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Update the Deep Review with latest Manubot #681

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Merged
dhimmel merged 202 commits into from
Nov 3, 2017
Merged

Update the Deep Review with latest Manubot #681

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b2059b5
fix codeclimate issues that were identified
Aug 5, 2016
b3cd5b0
merge
Aug 5, 2016
d3dcff6
add code climate to readme, test config
Aug 5, 2016
6160d00
Add markdown and citation information
dhimmel Aug 9, 2016
2b8425f
add initial status update to README
Aug 25, 2016
3e2be5a
incorporate suggestions from @gwaygenomics
Aug 25, 2016
e1b9588
more tuning of get involved list
Aug 25, 2016
86496b4
Merge pull request #90 from greenelab/status-update-readme
cgreene Aug 25, 2016
9bd1c34
add initial stub files
Oct 13, 2016
e0bb1fc
fix up pandoc stubs
Oct 13, 2016
917045f
Merge pull request #106 from greenelab/stubs
cgreene Oct 13, 2016
3f45fd6
Merge branch 'master' into categorize-draft
Oct 13, 2016
bb55bfe
reality has struck!
cgreene Oct 20, 2016
7162061
Merge pull request #115 from greenelab/cgreene-patch-1
agitter Oct 20, 2016
528f8ba
Merge branch 'categorize-draft' of github.com:greenelab/deep-review i…
Oct 25, 2016
419aaeb
Merge pull request #108 from greenelab/categorize-draft
cgreene Oct 25, 2016
69dfd7a
2016-10-26 status report
agitter Oct 26, 2016
a660556
Rearrange status update order
agitter Oct 27, 2016
9d6827e
Merge pull request #120 from greenelab/status
agitter Oct 27, 2016
1896d47
Merge pull request #121 from traversc/patch-1
agitter Oct 30, 2016
80807fd
Enable tag citations (#123)
dhimmel Oct 30, 2016
5015e16
URL citation guidelines
agitter Nov 13, 2016
66ba062
Merge pull request #143 from greenelab/contributing
agitter Nov 14, 2016
9c7881a
Merge remote-tracking branch 'origin' into more-intro-work
Dec 19, 2016
efaf691
Merge pull request #136 from greenelab/study-stubs
agitter Dec 20, 2016
4971905
12/21 Status Report
cgreene Dec 21, 2016
5dd62cc
2016 -> 2017
cgreene Dec 21, 2016
c74db29
Merge pull request #135 from greenelab/more-intro-work
cgreene Dec 21, 2016
daf1042
Merge branch 'master' into hardware-limitations-and-scaling
agitter Dec 21, 2016
13d1b14
Merge pull request #147 from evancofer/hardware-limitations-and-scaling
agitter Dec 21, 2016
b9e856c
link example PR
cgreene Dec 21, 2016
01e0594
link evan
cgreene Dec 21, 2016
d30b571
Merge pull request #165 from greenelab/status-report-update
cgreene Dec 21, 2016
fca06bb
Merge branch 'master' into intro_thoughts
cgreene Dec 28, 2016
141a05c
Merge pull request #166 from greenelab/intro_thoughts
cgreene Dec 28, 2016
95bdecf
Merge pull request #167 from cgreene/ehr-pattern-discovery
cgreene Dec 28, 2016
8733368
Add ignores
dhimmel Feb 24, 2017
a8ec509
Add ability to autogenerate citations
dhimmel Feb 24, 2017
ecef917
Enable Travis CI
dhimmel Feb 24, 2017
abf4474
Switch from notebook to script
dhimmel Feb 24, 2017
78c98b2
Switch to J R Soc Interface CSL
dhimmel Feb 24, 2017
ce0e9fd
Ignore all output files
dhimmel Feb 24, 2017
39ab303
Add ghp-import
dhimmel Feb 24, 2017
f6ff07e
Make generated directory
dhimmel Feb 24, 2017
06c672d
Improve status reporting
dhimmel Feb 24, 2017
feef8e2
Remove jupyter from environment
dhimmel Feb 25, 2017
ce8fd2b
Switch CC BY license to markdown
dhimmel Feb 25, 2017
e2f6521
Dual license code and data under CC0
dhimmel Feb 25, 2017
de59528
Merge pull request #257 from dhimmel/build-refs
dhimmel Feb 25, 2017
1a9dfe0
Cache generated citation metadata
dhimmel Feb 25, 2017
1fef464
Add GitHub SSH deploy key
dhimmel Feb 25, 2017
1a0b9c7
Wrap long line in .travis.yml
dhimmel Feb 25, 2017
736aedb
Add deployment script
dhimmel Feb 25, 2017
79ff70d
Merge pull request #259 from dhimmel/continuous
dhimmel Feb 25, 2017
de72db1
Attempt to fix ghp-import error
dhimmel Feb 25, 2017
da704b6
CI: fetch gh-pages and references branches
dhimmel Feb 26, 2017
cf19088
CI: transmit commit author details
dhimmel Feb 26, 2017
0645cad
Use long arguments with ghp-import
dhimmel Feb 26, 2017
b5ffb9e
Document references/generated directory
dhimmel Feb 26, 2017
9ba02f6
Build: print bracketed text that's not refs
dhimmel Feb 26, 2017
3c769b8
Merge pull request #260 from dhimmel/fix-refs
dhimmel Feb 26, 2017
7c97c64
Build only master branch
dhimmel Feb 26, 2017
0a4f2d8
Fix regex error
dhimmel Feb 26, 2017
ce520de
Add CSS style to HTML pandoc output (#263)
dhimmel Feb 26, 2017
420aee5
Clean up build code
dhimmel Feb 27, 2017
efa428f
Improve README CI and License doc
dhimmel Feb 27, 2017
b0f1a30
Pandoc: link-citations to bibliography (#272)
dhimmel Mar 3, 2017
bc72855
Switch Travis to trusty from precise (#273)
dhimmel Mar 3, 2017
3b763ff
Timestamp manuscripts with OpenTimestamps (#274)
dhimmel Mar 4, 2017
2d589e4
Fix blank output/README.md bug (#275)
dhimmel Mar 4, 2017
0d35012
Merge branch 'master' of git://github.com/gailrosen/deep-review into …
dhimmel Mar 16, 2017
c02ef7d
update expected date (#279)
cgreene Mar 17, 2017
95916fa
Merge pull request #278 from dhimmel/gailrosen-tags
dhimmel Apr 3, 2017
41428e0
fix conflicts; removed unused section
Apr 5, 2017
af6d0ee
Merge branch 'traversc-patch-1'
Apr 5, 2017
8371123
merge concluded
Apr 6, 2017
400ef7f
Merge pull request #243 from cgreene/master
cgreene Apr 6, 2017
c0c8e83
Style: flake8 formatting in references.py
dhimmel Apr 7, 2017
d3ee476
Style: flake8 citations.py
dhimmel Apr 7, 2017
de283be
pandoc-citeproc: fix multiple references in brackets
dhimmel Apr 7, 2017
cf5f5f9
Merge pull request #294 from dhimmel/multirefs
dhimmel Apr 7, 2017
0eaa638
Replace numbered citation_id with 5-byte blake2 hash (#298)
dhimmel Apr 10, 2017
72432d7
Fix indentation bug (#303)
dhimmel Apr 10, 2017
76b8ab8
Encode citation_ids using base62
dhimmel Apr 11, 2017
e11f8ea
CSL: remove malformated event field
dhimmel Apr 13, 2017
dedd021
Remove reference lists in CSL bibliography.json (#309)
dhimmel Apr 13, 2017
356668e
add timeline; notifications dates; etc (#310)
cgreene Apr 13, 2017
432232d
provide more info for contributors (#318)
cgreene Apr 19, 2017
0f5a322
expanded section on standards, inc. refs to ongoing projects
agapow Apr 24, 2017
0433a5e
Merge pull request #360 from greenelab/pre-merge-pa
cgreene Apr 26, 2017
b877fb6
Merge branch 'master' into ehr-additions
cgreene Apr 27, 2017
b79585f
Merge pull request #357 from enricoferrero/ehr-additions
cgreene Apr 27, 2017
b84bd9c
Merge branch 'master' into master
cgreene Apr 28, 2017
322dbd2
Merge pull request #246 from swamidass/master
cgreene Apr 28, 2017
6aa0227
Author approval (#389)
cgreene May 9, 2017
bd99c5c
Bibtex: use url not link attribute (#465)
dhimmel May 17, 2017
5e611e6
Get metadata for URL references using Greycite (#464)
dhimmel May 17, 2017
7762bfe
Use requests for Greycite (#472)
dhimmel May 17, 2017
cdd819a
Count references by type (#479)
dhimmel May 18, 2017
ca09d92
Fix GitHub markdown numbered list rendering (#481)
dhimmel May 18, 2017
7c220c5
Upgrade opentimestamps-client (#482)
dhimmel May 18, 2017
d5f29a0
Enable templating with jinja2 (#485)
dhimmel May 19, 2017
1efe954
Add continuous collaborative manuscript drafting section (#477)
dhimmel May 19, 2017
4eeb404
Improve duplicate citation text output (#488)
dhimmel May 19, 2017
883fca8
update title from @bdo311 closes #496 (#503)
cgreene May 23, 2017
055716a
Enable manual citeproc JSON for references
dhimmel May 24, 2017
23fd6b3
Merge pull request #509 from dhimmel/overide
dhimmel May 25, 2017
1023a0f
Style: display hyperlinks for all references
dhimmel May 24, 2017
b7e1b5a
Update DOI resolution URLs in citeproc
dhimmel May 24, 2017
ccaa852
Add URL attribute to PubMed citeproc
dhimmel May 24, 2017
16d0101
Merge pull request #510 from dhimmel/hyperlink
dhimmel May 25, 2017
c7f3798
Upgrade arXiv URLs to use HTTPS (#512)
dhimmel May 25, 2017
2869f11
Update README to note new manuscript status (#521)
cgreene May 29, 2017
6a3c3d3
Add Google Analytics to HTML output (#525)
dhimmel Jun 1, 2017
d36e341
Add anchor links to headers in the HTML version (#534)
rgieseke Jun 7, 2017
c3580b3
Convert author table from md to tsv (#541)
agitter Jun 12, 2017
0750b8c
Update build notes (#545)
agitter Jun 17, 2017
e055c18
Template for author counts (#546)
agitter Jun 18, 2017
bf9de06
Fix typo (#552)
rgieseke Jun 21, 2017
1a2afbb
Templates for author list, affiliations, and funding (#550)
agitter Jun 21, 2017
5999168
Migrate from deep-review to manubot-rootstock
dhimmel Jun 29, 2017
52a2841
Add references and sections directories
dhimmel Jun 29, 2017
b6efd17
Update deploy key for greenelab/manubot-rootstock
dhimmel Jun 29, 2017
2dd8f00
Update environment
dhimmel Jun 29, 2017
adcb25e
Add reference
dhimmel Jun 29, 2017
cf24601
Disable author parsing
dhimmel Jun 29, 2017
f82ae0d
On new repositories where gh-pages and references branches did not exist
dhimmel Jun 29, 2017
ef4e272
Use metabot package for metadata.py
dhimmel Jun 29, 2017
b1762ae
Fix output/README.md templating
dhimmel Jun 29, 2017
439bf03
Manual reference example (#5)
agitter Jul 5, 2017
b047fc6
Update shortened URLs (#9)
agitter Jul 10, 2017
a86d1c0
Use same locale for all builds (#11)
dhimmel Jul 11, 2017
f1b13a3
Rename sections to content
dhimmel Jul 10, 2017
e3acbe6
Use terse pathlib syntax
dhimmel Jul 10, 2017
8e45956
Fill authors.tsv. Add info to manuscript.
dhimmel Jul 10, 2017
bea6f31
Docs: mention deep review and authors.tsv
dhimmel Jul 11, 2017
49100ca
Improved error message
dhimmel Jul 11, 2017
33a54cb
citeproc_type_fixer: standard to entry
dhimmel Jul 11, 2017
84d9d92
Fix citeproc issue with catagories (#13)
dhimmel Jul 11, 2017
b03e1c3
Support for pandoc fignos, tablenos, eqnos
slochower Jul 7, 2017
047ac5e
Routine maintenance
dhimmel Jul 12, 2017
c227064
Fix formatting of missing author fields (#17)
vsmalladi Jul 13, 2017
1a118b9
Workaround for Travis timeout / termination (#19)
dhimmel Jul 15, 2017
7db3f4f
Add metadata.yaml and remove authors.tsv
evancofer Jul 12, 2017
8811e59
Address remaining issues with metadata.yaml
dhimmel Jul 15, 2017
1ad485b
Directly make PDF from HTML via wkhtmltopdf
dhimmel Jul 16, 2017
123b84b
Second attempt for Travis deploy timeout (#23)
dhimmel Jul 16, 2017
6c732a3
Fix typo in 03.figures.md (#22)
slochower Jul 16, 2017
2f51e26
Write source repo version info in manucript (#24)
dhimmel Jul 16, 2017
89e0cbc
Add GitHub, ORCID, Twitter icons (#21)
dhimmel Jul 17, 2017
83659ae
Shorten & simplify metadata author keys (#27)
dhimmel Jul 17, 2017
9117720
Fix typo in 02.equations.md (#30)
agitter Jul 18, 2017
a60ebd4
Minor edits to README.md (#29)
petebachant Jul 18, 2017
3773330
Add BUILD_DOCX option to export to DOCX (#26)
vsmalladi Jul 20, 2017
8993c17
Fix sh error when BUILD_DOCX=true (#34)
dhimmel Jul 20, 2017
d08d0bf
page-break control using HTML classes (#35)
dhimmel Jul 20, 2017
97d3714
Add date to output (#36)
dhimmel Jul 20, 2017
293050c
Use author-meta / date-meta to remove sed (#37)
dhimmel Jul 21, 2017
4be985c
Set print margins (#39)
dhimmel Jul 24, 2017
8c51432
Compute word count (#42)
agitter Jul 29, 2017
247fdbe
README: reference DOCX image embedding PR (#43)
vsmalladi Jul 30, 2017
6988107
README: link to cloning instructions (#44)
agitter Jul 31, 2017
64f3ddb
references/README: link to example CSL JSON Items (#46)
vsmalladi Aug 3, 2017
084e30d
Update for expanded manubot package (#48)
dhimmel Aug 9, 2017
b92226b
USAGE: recommend semantic linefeeds (#49)
dhimmel Aug 10, 2017
0a04405
Upgrade manubot version (#50)
dhimmel Aug 10, 2017
03de821
Set timezone to UTC in build.sh (#52)
dhimmel Aug 14, 2017
9f4deeb
Pandoc: use --html5 not --html5 for output (#56)
slochower Aug 15, 2017
28f460e
Add --mathjax to pandoc build
dhimmel Aug 15, 2017
795490c
Update Manubot
dhimmel Aug 15, 2017
868da10
Switch OpenTimestamps from submodule to pip (#60)
dhimmel Aug 27, 2017
69d0d5f
Autobuild: watchdog monitor content dir (#61)
dhimmel Aug 28, 2017
86851c0
Modify rootstock markdown files
dhimmel Aug 28, 2017
727ac1e
Add example manuscripts to USAGE.md
dhimmel Aug 28, 2017
719c9b5
SETUP.md: instructions for initializing instance
dhimmel Aug 28, 2017
5f1db0e
Delinieate README sections
dhimmel Aug 28, 2017
5eed755
Simplify metadata.yaml
dhimmel Aug 30, 2017
7b0c4ca
Travis CI: Attempt to fix "bad decrypt" issues (#64)
dhimmel Aug 31, 2017
99ce6d4
SETUP.md updates & Manubot version bumb (#66)
dhimmel Sep 1, 2017
26472cd
Prettify github-pandoc.css (#63)
dhimmel Sep 1, 2017
a51c064
Explicitly insert bibliography (#69)
dhimmel Sep 5, 2017
b5644db
Customize Manubot citation style (#68)
dhimmel Sep 6, 2017
2a87697
Examples: add bitcoin-whitepaper & rephetio-manuscript (#72)
dhimmel Sep 19, 2017
d323b8e
Fix typos
dhimmel Sep 6, 2017
3a42f6b
Update indents and ordering of manual-references.json
dhimmel Sep 19, 2017
7d64afa
Pin miniconda version (#76)
dhimmel Sep 28, 2017
72189b5
Note MIT licensed 3rd-party code (#75)
rgieseke Sep 28, 2017
47ee5f0
PDF export: use weasyprint not wkhtmltopdf (#78)
dhimmel Oct 4, 2017
aba5246
Specify width of front-matter SVGs (#79)
vsmalladi Oct 5, 2017
38effe8
Fix intra-sentence newline in README (#80)
dhimmel Oct 9, 2017
ec186c2
Update environment and documentation (#81)
dhimmel Nov 1, 2017
46824e6
USAGE.md: link to language tag documentation (#83)
dhimmel Nov 2, 2017
ea92847
Rename sections to 00.xxxx.md from 00_xxxx.md
dhimmel Nov 3, 2017
10f0e6e
Merge manubot-rootstock
dhimmel Nov 3, 2017
22c0936
Prepare sections for move to content
dhimmel Nov 3, 2017
14abf7b
Move sections to content directory
dhimmel Nov 3, 2017
f2244e6
Migrate authors.tsv to metadata.yaml
dhimmel Nov 3, 2017
12ce17c
Revise content for updated manubot syntax
dhimmel Nov 3, 2017
2ecee8d
Remove SETUP.md
dhimmel Nov 3, 2017
2f4b3a9
Fix output/README.md h1 header
dhimmel Nov 3, 2017
d4cb9b2
jinja2: fix author count template
dhimmel Nov 3, 2017
5bf0b34
Revert authors/author-order.ipynb
dhimmel Nov 3, 2017
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add initial stub files
  • Loading branch information
Casey Greene committed Oct 13, 2016
commit 9bd1c345cde3812ff6091f9b65d8cc6af8feb43b
2 changes: 2 additions & 0 deletions build.sh
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pandoc -f markdown -o review.pdf sections/*.md