| 2482af4 | Daniel Himmelstein | 25 May 2020, 14:59:47 UTC | PR #265 to update Rootstock on 2020-05-25 Switches to GitHub Actions from Travis CI | 25 May 2020, 14:59:47 UTC |
| 74805a2 | Daniel Himmelstein | 25 May 2020, 14:56:52 UTC | remove Travis CI: switching to GitHub Actions | 25 May 2020, 14:56:52 UTC |
| c9b1ee5 | Daniel Himmelstein | 25 May 2020, 14:50:04 UTC | Merge rootstock on 2020-05-25 | 25 May 2020, 14:50:04 UTC |
| b746270 | Daniel Himmelstein | 24 May 2020, 23:42:56 UTC | Update manubot for more flexible citation processing merges https://github.com/manubot/rootstock/pull/342 Includes major updates to how citations are processed by the pandoc-manubot-cite filter. See the following commit messages for more information: - https://github.com/manubot/manubot/commit/7055bcc6524fdf1ef97d838cf0158973e2061595 - https://github.com/manubot/manubot/commit/47b03e0c202e6a0561e6548ba08a4ad790f56eee Removes requirement to prefix certain citekeys with raw: or tag: Removes support for deprecated `content/citation-tags.tsv`. Switches from tag to alias terminology for citation aliases. closes https://github.com/manubot/manubot/issues/120 Removes pandas and jsonref dependencies, which are no longer needed. | 24 May 2020, 23:42:56 UTC |
| 8b9b5ce | Daniel Himmelstein | 07 May 2020, 14:59:18 UTC | move build/pandoc-defaults to build/pandoc/defaults (#340) merges https://github.com/manubot/rootstock/pull/340 * Move build/pandoc-defaults to build/pandoc/defaults Improves compatibility with Pandoc's directory naming expectations in case when setting --data-dir=build/assets in the future. Allows for other subdirectories like build/pandoc/filters * set pandoc --data-dir * update spellcheck filter to use build/pandoc/filters | 07 May 2020, 14:59:18 UTC |
| 92f0285 | Anthony Gitter | 05 May 2020, 16:21:58 UTC | Fix spellcheck bug and track unique spelling errors merges https://github.com/manubot/rootstock/pull/337 refs https://github.com/manubot/rootstock/issues/336 * Track unique spelling errors Fixes a bug in how unique words were calculated. Also stores the list of unique misspelled words in addition to the locations of the misspelled words. * Create separate spellcheck install script * Add spellcheck to GitHub Actions workflow * Search for expanded punctuation in misspelled words | 05 May 2020, 16:21:58 UTC |
| 1b69406 | Daniel Himmelstein | 01 May 2020, 16:46:56 UTC | USAGE: howto set citation style using pandoc defaults merges https://github.com/manubot/rootstock/pull/338 closes https://github.com/manubot/rootstock/issues/334 | 01 May 2020, 16:46:56 UTC |
| 2c28689 | Anthony Gitter | 29 April 2020, 03:11:35 UTC | Enable pandoc spellcheck filter merges https://github.com/manubot/rootstock/pull/333 Installs and runs aspell via the pandoc spellcheck filter when the SPELLCHECK environment variable is true. Spellcheck outputs candidate spelling errors and the filenames and line numbers in which they occur. Initially only supported in Travis CI and AppVeyor builds. | 29 April 2020, 03:11:35 UTC |
| 8dee14c | Anthony Gitter | 28 April 2020, 13:10:32 UTC | Add github to dictionary | 28 April 2020, 13:10:32 UTC |
| a63cb12 | Anthony Gitter | 28 April 2020, 12:08:37 UTC | Move true command to end of pipeline | 28 April 2020, 12:08:37 UTC |
| 311269d | Anthony Gitter | 28 April 2020, 11:58:41 UTC | Make grep exit with 0 grep exits with 1 if there is no match found, which makes the pipeline fail due to the pipefail option Also make grep case insensitive | 28 April 2020, 11:58:41 UTC |
| 24241ee | Anthony Gitter | 28 April 2020, 03:01:44 UTC | Document spellchecking | 28 April 2020, 03:01:44 UTC |
| eff3676 | Anthony Gitter | 28 April 2020, 02:53:59 UTC | Update custom dictionary Make dictionary lowercase now that case is ignored | 28 April 2020, 02:53:59 UTC |
| a63502f | Anthony Gitter | 28 April 2020, 02:47:12 UTC | Add file names alongside line numbers Co-authored-by: David Nicholson <dnicholson329@gmail.com> | 28 April 2020, 02:47:12 UTC |
| 14215d3 | Anthony Gitter | 27 April 2020, 22:43:32 UTC | Add line numbers for misspelled words Co-authored-by: David Nicholson <dnicholson329@gmail.com> | 27 April 2020, 22:43:32 UTC |
| 975fb61 | Anthony Gitter | 24 April 2020, 21:49:25 UTC | Ignore case during spellcheck | 24 April 2020, 21:49:25 UTC |
| 3199820 | Anthony Gitter | 24 April 2020, 21:36:42 UTC | Update custom dictionary with delete-me errors | 24 April 2020, 21:36:42 UTC |
| 2f30622 | Anthony Gitter | 20 April 2020, 22:01:35 UTC | Test spellcheck in Travis CI | 20 April 2020, 22:01:35 UTC |
| c2e7287 | Anthony Gitter | 20 April 2020, 21:59:01 UTC | Fix AppVeyor whitespace | 20 April 2020, 21:59:01 UTC |
| b20126f | Anthony Gitter | 20 April 2020, 21:47:49 UTC | Enable pandoc spellcheck filter in AppVeyor | 20 April 2020, 21:47:49 UTC |
| 073ce0e | Daniel Himmelstein | 18 April 2020, 13:41:51 UTC | upgrade manubot to fix webpage subprocess handling upgrade manubot to https://github.com/manubot/manubot/commit/890b76891f139a26d36cd9a4aa652f7e019501f8 fixes https://github.com/manubot/manubot/issues/222 previously, CI deployment could trigger the following Exception: ``` File "manubot/webpage/webpage_command.py", line 198, in ots_upgrade elif not process.stderr.strip() == "Success! Timestamp complete": AttributeError: 'NoneType' object has no attribute 'strip' ``` | 18 April 2020, 13:41:51 UTC |
| 6da6f5a | Daniel Himmelstein | 18 April 2020, 12:44:03 UTC | metadata: use list for author.funders closes https://github.com/manubot/rootstock/issues/329 upgrade manubot with author.funders processing added in https://github.com/manubot/manubot/commit/9c33b7a53f60aa5aba42424b925af0c32ea561fb | 18 April 2020, 12:44:03 UTC |
| 7c0f9c3 | Anthony Gitter | 22 March 2020, 13:10:07 UTC | Export environment variables needed for gh-pages readme merges https://github.com/manubot/rootstock/pull/326 | 22 March 2020, 13:10:07 UTC |
| 5ee04da | Anthony Gitter | 22 March 2020, 12:48:36 UTC | Export environment variables needed for gh-pages readme | 22 March 2020, 12:48:36 UTC |
| 1780fac | Daniel Himmelstein | 03 March 2020, 20:02:15 UTC | GitHub Actions: cache manubot files in ci/cache merges https://github.com/manubot/rootstock/pull/316 | 03 March 2020, 20:02:15 UTC |
| cde7fa2 | Daniel Himmelstein | 28 February 2020, 17:46:34 UTC | Update environment 2020-02-27 & citations usage merges https://github.com/manubot/rootstock/pull/315 Update environment on 2020-02-27 USAGE: clarify citation key syntax | 28 February 2020, 17:46:34 UTC |
| c25f8b8 | Daniel Himmelstein | 18 February 2020, 20:31:45 UTC | Simplify setup by creating branches later merges https://github.com/manubot/rootstock/pull/314 * Simplify setup by creating branches later For a new manuscript, the first deploy event won't be able to fetch gh-pages and output because they were not pushed during setup. However, the deploy script now ignores the error on fetch and continues with the deployment, creating those branches at the first deployment. All subsequent deployments work as they did previously. * SETUP: Update with how to workaround GITHUB_TOKEN not triggering Pages builds. | 18 February 2020, 20:31:44 UTC |
| cd8ce12 | Daniel Himmelstein | 18 February 2020, 16:25:59 UTC | fixup! GH Actions: skip deployment on forks | 18 February 2020, 16:25:59 UTC |
| 9bdf4c1 | Daniel Himmelstein | 18 February 2020, 16:08:48 UTC | GH Actions: skip deployment on forks merges https://github.com/manubot/rootstock/pull/313 Previously deployment was governed by the presence of MANUBOT_SSH_PRIVATE_KEY, but now that GITHUB_TOKEN is supported for deployment, forks with master branch commits attempted to deploy. | 18 February 2020, 16:08:48 UTC |
| d14dd7d | Daniel Himmelstein | 18 February 2020, 14:33:23 UTC | SETUP.md: fix double negative typo [skip ci] | 18 February 2020, 14:33:23 UTC |
| af2ef81 | Daniel Himmelstein | 18 February 2020, 14:24:55 UTC | GH Actions: no setup deployment using GITHUB_TOKEN merges https://github.com/manubot/rootstock/pull/310 Previously secrets.GITHUB_TOKEN did not work for deployment because the commits it pushed to `gh-pages` were unable to trigger a GitHub Pages build on public repositories. However, this issue seems to have been quietly resolved. There has been no official GitHub announcement about the change, so there is a risk that it will be temporary. Deployment now uses MANUBOT_SSH_PRIVATE_KEY over MANUBOT_ACCESS_TOKEN when both are set. The idea is that if GitHub's support for GITHUB_TOKEN is temporary (since no official commitment yet), then users who have configured MANUBOT_ACCESS_TOKEN will not be affected. Only users who did not set up MANUBOT_SSH_PRIVATE_KEY will be affected, but they could then set up MANUBOT_SSH_PRIVATE_KEY without having to upgrade Manubot Rootstock to get deployment to work. | 18 February 2020, 14:24:55 UTC |
| 7545592 | Daniel Himmelstein | 17 February 2020, 22:25:12 UTC | Update environment on 2020-02-17 merges https://github.com/manubot/rootstock/pull/311 Includes manubot update with yamllint output for invalid metadata.yaml files. | 17 February 2020, 22:25:12 UTC |
| 7412f76 | Olga Botvinnik | 14 February 2020, 22:55:51 UTC | .appveyor.yml: note about skipping branches with PR merges https://github.com/manubot/rootstock/pull/309 closes https://github.com/manubot/rootstock/issues/308 | 14 February 2020, 22:55:51 UTC |
| 40b0e5b | Olga Botvinnik | 30 January 2020, 21:44:14 UTC | SETUP.md: add table of contents merges https://github.com/manubot/rootstock/pull/304 autogenerated by https://ecotrust-canada.github.io/markdown-toc/ | 30 January 2020, 21:44:14 UTC |
| 8924d7d | Daniel Himmelstein | 30 January 2020, 19:10:22 UTC | CI deployment: update env vars Rename environment variables for deployment to: $CI_BUILD_WEB_URL $CI_JOB_WEB_URL Fix bug with $CI_JOB_WEB_URL on GitHub Actions | 30 January 2020, 19:10:22 UTC |
| 713000d | Daniel Himmelstein | 29 January 2020, 15:45:25 UTC | GitHub Actions: version artifact name merges https://github.com/manubot/rootstock/pull/305 Create artifacts that are named like manuscript-32632624-d1c4caf and contain the GitHub Actions run-id as well as the head of the triggering commit hash. Note that on a pull request, this is the commit that was added to the PR and not the auto-generated merge commit that the action is actually evaluating. | 29 January 2020, 15:45:25 UTC |
| 42669ce | Daniel Himmelstein | 28 January 2020, 19:08:25 UTC | Fix get_rootstock_commit on CI merges https://github.com/manubot/rootstock/pull/303 SETUP manubot upgrade instructions. add --no-rebase to git pull Upgrade Manubot to fix get_rootstock_commit GitHub Actions: fetch entire commit history to support get_rootstock_commit | 28 January 2020, 19:08:25 UTC |
| f6b6231 | Daniel Himmelstein | 19 January 2020, 00:33:09 UTC | Attempt to fix .travis.yml syntax error https://travis-ci.com/manubot/rootstock/builds/145087566#L2163 travis_run_after_success: command not found | 19 January 2020, 00:33:09 UTC |
| eab9b2a | Daniel Himmelstein | 19 January 2020, 00:26:15 UTC | CI: do not run deploy.sh if secrets are unset merges https://github.com/manubot/rootstock/pull/302 GitHub Actions: do not run deploy.sh if secrets.MANUBOT_SSH_PRIVATE_KEY is not set resulting in `env: MANUBOT_SSH_PRIVATE_KEY: ""` https://github.community/t5/GitHub-Actions/If-expression-with-context-variable/m-p/34560/highlight/true#M1959 Travis CI: condition deploy on MANUBOT_SSH_PRIVATE_KEY being set or variable name expansion for encrypted_*. https://unix.stackexchange.com/a/290296/294987 https://wiki.bash-hackers.org/syntax/pe#variable_name_expansion | 19 January 2020, 00:26:15 UTC |
| af52dea | Daniel Himmelstein | 17 January 2020, 20:57:48 UTC | Tweaks following up GitHub Actions | 17 January 2020, 20:57:48 UTC |
| f072e93 | Daniel Himmelstein | 17 January 2020, 20:35:17 UTC | GitHub Actions workflow for building and deployment merges https://github.com/manubot/rootstock/pull/297 | 17 January 2020, 20:35:17 UTC |
| 52211e1 | Daniel Himmelstein | 14 January 2020, 22:31:56 UTC | Minor environment updates on 2020-01-14 merges https://github.com/manubot/rootstock/pull/301 | 14 January 2020, 22:31:56 UTC |
| aa78ba9 | Daniel Himmelstein | 14 January 2020, 15:19:55 UTC | Merge PR #263: update Manubot on 2020-01-14 merges https://github.com/greenelab/meta-review/pull/263 Update Manubot on 2020-01-14 with pandoc-manubot-cite filter | 14 January 2020, 15:19:55 UTC |
| 4bbb0ea | Daniel Himmelstein | 14 January 2020, 15:09:26 UTC | Add citekey aliases to markdown Using suggested paragraph from https://travis-ci.org/greenelab/meta-review/builds/636940701#L863 | 14 January 2020, 15:09:26 UTC |
| bc66cec | Daniel Himmelstein | 14 January 2020, 15:04:01 UTC | Merge rootstock on 2020-01-14 | 14 January 2020, 15:04:01 UTC |
| 6636b91 | Daniel Himmelstein | 14 January 2020, 15:00:34 UTC | Process citations / references with pandoc-manubot-cite filter merges https://github.com/manubot/rootstock/pull/300 | 14 January 2020, 15:00:34 UTC |
| 06fb01d | Daniel Himmelstein | 04 January 2020, 22:27:12 UTC | build: configure pandoc using --defaults files merges https://github.com/manubot/rootstock/pull/290 The options for the pandoc commands in build/build.sh are now configured in YAML files that are passed to Pandoc using --defaults. export PANDOC_DEFAULTS_DIR to override the directory with pandoc --defaults files | 04 January 2020, 22:27:12 UTC |
| b5c196f | Daniel Himmelstein | 04 January 2020, 21:49:26 UTC | SETUP: better manubot update instructions merges https://github.com/manubot/rootstock/pull/298 | 04 January 2020, 21:49:26 UTC |
| 37b3378 | Daniel Himmelstein | 18 December 2019, 18:11:22 UTC | Update metadata.authors & USAGE Merges https://github.com/manubot/rootstock/pull/289 * Update metadata.yaml to use 'authors' * Mention delete-me.md in USAGE | 18 December 2019, 18:11:22 UTC |
| b7e6f58 | Vincent Rubinetti | 13 December 2019, 20:12:12 UTC | Update plugins for pandoc-xnos suite version 2.0 breaking changes merges https://github.com/manubot/rootstock/pull/286 closes https://github.com/manubot/rootstock/issues/284 - removes table scroll plugin - relies on pandoc-tablenos to wrap `<table>` elements in `<div>`s that can be scrolled - updates CSS such that breaks are forced when printing or when a table isn't given an id (and thus isn't wrapped with a `<div>` - simplifies plugins a bit as a result of pandoc-tablenos and pandoc-fignos changes - adds tolerance to scroll-out-of-bounds feature - adds support for equations in anchors plugin | 13 December 2019, 20:12:12 UTC |
| cf9e16b | Daniel Himmelstein | 20 November 2019, 20:53:36 UTC | frontmatter variable type: artifact_url must match variable name set by the manubot python package at https://github.com/manubot/manubot/blob/46768a8357c35541fc719e7ddc7fe8a65c42bb39/manubot/process/ci.py#L63 | 20 November 2019, 20:53:36 UTC |
| 6afcab4 | Daniel Himmelstein | 20 November 2019, 20:46:44 UTC | PR #262: update rootstock on 2019-11-20 Exposes improved HTML metadata | 20 November 2019, 20:46:44 UTC |
| d944b08 | Daniel Himmelstein | 20 November 2019, 20:40:07 UTC | Merge rootstock on 2019-11-20 | 20 November 2019, 20:40:07 UTC |
| 277a769 | Daniel Himmelstein | 20 November 2019, 17:03:06 UTC | Fix frontmatter date for new variables schema merges https://github.com/manubot/rootstock/pull/279 fixup following HTML <meta> and variables update fixup f1bf210b115607b1887c0dcfaed11cbe81543967 | 20 November 2019, 17:03:06 UTC |
| f1bf210 | Daniel Himmelstein | 20 November 2019, 15:55:00 UTC | Improved HTML metadata & thumbnail support merges https://github.com/manubot/rootstock/pull/277 closes https://github.com/manubot/rootstock/issues/176 closes https://github.com/manubot/rootstock/issues/267 Set extra <meta> fields in HTML <head>. Update manubot Python package to version that sets Pandoc's `header-includes` to provide scholarly metadata via HTML <head> fields. This update changes the schema of variables.json (templating variables available to jinja2). Frontmatter has been updated for the new variables format. Update usage with thumbnail instructions Multiple formats in AppVeyor notification: Upload HTML manuscript to AppVeyor | 20 November 2019, 15:55:00 UTC |
| 7cf9071 | Daniel Himmelstein | 01 November 2019, 17:41:38 UTC | Update manubot to fix webpage bug Closes https://github.com/manubot/manubot/issues/165 Includes fix from https://github.com/manubot/manubot/pull/166 | 01 November 2019, 17:41:38 UTC |
| a121e47 | Daniel Himmelstein | 31 October 2019, 21:44:04 UTC | Update environment on 2019-10-31 Merges https://github.com/manubot/rootstock/pull/274 Update environment on 2019-10-31. USAGE: note URL workaround for bad DOI metadata. | 31 October 2019, 21:44:04 UTC |
| 6859ada | Daniel Himmelstein | 11 October 2019, 16:05:31 UTC | Specify --pagesize=A4 during PDF export (clarifies default) Merges https://github.com/manubot/rootstock/pull/272 Closes https://github.com/manubot/rootstock/issues/270 The existence of two common pagesizes for physical paper, A4 and Letter, creates user confusion. Sometimes users print a PDF with A4 dimensions onto Letter paper and do not use the "scale to fit" printer setting. This leads to truncated text at the bottom of the page. Ultimately, it is not a Manubot issue, but confuses Manubot users nonetheless. When exporting the HTML to PDF, Manubot uses an A4 pagesize, which while less common in the U.S. is an international standard. This commit explicitly specifies the default behavior, such that there is no functional change. However, by specifying the pagesize, its more clear to Manubot users where pagesize gets set. This will hopefully spare users of some debugging. If manuscript viewers would like to export to a pagesize that is different from the one used by manuscript.pdf, the recommendation is for them to print the HTML page to PDF from their browser and specify the desired page size there. For this reason, our CSS style does not specify a default page size, but instead just a margin. Documentation of the relevant options: > athenapdf --pagesize <size> > page size of the generated PDF (default: A4, values: A3|A4|A5|Legal|Letter|Tabloid) We did not update the WeasyPrint build command because: > Currently, WeasyPrint does not provide support for adjusting page size or > document margins via command-line flags. | 11 October 2019, 16:05:31 UTC |
| 6cfc575 | Vincent Rubinetti | 20 September 2019, 15:12:47 UTC | add white background to thumbnail (#260) | 20 September 2019, 15:12:47 UTC |
| 9811137 | Ryan A. Hagenson | 18 September 2019, 14:28:40 UTC | Fix broken references to webpage.py Merges https://github.com/manubot/rootstock/pull/269 Follows up 188e51ab58dd25f14126670512b238b2221881b1 * python webpage.py -> manubot webpage * clarify CI use of manubot webpage in deploy.sh | 18 September 2019, 14:28:40 UTC |
| 6527dd4 | Vincent Rubinetti | 18 September 2019, 13:19:00 UTC | update meta-review thumbnail (#259) merges https://github.com/greenelab/meta-review/pull/259 includes SVG | 18 September 2019, 13:19:00 UTC |
| 5182135 | Daniel Himmelstein | 17 September 2019, 12:21:53 UTC | Typo: fix missing "a" https://github.com/greenelab/meta-review/pull/255#discussion_r325106032 | 17 September 2019, 12:21:53 UTC |
| 213d599 | Daniel Himmelstein | 16 September 2019, 17:33:32 UTC | Mention additional related tools in the discussion Merges https://github.com/greenelab/meta-review/pull/255 Closes https://github.com/greenelab/meta-review/issues/249 Add discussion paragraph on other cite-by-ID tools Mention dokieli, Texture, and pwcite. Hyphenate citation-by-identifier everywhere | 16 September 2019, 17:33:32 UTC |
| 85281e1 | Anthony Gitter | 14 September 2019, 16:46:33 UTC | Add thumbnail image (#258) Merges https://github.com/greenelab/meta-review/pull/258 Closes https://github.com/greenelab/meta-review/issues/257 Co-authored-by: Vincent Rubinetti <vince.rubinetti@gmail.com> | 14 September 2019, 16:46:33 UTC |
| 0dc5ea8 | Vincent Rubinetti | 11 September 2019, 17:14:44 UTC | Plugin to set HTML attributes via comments Merges https://github.com/manubot/rootstock/pull/251 Closes https://github.com/manubot/rootstock/issues/264 Refs https://github.com/manubot/rootstock/issues/240 Uses javascript to apply attributes extracted from HTML comments. | 11 September 2019, 17:14:44 UTC |
| 631b8a2 | Vincent Rubinetti | 06 September 2019, 16:07:38 UTC | CSS overflow-wrap: break-word to wrap long links Merges https://github.com/manubot/rootstock/pull/266 Fix link overflow & change word-break to overflow-wrap | 06 September 2019, 16:07:38 UTC |
| 52d0cb0 | Anthony Gitter | 06 September 2019, 11:16:38 UTC | Add MOOP paper (#256) | 06 September 2019, 11:16:38 UTC |
| 188e51a | Daniel Himmelstein | 05 September 2019, 21:34:58 UTC | Migrate to manubot webpage command Merges https://github.com/manubot/rootstock/pull/265 Follows up https://github.com/manubot/manubot/pull/132 Update timestamp related dependencies | 05 September 2019, 21:34:58 UTC |
| a609248 | Daniel Himmelstein | 02 September 2019, 23:11:34 UTC | Revert some PLOS formatting requirements (#254) Merges https://github.com/greenelab/meta-review/pull/254 Revert "Remove paragraph breaks from author summary" This reverts commit 95da0bdf3063b5a470f567f5df8f5e33e1823647. Revert citations to Manubot style Reverts part of 040638d25b9a45ad3d060afc9689a17f4c3a3045 Revert author formatting Update front-matter to link to compare changes since journal publication. | 02 September 2019, 23:11:34 UTC |
| b90923a | Daniel Himmelstein | 30 August 2019, 17:32:59 UTC | Merge PR #253 to update rootstock on 2019-08-30 | 30 August 2019, 17:32:59 UTC |
| ea21087 | Daniel Himmelstein | 30 August 2019, 17:23:19 UTC | Merge rootstock on 2019-08-30 Includes updates for AppVeyor PR builds | 30 August 2019, 17:23:19 UTC |
| 6a3ac95 | Daniel Himmelstein | 30 August 2019, 16:16:45 UTC | Use AppVeyor artifact URLs in manuscript front-matter Merges https://github.com/manubot/rootstock/pull/263 Update front-matter to use ci_source.manuscript_url Update environment on 2019-08-09 | 30 August 2019, 16:16:45 UTC |
| bc094bd | Anthony Gitter | 09 August 2019, 16:41:12 UTC | Add AppVeyor pull request previews Merges https://github.com/manubot/rootstock/pull/262 References https://github.com/manubot/rootstock/issues/198 Add an AppVeyor continuous integration file to enable manuscript build previews in pull requests. AppVeyorBot comments in pull requests with a link to the latest manuscript PDF. Move shared continuous integration steps to an install script. Change the continuous integration skip message in the deploy script to work across multiple continuous integration services. | 09 August 2019, 16:41:12 UTC |
| 579547d | Vincent Rubinetti | 04 August 2019, 19:26:38 UTC | Reduce chance of incomplete MathJax rendering Merges https://github.com/manubot/rootstock/pull/255 Closes https://github.com/manubot/rootstock/issues/252 Disable MathJax fast preview to reduce render time. Enable MANUBOT_ATHENAPDF_DELAY environment variable to set the athenapdf --delay option. Default to --delay=5000 (5 seconds) for CI builds, where ensuring rendering is complete is crucial and Travis instances may have high load. Default to --delay=1100 (1.1 seconds) for local builds, where there is a greater chance that users are running the command in real-time. | 04 August 2019, 19:26:38 UTC |
| 3defccf | Daniel Himmelstein | 02 August 2019, 15:30:32 UTC | Disable Jekyll processing on GitHub Pages Merges https://github.com/manubot/rootstock/pull/259 Specify --no-jekyll to add a .nojekyll file to the gh-pages branch. Manubot does not make use of Jekyll to do additional processing of webpage content hosted on GitHub Pages. Disable Jekyll to bypass an unnecessary CI job, which can slow down webpage deployment. https://github.blog/2009-12-29-bypassing-jekyll-on-github-pages/ | 02 August 2019, 15:30:32 UTC |
| de83608 | Michael Hoffman | 01 August 2019, 15:01:38 UTC | Make shell scripts executable Merges https://github.com/manubot/rootstock/pull/258 Closes https://github.com/manubot/rootstock/issues/257 Change corresponds to: chmod a+x **/*.sh | 01 August 2019, 15:01:38 UTC |
| a407617 | Daniel Himmelstein | 09 July 2019, 19:46:20 UTC | Update PLOS Comp Bio outputs from version 1 to 2 Merges https://github.com/greenelab/meta-review/pull/252 Downloaded on 2019-07-09 from: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007128&rev=2 | 09 July 2019, 19:46:20 UTC |
| 9e91827 | Daniel Himmelstein | 09 July 2019, 18:20:05 UTC | PR: upgrade rootstock on 2019-07-09 Merges https://github.com/greenelab/meta-review/pull/251 Includes updated deploy.sh SSH private key scripts. Will help test whether the SSH connection still works with encrypted files. | 09 July 2019, 18:20:05 UTC |
| 0e4f1b1 | Daniel Himmelstein | 09 July 2019, 18:08:12 UTC | Merge: update rootstock on 2019-07-09 | 09 July 2019, 18:08:12 UTC |
| 2a5e425 | Daniel Himmelstein | 09 July 2019, 17:13:52 UTC | Travis CI: use settings env var to store SSH private key Merges https://github.com/manubot/rootstock/pull/243 Closes https://github.com/manubot/rootstock/issues/91 Closes https://github.com/manubot/rootstock/issues/246 Switch to a Travis CI settings environment variable to store the SSH private key for GitHub deployment. Setup no longer requires the travis ruby gem, whose `travis encrypt` subcommand was incompatible with Windows. Setup is now supported on Windows systems with a Unix/Linux/POSIX-compliant shell with the proper dependencies, such as ssh-keygen & openssl. The SSH private key is stored in MANUBOT_SSH_PRIVATE_KEY, after being base64 encoded to remove newline characters. Remove files for the legacy encrypted file method. Deprecate the encrypted file decryption in deploy.sh. In the future, we may only support private key specification via MANUBOT_SSH_PRIVATE_KEY. | 09 July 2019, 17:13:52 UTC |
| 8bbd978 | Daniel Himmelstein | 09 July 2019, 16:47:54 UTC | Travis CI: replace after_success stage with deploy Merges https://github.com/manubot/rootstock/pull/250 Failures in after_success did not cause the entire build to fail. Now if deployment fails, the build should fail. References: https://docs.travis-ci.com/user/deployment/#conditional-releases-with-on https://docs.travis-ci.com/user/deployment/script/ https://github.com/travis-ci/travis-ci/issues/758 | 09 July 2019, 16:47:54 UTC |
| 1a41435 | Anthony Gitter | 08 July 2019, 20:32:27 UTC | Add customization instructions and catalog to USAGE (#245) * Link to catalog * Add formatting and CSL instructions * Remove examples and add try-manubot | 08 July 2019, 20:32:27 UTC |
| ed4158c | Anthony Gitter | 28 June 2019, 21:50:04 UTC | Improve documentation about build process (#238) * Improve documentation about build process * Additional rephrasing * Updates per dhimmel review | 28 June 2019, 21:50:04 UTC |
| ddb0288 | Daniel Himmelstein | 27 June 2019, 21:17:00 UTC | Harden shell scripts with improved robustness & verbosity (#233) Merges https://github.com/manubot/rootstock/pull/233 Hat tip to Michael Hoffman (https://hoffmanlab.org/) for feedback. * Apply shell best practices References: https://kvz.io/blog/2013/11/21/bash-best-practices/ https://www.davidpashley.com/articles/writing-robust-shell-scripts/ https://github.com/manubot/rootstock/pull/233#issuecomment-500898800 * Specify bash (not just sh). Other shellcheck suggestions Properly use command substitution and parameter expansion in the appropriate places. * echo diagnostic messages to stderr Previously echo defaulted to stdout https://stackoverflow.com/a/41766832/4651668 Placement of stderr redirect to: "echo >&2" * Update bash options: xtrace specified by calling command * Quote variable names * deploy.sh: use Travis env vars for CI build URLs These environment variables were added to Travis in late 2018 https://github.com/travis-ci/travis-ci/issues/8935#issuecomment-425185232 | 27 June 2019, 21:17:00 UTC |
| 2fd84f1 | Daniel Himmelstein | 25 June 2019, 18:44:41 UTC | Mention PLOS Comp Bio software article on Manubot Merges https://github.com/manubot/rootstock/pull/234 Also update URLs in 02.delete-me.md | 25 June 2019, 18:44:41 UTC |
| 22b9463 | Daniel Himmelstein | 25 June 2019, 16:43:13 UTC | Add PLOS Comp Bio publication links and outputs Merges https://github.com/greenelab/meta-review/pull/248 * Mention PLOS Comp Bio publication * Add PLOS Computational Biology outputs on 2019-06-25 These outputs correspond to the uncorrected proof and were downloaded from the PLOS website at https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007128 | 25 June 2019, 16:43:13 UTC |
| 518779d | Daniel Himmelstein | 25 June 2019, 14:53:31 UTC | Style of "webpage" & fix incorrect DOI in manual refs Merges https://github.com/greenelab/meta-review/pull/247 * Fix incorrect DOI in manual references Presumably this was a typo at some point in manual-references.json https://github.com/greenelab/meta-review/issues/244#issuecomment-505199526 * Consistent style: "web page" to "webpage" | 25 June 2019, 14:54:36 UTC |
| a0c392b | Anthony Gitter | 21 June 2019, 15:54:06 UTC | Track the docx files and manual changes (#245) | 21 June 2019, 15:54:06 UTC |
| eb7a64b | Anthony Gitter | 14 June 2019, 15:26:52 UTC | Update affiliation and Software Heritage (#243) * Swap city and state * Update manubot and rootstock Software Heritage ids * Update meta-review Software Heritage id | 14 June 2019, 15:26:52 UTC |
| e505f0c | Anthony Gitter | 14 June 2019, 13:07:12 UTC | PLOS figures: Fig1.eps and striking-image.png Merges https://github.com/greenelab/meta-review/pull/242 Closes https://github.com/greenelab/meta-review/issues/235 * Replace Figure 1 with version from PLOS * Add striking image by Vince Rubinetti, originally from https://github.com/manubot/manubot.org/raw/82ecfcdd5801e8ca51e08e3f194a4bf4bb97eed2/images/automated-1.png | 14 June 2019, 13:07:12 UTC |
| 9b7427b | Daniel Himmelstein | 13 June 2019, 16:45:17 UTC | Cleanup PLOS styled references Merges https://github.com/greenelab/meta-review/pull/241 Refs https://github.com/greenelab/meta-review/issues/233 * Add additional example manuscripts & citations * Update frozen references * Switch raw:dongbo-conversation to raw:paywall-movie. Now appears as: 21. Paywall: The Business of Scholarship [Internet]. 2018. Available: https://paywallthemovie.com/paywall Fixing of individual references as follows: * Fix math in reference title for doi:10.1103/physrevlett.114.191803 use title from https://www.ncbi.nlm.nih.gov/pubmed/26024162 * Update Kipoi citation Preprint has been published. * Remove errant DOI for https://hdl.handle.net/10261/160086 * Update Silva et al from preprint to mSphere DOI * Add book publisher place | 13 June 2019, 16:45:17 UTC |
| 040638d | Daniel Himmelstein | 11 June 2019, 18:06:44 UTC | Freeze references, use PLOS Comp Bio CSL style Merges https://github.com/greenelab/meta-review/pull/228 * Switch CSL to PLOS Comp Bio syle * Generate manual-reference on 2019-06-11 | 11 June 2019, 18:06:44 UTC |
| bdeae89 | Vincent Rubinetti | 11 June 2019, 16:34:17 UTC | Increase resolution of plugins figure (Fig 3 for PLOS Comp Bio) Merges https://github.com/greenelab/meta-review/pull/240 Refs https://github.com/greenelab/meta-review/issues/234 Increase resolution of plugin screenshots and store raw screenshots in analyses/plugin-screenshots. New resolution of plos-comp-bio/figures/Fig3.tif is 600 dpi with a width of 4500 pixels, equating to PLOS Comp Bio's max figure width of 7.5 inches. | 11 June 2019, 16:34:17 UTC |
| 225ee6f | Daniel Himmelstein | 10 June 2019, 21:13:30 UTC | PR: upgrade rootstock on 2019-06-10 Merges https://github.com/greenelab/meta-review/pull/239 Merges https://github.com/greenelab/meta-review/pull/238 (duplicate PR that was improperly merged) manual-references.json: use "id" not "standard_citation" field | 10 June 2019, 21:13:30 UTC |
| 0af9521 | Daniel Himmelstein | 10 June 2019, 19:10:38 UTC | manual-references.json: use "id" not "standard_citation" field | 10 June 2019, 19:10:38 UTC |
| a8dce08 | Daniel Himmelstein | 10 June 2019, 19:08:42 UTC | Upgrade rootstock on 2019-06-10 | 10 June 2019, 19:08:42 UTC |
| 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 |
| 362b839 | Daniel Himmelstein | 03 June 2019, 22:29:03 UTC | Switch affiliations to a numbered list Merges https://github.com/greenelab/meta-review/pull/236 Closes https://github.com/greenelab/meta-review/issues/230 Switch affiliations to a numbered list and add city / country to affiliations As per PLOS Computational Biology request: > Please modify the Affiliations section of your manuscript so that all affiliations listed contain a Department, Institution, City, and Country | 03 June 2019, 22:29:03 UTC |
