Colrev

Fixed

- paper_md: export BibTeX file and replace keys containing `.` to prevent pandoc error

Changed

- SearchTypes: API, TOC, MD are added, PDFS is replaced by FILES.
- SearchTypes are explained in the docs.
- Package documentation is imported to docs.
- colrev.pdfs_dir and colrev.video_dir are integrated into colrev.files_dir.

0.10. - 2023-10-02

Added

- SearchSources: SYNERGY datasets, OpenAlex, ERIC, IEEEXplore, ArXiv
- JournalRankings: index, prep, and prescreen
- CoLRev shell via cli-repl (`colrev shell`)
- prep operation: pause and resume
- Dashboard overview of the sample and project status
- Extended tests, updated documentation (especially for extension development)
- GitHub workflows to update dependencies (poetry update)
- Ruff linter

Changed

- Load: ris/csv/... files are loaded directly (without creating intermediate BibTeX file)
- Introduced namespaced fields (e.g., `colrev.pubmed.pubmedid` instead of `pubmedid`)
- Extracted quality checks to separate Quality Model
- Docs: instructions for development setup
- Code quality improvements (codacy)

Removed

- colrev-asreview: extracted to separate package
- watchdog-based service

Changed

- Introduced namespaced fields (e.g., `colrev.pubmed.pubmedid` instead of `pubmedid`).

Changed

- Updated colrev-asreview dependency (PyPI instead of GitHub)

Changed

- Integrated `load` into `SearchSource`. Removed `load_conversion` endpoint: `settings.json`, `packages`, `interface` etc.

Added

- The `quality_model` was created to check for quality defects
- The `auto_upgrade` flag allows users to enable/disable automated upgrades
- All-contributors bot to acknowledge contributions to CoLRev
- Implemented OpenLibrary as a SearchSource
- Pylint check for direct assignment of colrev_status
- Test battery for built-in SearchSources (heuristics, load, prep)
- Backward-search comparison with OpenCitations data

Changed

- Refactored `language_service`
- Refactored the tests (`conftest.py` now provides the `base_repo_review_manager` fixture)
- Changed pdf-hash (pdf to image) from poppler to mupdf for cross-platform compatibility (`cpid1` -> `cpid2`)
- Local settings changed from yaml to json
- Quality defects (colrev_masterdata_provenance notes) change
- The `colrev.global_ids_consistency_check` prep-endpoint is removed (integrated into the quality model)
- Individual quality checks can be disabled through the `prep/defects_to_ignore` settings
- Update the Github action workflows in CoLRev repositories

Removed

- `timeout-decorator` dependency (for better compatibility with MacOS)
- Docker image `pdf-hash-service` (replaced by mupdf)
- Redundant fields for the backward search are removed (`cited_by_file` and `cited_by_id`)

Fixed

- Documentation: typos and inconsistencies
- Codacy issues and refactored complex files [1](https://app.codacy.com/gh/CoLRev-Environment/colrev/dashboard)
- Windows paths in `iter_commit` (git history)