update to authors-block

MS/AC.qmd

@@ -1,13 +1,9 @@
 ---
 format:
   elsevier-html:
-    filters:
-      - author-info-blocks
     css: _extensions/inst/css/style.css
   docx:
     reference-doc: _extensions/inst/word/MS.docx
-    filters:
-      - author-info-blocks
   elsevier-pdf:
     latex-clean: false
     header-includes:
@@ -23,6 +19,8 @@ format:
       formatting: preprint
       model: 1p
       cite-style: authoryear
+filters:
+  - authors-block
 ---
 
 # CRediT authorship contribution statement {-}

MS/MS.qmd

@@ -14,41 +14,38 @@ format:
   elsevier-html:
     css: _extensions/inst/css/style.css
     keep-md: true
-    dplyr::filters:
-      - author-info-blocks
   epub: default
   docx:
     reference-doc: _extensions/inst/word/MS.docx
-    dplyr::filters:
+  elsevier-pdf:
-      - author-info-blocks
+    keep-tex: false
-#   elsevier-pdf:
+    keep-md: false
-#     keep-tex: false
+    include-in-header: "./_extensions/quarto-journals/elsevier/partials/revision.tex"
-#     keep-md: false
+    latex-clean: false
-#     include-in-header: "./_extensions/quarto-journals/elsevier/partials/revision.tex"
+    header-includes:
-#     latex-clean: false
+      # - \usepackage{threeparttable}
-#     header-includes:
+      # - \usepackage{fontspec}
-#       # - \usepackage{threeparttable}
+      # - \usepackage{endfloat}
-#       # - \usepackage{fontspec}
+      - \setmainfont{Calibri}
-#       # - \usepackage{endfloat}
+      - \usepackage[UTF8, scheme=plain]{ctex}
-#       - \setmainfont{Calibri}
+      - \usepackage{float}
-#       - \usepackage[UTF8, scheme=plain]{ctex}
+      - \usepackage[normalem]{ulem}
-#       - \usepackage{float}
+      - \usepackage[doublespacing]{setspace}
-#       - \usepackage[normalem]{ulem}
+      - \usepackage{lineno}
-#       - \usepackage[doublespacing]{setspace}
+      - \linenumbers
-#       - \usepackage{lineno}
+    journal:
-#       - \linenumbers
+      formatting: preprint # preprint | review | doublebind
-#     journal:
+      model: 1p
-#       formatting: preprint # preprint | review | doublebind
+      cite-style: authoryear
-#       model: 1p
+      # graphical-abstract: "![](../figures/GA3.pdf)"
-#       cite-style: authoryear
+      # highlights:
-#       # graphical-abstract: "![](../figures/GA3.pdf)"
+      #   - A comprehensive model was contructed to evaluate the risk of odor occurrences
-#       # highlights:
+      #   - Turbidity distribution determine underwater light and MIB-producing *Planktothrix*
-#       #   - A comprehensive model was contructed to evaluate the risk of odor occurrences
+      #   - Increasing flowrate increases turbidity that can control *Planktothrix* and MIB
-#       #   - Turbidity distribution determine underwater light and MIB-producing *Planktothrix*
+      #   - Odor control based on flow regulation in source water is "green" and fundamental
-#       #   - Increasing flowrate increases turbidity that can control *Planktothrix* and MIB
+filters:
-#       #   - Odor control based on flow regulation in source water is "green" and fundamental
+   - latex-environment
-# filters:
+   - authors-block
-#    - latex-environment
 commands: [clab]
 ---
 

MS/SM.qmd

@@ -5,13 +5,9 @@ bibliography: [../BB/Ref.bib, ../BB/localRef.bib]
 csl: _extensions/inst/tex/elsevier-harvard.csl
 format:
   elsevier-html:
-    filters:
-      - author-info-blocks
     css: _extensions/inst/css/style.css
   docx:
     reference-doc: _extensions/inst/word/MS.docx
-    filters:
-      - author-info-blocks
   elsevier-pdf:
     classoption: [nopreprintline]
     revision: true
@@ -35,6 +31,7 @@ format:
       - \linenumbers
 filters:
    - latex-environment
+   - authors-block
 commands: [clab]
 ---
 

_extensions/kapsner/authors-block/_extension.yml

@@ -0,0 +1,13 @@
+title: Authors-block
+authors:
+  - name: Lorenz A. Kapsner
+    orcid: 0000-0003-1866-860X
+  - name: Albert Krewinkel
+    orcid: 0000-0002-9455-0796
+  - name: Robert Winkler
+version: 0.2.1
+quarto-required: ">=1.3.0"
+contributes:
+  filters:
+    - authors-block.lua
+

_extensions/kapsner/authors-block/authors-block.lua

@@ -0,0 +1,64 @@
+--[[
+authors-block – affiliations block extension for quarto
+
+Copyright (c) 2023 Lorenz A. Kapsner
+
+Permission to use, copy, modify, and/or distribute this software for any purpose
+with or without fee is hereby granted, provided that the above copyright notice
+and this permission notice appear in all copies.
+
+THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
+REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
+INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
+TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
+THIS SOFTWARE.
+]]
+
+local List = require 'pandoc.List'
+
+-- [import]
+local from_utils = require "utils"
+local normalize_affiliations = from_utils.normalize_affiliations
+local normalize_authors = from_utils.normalize_authors
+local normalize_latex_authors = from_utils.normalize_latex_authors
+
+local from_authors = require "from_author_info_blocks"
+local default_marks = from_authors.default_marks
+local create_equal_contributors_block = from_authors.create_equal_contributors_block
+local create_affiliations_blocks = from_authors.create_affiliations_blocks
+local create_correspondence_blocks = from_authors.create_correspondence_blocks
+local is_corresponding_author = from_authors.is_corresponding_author
+local author_inline_generator = from_authors.author_inline_generator
+local create_authors_inlines = from_authors.create_authors_inlines
+-- [/import]
+
+-- This is the main-part
+function Pandoc(doc)
+  local meta = doc.meta
+  local body = List:new{}
+  
+  local mark = function (mark_name) return default_marks[mark_name] end
+
+  body:extend(create_equal_contributors_block(meta.authors, mark) or {})
+  body:extend(create_affiliations_blocks(meta.affiliations) or {})
+  body:extend(create_correspondence_blocks(meta.authors, mark) or {})
+  body:extend(doc.blocks)
+  
+  for _i, author in ipairs(meta.authors) do
+    author.test = is_corresponding_author(author)
+  end
+  
+  meta.affiliations = normalize_affiliations(meta.affiliations)
+  meta.author = meta.authors:map(normalize_authors(meta.affiliations))
+  
+  -- Overwrite authors with formatted values. We use a single, formatted
+  -- string for most formats. LaTeX output, however, looks nicer if we
+  -- provide a authors as a list.
+  meta.author = pandoc.MetaInlines(create_authors_inlines(meta.author, mark))
+  -- Institute info is now baked into the affiliations block.
+  meta.affiliations = nil
+  
+  return pandoc.Pandoc(body, meta)
+end

_extensions/kapsner/authors-block/from_author_info_blocks.lua

@@ -0,0 +1,197 @@
+-- https://github.com/pandoc/lua-filters/commit/ca72210b453cc0d045360e0ae36448d019d7dfbf
+--[[
+affiliation-blocks – generate title components
+
+Copyright © 2017–2021 Albert Krewinkel
+
+Permission to use, copy, modify, and/or distribute this software for any purpose
+with or without fee is hereby granted, provided that the above copyright notice
+and this permission notice appear in all copies.
+
+THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
+REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
+INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
+TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
+THIS SOFTWARE.
+]]
+
+-- from @kapsner
+-- [import]
+local from_utils = require "utils"
+local has_key = from_utils.has_key
+-- [/import]
+local M = {}
+
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
+local List = require 'pandoc.List'
+local utils = require 'pandoc.utils'
+local stringify = utils.stringify
+
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
+local default_marks
+local default_marks = {
+  corresponding_author = FORMAT == 'latex'
+    and {pandoc.RawInline('latex', '*')}
+    or {pandoc.Str '✉'},
+  equal_contributor = FORMAT == 'latex'
+    and {pandoc.RawInline('latex', '$\\dagger{}$')}
+    or {pandoc.Str '*'},
+}
+M.default_marks = default_marks
+
+-- modified by @kapsner
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
+local function is_equal_contributor(author)
+  if has_key(author, "attributes") then
+    return author.attributes["equal-contributor"]
+  end
+  return nil
+end
+
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
+--- Create equal contributors note.
+local function create_equal_contributors_block(authors, mark)
+  local has_equal_contribs = List:new(authors):find_if(is_equal_contributor)
+  if not has_equal_contribs then
+    return nil
+  end
+  local contributors = {
+    pandoc.Superscript(mark'equal_contributor'),
+    pandoc.Space(),
+    pandoc.Str 'These authors contributed equally to this work.'
+  }
+  return List:new{pandoc.Para(contributors)}
+end
+M.create_equal_contributors_block = create_equal_contributors_block
+
+
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
+local function intercalate(lists, elem)
+  local result = List:new{}
+  for i = 1, (#lists - 1) do
+    result:extend(lists[i])
+    result:extend(elem)
+  end
+  if #lists > 0 then
+    result:extend(lists[#lists])
+  end
+  return result
+end
+
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
+--- Check whether the given author is a corresponding author
+local function is_corresponding_author(author)
+  if has_key(author, "attributes") then
+    if author.attributes["corresponding"] then
+      return author.email
+    end
+  end
+  return nil
+end
+M.is_corresponding_author = is_corresponding_author
+
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
+--- Generate a block element containing the correspondence information
+local function create_correspondence_blocks(authors, mark)
+  local corresponding_authors = List:new{}
+  for _, author in ipairs(authors) do
+    if is_corresponding_author(author) then
+      local mailto = 'mailto:' .. utils.stringify(author.email)
+      local author_with_mail = List:new(
+        -- modified by @kapsner
+        author.name.literal .. List:new{pandoc.Space(),  pandoc.Str '<'} ..
+        author.email .. List:new{pandoc.Str '>'}
+      )
+      local link = pandoc.Link(author_with_mail, mailto)
+      table.insert(corresponding_authors, {link})
+    end
+  end
+  if #corresponding_authors == 0 then
+    return nil
+  end
+  local correspondence = List:new{
+    pandoc.Superscript(mark'corresponding_author'),
+    pandoc.Space(),
+    pandoc.Str'Correspondence:',
+    pandoc.Space()
+  }
+  local sep = List:new{pandoc.Str',',  pandoc.Space()}
+  return {
+    pandoc.Para(correspondence .. intercalate(corresponding_authors, sep))
+  }
+end
+M.create_correspondence_blocks = create_correspondence_blocks
+
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
+--- Create inlines for a single author (includes all author notes)
+local function author_inline_generator (get_mark)
+  return function (author)
+    local author_marks = List:new{}
+    -- modified by @kapsner
+    if has_key(author, "attributes") then
+      if author.attributes["equal-contributor"] then
+        author_marks[#author_marks + 1] = get_mark 'equal_contributor'
+      end
+    end
+    local idx_str
+    for _, idx in ipairs(author.affiliations) do
+      if type(idx) ~= 'table' then
+        idx_str = tostring(idx)
+      else
+        idx_str = stringify(idx)
+      end
+      author_marks[#author_marks + 1] = {pandoc.Str(idx_str)}
+    end
+    if is_corresponding_author(author) then
+      author_marks[#author_marks + 1] = get_mark 'corresponding_author'
+    end
+    -- modified by @kapsner
+    if FORMAT:match 'latex' then
+      author.name.literal[#author.name.literal + 1] = pandoc.Superscript(intercalate(author_marks, {pandoc.Str ','}))
+      return author
+    else
+      local res = List.clone(author.name.literal)
+      res[#res + 1] = pandoc.Superscript(intercalate(author_marks, {pandoc.Str ','}))
+      return res
+    end
+  end
+end
+M.author_inline_generator = author_inline_generator
+
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
+--- Generate a list of inlines containing all authors.
+local function create_authors_inlines(authors, mark)
+  local inlines_generator = author_inline_generator(mark)
+  local inlines = List:new(authors):map(inlines_generator)
+  local and_str = List:new{pandoc.Space(), pandoc.Str'and', pandoc.Space()}
+
+  local last_author = inlines[#inlines]
+  inlines[#inlines] = nil
+  local result = intercalate(inlines, {pandoc.Str ',', pandoc.Space()})
+  if #authors > 1 then
+    result:extend(List:new{pandoc.Str ","} .. and_str)
+  end
+  result:extend(last_author)
+  return result
+end
+M.create_authors_inlines = create_authors_inlines
+
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/author-info-blocks/author-info-blocks.lua
+--- Generate a block list all affiliations, marked with arabic numbers.
+local function create_affiliations_blocks(affiliations)
+  local affil_lines = List:new(affiliations):map(
+    function (affil, i)
+      local num_inlines = List:new{
+        pandoc.Superscript{pandoc.Str(affil.number)},
+        pandoc.Space()
+      }
+      return num_inlines .. affil.name
+    end
+  )
+  return {pandoc.Para(intercalate(affil_lines, {pandoc.LineBreak()}))}
+end
+M.create_affiliations_blocks = create_affiliations_blocks
+
+return M

_extensions/kapsner/authors-block/from_scholarly_metadata.lua

@@ -0,0 +1,59 @@
+--[[
+ScholarlyMeta – normalize author/affiliation meta variables
+
+Copyright (c) 2017-2021 Albert Krewinkel, Robert Winkler
+
+Permission to use, copy, modify, and/or distribute this software for any purpose
+with or without fee is hereby granted, provided that the above copyright notice
+and this permission notice appear in all copies.
+
+THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
+REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
+INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
+TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
+THIS SOFTWARE.
+]]
+
+local List = require 'pandoc.List'
+local utils = require 'pandoc.utils'
+local stringify = utils.stringify
+
+local M = {}
+
+
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/scholarly-metadata/scholarly-metadata.lua
+--- Returns a function which checks whether an object has the given ID.
+local function has_id(id)
+  return function(x) return x.id == id end
+end
+
+
+-- taken from https://github.com/pandoc/lua-filters/blob/1660794b991c3553968beb993f5aabb99b317584/scholarly-metadata/scholarly-metadata.lua
+--- Resolve institute placeholders to full named objects
+local function resolve_institutes(institute, known_institutes)
+  local unresolved_institutes
+  if institute == nil then
+    unresolved_institutes = {}
+  elseif type(institute) == "string" or type(institute) == "number" then
+    unresolved_institutes = {institute}
+  else
+    unresolved_institutes = institute
+  end
+
+  local result = List:new{}
+  for i, inst in ipairs(unresolved_institutes) do
+    -- this has been modified by @kapsner
+    --result[i] =
+    --  known_institutes[tonumber(inst)] or
+    --  known_institutes:find_if(has_id(pandoc.utils.stringify(inst))) or
+    --  to_named_object(inst)
+    intermed_val = known_institutes:find_if(has_id(stringify(inst)))
+    result[i] = pandoc.MetaString(stringify(intermed_val.index))
+  end
+  return result
+end
+M.resolve_institutes = resolve_institutes
+
+return M

_extensions/kapsner/authors-block/utils.lua

@@ -0,0 +1,62 @@
+--[[
+authors-block – affiliations block extension for quarto
+
+Copyright (c) 2023 Lorenz A. Kapsner
+
+Permission to use, copy, modify, and/or distribute this software for any purpose
+with or without fee is hereby granted, provided that the above copyright notice
+and this permission notice appear in all copies.
+
+THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
+REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
+INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
+TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
+THIS SOFTWARE.
+]]
+
+local List = require 'pandoc.List'
+local utils = require 'pandoc.utils'
+local stringify = utils.stringify
+
+-- [import]
+local from_scholarly = require "from_scholarly_metadata"
+local resolve_institutes = from_scholarly.resolve_institutes
+-- [/import]
+
+local M = {}
+
+-- from @kapsner
+local function normalize_affiliations(affiliations)
+  local affiliations_norm = List:new(affiliations):map(
+    function(affil, i)
+      affil.index = pandoc.MetaInlines(pandoc.Str(tostring(i)))
+      affil.id = pandoc.MetaString(stringify(affil.id))
+      return affil
+    end
+  )
+  return affiliations_norm
+end
+M.normalize_affiliations = normalize_affiliations
+
+-- from https://stackoverflow.com/a/2282547
+local function has_key(set, key)
+  return set[key] ~= nil
+end
+M.has_key = has_key
+
+-- from @kapsner
+local function normalize_authors(affiliations)
+  return function(auth)
+    auth.id = pandoc.MetaString(stringify(auth.name))
+    auth.affiliations = resolve_institutes(
+      auth.affiliations,
+      affiliations
+    )
+    return auth
+  end
+end
+M.normalize_authors = normalize_authors
+
+return M

_quarto.yml

@@ -125,8 +125,8 @@ website:
         file: MS/MS.qmd
       - text: "Supplementary Materials"
         file: MS/SM.qmd
-      - text: "Revision Notes"
+      # - text: "Revision Notes"
-        file: MS/RN.qmd
+      #   file: MS/RN.qmd
       - text: "Slides"
         file: SD/index.qmd
       - text: "Other"