Colrev

Added

- Add linter `colrev_records_variable_naming_convention`
- Test coverage increased from 71% to 80%

Changed

- Split `records`, `dataset`, created `records` package.
- Extracted `process` as a separate package.
- Implemented loaders as a separate package, created a standard interface. SearchSources now create the specific mapping of IDs, entrytypes and fields.
- Moved field standardization from `load` to SearchSources.
- Extended use of constants
- SearchSourceInterface: renamed `run_search` to `search`, prefer `prep_link_md` over `get_masterdata`
- Renamed and refactored `GeneralOriginFeed` to `SearchAPIFeed`
- Pass record objects instead of dicts (in `local_index` in particular)
- Replaced unnecessary keyword arguments by positional arguments
- Moved `zotero_translation_service` to `bibliography_export` package
- Consolidated code for reference parsing in `tei_parser`
- Upgraded Grobid to 0.8.0

Removed

- Removed dead code
- Dropped `INCONSISTENT_WITH_DOI_METADATA`
- `transitions` dependency

Fixed

- Do not require review_manager for `colrev env -i`
- Fixed `status_stats`, including special cases.
- Repository registration: resolve() and absolute() path

Added

- Separate PDF quality model ([268](https://github.com/CoLRev-Environment/colrev/pull/268))
- `download_from_website` pdf-get package
- Separate loader utilities for nbib, ris, bib
- SearchSources: SemanticScholar ([288](https://github.com/CoLRev-Environment/colrev/pull/288)), Arxiv ([#203](https://github.com/CoLRev-Environment/colrev/pull/203))
- Constants module for Fields, ENTRYTYPES, etc.
- CEP003 for SearchSources
- New default dedupe package based on [bib-dedupe](https://github.com/CoLRev-Environment/bib-dedupe)
- Colrev pandas for Jupyter notebooks
- GitHub actions: pip-install test, make documentation

Changed

- Integrated `colrev.resolve_crossrefs` into `load_utils_bib.py`
- Defect codes can be ignored based on the `IGNORE:` prefix ([269](https://github.com/CoLRev-Environment/colrev/pull/269))
- Documentation for setup (VM, MacOS, WSL)
- Revised interfaces for SearchSources
- Integrated: pdf_dir + video_dir > files_dir
- poetry extras
- Backward search: export of parameters and expected sample sizes
- Replace thefuzz witz rapidfuzz

Removed

- Package based on dedupe-io, including incompatible dependencies
- Crossref resolution package (integrated in bib-loader)

Fixed

- Removed unstable test case

Changed

- GitHub actions for CoLRev updates now install with Poetry because the fixed dependencies are more stable compared to pip installation

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