d80b2c9 | Daniel Himmelstein | 04 August 2018, 18:34:36 UTC | 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 | Daniel Himmelstein | 04 August 2018, 18:21:51 UTC | 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 | Daniel Himmelstein | 03 June 2018, 23:07:48 UTC | 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 | Daniel Himmelstein | 03 February 2018, 21:36:29 UTC | Variables: set ci_source.repo_owner / repo_name (#32) | 03 February 2018, 21:36:29 UTC |
7a4dd0f | Daniel Himmelstein | 17 January 2018, 20:35:11 UTC | Remove extra space between month and day (#30) | 17 January 2018, 20:35:11 UTC |
7ca386d | Daniel Himmelstein | 14 January 2018, 20:45:54 UTC | 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 | Daniel Himmelstein | 12 January 2018, 21:17:19 UTC | 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 | Daniel Himmelstein | 10 January 2018, 21:52:10 UTC | 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 | Daniel Himmelstein | 09 January 2018, 20:26:16 UTC | README: dev environment documentation (#23) | 09 January 2018, 20:26:16 UTC |
33ff367 | Daniel Himmelstein | 09 January 2018, 17:55:00 UTC | 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 | Daniel Himmelstein | 08 January 2018, 23:04:32 UTC | Improve arXiv published DOI warning (#17) | 08 January 2018, 23:04:32 UTC |
855c849 | Daniel Himmelstein | 29 November 2017, 19:02:15 UTC | Enable multiple --template-variables-path args (#19) Closes https://github.com/greenelab/manubot/issues/18 | 29 November 2017, 19:02:15 UTC |
367f0b5 | Daniel Himmelstein | 31 August 2017, 19:33:36 UTC | 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 | Daniel Himmelstein | 15 August 2017, 16:44:01 UTC | Doc: Improve README (#11) | 15 August 2017, 16:44:01 UTC |
33e512d | Daniel Himmelstein | 14 August 2017, 14:20:18 UTC | 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 | Daniel Himmelstein | 11 August 2017, 15:08:24 UTC | Log timezone and datetime.now (#8) Refs https://github.com/greenelab/manubot/issues/3 | 11 August 2017, 15:08:24 UTC |
1723a22 | Daniel Himmelstein | 10 August 2017, 19:52:53 UTC | Fix manual references bug (#7) Previousely, manual references were not getting used. | 10 August 2017, 19:52:53 UTC |
115fbbd | Daniel Himmelstein | 09 August 2017, 20:51:33 UTC | Newline at end of JSON files (#6) | 09 August 2017, 20:51:33 UTC |
bac27de | Daniel Himmelstein | 08 August 2017, 18:47:37 UTC | 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 | Daniel Himmelstein | 08 August 2017, 01:18:04 UTC | 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 | Daniel Himmelstein | 07 August 2017, 18:34:05 UTC | Remove typo text (#4) | 07 August 2017, 18:34:05 UTC |
ab4bb26 | Daniel Himmelstein | 07 August 2017, 16:26:23 UTC | Additional manuscript.py logging | 07 August 2017, 16:54:11 UTC |
c42092b | Daniel Himmelstein | 07 August 2017, 16:10:31 UTC | Test: add manuscript with template variables | 07 August 2017, 16:54:11 UTC |
dbacb45 | Daniel Himmelstein | 07 August 2017, 15:22:13 UTC | Rename test manuscripts | 07 August 2017, 16:54:11 UTC |
9636fe5 | Daniel Himmelstein | 04 August 2017, 21:25:24 UTC | Enable custom cache directory | 07 August 2017, 16:54:11 UTC |
f61d123 | Daniel Himmelstein | 04 August 2017, 19:08:17 UTC | Allow internal underscores in citation strings | 07 August 2017, 16:54:11 UTC |
4968bb8 | Daniel Himmelstein | 04 August 2017, 17:10:14 UTC | Improve metadata error logging Builds failing due to https://github.com/datacite/datacite/issues/187 | 07 August 2017, 16:54:11 UTC |
5542402 | Daniel Himmelstein | 04 August 2017, 15:48:23 UTC | 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 | Daniel Himmelstein | 03 August 2017, 17:51:39 UTC | 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 | Daniel Himmelstein | 02 August 2017, 19:05:41 UTC | DOI metadata: add shortDOI to citeproc | 07 August 2017, 16:54:11 UTC |
dade757 | Daniel Himmelstein | 02 August 2017, 18:43:50 UTC | Add citaiton-tags.tsv to example-manuscript | 07 August 2017, 16:54:11 UTC |
983241d | Daniel Himmelstein | 01 August 2017, 21:10:40 UTC | Enable requests-cache | 07 August 2017, 16:54:11 UTC |
6b1fbde | Daniel Himmelstein | 01 August 2017, 20:27:46 UTC | Test manubot command line script | 07 August 2017, 16:54:11 UTC |
b674c2f | Daniel Himmelstein | 01 August 2017, 20:26:39 UTC | Create manubot command line script | 07 August 2017, 16:54:11 UTC |
e3ab956 | Daniel Himmelstein | 30 July 2017, 20:34:02 UTC | Add pmid citation test | 07 August 2017, 16:54:11 UTC |
65d4237 | Daniel Himmelstein | 30 July 2017, 16:53:21 UTC | Travis CI: cache pip installs | 07 August 2017, 16:54:11 UTC |
bd8d1aa | Daniel Himmelstein | 30 July 2017, 00:58:04 UTC | 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 | Daniel Himmelstein | 30 July 2017, 00:45:44 UTC | Add manuscript citation functionality Refs https://github.com/greenelab/manubot-rootstock/issues/2 | 07 August 2017, 16:54:11 UTC |
ada2e23 | Daniel Himmelstein | 29 July 2017, 22:29:22 UTC | utilities.py: add get_citation_id function | 07 August 2017, 16:54:11 UTC |
9d0615f | Daniel Himmelstein | 29 July 2017, 21:59:02 UTC | Add gitignore | 07 August 2017, 16:54:11 UTC |
99306a8 | Daniel Himmelstein | 29 July 2017, 21:32:35 UTC | Remove metadata.get_doi_bibtex | 07 August 2017, 16:54:11 UTC |
78d7ece | Daniel Himmelstein | 29 July 2017, 21:14:07 UTC | Remove arxiv2bib dependency | 07 August 2017, 16:54:11 UTC |
ece9d00 | Daniel Himmelstein | 13 July 2017, 22:11:04 UTC | Fix package name | 13 July 2017, 22:11:04 UTC |
555a420 | Daniel Himmelstein | 13 July 2017, 19:39:24 UTC | Ensure DOI citeproc always has URL | 13 July 2017, 19:39:24 UTC |
b0da176 | Daniel Himmelstein | 29 June 2017, 15:45:49 UTC | Add metadata.py from the deep review From https://github.com/dhimmel/deep-review/commit/2d192d721f4584713f7e9ebf540203bef4fa7402 | 29 June 2017, 15:45:49 UTC |
54e11b7 | Daniel Himmelstein | 29 June 2017, 15:32:50 UTC | Configure Travis for CI | 29 June 2017, 15:34:23 UTC |
d1d2791 | Daniel Himmelstein | 29 June 2017, 15:32:29 UTC | Add setup.py | 29 June 2017, 15:32:29 UTC |
d898b56 | Daniel Himmelstein | 29 June 2017, 15:07:46 UTC | Initial commit | 29 June 2017, 15:07:46 UTC |