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d80b2c9 Attempt to fix PyPI deploy password Merges https://github.com/greenelab/manubot/pull/39 Follows up on https://github.com/greenelab/manubot/pull/38 04 August 2018, 18:34:36 UTC
5e02e99 Configure manubot upload to PyPI Merges https://github.com/greenelab/manubot/pull/38 * setup.py: markdown long_description * Configure PyPI deployment using Travis CI * AppVeyor: add Python 3.7 64-bit build 04 August 2018, 18:21:51 UTC
f456155 Configure AppVeyor for Windows CI testing (#35) * Configure AppVeyor for Windows CI testing Used the following as references: https://github.com/ogrisel/python-appveyor-demo/blob/3e6eb8b2f41d0aeaf2cf69105c0cf5aa608b200f/appveyor.yml https://github.com/krlmlr/r-appveyor/issues/82 https://github.com/Tomnl/appveyor-py-test/blob/d17e632c16f7ba571349e2e589e8ac9d031d9596/appveyor.yml * Workaround: subprocess pathlib windows bug Closes https://github.com/greenelab/manubot/issues/34 Thanks Alexander Dunkel for reporting the issue. 03 June 2018, 23:07:48 UTC
2745659 Variables: set ci_source.repo_owner / repo_name (#32) 03 February 2018, 21:36:29 UTC
7a4dd0f Remove extra space between month and day (#30) 17 January 2018, 20:35:11 UTC
7ca386d Better error messages for citations.tsv (#28) Log an error if there are any missing values. Retry read_table with delim_whitespace=True, which should parse lines that are space (rather than tab) delimited. Build continues. Closes https://github.com/greenelab/manubot/issues/26 14 January 2018, 20:45:54 UTC
c041bea Citation regex: negative lookahead for word chars (#27) No longer extract most email addresses as citations. Closes https://github.com/greenelab/manubot/issues/25 12 January 2018, 21:17:19 UTC
b53f487 PubMed ID citation support (#24) Migrates the previous pmid citations functionality (from NCBI Citation Exporter) to pmcid. This is more accurate because the NCBI Citation Exporter only works for records in PubMed Central. pmid citations are now supported that use the NCBI E-Utilities. pubmed.py enables parsing the XML returned by from E-Utilities into JSON CSL metadata. Merges https://github.com/greenelab/manubot/issues/24 Closes https://github.com/greenelab/manubot/issues/21 Refs https://github.com/ncbi/citation-exporter/issues/3 10 January 2018, 21:52:10 UTC
a44c110 README: dev environment documentation (#23) 09 January 2018, 20:26:16 UTC
33ff367 Author affiliation numbering (#22) Enables frontmatters to use numbered author affiliations. Switch to using a list for author affiliations in metadata.yaml. Deprecate non-list affiliations and log a DeprecationWarning. Except unrelated test that was failing. 09 January 2018, 17:55:00 UTC
bf60dce Improve arXiv published DOI warning (#17) 08 January 2018, 23:04:32 UTC
855c849 Enable multiple --template-variables-path args (#19) Closes https://github.com/greenelab/manubot/issues/18 29 November 2017, 19:02:15 UTC
367f0b5 Ensure CSL type is always valid (#12) Use "entry" for invalid types. https://github.com/citation-style-language/schema/blob/4846e02f0a775a8272819204379a4f8d7f45c16c/csl-types.rnc#L5-L39 http://citeproc-js.readthedocs.io/en/latest/csl-json/markup.html 31 August 2017, 19:33:36 UTC
31e1f7b Doc: Improve README (#11) 15 August 2017, 16:44:01 UTC
33e512d Fix lookahead in citation string regex (#10) Prevents substrings of longer citation strings from shortcircuiting the regex match and substitution. Closes https://github.com/greenelab/manubot/issues/9 14 August 2017, 14:20:18 UTC
e040b9d Log timezone and datetime.now (#8) Refs https://github.com/greenelab/manubot/issues/3 11 August 2017, 15:08:24 UTC
1723a22 Fix manual references bug (#7) Previousely, manual references were not getting used. 10 August 2017, 19:52:53 UTC
115fbbd Newline at end of JSON files (#6) 09 August 2017, 20:51:33 UTC
bac27de DOI citeproc URL: always overwrite URL (#5) Always set the URL for a DOI using the DOI. Fixes https://travis-ci.org/greenelab/manubot/builds/262063044#L1509-L1520 08 August 2017, 18:47:37 UTC
507fc21 Re-enable test_citation_to_citeproc_doi_datacite Upstream issue resolved https://github.com/datacite/datacite/issues/187#issuecomment-320792057 08 August 2017, 01:18:04 UTC
0fa0163 Remove typo text (#4) 07 August 2017, 18:34:05 UTC
ab4bb26 Additional manuscript.py logging 07 August 2017, 16:54:11 UTC
c42092b Test: add manuscript with template variables 07 August 2017, 16:54:11 UTC
dbacb45 Rename test manuscripts 07 August 2017, 16:54:11 UTC
9636fe5 Enable custom cache directory 07 August 2017, 16:54:11 UTC
f61d123 Allow internal underscores in citation strings 07 August 2017, 16:54:11 UTC
4968bb8 Improve metadata error logging Builds failing due to https://github.com/datacite/datacite/issues/187 07 August 2017, 16:54:11 UTC
5542402 Process empty manuscripts / zero citations Add test for a manuscript with zero files (missing content directory). Closes https://github.com/greenelab/manubot-rootstock/issues/47 07 August 2017, 16:54:11 UTC
901d9ba Enable user-provided template variables Provide JSON variables for jinja2 from either a path or URL. Add logging for jinja2 template variables in the manuscript that are undefined. 07 August 2017, 16:54:11 UTC
6bb78e0 DOI metadata: add shortDOI to citeproc 07 August 2017, 16:54:11 UTC
dade757 Add citaiton-tags.tsv to example-manuscript 07 August 2017, 16:54:11 UTC
983241d Enable requests-cache 07 August 2017, 16:54:11 UTC
6b1fbde Test manubot command line script 07 August 2017, 16:54:11 UTC
b674c2f Create manubot command line script 07 August 2017, 16:54:11 UTC
e3ab956 Add pmid citation test 07 August 2017, 16:54:11 UTC
65d4237 Travis CI: cache pip installs 07 August 2017, 16:54:11 UTC
bd8d1aa Remove requests-cache due to Travis CI error See https://travis-ci.org/greenelab/manubot/builds/258991246#L556 ``` error: The 'requests' distribution was not found and is required by manubot ``` 07 August 2017, 16:54:11 UTC
cecb00c Add manuscript citation functionality Refs https://github.com/greenelab/manubot-rootstock/issues/2 07 August 2017, 16:54:11 UTC
ada2e23 utilities.py: add get_citation_id function 07 August 2017, 16:54:11 UTC
9d0615f Add gitignore 07 August 2017, 16:54:11 UTC
99306a8 Remove metadata.get_doi_bibtex 07 August 2017, 16:54:11 UTC
78d7ece Remove arxiv2bib dependency 07 August 2017, 16:54:11 UTC
ece9d00 Fix package name 13 July 2017, 22:11:04 UTC
555a420 Ensure DOI citeproc always has URL 13 July 2017, 19:39:24 UTC
b0da176 Add metadata.py from the deep review From https://github.com/dhimmel/deep-review/commit/2d192d721f4584713f7e9ebf540203bef4fa7402 29 June 2017, 15:45:49 UTC
54e11b7 Configure Travis for CI 29 June 2017, 15:34:23 UTC
d1d2791 Add setup.py 29 June 2017, 15:32:29 UTC
d898b56 Initial commit 29 June 2017, 15:07:46 UTC
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