Manubot Versions Save

Commits

f62dd4c ai-revision: ModuleNotFoundError error message 6e6f6a5 drop py37, require pyrate-limiter <3

Commits

• f9abd4d pre-commit: replace checks with ruff
• 9d3edb8 lint with ruff & fix errors
• 57c3833 pre-commit autoupdate
• f6c1fcd test_get_doi_csl_item_zotero: changed author order
• d4242ff manubot ai-revision command
• b2e0bcf Fix broken link to docs (#361)
• ebf49f0 readme: fix CI badge

Code authors

• Anthony Gitter
• Daniel Himmelstein
• Milton Pividori

Commits

• 0533556 jinja2 keep_trailing_newline
• 4283d79 appveyor: reduce pytest to appveyor marked only (#351)
• 86a6903 test_webpage_command: remove appveyor mark
• 3c1f4a0 get_pubmed_csl_item: use retmode=xml (#355)
• e14df43 CSL schema: upgrade to v1.0.2 (#353)

Commits

• c6d02c8 pre-commit autoupdate
• fb39504 Skip citation processing for sec prefix (#334)
• 5fcee80 Use python=3.10 on conda developer environment.
• d919de2 Fix tests failing on main.
• 29dec5b isbnlib default timeout (#342)
• a2ba578 test_cite_pandoc_filter: updated date (#343)
• 3524f72 Swap first and last name in Citoid ISBN metadata (#345)
• da4161f GH actions: upgrade workflow dependencies
• ea096d3 CI: test on Python 3.11
• e2c5fd4 switch from raterlimiter to throttler
• 6df3ac8 pre-commit autoupdate
• 1729dae switch dependency: toml --> tomllib / tomli
• cbc0557 CI: revert max python version to 3.10
• a5b9acf CI: shorten job name to pytest
• e0a8c11 readme: remove Travis CI badge
• 455842d _request_eutils: throttler requires async
• 431daa1 use pyrate_limiter for rate limited requests (#347)
• 0809ff5 manuscript metadata: explicit date (#349)
• 43ef558 update bioregistry on 2022-11-12
• 35178e6 fix bioregistry test for gramene.growthstage:0007133
• 912aa0e Test on Python 3.11

Code authors

• Anthony Gitter
• Daniel Himmelstein
• Joshua Haase
• Matthew Turk
• xihh87

Commits

be8a96f Support metadata.manubot-randomize-author-order (#317) d5779de Use doi.org content negotiation only, fallback to resolved URL (#319) e2896f7 Drop Python 3.6 support, add Python 3.10 support (#318) 90925ee pre-commit: run pyupgrade --py37-plus (#321) 3551dec tool.black.target-version: remove py36 43de2af update bioregistry on 2022-03-02 (#324)

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)