Manubot

What's Changed

* Add command-line argument to skip adding the rootstock git remote by twrightsman in https://github.com/manubot/manubot/pull/292
* gh actions job_id: use GITHUB_RUN_ID by dhimmel in https://github.com/manubot/manubot/pull/300
* pandoc-manubot-cite link reference syntax with newline by dhimmel in https://github.com/manubot/manubot/pull/302
* Upgrade identifiers.org database on 2021-10-29 by dhimmel in https://github.com/manubot/manubot/pull/304
* CURIE support: switch to Bioregistry by dhimmel in https://github.com/manubot/manubot/pull/306
* get_doi_csl_item: try crosscite if datacite fails by dhimmel in https://github.com/manubot/manubot/pull/310
* get_doi_csl_item_negotiation: do not use partial by dhimmel in https://github.com/manubot/manubot/pull/312
* update bioregistry on 2022-01-08 by dhimmel in https://github.com/manubot/manubot/pull/311
* Prepare 0.5.2 release by dhimmel in https://github.com/manubot/manubot/pull/313

New Contributors

* twrightsman made their first contribution in https://github.com/manubot/manubot/pull/292

**Full Changelog**: https://github.com/manubot/manubot/compare/v0.5.1...v0.5.2

Commits
-------

- 0c2e5b2 switch default branch to main from master
- 3a6c41b fix exclusion of tests in wheel distribution (273)
- 96df839 move common pytest options to pyproject.toml
- 5b865c5 setup options: zip_safe = False
- 55c5e1e update rootstock default branch to main (275)
- 9d9c2e1 upgrade to pandoc 2.11.3.1 (276)
- 553090a Infer citekey prefixes (277)
- 3ff3000 cite requests: better error messages (279)
- 52aa09f Check pandoc-citeproc version only if required


Code authors
------------

- Daniel Himmelstein
- Sergey Lazarev

Commits
-------

- 6c40633 update CURIE export on 2020-12-05
- 980cc2e Use pre-commit hooks for formatting and linting (269)
- 53c69d8 package setup: use declarative config (268)
- 749f4a1 test_metadata.py: swap skip reasons
- 68556f6 manubot cite: remove --render & cslyaml support (267)
- aade9e1 Revise CSL Item notes added by Manubot (265)

Commits
-------

- 9a958c9 PR 261: cite filter options, bibliography-cache & YAML bibs
- d5227e6 test_cite_filter: do not use yaml_metadata_block for wrap
- 4c9e64b util flake8 lazy import type annotation
- 1b3edc7 pandoc-manubot-cite: improve options documentation
- 38b34f4 pandoc test_cite_filter: move options to YAML metadata
- 5540b1a test_citations_csl_serialization
- a78dcdc yaml.dump sort_keys=False to retain dict order
- 19e9f45 Citations.write_csl_items support for YAML
- 1c44271 disable manubot-bibliography-cache by default
- c6f1a3d manubot-pandoc-cite manubot-bibliography-cache
- c08e1a6 manubot.process.bibliography.load_bibliography docs
- 9858c0c note test_cite_pandoc_filter skipped on pandoc >= 2.11
- 4323275 do not append duplicate lines to a note
- daf56e6 manubot.cite.csl_item type annotations
- e61e86d ignore ratelimiter DeprecationWarning (259)
- 5d9e8e4 Support pandoc 2.11 (256)
- 406eed4 cite_filter.py: panflute<2, typing, doc.manubot (255)
- 01d69f0 More typing of manubot.cite modules (252)
- 7c03b4a Add typing to some manubot.cite modules (251)
- 1c764d0 Support and test on Python 3.9 (250)
- 0091846 get_url_csl_item_zotero: set missing URL (247)
- 1e807db Merge pull request 246 from agitter/update-test-output
- a50ecab black 20.8b1 formatting changes
- 568aa55 Fix failing cite filter text Update authors in Papernot et al. reference
- c543bd9 Fix oai logging (245)


Code authors
------------

- Anthony Gitter
- Daniel Himmelstein
- James

Contains enhancements and usability improvements to manubot cite.

Commits
-------

2c4cc8b Prepare 0.4.1 release
3d6d5d4 cite command: preserve order of input citekeys in output (241)
a57ccf0 Testing manuscript with missing CSL JSON fields (110)
217e514 cite command enhancements (238)
3bd4aab Fix inspection of CURIEs when namespaceEmbeddedInLui (237)

Includes backwards incompatable changes to the manubot.cite API.
Major enhancements to the flexibility of citation processing.

Commits
-------

- 12d4537 reduce travis and appveyor CI duties (232)
- 3196819 one-time reset of the CSL JSON Schema requests cache (235)
- 1c3c74b Update CSL JSON Schema processing & replace OrderedDicts (234)
- 2c5fb7a Update README badges
- 47b03e0 apply flexible class-based citation pipeline (225)
- a2c54c8 Adopt BSD-2-Clause-Patent license
- 20ba7e3 move linting, docs, and releases to github actions (228)
- f891508 Improve maintainability of cite command tests (227)
- 04cbe9f fix test_web_query_returns_single_result_pubmed_url
- 7055bcc Citation refactor: CiteKey & Handle classes, CURIE support (223)
- 4d3a97f actions: restore python-version functionality (224)
- 730527f style: ignore F541: f-string without any placeholders
- 7261220 cite.curie module for compact identifiers via identifiers.org (219)
- dc5ad40 relax test_unpaywall_from_csl_item_with_doi
- 890b768 webpage_command.py: fix bug in subprocess usage
- 9c33b7a metadata: convert author.funders to list (221)
- a4c826c get_continuous_integration_parameters: fix warning (215)
- b4a6238 subprocess calls: do not accidentally write to stdout (212)
- ea11343 CI: use r-lib/actions/setup-pandoc to install pandoc
- 10fa21b fix typo in cite.citeproc._remove_error warning message
- a022e71 manubot process: require --skip-citations (210)
- bc79746 Fix test_unpaywall_from_citekey
- e912856 DOI metadata: use DataCite Content Negotiation (206)
- 9a8c080 Fix test_get_arxiv_csl_item_oai: new OpenBioLink title
- 68ae7cf yamllint failing YAML files (205)
- e18fed8 Fix get_rootstock_commit on pull requests
- e88055f Update release instruction [skip ci]