| 5e2eeeb | Daniel Himmelstein | 07 October 2018, 12:03:30 UTC | Prepare v0.2.0 release Merges https://github.com/greenelab/manubot/pull/57 | 07 October 2018, 12:03:30 UTC |
| 48d5bba | Daniel Himmelstein | 06 October 2018, 22:53:03 UTC | For pandoc markdown/plain format, use --wrap=none Merges https://github.com/greenelab/manubot/pull/58 * For pandoc markdown and plain formats, use --wrap=none * Update CSL style commit hash Includes block spacing from https://github.com/greenelab/manubot-rootstock/pull/134 * Move expected rendered refs to files * Update rendered refs with block changes * Travis: update pandoc to v2.3.1 Fixes HTML output discrepency in rendered reference test. Issue resulted from change to the HTML writer in Pandoc: https://github.com/jgm/pandoc/releases/tag/2.3.1 > Don’t add uri class to presumed autolinks | 06 October 2018, 22:53:03 UTC |
| 1148689 | Daniel Himmelstein | 24 September 2018, 01:27:22 UTC | Enable lazy imports by the CLI & clear __init__.py files (#56) Merges https://github.com/greenelab/manubot/pull/56 * Move code in __init__.py submodule files to util.py. Enables manubot CLI to be called without running these files and triggering the imports Creates slightly more aesthetic import statements such as `import manubot.cite.util` rather than `import manubot.cite.cite`. * Configure subcommand argparsers in command.py Submodules are now lazily imported, when using the manubot CLI. * Use string function specs for citeproc_retrievers Enables lazy import of citation_retreiver functions. * manubot.cite: expose citation_to_citeproc & standardize_citation Define __all__ in manubot.cite.__init__.py to silence flake8 warning as per https://stackoverflow.com/a/49266468/4651668. | 24 September 2018, 01:27:22 UTC |
| b46e16b | Daniel Himmelstein | 24 September 2018, 01:23:57 UTC | Add Meta Review citation to README Merges https://github.com/greenelab/manubot/pull/60 Refs https://github.com/greenelab/manubot/issues/59 | 24 September 2018, 01:23:57 UTC |
| 472a646 | Daniel Himmelstein | 23 August 2018, 22:23:01 UTC | README: add Goals & Acknowledgments section Merges https://github.com/greenelab/manubot/pull/55 | 23 August 2018, 22:23:01 UTC |
| 66a6efc | Daniel Himmelstein | 21 August 2018, 23:13:38 UTC | Merge GH54: module reorganization & move --log-level to subcommands Merges https://github.com/greenelab/manubot/pull/54 process module, cite_command submodule, --log-level to subparser | 21 August 2018, 23:13:38 UTC |
| bdafbfa | Daniel Himmelstein | 21 August 2018, 19:57:19 UTC | Remove whitespace that offended flake8 | 21 August 2018, 19:57:19 UTC |
| d13987e | Daniel Himmelstein | 21 August 2018, 19:56:14 UTC | Move process code to submodule | 21 August 2018, 19:56:14 UTC |
| e24607a | Daniel Himmelstein | 21 August 2018, 16:47:57 UTC | Create process_command.py & minimize imports when calling CLI | 21 August 2018, 16:47:57 UTC |
| 2915179 | Daniel Himmelstein | 21 August 2018, 14:24:44 UTC | Capitalization of manubot process help messages | 21 August 2018, 14:32:20 UTC |
| c4d0e43 | Daniel Himmelstein | 21 August 2018, 14:18:05 UTC | argparse: relocate --log-level to subparser Closes https://github.com/greenelab/manubot/issues/52 | 21 August 2018, 14:32:20 UTC |
| eac9795 | Daniel Himmelstein | 21 August 2018, 14:04:59 UTC | Move manubot cite command infrastructure to submodule | 21 August 2018, 14:32:20 UTC |
| be7bdf6 | Daniel Himmelstein | 21 August 2018, 14:31:42 UTC | Do not import certain non-builtin packages unless needed Merges https://github.com/greenelab/manubot/pull/53 * Do not import jsonref & jsonschema unless CSL pruning Reduces the chance of code failing due to missing these dependencies. * Move base62 import to single calling function | 21 August 2018, 14:31:42 UTC |
| a26454e | Daniel Himmelstein | 21 August 2018, 13:57:28 UTC | CLI: manubot cite --render option Merges https://github.com/greenelab/manubot/pull/51 Closes https://github.com/greenelab/manubot/issues/48 | 21 August 2018, 13:57:28 UTC |
| ff601c5 | Daniel Himmelstein | 16 August 2018, 15:21:41 UTC | Prune CSL Items to validate JSON schema Merges https://github.com/greenelab/manubot/pull/49 Closes https://github.com/greenelab/manubot/issues/47 * Prune CSL Items to validate against JSON schema * Travis: install package using pip * Update manubot cite help in README * DOI CSL retriever: use shortDOI for URL * arxiv citeproc: replace arxiv_id with number * arxiv citeproc: use int for date-parts | 16 August 2018, 15:21:41 UTC |
| fdafa3e | Daniel Himmelstein | 14 August 2018, 14:32:20 UTC | Test fidelity of README codeblocks with command ouput Merges https://github.com/greenelab/manubot/pull/50 | 14 August 2018, 14:32:20 UTC |
| 4c40387 | Daniel Himmelstein | 07 August 2018, 15:13:33 UTC | Retrieve PMIDs / PMCIDs for DOI references Merges https://github.com/greenelab/manubot/pull/46 Closes https://github.com/greenelab/manubot/issues/45 Add PubMed IDs (when available) to CSL for DOI citations | 07 August 2018, 15:13:33 UTC |
| 6f41e15 | Daniel Himmelstein | 07 August 2018, 14:47:01 UTC | Use subcommands & add manubot cite CLI Merges https://github.com/greenelab/manubot/pull/42 Closes https://github.com/greenelab/manubot/issues/37 ATTENTION Backwards incompatabile API change. The `manubot` command is now `manubot process`. A new `manubot cite` CLI has been added to generate CSL for the specified citations. * Switch manubot's argparse to use subcommands * Add `manubot cite`: CLI to output CSL for citations * Create command module with console_script entry point * Separate process code into module * Add `manubot --version` argument * DOC: add sub-command usage to README.md * Ignore .pytest_cache/ dicectory * Ignore flake8 line too long | 07 August 2018, 14:47:01 UTC |
| 286d634 | Daniel Himmelstein | 06 August 2018, 14:39:55 UTC | Travis CI deploy config: fix indent typo Merges https://github.com/greenelab/manubot/pull/44 | 06 August 2018, 14:39:55 UTC |
| 693fbb7 | Daniel Himmelstein | 05 August 2018, 15:20:29 UTC | Move citation code to manubot.cite module Merges https://github.com/greenelab/manubot/pull/41 Refs https://github.com/greenelab/manubot/issues/37 * Move citation code into manubot/cite * Update imports with cite submodule * Move each metadata resource to its own submodule * Move citeproc / CSL code to submodule * setup.py: use setuptools.find_packages * Unrelated flake8 change | 05 August 2018, 15:20:29 UTC |
| f8e04d8 | Daniel Himmelstein | 04 August 2018, 18:45:16 UTC | Update release instructions Merges https://github.com/greenelab/manubot/pull/40 | 04 August 2018, 18:45:16 UTC |
| 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 |
