| aa09b78 | Anthony Gitter | 08 June 2019, 10:47:22 UTC | Add manubot version details to build readme (#232) | 08 June 2019, 10:47:22 UTC |
| 9f16be0 | Michael Hoffman | 07 June 2019, 15:53:21 UTC | build.sh: always set DOCKER_EXISTS with a zero exit status Merges https://github.com/manubot/rootstock/pull/230 Closes https://github.com/manubot/rootstock/issues/229 Previously, `command -v docker` returned a non-zero exit status when docker did not exist. Because build.sh uses `set -o errexit`, this caused the build script to exit. By appending `|| true`, the exit status will always be zero. Use recommended $() instead of backticks for command substitution. https://stackoverflow.com/a/24592916/4651668 | 07 June 2019, 15:53:21 UTC |
| b9e1d42 | Daniel Himmelstein | 05 June 2019, 18:05:41 UTC | Dependency upgrade on 2019-06-03 with multiple ref file support Merges https://github.com/manubot/rootstock/pull/227 * Upgrade dependencies on 2019-06-03 Keep python at 3.6 to avoid introducing collections.abc warnings from jinja2. Keep cairo, pango, and weasyprint at previous versions to avoid dealing with any difficulties. * Upgrade manubot to include new citation infrastructure. Includes support for multiple manual reference files of multiple formats. Rewrite USAGE.md to document new functionality. * environment.yml: remove `conda-forge::` prefix, which should not be necessary since we specify conda-forge as the channel. This change is meant to resolve conda warning: > you have pip-installed dependencies in your environment file, but you do not list pip itself as one of your conda dependencies https://travis-ci.com/manubot/rootstock/builds/114188607#L507 * Update .gitignore with vscode directory | 05 June 2019, 18:05:41 UTC |
| dcb3cc4 | Daniel Himmelstein | 17 May 2019, 20:15:10 UTC | Use 90. prefix for back-matter.md Merges https://github.com/manubot/rootstock/pull/222 Closes https://github.com/manubot/manubot/issues/106 Enables creating two-digit prefixed content markdown files that will sort to come after back-matter. While back matter is intended to be the final markdown file, some users may want to place content after it. | 17 May 2019, 20:15:10 UTC |
| 5da1d32 | Daniel Himmelstein | 14 May 2019, 15:19:04 UTC | CSL author macro: substitute editor/venue Merges https://github.com/manubot/rootstock/pull/219 Ensures there is a newline between the title and venue, when authors are missing. Closes https://github.com/manubot/rootstock/issues/218 Supersedes https://github.com/manubot/rootstock/pull/158 Substitutes editors for authors when authors are missing. Editors are labeled like "Sönke Bartling, Sascha Friesike (editors)". | 14 May 2019, 15:19:04 UTC |
| 1eb6da8 | David Slochower | 13 May 2019, 18:48:11 UTC | Increase shared memory of athenapdf container Merges https://github.com/manubot/rootstock/pull/220 Closes https://github.com/arachnys/athenapdf/issues/195 Increase --shm-size from the default value of 64m to 1g when running the athenapdf Docker image. Resolves athena issue: `The renderer process has crashed` Switch to using equal sign to separate Docker arguments and values for consistency. https://stackoverflow.com/q/50319060/4651668 | 13 May 2019, 18:48:11 UTC |
| 8d74236 | Anthony Gitter | 01 May 2019, 02:31:38 UTC | Add meta review link to readme Merges https://github.com/manubot/rootstock/pull/217 Closes https://github.com/manubot/rootstock/issues/216 | 01 May 2019, 02:31:38 UTC |
| 0e29315 | Daniel Himmelstein | 24 April 2019, 15:53:50 UTC | Use Athena to build PDF, if Docker installed Merges https://github.com/manubot/rootstock/pull/210 Closes https://github.com/manubot/rootstock/issues/170 More information about Athena is available at https://github.com/arachnys/athenapdf Based on meta-review commit: https://github.com/greenelab/meta-review/commit/cffcfeaea0b6859051d16ab1e263d8bcf62a24b1 | 24 April 2019, 15:53:50 UTC |
| 0399e5f | Daniel Himmelstein | 18 April 2019, 19:27:56 UTC | webpage.py: note to ignore error in versions checkout Merges https://github.com/manubot/rootstock/pull/211 Closes https://github.com/manubot/rootstock/issues/183 | 18 April 2019, 19:27:56 UTC |
| 091ca8d | Vincent Rubinetti | 08 April 2019, 16:42:21 UTC | HTML view: theme & plugin improvements Merges https://github.com/manubot/rootstock/pull/204 Closes https://github.com/manubot/rootstock/issues/197 Lightbox figure zoom: add centerZoom option (default behavior unchanged). Closes https://github.com/manubot/rootstock/issues/202 Remove tooltip keepHorizontal option Closes https://github.com/manubot/rootstock/issues/199 Miscellaneous refactors and theme improvements | 08 April 2019, 16:42:21 UTC |
| 3c37239 | Vincent Rubinetti | 05 April 2019, 13:54:14 UTC | Compactify HTML print view & PDF Merges https://github.com/manubot/rootstock/pull/201 Closes https://github.com/manubot/rootstock/issues/192 Change print CSS rules to reduce the number of pages when printing: - smaller overall font size - even smaller table and figure font size - smaller line spacing - smaller page margins (0.75in -> 0.5in) - smaller heading margins - smaller table cell padding - smaller button icons | 05 April 2019, 13:54:14 UTC |
| fea9eb8 | Vincent Rubinetti | 22 March 2019, 15:49:28 UTC | webpage TOC plugin: fix open/close option issues Merges https://github.com/manubot/rootstock/pull/194 | 22 March 2019, 15:49:28 UTC |
| 4d27314 | Vincent Rubinetti | 20 March 2019, 18:01:21 UTC | images: specify explicit size for icon SVGs Merges https://github.com/manubot/rootstock/pull/195 Sometimes you can see a 'flash' of a very large svg image while the page is loading. This is because the svg has loaded before the css specifying its size has. To fix, specify a reasonable size explicitly in the svg (so it will load at that size by default and then been overridden by whatever size the css tells it to be). | 20 March 2019, 18:01:21 UTC |
| 723319f | Vincent Rubinetti | 15 March 2019, 20:53:33 UTC | HTML: fix auto setting for TOC plugin, revert margin to 0.75in Merges https://github.com/manubot/rootstock/pull/193 | 15 March 2019, 20:53:33 UTC |
| 40a6de3 | Vincent Rubinetti | 14 March 2019, 21:59:08 UTC | HTML plugins: lightbox, tooltips, toc tweaks Merges https://github.com/manubot/rootstock/pull/191 | 14 March 2019, 21:59:08 UTC |
| b422130 | Vincent Rubinetti | 13 March 2019, 21:51:46 UTC | CSS: background colors, alignment classes, print control Merges https://github.com/manubot/rootstock/pull/188 Miscellaneous changes to default.html style including background colors, text/page alignment classes, print control styles. Switch margins to 0.75 inches to reduce pages needed to print manuscript. | 13 March 2019, 21:51:46 UTC |
| 3b5bf5c | Vincent Rubinetti | 13 March 2019, 21:41:01 UTC | Update content/02.delete-me.md to show formatting Merges https://github.com/manubot/rootstock/pull/169 | 13 March 2019, 21:41:01 UTC |
| af1d47a | Vincent Rubinetti | 12 March 2019, 14:21:45 UTC | HTML: add modular plugins for webpage interactivity Merges https://github.com/manubot/rootstock/pull/179 Closes https://github.com/manubot/rootstock/issues/185 Improves https://github.com/manubot/rootstock/issues/165 Adds plugins that can be included in the pandoc build commands to enable various interactive frontend features. Plugins are located in `build/plugins/` and consist of: - accordion (new) - analytics (modified) - anchors (replaced) - hypothesis (modified) - jump-to-first (new) - lightbox (new) - link-highlight (new) - math (modifies how MathJax is loaded) - table-of-contents (new) - table-scroll (new) - tooltips (new) | 12 March 2019, 14:21:45 UTC |
| 6303fcf | Anthony Gitter | 12 March 2019, 13:28:23 UTC | Update rootstock manual JSON CSL in example reference Merges https://github.com/manubot/rootstock/pull/186 | 12 March 2019, 13:28:23 UTC |
| e5ab24a | Vincent Rubinetti | 08 March 2019, 23:05:00 UTC | HTML: default theme updates Merges https://github.com/manubot/rootstock/pull/178 Various aesthetic updates, refactoring, edits for plugins, and additional comments | 08 March 2019, 23:05:00 UTC |
| 720febe | Daniel Himmelstein | 02 March 2019, 12:37:29 UTC | CI: only deploy on push TRAVIS_EVENT_TYPE Merges https://github.com/manubot/rootstock/pull/184 Previously, ci/deploy.sh could be run for push, api, or cron builds, but not for pull_request builds. This commit further restricts when deployment is run to just push builds. | 02 March 2019, 12:37:29 UTC |
| 717630e | David Slochower | 28 February 2019, 09:16:32 UTC | Fix SETUP.md random string & psutil install Merges https://github.com/manubot/rootstock/pull/182 Update SETUP.md to replace the correct random string Fix missing x86_64-conda_cos6-linux-gnu-gcc in psutil install by installing psutil using conda. .travis.yml: one configuration option per line (non-functional whitespace change) | 28 February 2019, 09:16:32 UTC |
| 2a4c813 | Daniel Himmelstein | 13 February 2019, 01:11:25 UTC | Relocate repository to manubot/rootstock Merges https://github.com/manubot/rootstock/pull/180 Closes https://github.com/greenelab/manubot-rootstock/issues/175 Closes https://github.com/greenelab/manubot-rootstock/pull/124 (supersedes) Relocate repository from https://github.com/greenelab/manubot-rootstock to https://github.com/manubot/rootstock. Relocate continuous integration from https://travis-ci.org/greenelab/manubot-rootstock to https://travis-ci.com/manubot/rootstock | 13 February 2019, 01:11:25 UTC |
| f559600 | Daniel Himmelstein | 06 February 2019, 16:24:17 UTC | shortDOI support & update environment on 2019-02-06 Merges https://github.com/greenelab/manubot-rootstock/pull/174 * Environment update on 2019-02-06 Does not upgrade weasyprint or cairo, due to the following error during WeasyPrint execution: OSError: dlopen() failed to load a library: cairo / cairo-2 / cairo-gobject-2 Specify cairocffi dependency in environment.yml, since v0.9 from PyPI seemed to trigger the OSError. * Add shortDOI support & usage Update repo to https://github.com/manubot/manubot greenelab/manubot relocated to manubot/manubot as per https://github.com/manubot/manubot/issues/94. 02.delete-me.md still references greenelab/manubot, however it is not worth creating merge conflicts to update just this. | 06 February 2019, 16:24:17 UTC |
| 658bcd7 | Vincent Rubinetti | 01 February 2019, 22:48:56 UTC | HTML themes: rewrite default.html with new style Merges https://github.com/greenelab/manubot-rootstock/pull/171 Various display improvements, simplified code structure with modern best practices. | 01 February 2019, 22:48:56 UTC |
| ec359f6 | Vincent Rubinetti | 29 January 2019, 17:09:18 UTC | Explicit fill color in icon SVGs Merges https://github.com/greenelab/manubot-rootstock/pull/172 Fixes issue that fill="currentColor" did not work as expected because SVGs are loaded from URLs rather than defined inline. Hence, revert to specifying a specific color. | 29 January 2019, 17:09:18 UTC |
| 96b580d | Vincent Rubinetti | 28 January 2019, 19:53:52 UTC | Update frontmatter author icons Merges https://github.com/greenelab/manubot-rootstock/pull/166 Improves formatting and centering of icons. Uses github and twitter icons from https://fontawesome.com | 28 January 2019, 19:53:52 UTC |
| fa7949f | Vincent Rubinetti | 28 January 2019, 16:10:50 UTC | Refactor HTML assets to build/themes & build/plugins Merges https://github.com/greenelab/manubot-rootstock/pull/168 Refs https://github.com/greenelab/manubot-rootstock/issues/163 | 28 January 2019, 16:10:50 UTC |
| eb4cb3e | Vincent Rubinetti | 22 January 2019, 21:34:14 UTC | CSS improvements to github-pandoc.css Merges https://github.com/greenelab/manubot-rootstock/pull/159 When printing, hide hypothesis toolbar and fix page margins. Fix pandoc syntax highlighting quirk: long width code boxes overflow outside of container. Fix superscript size issue documented at https://github.com/greenelab/meta-review/pull/88#issuecomment-408546057 | 22 January 2019, 21:34:14 UTC |
| b1b274d | Daniel Himmelstein | 21 January 2019, 21:36:39 UTC | front-matter: omit null or empty author fields Merges https://github.com/greenelab/manubot-rootstock/pull/161 | 21 January 2019, 21:36:39 UTC |
| 4103ad3 | Daniel Himmelstein | 03 January 2019, 23:36:22 UTC | Update environment & examples on 2019-01-03 Merges https://github.com/greenelab/manubot-rootstock/pull/153 Updates pandoc to v2.5. | 03 January 2019, 23:37:14 UTC |
| 9e6a00b | Daniel Himmelstein | 18 December 2018, 17:13:34 UTC | Upgrades on 2018-12-18 including wikidata citation support Merges https://github.com/greenelab/manubot-rootstock/pull/151 * Upgrade manubot python package with Wikidata citations * Remove DataCite DOI from 02.delete-me.md * Add additional manuscripts to USAGE examples | 18 December 2018, 17:13:34 UTC |
| aa664b4 | Daniel Himmelstein | 11 December 2018, 16:06:20 UTC | webpage utility: upgrade preexisting timestamps Merges https://github.com/greenelab/manubot-rootstock/pull/150 Attempt to upgrade preexisting timestamps during continuous deployment, such that manually upgrading incomplete timestamps should no longer be necessary. Add two mutually exclusive arguments to webpage.py: --ots-cache and --no-ots-cache for configuring the OTS client caching. Disable timestamp caching for deploy.sh (i.e. on Travis CI) | 11 December 2018, 16:06:20 UTC |
| 1614fa3 | Daniel Himmelstein | 20 November 2018, 16:06:40 UTC | Enable ISBN citation support Merges https://github.com/greenelab/manubot-rootstock/pull/149 * Enable ISBN citaiton support * Update URL citation Previous URL citation contained "?", therefore requiring a citation tag. | 20 November 2018, 16:06:40 UTC |
| a4428b5 | Daniel Himmelstein | 16 November 2018, 14:56:18 UTC | SETUP.py: add checkout command to rootstock upgrade Merges https://github.com/greenelab/manubot-rootstock/pull/148 Co-Authored-By: Daniel Himmelstein <daniel.himmelstein@gmail.com> Co-Authored-By: Anthony Gitter <agitter@users.noreply.github.com> | 16 November 2018, 14:57:41 UTC |
| 4e68632 | Daniel Himmelstein | 15 November 2018, 19:43:06 UTC | Update manubot to v0.2.1 with PMCID fix Merges https://github.com/greenelab/manubot-rootstock/pull/147 Update manubot version on 2018-11-15 to https://github.com/greenelab/manubot/commit/afa55f83a4a27645b07bdf0a25092a45b814df35 Includes migration of PMCID citations to Literature Citation Exporter. Update conda-forge dependencies | 15 November 2018, 19:43:06 UTC |
| 66214ac | Daniel Himmelstein | 12 November 2018, 21:59:31 UTC | Add pango to conda environment Closes https://github.com/greenelab/manubot-rootstock/issues/144 Merges https://github.com/greenelab/manubot-rootstock/pull/146 pango is required by WeasyPrint during the PDF build. While usually built-in to the OS on Linux, it is not pre-installed on macOS. macOS were installing pango using homebrew, which led to a segmentation fault error. Pango is available on conda-forge for linux and mac: https://anaconda.org/conda-forge/pango https://github.com/conda-forge/pango-feedstock Adding pango to environment.yml prevents conda environment installation on Windows, but has the benefits of standardizing the pango version on linux and mac platforms and preventing the mac homebrew issue. | 12 November 2018, 21:59:31 UTC |
| 44c5d35 | Daniel Himmelstein | 09 November 2018, 21:26:22 UTC | Support BUILD_PDF=false environment variable Merges https://github.com/greenelab/manubot-rootstock/pull/145 Closes https://github.com/greenelab/manubot-rootstock/issues/122 * Add BUILD_PDF environment variable BUILD_PDF is considered "true" unless specifically set to "false" webpage.py: tolerate missing output/manuscript.pdf Refs https://github.com/greenelab/manubot-rootstock/issues/144#issuecomment-437119645 ots stamp in deploy.sh: do not fail if BUILD_PDF=false * Delete existing images symlink in PDF build script When an images directory exists, do not create a symbolic link with source images/images. More info in ln documentation: - https://ss64.com/osx/ln.html - https://linux.die.net/man/1/ln Ignore /images temporary symlink | 09 November 2018, 21:26:22 UTC |
| 135f451 | Daniel Himmelstein | 02 November 2018, 17:23:22 UTC | Ignore OS specific files Merges https://github.com/greenelab/manubot-rootstock/pull/142 | 02 November 2018, 17:23:22 UTC |
| 895924e | Daniel Himmelstein | 30 October 2018, 19:28:24 UTC | Enable raw citations & small USAGE updates Merges https://github.com/greenelab/manubot-rootstock/pull/141 * Update USAGE with current URLs & recs Use HTTPS URLs where possible Switch SVG embedding solution from rawgit.com, which is shutting down, to the native GitHub solution. https://twitter.com/dhimmel/status/1049361799244664834 * Enable raw citations Update USAGE.md with raw citation example. Also update citations in delete-me.md. | 30 October 2018, 19:29:31 UTC |
| dcfe402 | Daniel Himmelstein | 23 October 2018, 19:23:20 UTC | Bugfix environment updates on 2018-10-23 Merges https://github.com/greenelab/manubot-rootstock/pull/140 Closes https://github.com/greenelab/manubot-rootstock/issues/136 Updates Manubot to fix empty date-parts issue Fix opentimestamps incompatible pinned versions | 23 October 2018, 19:23:20 UTC |
| 6bb804c | Anthony Gitter | 09 October 2018, 16:20:08 UTC | Case sensitive environment variables in setup instructions Merges https://github.com/greenelab/manubot-rootstock/pull/138 Closes https://github.com/greenelab/manubot-rootstock/issues/137 * Case sensitive environment variables * Update phrasing borrowing dhimmel ideas * Change account to username | 09 October 2018, 16:20:08 UTC |
| 830cdc0 | Daniel Himmelstein | 08 October 2018, 19:12:33 UTC | Update USAGE.md & environment on 2018-10-08 Merges https://github.com/greenelab/manubot-rootstock/pull/135 Closes https://github.com/greenelab/manubot/issues/59 * USAGE.md: suggested citation & acknowledgments Mostly copied from https://github.com/greenelab/manubot/blob/9d97ec347882bcd85ab6aee7a3b4734105ebfc15/README.md * Update environment on 2018-10-08 Updates to https://github.com/greenelab/manubot@9d97ec347882bcd85ab6aee7a3b4734105ebfc15 which is slightly past the manubot v0.2.0 release. jsonschema & jsonref should have been added to the environment previousely since they are required by manubot for JSON schema validation, but were not added. Do not upgrade to Python 3.7 due to collections DeprecationWarnings in several packages. Fixed warning in https://github.com/gazpachoking/jsonref/pull/26, but several remain. * Travis CI: update miniconda to 4.5.11 | 08 October 2018, 19:12:33 UTC |
| e83e51d | Daniel Himmelstein | 06 October 2018, 14:01:27 UTC | CSL: display="block" every other group Merges https://github.com/greenelab/manubot-rootstock/pull/134 Previous blocks were causing a blank line after the author line before the journal-date-URL line in markdown output. Placing blocks at every other line seems to be the solution required for pandoc-citeproc / pandoc to properly place the newlines. | 06 October 2018, 14:01:27 UTC |
| 3df864e | Daniel Himmelstein | 31 August 2018, 16:42:31 UTC | Upgrade manubot & environment on 2018-08-22 Merges https://github.com/greenelab/manubot-rootstock/pull/132 * Upgrade manubot to use process subcommand * Upgrade environment to latest versions on 2018-08-22 * CSL style: block to display identifiers | 31 August 2018, 16:42:31 UTC |
| 22b5260 | Daniel Himmelstein | 03 August 2018, 22:50:14 UTC | CSS: figure & table caption alignment Merges https://github.com/greenelab/manubot-rootstock/pull/131 Closes https://github.com/greenelab/manubot-rootstock/issues/130 * Left-align table caption text * figure img style: center img, left-align text | 03 August 2018, 22:50:14 UTC |
| 9aec6f5 | Daniel Himmelstein | 10 July 2018, 15:54:40 UTC | Add 3 additional example manuscripts to USAGE.md Merges https://github.com/greenelab/manubot-rootstock/pull/127 Add TFSEE, global emissions, & yt 3.0 manuscripts | 10 July 2018, 15:54:40 UTC |
| 9088481 | Anthony Gitter | 18 June 2018, 15:06:37 UTC | build/README.md: minor fix to build instructions Merges https://github.com/greenelab/manubot-rootstock/pull/125 | 18 June 2018, 15:06:37 UTC |
| 81945d9 | Daniel Himmelstein | 05 April 2018, 20:13:07 UTC | build.sh: remove long args incompatible with macOS Merges https://github.com/greenelab/manubot-rootstock/pull/123 Refs https://github.com/greenelab/manubot-rootstock/issues/120 | 05 April 2018, 20:13:07 UTC |
| f4cc39a | Ogun Adebali | 31 March 2018, 11:13:22 UTC | travis login information added (https://github.com/greenelab/manubot-rootstock/pull/119) * travis login information added * single quote and inline sentence * Add newline | 31 March 2018, 11:13:22 UTC |
| d91a7bd | Daniel Himmelstein | 29 March 2018, 02:13:30 UTC | CSL: do not collapse numeric citations Change style of citations from [1–4] to [1,2,3,4] Merges https://github.com/greenelab/manubot-rootstock/pull/121 | 29 March 2018, 02:13:30 UTC |
| fffcaf0 | Daniel Himmelstein | 26 February 2018, 22:36:22 UTC | front matter: hyperlink permalink for brevity Merges https://github.com/greenelab/manubot-rootstock/pull/114 | 26 February 2018, 22:36:22 UTC |
| 9438011 | Daniel Himmelstein | 26 February 2018, 22:35:12 UTC | Upgrade miniconda on Travis to 4.4.10 Merges https://github.com/greenelab/manubot-rootstock/pull/115 The method for enabling conda has changed. See notes at https://github.com/conda/conda/blob/53954c0d6785510587cd755a0cee4e177dca8455/CHANGELOG.md#recommended-change-to-enable-conda-in-your-shell | 26 February 2018, 22:35:12 UTC |
| b7a9de8 | Daniel Himmelstein | 17 February 2018, 17:51:13 UTC | autobuild.sh: include webpage.py execution (#113) Most autobuild users will want to automatically update the webpage. See discussion at https://github.com/greenelab/manubot-rootstock/pull/101#issuecomment-366405495 Update README to better document autobuild. | 17 February 2018, 17:51:13 UTC |
| 29cd993 | Daniel Himmelstein | 16 February 2018, 18:49:56 UTC | Versioned webpage using commit directories (#101) Closes https://github.com/greenelab/manubot-rootstock/issues/96 | 16 February 2018, 18:49:56 UTC |
| cc3b508 | Daniel Himmelstein | 15 February 2018, 18:39:07 UTC | Fix name with space issue (#110) git's user.name config was being set to first names only, since names are space separated. Add quotes to prevent this. | 15 February 2018, 18:39:07 UTC |
| 310dd07 | Daniel Himmelstein | 06 February 2018, 20:35:47 UTC | Update environment on 2018-02-06 (#108) Fix upstream issues: Extra brackets around citations in figure captions https://github.com/jgm/pandoc/issues/4272 WeasyPrint 0.42 gets stuck https://github.com/Kozea/WeasyPrint/issues/560 Updated pandoc-xnos with better semantic versioning https://github.com/tomduck/pandoc-fignos/issues/46 | 06 February 2018, 20:35:47 UTC |
| a535f7b | Daniel Himmelstein | 01 February 2018, 11:55:51 UTC | Webpage: specify letter page size in CSS (#107) Closes https://github.com/greenelab/manubot-rootstock/issues/105 | 01 February 2018, 11:55:51 UTC |
| 59af0a2 | Anthony Gitter | 19 January 2018, 18:51:18 UTC | Merge pull request #103 from agitter/issues Suggest issues for general inquiries | 19 January 2018, 18:51:18 UTC |
| 0156d68 | Anthony Gitter | 19 January 2018, 17:29:25 UTC | Suggest issues for general inquiries | 19 January 2018, 17:29:25 UTC |
| 930b81b | Anthony Gitter | 16 January 2018, 21:06:29 UTC | Merge pull request #102 from greenelab/citation-tags Update usage instructions for citation tags | 16 January 2018, 21:06:29 UTC |
| d946d9c | Anthony Gitter | 16 January 2018, 20:18:16 UTC | Update usage instructions for citation tags | 16 January 2018, 20:18:16 UTC |
| 744a8ca | Daniel Himmelstein | 14 January 2018, 21:04:54 UTC | Environment updates on 2018-01-14 (#100) Upgrade Manubot with citations.tsv error message improvements Upgrade to weasyprint v0.42 http://weasyprint.readthedocs.io/en/latest/changelog.html#version-0-42 | 14 January 2018, 21:04:54 UTC |
| a673a3e | Daniel Himmelstein | 14 January 2018, 19:39:19 UTC | environment: explicitly set pandoc-xnos version (#99) Pinning pandoc-eqnos, pandoc-fignos, and pandoc-tablenos, but allowing them to trigger the installation of the latest pandoc-xnos version (which is a dependency) caused issues. See https://github.com/greenelab/deep-review/pull/774#issuecomment-357520693 | 14 January 2018, 19:39:19 UTC |
| b140c76 | Daniel Himmelstein | 11 January 2018, 18:19:28 UTC | Enable PubMed ID citations (#98) Upgrade Manubot to https://github.com/greenelab/manubot/commit/b53f487026954729ce80ca963f3838ebca85a144 Refs https://github.com/greenelab/manubot/pull/24 | 11 January 2018, 18:19:28 UTC |
| c31c5d0 | Daniel Himmelstein | 09 January 2018, 18:48:15 UTC | MAINT: update packages on 2018-01-09 Update pandoc to 2.1 Reference 2018 development proposal in USAGE.md Remove temporarily broken DOI: https://twitter.com/dhimmel/status/950443969313419264 | 09 January 2018, 22:44:45 UTC |
| b030529 | Daniel Himmelstein | 09 January 2018, 18:23:55 UTC | Manubot numbered affiliations upgrade Refs https://github.com/greenelab/manubot/pull/22 | 09 January 2018, 22:44:45 UTC |
| f165f60 | Daniel Himmelstein | 07 December 2017, 20:37:45 UTC | HTML output: enable Hypothesis embedding https://h.readthedocs.io/projects/client/en/latest/publishers/embedding/ Closes https://github.com/greenelab/manubot-rootstock/issues/90 | 07 December 2017, 21:41:33 UTC |
| d209731 | Dan Siddoway | 07 December 2017, 18:21:27 UTC | Fix Hypothesis adder positioning By positioning the `body` element, we tell Hypothesis to use it (rather than the document) as the container element for the adder. (See hypothesis/client#487 for more information.) Closes: #90, hypothesis/client#619 | 07 December 2017, 21:41:33 UTC |
| 4149215 | Daniel Himmelstein | 04 December 2017, 21:37:55 UTC | Update environment.yml on 2017-12-04 (#94) Update depedencies to latest versions Update minoconda to 4.3.30: https://github.com/conda/conda/blob/c72c237a354c3fd9629d800311ba6a2b8a95d1d1/CHANGELOG.md#4330-2017-10-17 Update pandoc to 2.0.4: https://github.com/jgm/pandoc/releases/tag/2.0.4 Update cairo to 1.14.10: https://cairographics.org/news/cairo-1.14.10/ Update cffi to 1.11.2: https://cffi.readthedocs.io/en/latest/whatsnew.html#v1-11-2 Update jinja2 to 2.10: http://jinja.pocoo.org/docs/2.10/changelog/#version-2-10 manubot update to support multiple --template-variables-path args | 04 December 2017, 21:37:55 UTC |
| fffae41 | Daniel Himmelstein | 16 November 2017, 19:08:49 UTC | Update SETUP.md based on OpenCon do-a-thon (#89) * Update SETUP.md based on OpenCon do-a-thon https://github.com/sparcopen/doathon/issues/21 * git diff --color-words, not --word-diff * Specify no Windows support in SETUP.md https://github.com/greenelab/manubot-rootstock/issues/91 * Doc: conda env installs on macOS I installed the environment on macOS 10.12.6 on 2017-11-16 and ran `sh build/build.sh` successfully. | 16 November 2017, 19:08:49 UTC |
| 4274f35 | Daniel Himmelstein | 16 November 2017, 18:56:55 UTC | Use .html not .js for inserted HTML snippets (#93) | 16 November 2017, 18:56:55 UTC |
| 64af604 | Venkat Malladi | 07 November 2017, 18:24:29 UTC | SETUP.md shell command macOS compatibility (#84) Closes https://github.com/greenelab/manubot-rootstock/issues/74 SETUP.md commands should now work on both Linux and macOS. Requires Python on system. | 07 November 2017, 18:30:44 UTC |
| 46824e6 | Daniel Himmelstein | 02 November 2017, 13:06:28 UTC | USAGE.md: link to language tag documentation (#83) https://github.com/greenelab/manubot-rootstock/pull/81#discussion_r148344009 | 02 November 2017, 13:06:28 UTC |
| ec186c2 | Daniel Himmelstein | 01 November 2017, 16:46:34 UTC | Update environment and documentation (#81) Pandoc upgraded to v2.0.0.1 Swap anaconda packages to conda-forge Update build.sh for pandoc 2.0 WeasyPrint was not renderring MathJax, so use --webtex to convert equations to SVGs for PDF output. See https://github.com/Kozea/WeasyPrint/issues/59 | 01 November 2017, 16:46:34 UTC |
| 38effe8 | Daniel Himmelstein | 09 October 2017, 17:25:06 UTC | Fix intra-sentence newline in README (#80) | 09 October 2017, 17:25:06 UTC |
| aba5246 | Venkat Malladi | 05 October 2017, 16:54:28 UTC | Specify width of front-matter SVGs (#79) Now width and height are both specified at 13 pixels, to constrain the aspect ratio of these SVGs as square. Previously, the icons appeared squished in DOCX exports. See https://github.com/greenelab/manubot-rootstock/pull/40 | 05 October 2017, 16:54:28 UTC |
| 47ee5f0 | Daniel Himmelstein | 04 October 2017, 21:57:27 UTC | PDF export: use weasyprint not wkhtmltopdf (#78) * PDF export: use weasyprint not wkhtmltopdf Closes https://github.com/greenelab/manubot-rootstock/issues/77 * USAGE: specify SVG size Refs https://github.com/Kozea/WeasyPrint/issues/442 * Install cairocffi from pip not conda-forge | 04 October 2017, 21:57:27 UTC |
| 72189b5 | Robert Gieseke | 28 September 2017, 18:25:28 UTC | Note MIT licensed 3rd-party code (#75) | 28 September 2017, 18:25:28 UTC |
| 7d64afa | Daniel Himmelstein | 28 September 2017, 18:12:08 UTC | Pin miniconda version (#76) Do not use latest miniconda, since updates can cause bugs, which happened in https://github.com/greenelab/manubot-rootstock/pull/75#issuecomment-332914877 due to https://stackoverflow.com/a/46457813/4651668 | 28 September 2017, 18:12:08 UTC |
| 3a42f6b | Daniel Himmelstein | 19 September 2017, 19:12:19 UTC | Update indents and ordering of manual-references.json | 19 September 2017, 19:35:04 UTC |
| d323b8e | Daniel Himmelstein | 06 September 2017, 17:56:45 UTC | Fix typos | 19 September 2017, 19:35:04 UTC |
| 2a87697 | Daniel Himmelstein | 19 September 2017, 19:34:47 UTC | Examples: add bitcoin-whitepaper & rephetio-manuscript (#72) | 19 September 2017, 19:34:47 UTC |
| b5644db | Daniel Himmelstein | 06 September 2017, 00:53:15 UTC | Customize Manubot citation style (#68) Simplify the CSL specification as per https://github.com/greenelab/manubot-rootstock/issues/53 | 06 September 2017, 00:53:15 UTC |
| a51c064 | Daniel Himmelstein | 05 September 2017, 21:21:11 UTC | Explicitly insert bibliography (#69) Enables content that follows the bibliography From https://github.com/jgm/pandoc-citeproc/blame/5a7f26b61c8577916093851cdeb31fa9a198edcb/man/pandoc-citeproc.1.md#L126-L128 > a bibliography will be inserted into each Div element with id refs. If there is no such Div, one will be created at the end of the document. | 05 September 2017, 21:21:11 UTC |
| 26472cd | Daniel Himmelstein | 01 September 2017, 19:01:06 UTC | Prettify github-pandoc.css (#63) | 01 September 2017, 19:01:06 UTC |
| 99ce6d4 | Daniel Himmelstein | 01 September 2017, 19:00:48 UTC | SETUP.md updates & Manubot version bumb (#66) * Upgrade Manubot version * SETUP.md: small doc enhancements * Travis CI: limit concurrent jobs to 1 https://blog.travis-ci.com/2014-07-18-per-repository-concurrency-setting/ https://docs.travis-ci.com/user/customizing-the-build/#Limiting-Concurrent-Builds * Delete uneeded files * Change References to h2 header | 01 September 2017, 19:00:48 UTC |
| 7b0c4ca | Daniel Himmelstein | 31 August 2017, 18:06:02 UTC | Travis CI: Attempt to fix "bad decrypt" issues (#64) Deployment was failing due to deploy.key.enc failing to decrypt. This commit regenerates deploy.key and deploy.key.pub and reruns travis encrypt-file. https://github.com/greenelab/manubot-rootstock/commit/5eed755f0e2806eff4b42226864b084c48e20fc3#commitcomment-23985090 | 31 August 2017, 18:06:02 UTC |
| 5eed755 | Daniel Himmelstein | 30 August 2017, 14:35:23 UTC | Simplify metadata.yaml | 30 August 2017, 19:10:59 UTC |
| 5f1db0e | Daniel Himmelstein | 28 August 2017, 18:48:44 UTC | Delinieate README sections | 30 August 2017, 19:10:59 UTC |
| 719c9b5 | Daniel Himmelstein | 28 August 2017, 03:15:58 UTC | SETUP.md: instructions for initializing instance Refs https://github.com/greenelab/manubot-rootstock/issues/6#issuecomment-314541837 | 30 August 2017, 19:10:59 UTC |
| 727ac1e | Daniel Himmelstein | 28 August 2017, 00:51:39 UTC | Add example manuscripts to USAGE.md | 30 August 2017, 19:10:59 UTC |
| 86851c0 | Daniel Himmelstein | 28 August 2017, 00:36:18 UTC | Modify rootstock markdown files | 30 August 2017, 19:10:59 UTC |
| 69d0d5f | Daniel Himmelstein | 28 August 2017, 14:59:13 UTC | Autobuild: watchdog monitor content dir (#61) Refs https://github.com/greenelab/manubot-rootstock/issues/58#issuecomment-325056265 | 28 August 2017, 14:59:13 UTC |
| 868da10 | Daniel Himmelstein | 27 August 2017, 17:07:49 UTC | Switch OpenTimestamps from submodule to pip (#60) Closes https://github.com/greenelab/manubot-rootstock/issues/59 | 27 August 2017, 17:07:49 UTC |
| 795490c | Daniel Himmelstein | 15 August 2017, 15:58:49 UTC | Update Manubot | 15 August 2017, 16:00:26 UTC |
| 28f460e | Daniel Himmelstein | 15 August 2017, 15:52:54 UTC | Add --mathjax to pandoc build Closes https://github.com/greenelab/manubot-rootstock/issues/55 Also reorder some pandoc CLI arguments. | 15 August 2017, 16:00:26 UTC |
| 9f4deeb | David Slochower | 15 August 2017, 00:05:36 UTC | Pandoc: use --html5 not --html5 for output (#56) Refs https://github.com/greenelab/manubot-rootstock/issues/55#issuecomment-322338743 | 15 August 2017, 00:05:36 UTC |
| 03de821 | Daniel Himmelstein | 14 August 2017, 13:20:19 UTC | Set timezone to UTC in build.sh (#52) Closes https://github.com/greenelab/manubot/issues/3 | 14 August 2017, 13:20:19 UTC |
| 0a04405 | Daniel Himmelstein | 10 August 2017, 21:43:24 UTC | Upgrade manubot version (#50) Fixes issue where manual references were not respected. | 10 August 2017, 21:43:24 UTC |
