From 2191d929a12a233347ee79c673b8f2971c10e6dd Mon Sep 17 00:00:00 2001 From: Daniel Himmelstein Date: Sun, 27 Dec 2020 18:12:42 -0500 Subject: [PATCH 01/54] enable citekey prefix inference merges https://github.com/manubot/rootstock/pull/404 refs https://github.com/manubot/manubot/issues/123 --- USAGE.md | 15 ++++++++++++++- build/environment.yml | 2 +- 2 files changed, 15 insertions(+), 2 deletions(-) diff --git a/USAGE.md b/USAGE.md index a7e446b..5bd004a 100644 --- a/USAGE.md +++ b/USAGE.md @@ -110,6 +110,19 @@ When choosing which source to use for a citation, we recommend the following ord 9. For references that do not have any of the above persistent identifiers, the citation key does not need to include a prefix. Citing `@old-manuscript` will work, but only if reference metadata is [provided manually](#reference-metadata). +Manubot is able to infer certain prefixes, +such some citations can be formatted like `@accession` (without a prefix). +Examples includes DOIs like `@10.15363/thinklab.4` or `@10/993`, +PMC / PubMed identifiers like `@PMC4497619` or `@26158728`, +arXiv identifier like `@1508.06576v2`, +and Wikidata identifiers like `@Q50051684`. +To disable citekey prefix inference, add the following to `metadata.yaml`: + +```yaml +pandoc: + manubot-infer-citekey-prefixes: false +``` + Cite multiple items at once like: ```md @@ -136,7 +149,7 @@ By default, `pandoc-manubot-cite` does not fail upon invalid citations, although ```yaml pandoc: - manubot-fail-on-errors: True + manubot-fail-on-errors: true ``` #### Citation aliases diff --git a/build/environment.yml b/build/environment.yml index f81dfc8..abee7fb 100644 --- a/build/environment.yml +++ b/build/environment.yml @@ -21,7 +21,7 @@ dependencies: - yamllint=1.25.0 - pip: - errorhandler==2.0.1 - - git+https://github.com/manubot/manubot@55c5e1e526261ebadd2aefed2c2757792d8d2ebf + - git+https://github.com/manubot/manubot@553090a16ac24a9fdc3f8df241a91b790c140865 - isbnlib==3.10.3 - opentimestamps-client==0.7.0 - opentimestamps==0.4.1 From 87c11957cf69b73ebed5518f7928b99adb1dc5d6 Mon Sep 17 00:00:00 2001 From: Vincent Rubinetti Date: Fri, 5 Feb 2021 12:43:51 -0500 Subject: [PATCH 02/54] Webpage: refactor plugins & add scite plugin merges https://github.com/manubot/rootstock/pull/409 * moves repeated and shared/generic functions to separate "core" plugin * reorganizes html.yaml config into first and third party plugins * removes functionality to set plugin options from url * reformats plugins with Prettier (eg 4 space tabs to 2 space) * removes anonymizer wrapper. Just make + + diff --git a/build/plugins/analytics.html b/build/plugins/analytics.html index 0e641a1..cbab532 100644 --- a/build/plugins/analytics.html +++ b/build/plugins/analytics.html @@ -1,3 +1,5 @@ - - - + diff --git a/build/plugins/anchors.html b/build/plugins/anchors.html index 4f2e6ba..68f1225 100644 --- a/build/plugins/anchors.html +++ b/build/plugins/anchors.html @@ -1,144 +1,127 @@ - - - + + diff --git a/build/plugins/attributes.html b/build/plugins/attributes.html index b968198..7009782 100644 --- a/build/plugins/attributes.html +++ b/build/plugins/attributes.html @@ -1,130 +1,84 @@ - - - diff --git a/build/plugins/core.html b/build/plugins/core.html new file mode 100644 index 0000000..4c680a4 --- /dev/null +++ b/build/plugins/core.html @@ -0,0 +1,129 @@ + + + diff --git a/build/plugins/d3.html b/build/plugins/d3.html index 48c16d8..d04226e 100644 --- a/build/plugins/d3.html +++ b/build/plugins/d3.html @@ -1,16 +1,12 @@ - + + src="https://cdnjs.cloudflare.com/ajax/libs/d3/6.2.0/d3.min.js" + integrity="sha512-C2RveGuPIWqkaLAluvoxyiaN1XYNe5ss11urhZWZYBUA9Ydgj+hfGKPcxCzTwut1/fmjEZR7Ac35f2aycT8Ogw==" + crossorigin="anonymous" +> diff --git a/build/plugins/hypothesis.html b/build/plugins/hypothesis.html index 7bd1691..1986d36 100644 --- a/build/plugins/hypothesis.html +++ b/build/plugins/hypothesis.html @@ -1,104 +1,166 @@ - + + + diff --git a/build/plugins/inline-svg.html b/build/plugins/inline-svg.html index be40242..619a3a1 100644 --- a/build/plugins/inline-svg.html +++ b/build/plugins/inline-svg.html @@ -1,62 +1,53 @@ - - - diff --git a/build/plugins/jump-to-first.html b/build/plugins/jump-to-first.html index e8a8088..d205093 100644 --- a/build/plugins/jump-to-first.html +++ b/build/plugins/jump-to-first.html @@ -1,272 +1,102 @@ - - - + + diff --git a/build/plugins/lightbox.html b/build/plugins/lightbox.html index 6b9f2ae..1fbdf77 100644 --- a/build/plugins/lightbox.html +++ b/build/plugins/lightbox.html @@ -1,620 +1,660 @@ - - - + + diff --git a/build/plugins/link-highlight.html b/build/plugins/link-highlight.html index 4462f50..04263a8 100644 --- a/build/plugins/link-highlight.html +++ b/build/plugins/link-highlight.html @@ -1,184 +1,157 @@ - - - + + diff --git a/build/plugins/math.html b/build/plugins/math.html deleted file mode 100644 index f47b24d..0000000 --- a/build/plugins/math.html +++ /dev/null @@ -1,27 +0,0 @@ - - - - - - - diff --git a/build/plugins/mathjax.html b/build/plugins/mathjax.html new file mode 100644 index 0000000..14ba331 --- /dev/null +++ b/build/plugins/mathjax.html @@ -0,0 +1,53 @@ + + + + + + + diff --git a/build/plugins/scite.html b/build/plugins/scite.html new file mode 100644 index 0000000..d01fe51 --- /dev/null +++ b/build/plugins/scite.html @@ -0,0 +1,61 @@ + + + + + + + + diff --git a/build/plugins/table-of-contents.html b/build/plugins/table-of-contents.html index e415945..ea24c97 100644 --- a/build/plugins/table-of-contents.html +++ b/build/plugins/table-of-contents.html @@ -1,315 +1,404 @@ - + + diff --git a/build/plugins/tooltips.html b/build/plugins/tooltips.html index f9cbc60..b6fc505 100644 --- a/build/plugins/tooltips.html +++ b/build/plugins/tooltips.html @@ -1,614 +1,507 @@ - - - + + diff --git a/build/themes/default.html b/build/themes/default.html index 4022f31..2396cc4 100644 --- a/build/themes/default.html +++ b/build/themes/default.html @@ -1,60 +1,525 @@ From 52ab9dc8bba4d0c6cee348fa9d7b0b764a89ffcf Mon Sep 17 00:00:00 2001 From: Vincent Rubinetti Date: Fri, 12 Feb 2021 10:49:07 -0500 Subject: [PATCH 03/54] Update scite plugin merges https://github.com/manubot/rootstock/pull/415 --- build/plugins/scite.html | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/build/plugins/scite.html b/build/plugins/scite.html index d01fe51..4d62049 100644 --- a/build/plugins/scite.html +++ b/build/plugins/scite.html @@ -5,11 +5,6 @@ See https://scite.ai/. --> -