From 7e681492040da157c293b8262d6b5fd67e921d98 Mon Sep 17 00:00:00 2001
From: Jonas Smedegaard <dr@jones.dk>
Date: Sat, 15 Mar 2025 07:36:30 +0100
Subject: embed filter extensions in format extension

---
 .../pandoc-ext/abstract-section/_extension.yaml    |  6 --
 .../abstract-section/abstract-section.lua          | 85 ----------------------
 .../ruc-play/stylish-report/_extension.yaml        |  3 +
 .../pandoc-ext/abstract-section/_extension.yaml    |  6 ++
 .../abstract-section/abstract-section.lua          | 85 ++++++++++++++++++++++
 .../ruc-play/stylish-roles/_extension.yaml         |  6 ++
 .../ruc-play/stylish-roles/stylish-roles.lua       | 54 ++++++++++++++
 _extensions/ruc-play/stylish-roles/_extension.yaml |  6 --
 .../ruc-play/stylish-roles/stylish-roles.lua       | 54 --------------
 _quarto.yml                                        |  4 -
 10 files changed, 154 insertions(+), 155 deletions(-)
 delete mode 100644 _extensions/pandoc-ext/abstract-section/_extension.yaml
 delete mode 100644 _extensions/pandoc-ext/abstract-section/abstract-section.lua
 create mode 100644 _extensions/ruc-play/stylish-report/_extensions/pandoc-ext/abstract-section/_extension.yaml
 create mode 100644 _extensions/ruc-play/stylish-report/_extensions/pandoc-ext/abstract-section/abstract-section.lua
 create mode 100644 _extensions/ruc-play/stylish-report/_extensions/ruc-play/stylish-roles/_extension.yaml
 create mode 100644 _extensions/ruc-play/stylish-report/_extensions/ruc-play/stylish-roles/stylish-roles.lua
 delete mode 100644 _extensions/ruc-play/stylish-roles/_extension.yaml
 delete mode 100644 _extensions/ruc-play/stylish-roles/stylish-roles.lua

diff --git a/_extensions/pandoc-ext/abstract-section/_extension.yaml b/_extensions/pandoc-ext/abstract-section/_extension.yaml
deleted file mode 100644
index f6a946b..0000000
--- a/_extensions/pandoc-ext/abstract-section/_extension.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-name: abstract-section
-author: Albert Krewinkel
-version: 1.2.0
-contributes:
-  filters:
-    - abstract-section.lua
diff --git a/_extensions/pandoc-ext/abstract-section/abstract-section.lua b/_extensions/pandoc-ext/abstract-section/abstract-section.lua
deleted file mode 100644
index 4badeb4..0000000
--- a/_extensions/pandoc-ext/abstract-section/abstract-section.lua
+++ /dev/null
@@ -1,85 +0,0 @@
---[[
-abstract-section – move an "abstract" section into document metadata
-
-Copyright: © 2017–2023 Albert Krewinkel
-License:   MIT – see LICENSE file for details
-]]
-local stringify = (require 'pandoc.utils').stringify
-local section_identifiers = {
-  abstract = true,
-}
-local collected = {}
---- The level of the highest heading that was seen so far. Abstracts
---- must be at or above this level to prevent nested sections from being
---- treated as metadata. Only top-level sections should become metadata.
-local toplevel = 6
-
---- Extract abstract from a list of blocks.
-local function abstract_from_blocklist (blocks)
-  local body_blocks = {}
-  local looking_at_section = false
-
-  for _, block in ipairs(blocks) do
-    if block.t == 'Header' and block.level <= toplevel then
-      toplevel = block.level
-      if section_identifiers[block.identifier] then
-        looking_at_section = block.identifier
-        collected[looking_at_section] = {}
-      else
-        looking_at_section = false
-        body_blocks[#body_blocks + 1] = block
-      end
-    elseif looking_at_section then
-      if block.t == 'HorizontalRule' then
-        looking_at_section = false
-      else
-        local collect = collected[looking_at_section]
-        collect[#collect + 1] = block
-      end
-    else
-      body_blocks[#body_blocks + 1] = block
-    end
-  end
-
-  return body_blocks
-end
-
-Pandoc = function (doc)
-  local meta = doc.meta
-
-  -- configure
-  section_identifiers_list =
-    (doc.meta['abstract-section'] or {})['section-identifiers']
-  if section_identifiers_list and #section_identifiers_list > 0 then
-    section_identifiers = {}
-    for i, ident in ipairs(section_identifiers_list) do
-      section_identifiers[stringify(ident)] = true
-    end
-  end
-  -- unset config in meta
-  doc.meta['abstract-section'] = nil
-
-  local blocks = {}
-  if PANDOC_VERSION >= {2,17} then
-    -- Walk all block lists by default
-    blocks = doc.blocks:walk{Blocks = abstract_from_blocklist}
-  elseif PANDOC_VERSION >= {2,9,2} then
-    -- Do the same with pandoc versions that don't have walk methods but the
-    -- `walk_block` function.
-    blocks = pandoc.utils.walk_block(
-      pandoc.Div(doc.blocks),
-      {Blocks = abstract_from_blocklist}
-    ).content
-  else
-    -- otherwise, just check the top-level block-list
-    blocks = abstract_from_blocklist(doc.blocks)
-  end
-  for metakey in pairs(section_identifiers) do
-    metakey = stringify(metakey)
-    local abstract = collected[metakey]
-    if not meta[metakey] and abstract and #abstract > 0 then
-      meta[metakey] = pandoc.MetaBlocks(abstract)
-    end
-  end
-  return pandoc.Pandoc(blocks, meta)
-end
diff --git a/_extensions/ruc-play/stylish-report/_extension.yaml b/_extensions/ruc-play/stylish-report/_extension.yaml
index 507eeaa..58eb145 100644
--- a/_extensions/ruc-play/stylish-report/_extension.yaml
+++ b/_extensions/ruc-play/stylish-report/_extension.yaml
@@ -4,6 +4,9 @@ version: 0.0.3
 contributes:
  formats:
   common:
+    filters:
+    - stylish-roles
+    - abstract-section
   pdf:
     number-sections: true
     toc: true
diff --git a/_extensions/ruc-play/stylish-report/_extensions/pandoc-ext/abstract-section/_extension.yaml b/_extensions/ruc-play/stylish-report/_extensions/pandoc-ext/abstract-section/_extension.yaml
new file mode 100644
index 0000000..f6a946b
--- /dev/null
+++ b/_extensions/ruc-play/stylish-report/_extensions/pandoc-ext/abstract-section/_extension.yaml
@@ -0,0 +1,6 @@
+name: abstract-section
+author: Albert Krewinkel
+version: 1.2.0
+contributes:
+  filters:
+    - abstract-section.lua
diff --git a/_extensions/ruc-play/stylish-report/_extensions/pandoc-ext/abstract-section/abstract-section.lua b/_extensions/ruc-play/stylish-report/_extensions/pandoc-ext/abstract-section/abstract-section.lua
new file mode 100644
index 0000000..4badeb4
--- /dev/null
+++ b/_extensions/ruc-play/stylish-report/_extensions/pandoc-ext/abstract-section/abstract-section.lua
@@ -0,0 +1,85 @@
+--[[
+abstract-section – move an "abstract" section into document metadata
+
+Copyright: © 2017–2023 Albert Krewinkel
+License:   MIT – see LICENSE file for details
+]]
+local stringify = (require 'pandoc.utils').stringify
+local section_identifiers = {
+  abstract = true,
+}
+local collected = {}
+--- The level of the highest heading that was seen so far. Abstracts
+--- must be at or above this level to prevent nested sections from being
+--- treated as metadata. Only top-level sections should become metadata.
+local toplevel = 6
+
+--- Extract abstract from a list of blocks.
+local function abstract_from_blocklist (blocks)
+  local body_blocks = {}
+  local looking_at_section = false
+
+  for _, block in ipairs(blocks) do
+    if block.t == 'Header' and block.level <= toplevel then
+      toplevel = block.level
+      if section_identifiers[block.identifier] then
+        looking_at_section = block.identifier
+        collected[looking_at_section] = {}
+      else
+        looking_at_section = false
+        body_blocks[#body_blocks + 1] = block
+      end
+    elseif looking_at_section then
+      if block.t == 'HorizontalRule' then
+        looking_at_section = false
+      else
+        local collect = collected[looking_at_section]
+        collect[#collect + 1] = block
+      end
+    else
+      body_blocks[#body_blocks + 1] = block
+    end
+  end
+
+  return body_blocks
+end
+
+Pandoc = function (doc)
+  local meta = doc.meta
+
+  -- configure
+  section_identifiers_list =
+    (doc.meta['abstract-section'] or {})['section-identifiers']
+  if section_identifiers_list and #section_identifiers_list > 0 then
+    section_identifiers = {}
+    for i, ident in ipairs(section_identifiers_list) do
+      section_identifiers[stringify(ident)] = true
+    end
+  end
+  -- unset config in meta
+  doc.meta['abstract-section'] = nil
+
+  local blocks = {}
+  if PANDOC_VERSION >= {2,17} then
+    -- Walk all block lists by default
+    blocks = doc.blocks:walk{Blocks = abstract_from_blocklist}
+  elseif PANDOC_VERSION >= {2,9,2} then
+    -- Do the same with pandoc versions that don't have walk methods but the
+    -- `walk_block` function.
+    blocks = pandoc.utils.walk_block(
+      pandoc.Div(doc.blocks),
+      {Blocks = abstract_from_blocklist}
+    ).content
+  else
+    -- otherwise, just check the top-level block-list
+    blocks = abstract_from_blocklist(doc.blocks)
+  end
+  for metakey in pairs(section_identifiers) do
+    metakey = stringify(metakey)
+    local abstract = collected[metakey]
+    if not meta[metakey] and abstract and #abstract > 0 then
+      meta[metakey] = pandoc.MetaBlocks(abstract)
+    end
+  end
+  return pandoc.Pandoc(blocks, meta)
+end
diff --git a/_extensions/ruc-play/stylish-report/_extensions/ruc-play/stylish-roles/_extension.yaml b/_extensions/ruc-play/stylish-report/_extensions/ruc-play/stylish-roles/_extension.yaml
new file mode 100644
index 0000000..190c698
--- /dev/null
+++ b/_extensions/ruc-play/stylish-report/_extensions/ruc-play/stylish-roles/_extension.yaml
@@ -0,0 +1,6 @@
+name: stylish-roles
+author: Jonas Smedegaard
+version: 0.0.1
+contributes:
+  filters:
+    - stylish-roles.lua
diff --git a/_extensions/ruc-play/stylish-report/_extensions/ruc-play/stylish-roles/stylish-roles.lua b/_extensions/ruc-play/stylish-report/_extensions/ruc-play/stylish-roles/stylish-roles.lua
new file mode 100644
index 0000000..50caf71
--- /dev/null
+++ b/_extensions/ruc-play/stylish-report/_extensions/ruc-play/stylish-roles/stylish-roles.lua
@@ -0,0 +1,54 @@
+--[[
+stylish-roles - provide existence hints for attributes and CrediT roles
+as authors[*].metadata.credit[role], by-author[*].metadata.credit[role],
+some-author-has[*].credit[role] and some-author-has.attributes[attribute].
+
+Copyright: © 2024 Jonas Smedegaard <dr@jones.dk
+License:   MIT – see LICENSE file for details
+]]
+function Meta(meta)
+    local attributes = {"corresponding", "equal-contributor"}
+
+    for _, author in ipairs(meta.authors) do
+        if author.roles then
+            local _by = meta["by-author"][tonumber(author.number)]
+            local _some = meta["some-author-has"]
+
+            for _, role in ipairs(author.roles) do
+                if role["vocab-term"] then
+
+                    -- create if missing
+                    author.metadata.credit = author.metadata.credit or {}
+                    _by.metadata.credit = _by.metadata.credit or {}
+                    meta["some-author-has"] = meta["some-author-has"] or {}
+                    meta["some-author-has"].credit = meta["some-author-has"].credit or {}
+
+                    author.metadata.credit[role["vocab-term"]] = true
+                    _by.metadata.credit[role["vocab-term"]] = true
+                    meta["some-author-has"].credit[role["vocab-term"]] = true
+
+                    -- debugging aid
+                    --error(pandoc.utils.stringify(author.name.literal)
+                    --    .. " does " .. role["vocab-term"] .. ".")
+                end
+            end
+
+            for _, attr in ipairs(attributes) do
+                if author.attributes and author.attributes[attr] then
+                    -- create if missing
+                    meta["some-author-has"].attributes = meta["some-author-has"].attributes or {}
+
+                    meta["some-author-has"].attributes[attr] = true
+                end
+            end
+        end
+    end
+
+    -- debugging aid
+    --quarto.utils.dump(meta)
+    --quarto.utils.dump(meta["authors"])
+    --quarto.utils.dump(meta["by-author"])
+    --quarto.utils.dump(meta["some-author-has"])
+
+    return meta
+end
diff --git a/_extensions/ruc-play/stylish-roles/_extension.yaml b/_extensions/ruc-play/stylish-roles/_extension.yaml
deleted file mode 100644
index 190c698..0000000
--- a/_extensions/ruc-play/stylish-roles/_extension.yaml
+++ /dev/null
@@ -1,6 +0,0 @@
-name: stylish-roles
-author: Jonas Smedegaard
-version: 0.0.1
-contributes:
-  filters:
-    - stylish-roles.lua
diff --git a/_extensions/ruc-play/stylish-roles/stylish-roles.lua b/_extensions/ruc-play/stylish-roles/stylish-roles.lua
deleted file mode 100644
index 50caf71..0000000
--- a/_extensions/ruc-play/stylish-roles/stylish-roles.lua
+++ /dev/null
@@ -1,54 +0,0 @@
---[[
-stylish-roles - provide existence hints for attributes and CrediT roles
-as authors[*].metadata.credit[role], by-author[*].metadata.credit[role],
-some-author-has[*].credit[role] and some-author-has.attributes[attribute].
-
-Copyright: © 2024 Jonas Smedegaard <dr@jones.dk
-License:   MIT – see LICENSE file for details
-]]
-function Meta(meta)
-    local attributes = {"corresponding", "equal-contributor"}
-
-    for _, author in ipairs(meta.authors) do
-        if author.roles then
-            local _by = meta["by-author"][tonumber(author.number)]
-            local _some = meta["some-author-has"]
-
-            for _, role in ipairs(author.roles) do
-                if role["vocab-term"] then
-
-                    -- create if missing
-                    author.metadata.credit = author.metadata.credit or {}
-                    _by.metadata.credit = _by.metadata.credit or {}
-                    meta["some-author-has"] = meta["some-author-has"] or {}
-                    meta["some-author-has"].credit = meta["some-author-has"].credit or {}
-
-                    author.metadata.credit[role["vocab-term"]] = true
-                    _by.metadata.credit[role["vocab-term"]] = true
-                    meta["some-author-has"].credit[role["vocab-term"]] = true
-
-                    -- debugging aid
-                    --error(pandoc.utils.stringify(author.name.literal)
-                    --    .. " does " .. role["vocab-term"] .. ".")
-                end
-            end
-
-            for _, attr in ipairs(attributes) do
-                if author.attributes and author.attributes[attr] then
-                    -- create if missing
-                    meta["some-author-has"].attributes = meta["some-author-has"].attributes or {}
-
-                    meta["some-author-has"].attributes[attr] = true
-                end
-            end
-        end
-    end
-
-    -- debugging aid
-    --quarto.utils.dump(meta)
-    --quarto.utils.dump(meta["authors"])
-    --quarto.utils.dump(meta["by-author"])
-    --quarto.utils.dump(meta["some-author-has"])
-
-    return meta
-end
diff --git a/_quarto.yml b/_quarto.yml
index c8dcecb..64892a2 100644
--- a/_quarto.yml
+++ b/_quarto.yml
@@ -26,7 +26,3 @@ bibliography: ref.bib
 csl: apa
 resource-path:
 - /usr/share/citation-style-language/styles
-
-filters:
-  - abstract-section
-  - stylish-roles
-- 
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