code > span.co { color: #93A1A1; font-weight: normal; font-style: italic; } /* Comment */
104 | code > span.ot { color: #268BD2; font-weight: normal; font-style: normal; } /* Other */
105 | code > span.al { color: #DC322F; font-weight: bold;   font-style: normal; } /* Alert */
106 | code > span.fu { color: #268BD2; font-weight: normal; font-style: normal; } /* Function */
107 | code > span.er { color: #DC322F; font-weight: bold;   font-style: normal; } /* Error */
108 | code > span.wa { color: #CB4B16; font-weight: bold;   font-style: italic; } /* Warning */
109 | code > span.cn { color: #2AA198; font-weight: normal; font-style: normal; } /* Constant */
110 | code > span.sc { color: #DC322F; font-weight: normal; font-style: normal; } /* SpecialChar */
111 | code > span.vs { color: #657B83; font-weight: normal; font-style: normal; } /* VerbatimString */
112 | code > span.ss { color: #DC322F; font-weight: normal; font-style: normal; } /* SpecialString */
113 | code > span.im { color: #657B83; font-weight: normal; font-style: normal; } /* Import */
114 | code > span.va { color: #268BD2; font-weight: normal; font-style: normal; } /* Variable */
115 | code > span.cf { color: #859900; font-weight: bold;   font-style: normal; } /* ControlFlow */
116 | code > span.op { color: #859900; font-weight: bold;   font-style: normal; } /* Operator */
117 | code > span.bu { color: #657B83; font-weight: normal; font-style: normal; } /* BuiltIn */
118 | code > span.ex { color: #657B83; font-weight: normal; font-style: normal; } /* Extension */
119 | code > span.pp { color: #CB4B16; font-weight: normal; font-style: normal; } /* Preprocessor */
120 | code > span.at { color: #657B83; font-weight: normal; font-style: normal; } /* Attribute */
121 | code > span.do { color: #93A1A1; font-weight: normal; font-style: italic; } /* Documentation */
122 | code > span.an { color: #93A1A1; font-weight: bold;   font-style: italic; } /* Annotation */
123 | code > span.cv { color: #93A1A1; font-weight: bold;   font-style: italic; } /* CommentVar */
124 | code > span.in { color: #93A1A1; font-weight: bold;   font-style: italic; } /* Information */
125 | 


--------------------------------------------------------------------------------
/test.bib:
--------------------------------------------------------------------------------
  1 | @article{barrett2015,
  2 |   author = {Barrett, LF and Simmons, WK},
  3 |   title = {Interoceptive Predictions in the Brain},
  4 |   journal = {Nature Reviews Neuroscience},
  5 |   volume = {16},
  6 |   number = {7},
  7 |   pages = {419-429},
  8 |   doi = "10.1038/nrn3950",
  9 |   year = {2015}
 10 | }
 11 | @article{copenhaver2014,
 12 |   author = {Copenhaver, Rebecca},
 13 |   title = {Berkeley on the Language of Nature and the Objects of Vision},
 14 |   journal = {Res Philosophica},
 15 |   volume = {91},
 16 |   number = {1},
 17 |   pages = {29-46},
 18 |   doi = "10.11612/resphil.2014.91.1.2",
 19 |   year = {2014}
 20 | }
 21 | @article{crivellato2007,
 22 |   author = {Crivellato, Enrico and Ribatti, Domenico},
 23 |   title = {Soul, Mind, Brain: {Greek} Philosophy and the Birth of Neuroscience},
 24 |   journal = {Journal of Anatomy},
 25 |   volume = {71},
 26 |   number = {4},
 27 |   pages = {327-336},
 28 |   doi = "10.1016/j.brainresbull.2006.09.020",
 29 |   year = {2007}
 30 | }
 31 | @article{hoffman2014,
 32 |   author = {Hoffman, Donald D. and Prakash, Chetan},
 33 |   title = {Objects of Consciousness},
 34 |   journal = {Frontiers in psychology},
 35 |   volume = {5},
 36 |   pages = {577},
 37 |   doi = "10.3389/fpsyg.2014.00577",
 38 |   year = {2014}
 39 | }
 40 | @incollection{siegel2015,
 41 |   author = {Siegel, Susanna and Silins, Nicholas},
 42 |   editor = {Matthen, Mohan},
 43 |   publisher = {Oxford University Press},
 44 |   title = {The Epistemology of Perception},
 45 |   booktitle = {The oxford handbook of philosophy of perception},
 46 |   pages = {781-811},
 47 |   doi = "10.1093/oxfordhb/9780199600472.013.040",
 48 |   year = {2015},
 49 |   address = {Oxford}
 50 | }
 51 | @incollection{simmons2013,
 52 |   author = {Simmons, Alison},
 53 |   editor = {Matthen, Mohan},
 54 |   publisher = {Oxford University Press},
 55 |   title = {Perception in Early Modern Philosophy},
 56 |   booktitle = {The oxford handbook of philosophy of perception},
 57 |   pages = {81-99},
 58 |   doi = "10.1093/oxfordhb/9780199600472.013.015",
 59 |   year = {2015},
 60 |   address = {Oxford}
 61 | }
 62 | @article{dirac1953,
 63 |   title   = "The lorentz transformation and absolute time",
 64 |   journal = "Physica",
 65 |   volume  = "19",
 66 |   number  = "1--12",
 67 |   pages   = "888--896",
 68 |   year    = "1953",
 69 |   doi     = "10.1016/S0031-8914(53)80099-6",
 70 |   author  = "P.A.M. Dirac"
 71 | }
 72 | @article{feynman1963,
 73 |   title   = "The theory of a general quantum system interacting with a linear dissipative system",
 74 |   journal = "Annals of Physics",
 75 |   volume  = "24",
 76 |   pages   = "118--173",
 77 |   year    = "1963",
 78 |   doi     = "10.1016/0003-4916(63)90068-X",
 79 |   author  = "R.P Feynman and F.L {Vernon Jr.}"
 80 | }
 81 | 
 82 | @Article{schrodinger1926,
 83 |   author =       "Erwin Schrödinger",
 84 |   title =        "{Quantisierung als Eigenwertproblem (Dritte
 85 |                  Mitteilung: Störungstheorie, mit Anwendung auf den
 86 |                  Starkeffekt der Balmerlinien)}. ({German})
 87 |                  [{Quantization as an eigenvalue problem (Third report:
 88 |                  perturbation theory, with application to the Stark
 89 |                  effect of the Balmer lines)}]",
 90 |   journal =      "Annalen der Physik (1900)",
 91 |   volume =       "385",
 92 |   number =       "13",
 93 |   pages =        "437--490",
 94 |   month =        "????",
 95 |   year =         "1926",
 96 |   DOI =          "10.1002/andp.19263851302",
 97 |   ISSN =         "1521-3889",
 98 |   language =     "German",
 99 | }
100 | 


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