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Revision Author Date Message Commit Date
2a99f4a process command: make parent directories Merges Closes Make any missing parent directories for the --output-directory and --cache-directory arguments of `manubot process`. 04 June 2019, 15:58 UTC
1da2ecf Python 3.7 on Travis & fix YAMLLoadWarning Merges Travis CI: test on Python 3.7 Use yaml.safe_load to prevent YAMLLoadWarning Refs 04 June 2019, 15:38 UTC
f220999 Internal citation nomenclature & design refactor Merges Refs Do not include @ as part of citation This behavior seems most consistent with Pandoc and CSL behavior. @ is used to signify a citation, but should not be part of the actual citation identifier. Improve citation nomenclature. Rename columns of citation_df to: - manuscript_id: citation ids extracted from the manuscript content files. - detagged_id: manuscript_id but with tag citations dereferenced - standard_id: detagged_id standardized - short_id: standard_id hashed to create a short base 03 June 2019, 21:50 UTC
351f4ba use package_data not MANIFEST to include data files Merges Refs Follows up on * Use package_data rather than Hat tip: Anthony Schmieder * Fix manubot.cite.tests.test_web_query failure Title on website has changed to "Meet the Robin Hood of Science, Alexandra Elbakyan" 23 May 2019, 14:16 UTC
37a9c69 Allow multiple manual-reference files of many formats Merges Closes Support multiple manual reference files, including files of any format that is supported by `pandoc-citeproc --bib2json`. Support specifying standard citation ids by the CSL `id` field, the non-standard-for-CSL-JSON `standard_citation` field (previous method, now deprecated), and the `note` field. Support for parsing key-value pairs from CSL notes. Notes are now used to log details from the citation-by-identifier process. When CSL ids do not specify a source, a raw citation is now assumed for greater compatibility with existing manual reference files that do not conform to manubot's standard citation identifier syntax. 17 May 2019, 18:37 UTC
6b92c18 Update meta-review citation in README 17 May 2019, 14:31 UTC
46bfed2 Tests: update pandoc version & expected output Merges Update expected test_cite_command_render_stdout output. arxiv citation now includes a DOI and pandoc upgrade introduces changes. CI: update pandoc version to 2.7.2 08 May 2019, 13:51 UTC
a2eb7d8 Create pandoc submodule Merges Move get_pandoc_info to manubot.pandoc.util. Use packaging.version.parse to parse pandoc version string 29 March 2019, 15:15 UTC
81394c0 Fix Travis PyPI deployment fail PyPI deployment failed with the following error in the Travis log ``` HTTPError: 403 Client Error: Invalid or non-existent authentication information. for url: ``` ``` Could not restore untracked files from stash entry PyPI upload failed. failed to deploy ``` Regenerated encyrpted password using: ``` travis encrypt --store-repo manubot/manubot --com --add deploy.password XXXXXXXXXXXX ``` See 12 February 2019, 03:09 UTC
fc67139 Prepare v0.2.3 release Merges * Prepare v0.2.3 release Travis CI: update encrypted PyPI deploy password * Fix test_citation_to_citeproc_pmc and test_citation_to_citeproc_pubmed_1 PubMed XML response changed values 12 February 2019, 00:03 UTC
4505db3 Support shortDOI citation Merges Closes Cite like @doi:10/98p * Create function to expand shortDOI: manubot.cite.doi.expand_short_doi. standardize_citation calls this function to expand shortDOIs to regular DOIs, such that standardized citations should never be short unless the shortDOI was invalid. * Restructure DOI inspection to differentiate between regular and short DOIs. * Error handling for non-existent shortDOIs. Use existing error handling rather than introducing error handling into the standardize_citation mapping stage. * Cache cite.util.standardize_citation Prevents standardize_citation from logging the same error twice if called multiple times. Also can save time if the same citation is referenced many times. 05 February 2019, 21:22 UTC
1b3ac66 Relocate repo to manubot/manubot Merges Relocates repo from to 02 February 2019, 21:32 UTC
3b3b2f3 Switch pandas.read_table to read_csv Merges read_table deprecated as of pandas v0.24 31 January 2019, 17:47 UTC
719a369 Allow null authors in metadata.yaml Merges Previously, the following metadata.yaml would cause the following exception: ```yaml title: "Title" lang: en-US author_info: ``` ```python-traceback File "manubot/process/", line 199, in get_metadata_and_variables metadata['author-meta'] = [author['name'] for author in authors] TypeError: 'NoneType' object is not iterable ``` Instead, we should treat null authors field as an empty array/list. 04 January 2019, 21:26 UTC
552dd99 translation-server queries: force single result Merges translation-server web query: specify single=1 to use only translators that return a single result. Currently, this disables the DOI web translator. Refs Remove child notes in Zotero data. Keep only first item of a Zotero data list (JSON array). See _passthrough_zotero_data. Refs Improve export_as_csl error handling. When an error status code is returned, provide a more specific exception rather than JSON parsing failed. translation-server test coverage improvements: * test that web_query returns single result * test ISBN which previously failed due to containing child notes * test_zotero: test all ID types for /search * get_url_citeproc_zotero: test manubot & GitHub URLs 31 December 2018, 12:49 UTC
dae5703 Prepare version 0.2.2 release Merges * v0.2.2 release notes * Do not skip wikidata author ordering test since Manubot's translation-server is now updated to include the fix from Co-Authored-By: Daniel Himmelstein <> Co-Authored-By: Anthony Gitter <> 17 December 2018, 21:54 UTC
15eae64 Reorganize and clean up tests Merges Move tests into package directory to locate tests closer to the code they're testing in the project's directory tree. Split test modules to correspond one-to-one to source code modules. Add to test directories to allow test modules with the same name. Travis CI: call pytest, not py.test, on its own line. Update pandoc to 2.5 on Travis. Fix NCBI E-Utilities too many requests error using ratelimiter. test_cite_command_render_stdout: skip test if Pandoc is outdated. Update expected output for Pandoc 2.5 & replace DataCite doi because DOI Content Negotiation for DataCite DOIs is often down. AppVeyor CI. Show why pytest tests are skipped. Update chocolatey pandoc path and version pandoc install 17 December 2018, 18:32 UTC
26a6fbd Enable wikidata citations using translation-server Merges Closes Supersedes Adds support for `wikidata` citations such as `wikidata:Q50051684`. 12 December 2018, 23:25 UTC
36bf2ce cite.zotero: query translation-server for URL & ISBN metadata Merges Closes Refs Queries Manubot's translation-server instance at Setup information for this instance is available at Adds functions in manubot.cite.zotero to query the web, search, and export endpoints of a translation-server. Adds tests in covering this functionality. translation-server queries are now used for USL and ISBN citation metadata retrieval. These methods now use fallbacks, such that metadata is first collected via translation-server, but if that fails, then the preexisting methods are used. 10 December 2018, 17:05 UTC
77dabbb Update .gitignore with system files Merges Adopt system specific files from With the addition of .vscode for Visual Studio Code. 07 December 2018, 15:42 UTC
7440a8b API calls: set User-Agent header & E-Utility rate limits Merges Add platform information and Manubot contact email to User-Agent header used for API calls. On my system, get_manubot_user_agent returned: manubot/0.2.1 (Linux; Python/3.6) <> Move get_manubot_user_agent to util module. Rate limit NCBI E-Utilities API calls to 3 per second to address status code 429. Adds dependency on ratelimiter package: - - 07 December 2018, 15:15 UTC
3318c8f Support ISBN citations Merges Closes Retrieves ISBN metadata using Citoid. Metadata via isbnlib implemented but not used by default. ISBN-10 identifiers are converted to ISBN-13 as part of citation standardization. 19 November 2018, 18:20 UTC
afa55f8 Prepare v0.2.1 release with citation improvements Merges 15 November 2018, 18:56 UTC
53bb682 get_pmc_citeproc: switch to Literature Citation Exporter Merges NCBI Citation Exporter was taken offline without notice: New resource is available at Improve citation error messages 15 November 2018, 18:50 UTC
f9673fe Improve citation error messages Merges Closes * Improve citation string error message * Add citation validation checks in is_valid_citation_string * Detect source capitalization issues * is_valid_citation_string enable allow_* options to properly distinguish the validation needs of manuscript citation strings versus cite command citation strings. * manubot cite CLI: validate citations & do not attempt CSL if invalid citation * Reformat process.util.get_citation_df error message * Improve process.manuscript.get_citation_strings docstring 13 November 2018, 18:35 UTC
a008126 cite command error handling Merges Do not exit program when a citation_to_citeproc lookup fails. Instead set a nonzero exit code, but proceed with passing citaitons. Error messages are logged, full stacktrace is logged at INFO level. 24 October 2018, 19:08 UTC
25a8faa Support raw citations Merges Closes * Support raw citations where users must provide CSL JSON * Pass manual references through citeproc_passthrough with CSL JSON Schema pruning * Rename since it tests manubot.process only * Test raw citations in example manuscript 23 October 2018, 19:04 UTC
4e6a0f6 CSL JSON pruning: support minItems & recursion Merges Fixes empty issued date-parts bug reported in the following issues: - Closes - Closes - Fixes Recursively remove errors in remove_jsonschema_errors. Combined with a CSL JSON schema that specifies minItems for date-parts, this change fixes the above issues. See for the CSL JSON schema changes that are intended to be present in the CSL schema loaded by this package. Tests removal of empty date-parts for issued object. 23 October 2018, 17:06 UTC
67d3496 Allow integer months in PMID citations (#72) * Add test case for PMID date error * Allow integer months in PMID citations * Only assert correct date in numeric month test 12 October 2018, 14:39 UTC
9d97ec3 Add manubot cite terminal recording Merges Closes Add manubot cite terminal recording Set speed to 2x on asciinema and GIF 08 October 2018, 14:33 UTC
5e2eeeb Prepare v0.2.0 release Merges 07 October 2018, 12:03 UTC
48d5bba For pandoc markdown/plain format, use --wrap=none Merges * For pandoc markdown and plain formats, use --wrap=none * Update CSL style commit hash Includes block spacing from * 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: > Don’t add uri class to presumed autolinks 06 October 2018, 22:53 UTC
1148689 Enable lazy imports by the CLI & clear files (#56) Merges * Move code in submodule files to 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 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 to silence flake8 warning as per 24 September 2018, 01:27 UTC
b46e16b Add Meta Review citation to README Merges Refs 24 September 2018, 01:23 UTC
472a646 README: add Goals & Acknowledgments section Merges 23 August 2018, 22:23 UTC
66a6efc Merge GH54: module reorganization & move --log-level to subcommands Merges process module, cite_command submodule, --log-level to subparser 21 August 2018, 23:13 UTC
bdafbfa Remove whitespace that offended flake8 21 August 2018, 19:57 UTC
d13987e Move process code to submodule 21 August 2018, 19:56 UTC
e24607a Create & minimize imports when calling CLI 21 August 2018, 16:47 UTC
2915179 Capitalization of manubot process help messages 21 August 2018, 14:32 UTC
c4d0e43 argparse: relocate --log-level to subparser Closes 21 August 2018, 14:32 UTC
eac9795 Move manubot cite command infrastructure to submodule 21 August 2018, 14:32 UTC
be7bdf6 Do not import certain non-builtin packages unless needed Merges * 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 UTC
a26454e CLI: manubot cite --render option Merges Closes 21 August 2018, 13:57 UTC
ff601c5 Prune CSL Items to validate JSON schema Merges Closes * 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 UTC
fdafa3e Test fidelity of README codeblocks with command ouput Merges 14 August 2018, 14:32 UTC
4c40387 Retrieve PMIDs / PMCIDs for DOI references Merges Closes Add PubMed IDs (when available) to CSL for DOI citations 07 August 2018, 15:13 UTC
6f41e15 Use subcommands & add manubot cite CLI Merges Closes 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 * Ignore .pytest_cache/ dicectory * Ignore flake8 line too long 07 August 2018, 14:47 UTC
286d634 Travis CI deploy config: fix indent typo Merges 06 August 2018, 14:39 UTC
693fbb7 Move citation code to manubot.cite module Merges Refs * 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 * use setuptools.find_packages * Unrelated flake8 change 05 August 2018, 15:20 UTC
f8e04d8 Update release instructions Merges 04 August 2018, 18:45 UTC
d80b2c9 Attempt to fix PyPI deploy password Merges Follows up on 04 August 2018, 18:34 UTC
5e02e99 Configure manubot upload to PyPI Merges * markdown long_description * Configure PyPI deployment using Travis CI * AppVeyor: add Python 3.7 64-bit build 04 August 2018, 18:21 UTC
f456155 Configure AppVeyor for Windows CI testing (#35) * Configure AppVeyor for Windows CI testing Used the following as references: * Workaround: subprocess pathlib windows bug Closes Thanks Alexander Dunkel for reporting the issue. 03 June 2018, 23:07 UTC
2745659 Variables: set ci_source.repo_owner / repo_name (#32) 03 February 2018, 21:36 UTC
7a4dd0f Remove extra space between month and day (#30) 17 January 2018, 20:35 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 14 January 2018, 20:45 UTC
c041bea Citation regex: negative lookahead for word chars (#27) No longer extract most email addresses as citations. Closes 12 January 2018, 21:17 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. enables parsing the XML returned by from E-Utilities into JSON CSL metadata. Merges Closes Refs 10 January 2018, 21:52 UTC
a44c110 README: dev environment documentation (#23) 09 January 2018, 20:26 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 UTC
bf60dce Improve arXiv published DOI warning (#17) 08 January 2018, 23:04 UTC
855c849 Enable multiple --template-variables-path args (#19) Closes 29 November 2017, 19:02 UTC
367f0b5 Ensure CSL type is always valid (#12) Use "entry" for invalid types. 31 August 2017, 19:33 UTC
31e1f7b Doc: Improve README (#11) 15 August 2017, 16:44 UTC
33e512d Fix lookahead in citation string regex (#10) Prevents substrings of longer citation strings from shortcircuiting the regex match and substitution. Closes 14 August 2017, 14:20 UTC
e040b9d Log timezone and (#8) Refs 11 August 2017, 15:08 UTC
1723a22 Fix manual references bug (#7) Previousely, manual references were not getting used. 10 August 2017, 19:52 UTC
115fbbd Newline at end of JSON files (#6) 09 August 2017, 20:51 UTC
bac27de DOI citeproc URL: always overwrite URL (#5) Always set the URL for a DOI using the DOI. Fixes 08 August 2017, 18:47 UTC
507fc21 Re-enable test_citation_to_citeproc_doi_datacite Upstream issue resolved 08 August 2017, 01:18 UTC
0fa0163 Remove typo text (#4) 07 August 2017, 18:34 UTC
ab4bb26 Additional logging 07 August 2017, 16:54 UTC
c42092b Test: add manuscript with template variables 07 August 2017, 16:54 UTC
dbacb45 Rename test manuscripts 07 August 2017, 16:54 UTC
9636fe5 Enable custom cache directory 07 August 2017, 16:54 UTC
f61d123 Allow internal underscores in citation strings 07 August 2017, 16:54 UTC
4968bb8 Improve metadata error logging Builds failing due to 07 August 2017, 16:54 UTC
5542402 Process empty manuscripts / zero citations Add test for a manuscript with zero files (missing content directory). Closes 07 August 2017, 16:54 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 UTC
6bb78e0 DOI metadata: add shortDOI to citeproc 07 August 2017, 16:54 UTC
dade757 Add citaiton-tags.tsv to example-manuscript 07 August 2017, 16:54 UTC
983241d Enable requests-cache 07 August 2017, 16:54 UTC
6b1fbde Test manubot command line script 07 August 2017, 16:54 UTC
b674c2f Create manubot command line script 07 August 2017, 16:54 UTC
e3ab956 Add pmid citation test 07 August 2017, 16:54 UTC
65d4237 Travis CI: cache pip installs 07 August 2017, 16:54 UTC
bd8d1aa Remove requests-cache due to Travis CI error See ``` error: The 'requests' distribution was not found and is required by manubot ``` 07 August 2017, 16:54 UTC
cecb00c Add manuscript citation functionality Refs 07 August 2017, 16:54 UTC
ada2e23 add get_citation_id function 07 August 2017, 16:54 UTC
9d0615f Add gitignore 07 August 2017, 16:54 UTC
99306a8 Remove metadata.get_doi_bibtex 07 August 2017, 16:54 UTC
78d7ece Remove arxiv2bib dependency 07 August 2017, 16:54 UTC
ece9d00 Fix package name 13 July 2017, 22:11 UTC
555a420 Ensure DOI citeproc always has URL 13 July 2017, 19:39 UTC
b0da176 Add from the deep review From 29 June 2017, 15:45 UTC
54e11b7 Configure Travis for CI 29 June 2017, 15:34 UTC
d1d2791 Add 29 June 2017, 15:32 UTC
d898b56 Initial commit 29 June 2017, 15:07 UTC
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