From 57c9d4ad99cc4ca547eef41cea1ed826b5fb0649 Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Mon, 9 Nov 2020 21:26:24 -0500
Subject: [PATCH 01/10] upgrade pandoc to version 2.13
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

new citeproc filter name

upgrade pandoc-xnos packages

refs https://github.com/tomduck/pandoc-fignos/issues/85

upgrade panflute to 2.0.5

includes fix to https://github.com/manubot/rootstock/pull/386#issuecomment-724926969:
Element "MetaList" received "CSL_Item" but expected <class 'panflute.base.MetaValue'>

pandoc html: disable document-css in template

From pandoc 2.11 (2020-10-11) changelog:

> Add CSS to default HTML template (#6601, Mauro Bieg). This greatly
improves the default typography in pandoc’s HTML output. The CSS is
sensitive to a number of variables (e.g. mainfont, fontsize, linestretch):
see the manual for details. To restore the earlier, more spartan output,
you can disable this with -M document-css=false.

pandoc 2.11.3

https://github.com/jgm/pandoc/releases/tag/2.11.3
---
 build/environment.yml             | 16 ++++++++--------
 build/pandoc/defaults/common.yaml |  2 +-
 build/pandoc/defaults/html.yaml   |  1 +
 3 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/build/environment.yml b/build/environment.yml
index abee7fb1..247d9201 100644
--- a/build/environment.yml
+++ b/build/environment.yml
@@ -5,11 +5,10 @@ dependencies:
   - cairo=1.14.12
   - cairocffi=0.8.0
   - cffi=1.12.3
-  - ghp-import=0.5.5
+  - ghp-import=1.0.0
   - jinja2=2.11.2
   - jsonschema=3.2.0
-  - pandoc=2.9.2
-  - panflute=1.12.5
+  - pandoc=2.11.3
   - pango=1.40.14
   - pip=20.2
   - psutil=5.7.3
@@ -21,14 +20,15 @@ dependencies:
   - yamllint=1.25.0
   - pip:
     - errorhandler==2.0.1
-    - git+https://github.com/manubot/manubot@553090a16ac24a9fdc3f8df241a91b790c140865
+    - git+https://github.com/manubot/manubot@01d69f066eaf6554111e6bcf197f7ee1fcfb240b
     - isbnlib==3.10.3
     - opentimestamps-client==0.7.0
     - opentimestamps==0.4.1
-    - pandoc-eqnos==2.3.0
-    - pandoc-fignos==2.3.1
-    - pandoc-tablenos==2.2.2
-    - pandoc-xnos==2.4.3
+    - pandoc-eqnos==2.4.0
+    - pandoc-fignos==2.4.0
+    - pandoc-tablenos==2.3.0
+    - pandoc-xnos==2.5.0
+    - panflute==2.0.5
     - pybase62==0.4.3
     - pysha3==1.0.2
     - python-bitcoinlib==0.10.2
diff --git a/build/pandoc/defaults/common.yaml b/build/pandoc/defaults/common.yaml
index 12c0c343..bfa5d971 100644
--- a/build/pandoc/defaults/common.yaml
+++ b/build/pandoc/defaults/common.yaml
@@ -6,7 +6,7 @@ filters:
 - pandoc-eqnos
 - pandoc-tablenos
 - pandoc-manubot-cite
-- pandoc-citeproc
+- citeproc
 wrap: preserve
 metadata:
   csl: build/assets/style.csl
diff --git a/build/pandoc/defaults/html.yaml b/build/pandoc/defaults/html.yaml
index 50d29812..8aff336a 100644
--- a/build/pandoc/defaults/html.yaml
+++ b/build/pandoc/defaults/html.yaml
@@ -25,6 +25,7 @@ include-after-body:
 - build/plugins/mathjax.html
 #- build/plugins/scite.html
 variables:
+  document-css: false
   math: ""
 html-math-method:
   method: mathjax

From 088132507f78348b72c2f34f8119bced45f59ddd Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Sat, 29 May 2021 11:48:08 -0400
Subject: [PATCH 02/10] upgrade environment

---
 build/environment.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/build/environment.yml b/build/environment.yml
index 247d9201..7b0da108 100644
--- a/build/environment.yml
+++ b/build/environment.yml
@@ -20,15 +20,15 @@ dependencies:
   - yamllint=1.25.0
   - pip:
     - errorhandler==2.0.1
-    - git+https://github.com/manubot/manubot@01d69f066eaf6554111e6bcf197f7ee1fcfb240b
+    - git+https://github.com/manubot/manubot@2c028a7a87be24a76e2dec3ac7db6e8754ae6d4a
     - isbnlib==3.10.3
     - opentimestamps-client==0.7.0
     - opentimestamps==0.4.1
-    - pandoc-eqnos==2.4.0
+    - pandoc-eqnos==2.5.0
     - pandoc-fignos==2.4.0
     - pandoc-tablenos==2.3.0
     - pandoc-xnos==2.5.0
-    - panflute==2.0.5
+    - panflute==2.1.0
     - pybase62==0.4.3
     - pysha3==1.0.2
     - python-bitcoinlib==0.10.2

From a6d315c0f42db90a823e54c086e55066c8fd59c8 Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Sat, 29 May 2021 11:57:41 -0400
Subject: [PATCH 03/10] CSL style: remove handing indent

---
 build/assets/style.csl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build/assets/style.csl b/build/assets/style.csl
index 942a0434..b836f7b9 100644
--- a/build/assets/style.csl
+++ b/build/assets/style.csl
@@ -47,7 +47,7 @@
       <text variable="citation-number"/>
     </layout>
   </citation>
-  <bibliography hanging-indent="true" second-field-align="flush">
+  <bibliography second-field-align="flush">
     <layout>
       <text variable="citation-number" suffix=". "/>
       <group delimiter=" ">

From fd7ff49eb2f8e5eb355dc79a5c9ef132dea0f8a1 Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Mon, 31 May 2021 15:44:38 -0400
Subject: [PATCH 04/10] update pandoc to 2.14

---
 build/environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build/environment.yml b/build/environment.yml
index 7b0da108..40abf49e 100644
--- a/build/environment.yml
+++ b/build/environment.yml
@@ -8,7 +8,7 @@ dependencies:
   - ghp-import=1.0.0
   - jinja2=2.11.2
   - jsonschema=3.2.0
-  - pandoc=2.11.3
+  - pandoc=2.14
   - pango=1.40.14
   - pip=20.2
   - psutil=5.7.3

From fe18096c82f00996b4cfe22b6f2401e282bc635d Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Mon, 31 May 2021 19:08:06 -0400
Subject: [PATCH 05/10] USAGE: document curly-brace citation keys

---
 USAGE.md                | 25 +++++++++++++++++--------
 content/02.delete-me.md |  2 +-
 2 files changed, 18 insertions(+), 9 deletions(-)

diff --git a/USAGE.md b/USAGE.md
index 5bd004a1..4d2f9508 100644
--- a/USAGE.md
+++ b/USAGE.md
@@ -133,14 +133,23 @@ Note that multiple citations must be semicolon separated.
 Be careful not to cite the same study using identifiers from multiple sources.
 For example, the following citations all refer to the same study, but will be treated as separate references: `[@doi:10.7717/peerj.705; @pmc:PMC4304851; @pubmed:25648772]`.
 
-Citation keys must adhere to the syntax described in the [Pandoc manual](https://pandoc.org/MANUAL.html#citations):
-
-> The citation key must begin with a letter, digit, or `_`, and may contain alphanumerics, `_`, and internal punctuation characters (`:.#$%&-+?<>~/`).
-
-To evaluate whether a citation key fully matches this syntax, try [this online regex](https://regex101.com/r/mXZyY2/latest).
-If the citation key is not valid, use the [citation aliases](#citation-aliases) workaround below.
-This is required for citation keys that contain forbidden characters such as `;` or `=` or end with a non-alphanumeric character such as `/`.
-<!-- See [jgm/pandoc#6026](https://github.com/jgm/pandoc/issues/6026) for progress on a more flexible Markdown citation key syntax. -->
+The citation key syntax is described in the [Pandoc manual](https://pandoc.org/MANUAL.html#citations):
+
+> Unless a citation key start with a letter, digit, or `_`,
+> and contains only alphanumerics and internal punctuation characters (`:.#$%&-+?<>~/`),
+> it must be surrounded by curly braces,
+> which are not considered part of the key.
+> In `@Foo_bar.baz.`, the key is `Foo_bar.baz`.
+> The final period is not *internal* punctuation,
+> so it is not included in the key.
+> In `@{Foo_bar.baz.}`, the key is `Foo_bar.baz.`, including the final period.
+> The curly braces are recommended if you use URLs as keys:
+> `[@{https://example.com/bib?name=foobar&date=2000}, p. 33]`.
+
+If a citation key does not fully match [this online regex](https://regex101.com/r/mXZyY2/latest)
+(for example, contains characters such as `;` or `=` or end with a non-alphanumeric character such as `/`),
+make sure to surround it with curly braces or use the [citation aliases](#citation-aliases) workaround below.
+<!-- See [jgm/pandoc#6026](https://github.com/jgm/pandoc/issues/6026) on the curly-brace syntax for Markdown citation keys, which was introduced in Pandoc 2.14. -->
 
 Prior to Rootstock commit [`6636b91`](https://github.com/manubot/rootstock/commit/6636b912c6b41593acd2041d34cd4158c1b317fb) on 2020-01-14, Manubot processed citations separately from Pandoc.
 Switching to a Pandoc filter improved reliability on complex documents, but restricted the syntax of citation keys slightly.
diff --git a/content/02.delete-me.md b/content/02.delete-me.md
index c2b1fd0c..387c467f 100644
--- a/content/02.delete-me.md
+++ b/content/02.delete-me.md
@@ -107,7 +107,7 @@ Citation by Wikidata ID [@wikidata:Q56458321].
 
 Citation by ISBN [@isbn:9780262517638].
 
-Citation by URL [@https://greenelab.github.io/meta-review/].
+Citation by URL [@{https://greenelab.github.io/meta-review/}].
 
 Citation by alias [@deep-review].
 

From b5233d9c9525d8c5579930bc89c141ecc989934c Mon Sep 17 00:00:00 2001
From: Vincent Rubinetti <vince.rubinetti@gmail.com>
Date: Wed, 2 Jun 2021 18:27:59 -0400
Subject: [PATCH 06/10] upgrade pandoc to 2.13 and fix plugin breaks

---
 build/plugins/anchors.html       |  3 ++-
 build/plugins/jump-to-first.html | 10 ++++++----
 build/plugins/tooltips.html      |  8 ++++----
 build/themes/default.html        | 13 ++++++++++---
 4 files changed, 22 insertions(+), 12 deletions(-)

diff --git a/build/plugins/anchors.html b/build/plugins/anchors.html
index 68f1225b..7149501b 100644
--- a/build/plugins/anchors.html
+++ b/build/plugins/anchors.html
@@ -10,7 +10,8 @@
 <script type="module">
   // which types of elements to add anchors next to, in "document.querySelector"
   // format
-  const typesQuery = 'h1, h2, h3, [id^="fig:"], [id^="tbl:"], [id^="eq:"]';
+  const typesQuery =
+    'h1, h2, h3, div[id^="fig:"], div[id^="tbl:"], span[id^="eq:"]';
 
   // start script
   function start() {
diff --git a/build/plugins/jump-to-first.html b/build/plugins/jump-to-first.html
index d2050933..da7df4a9 100644
--- a/build/plugins/jump-to-first.html
+++ b/build/plugins/jump-to-first.html
@@ -15,9 +15,11 @@
 
   // start script
   function start() {
-    if (references !== "false") makeButtons("ref-", "p", "reference");
-    if (figures !== "false") makeButtons("fig:", "figcaption", "figure");
-    if (tables !== "false") makeButtons("tbl:", "caption", "table");
+    if (references !== "false")
+      makeButtons(`div[id^="ref-"]`, ".csl-left-margin", "reference");
+    if (figures !== "false")
+      makeButtons(`div[id^="fig:"]`, "figcaption", "figure");
+    if (tables !== "false") makeButtons(`div[id^="tbl:"]`, "caption", "table");
   }
 
   // when jump button clicked
@@ -45,7 +47,7 @@
 
   // add button next to each reference entry, figure, or table
   function makeButtons(query, containerQuery, subject) {
-    const elements = document.querySelectorAll(`[id^="${query}"`);
+    const elements = document.querySelectorAll(query);
     for (const element of elements) {
       const id = element.id;
       const buttonContainer = element.querySelector(containerQuery);
diff --git a/build/plugins/tooltips.html b/build/plugins/tooltips.html
index b6fc5057..e023e3a7 100644
--- a/build/plugins/tooltips.html
+++ b/build/plugins/tooltips.html
@@ -230,6 +230,7 @@
       "data-selected",
       "data-highlighted",
       "data-glow",
+      "class",
     ];
     for (const attribute of attributes) {
       sourceCopy.removeAttribute(attribute);
@@ -290,9 +291,8 @@
     prevButton.classList.add("icon_button");
     nextButton.classList.add("icon_button");
     prevButton.innerHTML = document.querySelector(".icon_caret_left").innerHTML;
-    nextButton.innerHTML = document.querySelector(
-      ".icon_caret_right"
-    ).innerHTML;
+    nextButton.innerHTML =
+      document.querySelector(".icon_caret_right").innerHTML;
     navBar.appendChild(prevButton);
     navBar.appendChild(document.createTextNode(text));
     navBar.appendChild(nextButton);
@@ -336,7 +336,7 @@
     if (!target) return;
 
     // if ref or figure, modify target to get expected element
-    if (id.indexOf("ref-") === 0) target = target.querySelector("p");
+    if (id.indexOf("ref-") === 0) target = target.querySelector(":nth-child(2)");
     else if (id.indexOf("fig:") === 0) target = target.querySelector("figure");
 
     return target;
diff --git a/build/themes/default.html b/build/themes/default.html
index 2396cc4d..0c855a3f 100644
--- a/build/themes/default.html
+++ b/build/themes/default.html
@@ -267,8 +267,7 @@
   }
 
   /* table auto-number */
-  table > caption > span:first-of-type,
-  div.table_wrapper > table > caption > span:first-of-type {
+  table > caption > span:first-of-type {
     font-weight: bold;
     margin-right: 5px;
   }
@@ -495,6 +494,15 @@
     top: 0.125em;
   }
 
+  /* -------------------------------------------------- */
+  /* references */
+  /* -------------------------------------------------- */
+
+  .csl-entry {
+    margin-top: 20px;
+    margin-bottom: 20px;
+  }
+
   /* -------------------------------------------------- */
   /* print control */
   /* -------------------------------------------------- */
@@ -626,7 +634,6 @@
 
   /* tablenos wrapper */
   .tablenos {
-    /* show scrollbar on tables if necessary to prevent overflow */
     width: 100%;
     margin: 20px 0;
   }

From ea9a48f949b162a425f321e8aa44c82d4f16f444 Mon Sep 17 00:00:00 2001
From: Vincent Rubinetti <vince.rubinetti@gmail.com>
Date: Thu, 3 Jun 2021 12:00:43 -0400
Subject: [PATCH 07/10] update csl entry margins

---
 build/themes/default.html | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/build/themes/default.html b/build/themes/default.html
index 0c855a3f..b3298fe7 100644
--- a/build/themes/default.html
+++ b/build/themes/default.html
@@ -499,8 +499,8 @@
   /* -------------------------------------------------- */
 
   .csl-entry {
-    margin-top: 20px;
-    margin-bottom: 20px;
+    margin-top: 15px;
+    margin-bottom: 15px;
   }
 
   /* -------------------------------------------------- */

From 21617d81c975b31b327814d182199c68ed9f07d1 Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Thu, 10 Jun 2021 09:08:20 -0400
Subject: [PATCH 08/10] Update USAGE.md

Co-authored-by: Anthony Gitter <agitter@users.noreply.github.com>
---
 USAGE.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/USAGE.md b/USAGE.md
index 4d2f9508..0b2ee470 100644
--- a/USAGE.md
+++ b/USAGE.md
@@ -133,7 +133,7 @@ Note that multiple citations must be semicolon separated.
 Be careful not to cite the same study using identifiers from multiple sources.
 For example, the following citations all refer to the same study, but will be treated as separate references: `[@doi:10.7717/peerj.705; @pmc:PMC4304851; @pubmed:25648772]`.
 
-The citation key syntax is described in the [Pandoc manual](https://pandoc.org/MANUAL.html#citations):
+The citation key syntax is described in the [Pandoc manual](https://pandoc.org/MANUAL.html#citation-syntax):
 
 > Unless a citation key start with a letter, digit, or `_`,
 > and contains only alphanumerics and internal punctuation characters (`:.#$%&-+?<>~/`),

From 9ae8d19a91801713c8a85b70176945024c7dc485 Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Thu, 10 Jun 2021 09:10:05 -0400
Subject: [PATCH 09/10] use conda for panflute

---
 build/environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build/environment.yml b/build/environment.yml
index 40abf49e..78eb2563 100644
--- a/build/environment.yml
+++ b/build/environment.yml
@@ -9,6 +9,7 @@ dependencies:
   - jinja2=2.11.2
   - jsonschema=3.2.0
   - pandoc=2.14
+  - panflute=2.1.0
   - pango=1.40.14
   - pip=20.2
   - psutil=5.7.3
@@ -28,7 +29,6 @@ dependencies:
     - pandoc-fignos==2.4.0
     - pandoc-tablenos==2.3.0
     - pandoc-xnos==2.5.0
-    - panflute==2.1.0
     - pybase62==0.4.3
     - pysha3==1.0.2
     - python-bitcoinlib==0.10.2

From eb824cee8f84f279a7d73ac66ef5602460bf5481 Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Thu, 10 Jun 2021 19:08:04 -0400
Subject: [PATCH 10/10] Revert "use conda for panflute"

This reverts commit 9ae8d19a91801713c8a85b70176945024c7dc485.
---
 build/environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build/environment.yml b/build/environment.yml
index 78eb2563..40abf49e 100644
--- a/build/environment.yml
+++ b/build/environment.yml
@@ -9,7 +9,6 @@ dependencies:
   - jinja2=2.11.2
   - jsonschema=3.2.0
   - pandoc=2.14
-  - panflute=2.1.0
   - pango=1.40.14
   - pip=20.2
   - psutil=5.7.3
@@ -29,6 +28,7 @@ dependencies:
     - pandoc-fignos==2.4.0
     - pandoc-tablenos==2.3.0
     - pandoc-xnos==2.5.0
+    - panflute==2.1.0
     - pybase62==0.4.3
     - pysha3==1.0.2
     - python-bitcoinlib==0.10.2