PR to merge rootstock changes on 2019-03-14 #5

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

12/21 Status Report

@brettbj

Merging @brettbj's updates.

Pattern Discovery / Categorize

License text from https://github.com/idleberg/Creative-Commons-Markdown/blob/95edd678ba1996e10fa576d23b35900dbb310692/4.0/by.markdown. License title collapsed to a single h1 line.

CC0 1.0 license text from greenelab/deep-review@86f159e.

Automatically extract & process references using Travis Dual license code/data as CC BY and CC0.

Continuously analyze repo for automatic manuscript deployment

Error is: ``` ghp-import: error: No import directory specified. ``` Testing "double quotes" and 'single quotes'

Modify auto-generated commit message

As as result of c-w/ghp-import#62.

Fix references and test CI of multiple PR merges

@dashed

From https://gist.github.com/dashed/6714393 by @dashed. MIT Licensed. Versioned link https://git.io/vykxo.

Improve build error reporting Remove notebook relics

See #271

Improve build wait times. See https://docs.travis-ci.com/user/trusty-ci-environment/

Closes greenelab/deep-review#269

Affects gh-pages branch only. Fixed to allow reading from and writing to the same file. See http://stackoverflow.com/a/3897483/4651668 Bug introduced in greenelab/deep-review#274.

…gailrosen-tags

@gailrosen

Update tags.tsv with placeholder references left by @gailrosen

Clarify Introduction

Closes greenelab/deep-review#290

Support multiple citations within brakets in pandoc output

* Replace numbered citation_id with 5-byte blake2 hash * Use base32 encoding for 5 bytes in 8 chars * Check for citation_id collisions

The event field of CSL data should be a string (https://git.io/vSSug). Instead the event key returns an object as shown below: ```sh curl --location \ --header "Accept: application/vnd.citationstyles.csl+json" \ https://doi.org/10.1109/icnn.1994.374637 \ | python -m json.tool ``` ```json "event": { "name": "1994 IEEE International Conference on Neural Networks (ICNN'94)", "location": "Orlando, FL, USA", "acronym": "ICNN-94" }, ``` Related to CrossRef/rest-api-doc#187. DOI content negotiation returns invalid CSL

Assuming the `reference` field was recently added. See https://doi.org/10.1126/science.aal1012.

Suggested additions/changes to Categorize/EHR

* add initial approval/contact form * add grants to cite col * update readme to match

Refs greenelab/deep-review#381 * Enable Greycite URL metadata fetching * Use urllib not requests for Greycite API Refs https://github.com/kennethreitz/requests/issues/4023 * Fix URL references for Greycite http://www.ncrr.nih.gov/publications/informatics/ehr.pdf is a broken link for a 2006 report titled "Electronic Health Records Overview" by the MITRE Corporation. See https://www.scribd.com/document/51496338 Greycite was struggling with http://dl.acm.org/citation.cfm?id=2188395 Returned a 404 for its API call. Replaced with an alternative location. * Greycite workarounds

@Lukasa

Uses `Connection: close` workaround by @Lukasa. See https://github.com/kennethreitz/requests/issues/4023#issuecomment-302164405

* Upgrade opentimestamps-client Upgrades to opentimestamps/opentimestamps-client@e1ff983 * Add pysha3 PyPI dependency

* Section: Continuous collaborative manuscript drafting * Add reference by type counts https://travis-ci.org/greenelab/deep-review/builds/233712348#L396-L400 * Revisions based on review comments * Template reference counts Refs greenelab/deep-review#485 * Rearrange sections * Remove duplicated import

Refs greenelab/deep-review#381 (comment) In manual-references.json use standard_citation not citation_id Closes greenelab/deep-review#506

Enable manual citeproc JSON for references

Update references to all have hyperlinks

* note submitted * Add bioRxiv link

Closes greenelab/deep-review#524

Add anchor links to headers in the HTML version The MIT-licensed AnchorJS library is used: <https://www.bryanbraun.com/anchorjs/> `build/assets/anchors.js` derives from https://github.com/bryanbraun/anchorjs/blob/bf22c0f9832ca160b361a3bbc4112528bc84b460/anchor.min.js

* Convert author table from md to tsv * Convert tsv from Unicode to UTF-8 * Machine readable column headers

* Update build notes * Add note about Linux requirement

* Test template with hard-coded author count * Move hard-coded author counts to authors.py * Dynamically get author count for template * Rename authors file and switch to OrderedDict

* Temporarily add exported HTML manuscript to support subsequent diff * Derive author initials and confirm authors approve manuscript * Standardize funders in author table * Further standardize funding information in author table * Add functions to format funding information for templates * Add templates for funding information * Add predetermined author order to prepare for additional templating * Generate affiliation numbers * Refactor affiliation code and add annotation to first author * Add corresponding author annotation * Better support for multiple middle initials * Remove trailing whitespace * Add template for corresponding author contact information * Replace defaultdict with setdefault * Sort author table and remove author ordering column * Switch to OrderedDict for funding information * Separate author name, affiliation, and symbol for template * Improve code style * Format affiliations in jinja2 * Ignore and remove exported HTML manuscipt

History proceeding this commit was generated from greenelab/deep-review@daef821 by running: git filter-branch \ --index-filter 'git rm --cached --ignore-unmatch -r authors references sections .codeclimate.yml author_contact_approve.md authors.tsv'\ --prune-empty -- --all

on GitHub, the following error occurred: fatal: Couldn't find remote ref gh-pages From the line: git fetch origin gh-pages:gh-pages references:references Now initialize.sh creates these branches

Closes manubot/rootstock#3 * URL reference for manual reference example * Add intructions for manual references * Fix relative link * Add manual reference example * Rephrasing

Refs greenelab/deep-review#569

So directory can contain additional information such as authors.tsv. Potentially even tags.tsv and manual-references.json should go here.

Closes manubot/rootstock#7

Full error: pandoc-citeproc: Error in $[26].categories[0][0]: failed to parse field categories: mempty CallStack (from HasCallStack): error, called at src/Text/CSL/Input/Bibutils.hs:50:49 in pandoc-citeproc-0.10.4-36ROWpY3Inr1fCxMvEajRL:Text.CSL.Input.Bibutils pandoc: Error running filter pandoc-citeproc

@dhimmel

Add table, figure, & equation to manuscript Fix jinja2 environment comment detection for pandoc-fignos compatability. Merges manubot/rootstock#8. Small edits by @dhimmel to deal with new directory structure.

Closes manubot/rootstock#15

Deployment was failing due to travis-ci/travis-ci#8082

Squashed and rebased version of manubot/rootstock#16

Refs manubot/rootstock#18 (comment)

Follows up on the unsuccessful manubot/rootstock#19 Addresses travis-ci/travis-ci#8082 Attempt to fix build error https://travis-ci.org/greenelab/manubot-rootstock/builds/254181411#L1379

LigGen → LibGen

Only applies to manuscripts built on Travis.

@slochower

* Add GitHub, ORCID, Twitter icons Adds images directory as pioneered by @slochower in manubot/rootstock#8. Uses symbolic link so content/images maps to output/images. Fix https://twitter.com/gcabanac/status/886587167333642240 Makes affiliations & funding small text. * Modify SVG icons to be gray * Make ORCID display conditional

Fix typo: delimeters → delimiters Closes manubot/rootstock#25

Follows up on manubot/rootstock#26 https://stackoverflow.com/a/3411105/4651668

Refs wkhtmltopdf/wkhtmltopdf#2982 (comment)

Refs manubot/rootstock#32 (comment) Also ignore manuscript.docx output

Closes manubot/rootstock#38

Refs #40

* Add cloning instructions to readme * Remove initialize script

Closes manubot/rootstock#28

* Update for expanded manubot package * Create distinct caching directory * Deployment: references branch now output * Rewrite documentation * Rename CONTRIBUTING.md to USAGE.md Refs manubot/manubot#2

Fixes issue where manual references were not respected.

Closes manubot/manubot#3

Refs manubot/rootstock#55 (comment)

Closes manubot/rootstock#55 Also reorder some pandoc CLI arguments.

Closes manubot/rootstock#59

Refs manubot/rootstock#58 (comment)

Refs manubot/rootstock#6 (comment)

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. manubot/rootstock@5eed755#commitcomment-23985090

* 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

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.

Simplify the CSL specification as per manubot/rootstock#53

Do not use latest miniconda, since updates can cause bugs, which happened in manubot/rootstock#75 (comment) due to https://stackoverflow.com/a/46457813/4651668

* PDF export: use weasyprint not wkhtmltopdf Closes manubot/rootstock#77 * USAGE: specify SVG size Refs Kozea/WeasyPrint#442 * Install cairocffi from pip not conda-forge

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 manubot/rootstock#40

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 Kozea/WeasyPrint#59

manubot/rootstock#81 (comment)

Closes manubot/rootstock#74 SETUP.md commands should now work on both Linux and macOS. Requires Python on system.

* Update SETUP.md based on OpenCon do-a-thon sparcopen/doathon#21 * git diff --color-words, not --word-diff * Specify no Windows support in SETUP.md manubot/rootstock#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.

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

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

https://h.readthedocs.io/projects/client/en/latest/publishers/embedding/ Closes manubot/rootstock#90

Refs manubot/manubot#22

Update pandoc to 2.1 Reference 2018 development proposal in USAGE.md Remove temporarily broken DOI: https://twitter.com/dhimmel/status/950443969313419264

Upgrade Manubot to manubot/manubot@b53f487 Refs manubot/manubot#24

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 greenelab/deep-review#774 (comment)

Upgrade Manubot with citations.tsv error message improvements Upgrade to weasyprint v0.42 http://weasyprint.readthedocs.io/en/latest/changelog.html#version-0-42

Update usage instructions for citation tags

Suggest issues for general inquiries

Closes manubot/rootstock#105

Fix upstream issues: Extra brackets around citations in figure captions jgm/pandoc#4272 WeasyPrint 0.42 gets stuck Kozea/WeasyPrint#560 Updated pandoc-xnos with better semantic versioning tomduck/pandoc-fignos#46

git's user.name config was being set to first names only, since names are space separated. Add quotes to prevent this.

Closes manubot/rootstock#96

Most autobuild users will want to automatically update the webpage. See discussion at manubot/rootstock#101 (comment) Update README to better document autobuild.

Merges manubot/rootstock#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

Merges manubot/rootstock#114

Change style of citations from [1–4] to [1,2,3,4] Merges manubot/rootstock#121

* travis login information added * single quote and inline sentence * Add newline

Merges manubot/rootstock#123 Refs manubot/rootstock#120

Merges manubot/rootstock#125

Merges manubot/rootstock#127 Add TFSEE, global emissions, & yt 3.0 manuscripts

Merges manubot/rootstock#131 Closes manubot/rootstock#130 * Left-align table caption text * figure img style: center img, left-align text

Merges manubot/rootstock#132 * Upgrade manubot to use process subcommand * Upgrade environment to latest versions on 2018-08-22 * CSL style: block to display identifiers

Merges manubot/rootstock#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.

Merges manubot/rootstock#135 Closes manubot/manubot#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 gazpachoking/jsonref#26, but several remain. * Travis CI: update miniconda to 4.5.11

Merges manubot/rootstock#138 Closes manubot/rootstock#137 * Case sensitive environment variables * Update phrasing borrowing dhimmel ideas * Change account to username

Merges manubot/rootstock#140 Closes manubot/rootstock#136 Updates Manubot to fix empty date-parts issue Fix opentimestamps incompatible pinned versions

Merges manubot/rootstock#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.

Merges manubot/rootstock#142

Merges manubot/rootstock#145 Closes manubot/rootstock#122 * Add BUILD_PDF environment variable BUILD_PDF is considered "true" unless specifically set to "false" webpage.py: tolerate missing output/manuscript.pdf Refs manubot/rootstock#144 (comment) 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

Closes manubot/rootstock#144 Merges manubot/rootstock#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.

Merges manubot/rootstock#147 Update manubot version on 2018-11-15 to manubot/manubot@afa55f8 Includes migration of PMCID citations to Literature Citation Exporter. Update conda-forge dependencies

Merges manubot/rootstock#148 Co-Authored-By: Daniel Himmelstein <[email protected]> Co-Authored-By: Anthony Gitter <[email protected]>

Merges manubot/rootstock#149 * Enable ISBN citaiton support * Update URL citation Previous URL citation contained "?", therefore requiring a citation tag.

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#161

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#168 Refs manubot/rootstock#163

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#186

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#169

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 ```

Commits on Oct 26, 2016

2016-10-26 status report

agitter committed Oct 26, 2016

Configuration menu

View commit details

Copy full SHA for 69dfd7a

Browse repository at this point

Copy the full SHA

69dfd7a View commit details

Browse the repository at this point in the history

Commits on Nov 13, 2016

URL citation guidelines

agitter committed Nov 13, 2016

Configuration menu

View commit details

Copy full SHA for 5015e16

Browse repository at this point

Copy the full SHA

5015e16 View commit details

Browse the repository at this point in the history

Commits on Apr 19, 2017

provide more info for contributors (#318)

cgreene authored Apr 19, 2017

Configuration menu

View commit details

Copy full SHA for 432232d

Browse repository at this point

Copy the full SHA

432232d View commit details

Browse the repository at this point in the history

Commits on Oct 9, 2017

Fix intra-sentence newline in README (#80)

dhimmel authored Oct 9, 2017

Configuration menu

View commit details

Copy full SHA for 38effe8

Browse repository at this point

Copy the full SHA

38effe8 View commit details

Browse the repository at this point in the history

PR to merge rootstock changes on 2019-03-14 #5

PR to merge rootstock changes on 2019-03-14 #5

Commits on Aug 5, 2016

Commits on Aug 9, 2016

Commits on Aug 25, 2016

Commits on Oct 13, 2016

Commits on Oct 20, 2016

Commits on Oct 25, 2016

Commits on Oct 26, 2016

Commits on Oct 27, 2016

Commits on Oct 30, 2016

Commits on Nov 13, 2016

Commits on Nov 14, 2016

Commits on Dec 19, 2016

Commits on Dec 20, 2016

Commits on Dec 21, 2016

Commits on Dec 28, 2016

Commits on Feb 24, 2017

Commits on Feb 25, 2017

Commits on Feb 26, 2017

Commits on Feb 27, 2017

Commits on Mar 3, 2017

Commits on Mar 4, 2017

Commits on Mar 16, 2017

Commits on Mar 17, 2017

Commits on Apr 3, 2017

Commits on Apr 5, 2017

Commits on Apr 6, 2017

Commits on Apr 7, 2017

Commits on Apr 10, 2017

Commits on Apr 13, 2017

Commits on Apr 19, 2017

Commits on Apr 26, 2017

Commits on Apr 27, 2017

Commits on Apr 28, 2017

Commits on May 9, 2017

Commits on May 17, 2017

Commits on May 18, 2017

Commits on May 19, 2017

Commits on May 23, 2017

Commits on May 24, 2017

Commits on May 25, 2017

Commits on May 29, 2017

Commits on Jun 1, 2017

Commits on Jun 7, 2017

Commits on Jun 12, 2017

Commits on Jun 17, 2017

Commits on Jun 18, 2017

Commits on Jun 21, 2017

Commits on Jun 29, 2017

Commits on Jul 5, 2017

Commits on Jul 10, 2017

Commits on Jul 11, 2017

Commits on Jul 12, 2017

Commits on Jul 13, 2017

Commits on Jul 15, 2017

Commits on Jul 16, 2017

Commits on Jul 17, 2017

Commits on Jul 18, 2017

Commits on Jul 20, 2017

Commits on Jul 21, 2017

Commits on Jul 24, 2017

Commits on Jul 29, 2017

Commits on Jul 30, 2017

Commits on Jul 31, 2017

Commits on Aug 3, 2017

Commits on Aug 9, 2017

Commits on Aug 10, 2017

Commits on Aug 14, 2017

Commits on Aug 15, 2017

Commits on Aug 27, 2017

Commits on Aug 28, 2017

Commits on Aug 30, 2017

Commits on Aug 31, 2017

Commits on Sep 1, 2017

Commits on Sep 5, 2017

Commits on Sep 6, 2017

Commits on Sep 19, 2017

Commits on Sep 28, 2017

Commits on Oct 4, 2017