PR to merge rootstock changes on 2019-03-14 #5
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Related to comment at greenelab/deep-review#2 (comment)
Provide 8/25 status update
Add in stub files so that we can start writing.
reality has struck!
…nto cgreene-patch-1
Start to stub in categorize section
2016-10-26 status report
Update 02_intro.md
* Enable tag citations See greenelab/deep-review#2 (comment). * Reflow text to satisfy codeclimate
URL citation guidelines
Outline the Study section
Fill in more of the introduction
Hardware Limitations and Scaling
Merges manubot/rootstock#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)
Merges manubot/rootstock#151 * Upgrade manubot python package with Wikidata citations * Remove DataCite DOI from 02.delete-me.md * Add additional manuscripts to USAGE examples
Merges manubot/rootstock#153 Updates pandoc to v2.5.
Merges manubot/rootstock#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 greenelab/meta-review#88 (comment)
Merges manubot/rootstock#166 Improves formatting and centering of icons. Uses github and twitter icons from https://fontawesome.com
Merges manubot/rootstock#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.
Merges manubot/rootstock#171 Various display improvements, simplified code structure with modern best practices.
Merges manubot/rootstock#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 manubot/manubot#94. 02.delete-me.md still references greenelab/manubot, however it is not worth creating merge conflicts to update just this.
Merges manubot/rootstock#180 Closes manubot/rootstock#175 Closes manubot/rootstock#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
Merges manubot/rootstock#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)
Merges manubot/rootstock#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.
Merges manubot/rootstock#178 Various aesthetic updates, refactoring, edits for plugins, and additional comments
Merges manubot/rootstock#179 Closes manubot/rootstock#185 Improves manubot/rootstock#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)
Merges manubot/rootstock#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.
Used code like: ``` git checkout -b rootstock-`date '+%Y-%m-%d'` git pull --allow-unrelated-histories --no-ff --no-commit rootstock master git checkout --ours FILE_PATH git checkout --theirs FILE_PATH ```
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Deployedment of the merged squashed commit (1ddd48d) failed according to the build log: |
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This build is based on 1ddd48d. This commit was created by the following Travis CI build and job: https://travis-ci.org/dhimmel/rephetio-manuscript/builds/506344659 https://travis-ci.org/dhimmel/rephetio-manuscript/jobs/506344668 [ci skip] The full commit message that triggered this build is copied below: PR to merge rootstock changes on 2019-03-14 Merges #5
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This build is based on 1ddd48d. This commit was created by the following Travis CI build and job: https://travis-ci.org/dhimmel/rephetio-manuscript/builds/506344659 https://travis-ci.org/dhimmel/rephetio-manuscript/jobs/506344668 [ci skip] The full commit message that triggered this build is copied below: PR to merge rootstock changes on 2019-03-14 Merges #5
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According to https://github.com/dhimmel/rephetio-manuscript/settings/keys there are no deploy keys... that could explain the issue. Added the public key with write as a deploy key on github and restarted the build. |
dhimmel
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Using method described in #5 (comment)
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merges #8 updates rootstock to manubot/rootstock@277a769 used squash method for updating described at #5 (comment)
dhimmel
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This build is based on d020443. This commit was created by the following Travis CI build and job: https://travis-ci.org/dhimmel/rephetio-manuscript/builds/614673307 https://travis-ci.org/dhimmel/rephetio-manuscript/jobs/614673308 The full commit message that triggered this build is copied below: Update rootstock on 2019-11-20 (#8) merges #8 updates rootstock to manubot/rootstock@277a769 used squash method for updating described at #5 (comment)
dhimmel
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Nov 20, 2019
This build is based on d020443. This commit was created by the following Travis CI build and job: https://travis-ci.org/dhimmel/rephetio-manuscript/builds/614673307 https://travis-ci.org/dhimmel/rephetio-manuscript/jobs/614673308 The full commit message that triggered this build is copied below: Update rootstock on 2019-11-20 (#8) merges #8 updates rootstock to manubot/rootstock@277a769 used squash method for updating described at #5 (comment)
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Since this repo used a squash method to clone rootstock as discussed in manubot/rootstock#65, merging rootstock changes is a bit more difficult.
I used the following workflow for this PR: