Colrev

Changed

- CoLRev pdf IDs are now based on the mupdf library

Fixed

- Fix InvalidGitRepositoryError (raised upon status in empty directories)

Changed

- Update the Github action workflows in CoLRev repositories
- Add auto-upgrade flag to settings

Added

- Unit tests: increased test coverage to 70%, added Github actions matrix tests across OS and Python versions
- Completed OpenSSF Best Practices checks ([1](https://bestpractices.coreinfrastructure.org/de/projects/7148))
- Added forward and backward searches based on [OpenCitations](https://opencitations.net/)
- Moved documentation to [readthedocs](https://colrev.readthedocs.io/en/latest/) and revised documentation
- Added dependabot and pre-commit.ci: automated code and secrity checks
- Added support for Github actions, distinguishing packages that are supported in ci-environments (``ci_supported`` flag)
- Added Pubmed API searches and metadata preparation support
- Option to initialize and run CoLRev repositories without requiring Docker
- Overview video presented at ESMARConf2023 [1](https://www.youtube.com/watch?v=fuLpu8X1Mr0)
- CITATION.cff and Zenodo
- API-searches for the AIS eLibrary

Changed

- Numerous modifications based on the [user tests](https://github.com/CoLRev-Environment/colrev/issues/41)
- Replaced OpenSearch with sqlite
- SearchSource interface: ``run_search`` and ``add_package`` are now mandatory
- Documentation review, including detailed information on development status
- Consistent setup of Github actions (test, publish to PyPI)
- Built-in packages renamed from ``colrev_built_in`` to ``colrev``
- Data package ``manuscript``renamed to ``paper_md``
- Simplified upgrade operation and activated upgrades per default
- Extracted and refactored language-service

Fixed

- Several bugfixes

Changed

- Changed package prefix from ``colrev_built_in`` to ``colrev``

Added

- Add retrieve and pdfs as high-level operations
- Metadata preparation can add records to separate origin feeds
- Initial package manager functionality (registering packages and displaying them in the docs)
- Search: update of records and propagation of changes
- Several SearchSources (including SearchSource query validation)
- Revisions of CLI (verbose mode, user feedback)
- Colrev merge (reconciliation coding when merging git branches)
- dedupe --merge/--unmerge
- Integrated colrev pre-commit hooks
- PRISMA diagram (data endpoint)
- Obsidian (data endpoint)
- Preparation: not-in-toc exception/warning
- Setup of pytests

Changed

- Curated records are now explicitly identified through curation_IDs
- Revise colrev validate (commits, users, properties)
- Detailed advisor (using get_advice() for data endpoints)
- Performance improvements and simplification of status (cli)
- Moved correction functionality to SearchSources (refactored correction path)
- Preparation: simplified preparation rounds (default settings)
- Retrieve TEIs through local_index (if available) instead of recreating it
- Replace pathos by Threadpool
- Revise the documentation
- Revise and extend exceptions

Removed

- Remove persistent colrev-ids
- Remove realtime review
- Dependencies ansiwrap and p-tqdm

Fixed

- **kwargs calls in ReviewManager
- Indexing of non-curated records
- Address special cases in dedupe (active learning)