release 0.16.0

Author: Gerit Wagner

.github/workflows/tests.yml

@@ -71,18 +71,10 @@ jobs:
           python-version: ${{ matrix.python-version }}
           enable-cache: true
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version-file: "pyproject.toml"
-
-      - name: List files after clone
-        run: find . -type f
-
       - name: Install dependencies with uv
         run: |
           uv sync --all-extras --dev
-          colrev install --uv ${{ env.COLREV_PACKAGES }}
+          uv run colrev install --uv ${{ env.COLREV_PACKAGES }}
 
       - name: Setup git
         run: |
@@ -110,15 +102,10 @@ jobs:
           python-version: ${{ matrix.python-version }}
           enable-cache: true
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version-file: "pyproject.toml"
-
       - name: Install dependencies with uv
         run: |
           uv sync --all-extras --dev
-          colrev install --uv ${{ env.COLREV_PACKAGES }}
+          uv run colrev install --uv ${{ env.COLREV_PACKAGES }}
 
       - name: Setup git
         run: |
@@ -134,14 +121,14 @@ jobs:
     needs: test-minimal-deps
     strategy:
       matrix:
-        platform: [ubuntu-latest,  macos-latest, windows-latest]
+        platform: [ubuntu-latest, macos-latest, windows-latest]
         python-version: ['3.10', '3.11', '3.12']
     runs-on: ${{ matrix.platform }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 

.pre-commit-config.yaml

@@ -12,7 +12,7 @@ ci:
 
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
     -   id: trailing-whitespace
         exclude: bib$|txt$|ris$|enl$|xml$|extensions_index/
@@ -27,7 +27,7 @@ repos:
     -   id: name-tests-test
         exclude: "tests/data/package_init/"
 -   repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 25.1.0
+    rev: 26.1.0
     hooks:
       - id: black
         language_version: python3
@@ -37,32 +37,26 @@ repos:
     hooks:
     -   id: autoflake
 -   repo: https://github.com/PyCQA/flake8
-    rev: 7.2.0
+    rev: 7.3.0
     hooks:
     -   id: flake8
         additional_dependencies: [flake8-typing-imports==1.12.0]
         args: ['--max-line-length=110', '--extend-ignore=E203,TYP006']
         exclude: "tests/data/package_init/"
--   repo: https://github.com/asottile/reorder-python-imports
-    rev: v3.14.0
-    hooks:
-    -   id: reorder-python-imports
-        args: [--py3-plus]
-        exclude: "tests/data/package_init/search_source.py"
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.19.1
+    rev: v3.21.2
     hooks:
     -   id: pyupgrade
         args: [--py36-plus, --keep-runtime-typing]
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v1.15.0'
+    rev: 'v1.19.1'
     hooks:
     -   id: mypy
         args: [--disallow-untyped-defs, --disallow-incomplete-defs, --disallow-untyped-calls]
         additional_dependencies: [types-toml]
         exclude: "tests/data/package_init/"
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.11.6
+  rev: v0.14.14
   hooks:
     - id: ruff # runs faster than pylint
       args: [--fix, --exit-non-zero-on-fix]

CHANGELOG.md

@@ -17,6 +17,26 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0).
 ### Fixed
 -->
 
+## 0.16.0 - 2026-01-28
+
+### Added
+
+- tei-parser: add iter_paragraphs()
+- prescreen-cli (entrypoint1)
+
+### Changed
+
+- loader/bib: allow keys with :/+
+- Dependency update: search-query 0.14.1 and bib-dedupe 0.11.0
+- dblp: handle timeout gracefully
+- package --check: test whether colrev loads the package
+- search-api-feed: add ENTRYTYPE if missing
+- pdf-prep and unpaywall: handle pymupdf.FileDataError
+- package-manager: install packages individually
+- crossref: ignore NA/UNKNOWN in url generation
+- Dataset: lazy-load git-repo
+- github: export more fields
+
 ## 0.15.0 - 2025-10-24
 
 ### Added

CITATION.cff

@@ -8,9 +8,9 @@ authors:
   given-names: "Julian"
   orcid: "https://orcid.org/0000-0003-2682-8036"
 title: "CoLRev: An open-source environment for collaborative reviews"
-version: 0.14.0
+version: 0.16.0
 identifiers:
   - type: doi
     value: 10.5281/zenodo.7707481
-date-released: 2025-02-21
+date-released: 2026-01-28
 url: "https://github.com/CoLRev-Environment/colrev"

colrev/constants.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 """Constants, including filepaths, fields, entrytypes, colrev_status, etc."""
+
 # pylint: disable=too-few-public-methods
 # pylint: disable=colrev-missed-constant-usage
 import importlib.util

colrev/dataset.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python3
 """Dataset class providing functionality for data/records.bib and git repository."""
+
 from __future__ import annotations
 
 import os
@@ -31,6 +32,7 @@ def __init__(self, *, review_manager: colrev.review_manager.ReviewManager) -> No
 
     @cached_property
     def git_repo(self) -> GitRepo:
+        """Get the GitRepo object for the review_manager path"""
         return GitRepo(path=self.review_manager.path)
 
     def get_origin_state_dict(self, records_string: str = "") -> dict:

colrev/env/docker_manager.py

@@ -1,5 +1,6 @@
 #! /usr/bin/env python
 """Manages Docker"""
+
 from __future__ import annotations
 
 import typing

colrev/env/environment_manager.py

@@ -1,5 +1,6 @@
 #! /usr/bin/env python
 """Manages environment registry, services, and stauts"""
+
 from __future__ import annotations
 
 import json

colrev/env/grobid_service.py

@@ -1,5 +1,6 @@
 #! /usr/bin/env python
 """GROBID service to extract and annotate PDF contents."""
+
 from __future__ import annotations
 
 import logging

colrev/env/language_service.py

@@ -1,5 +1,6 @@
 #! /usr/bin/env python
 """Service to detect languages and handle language codes"""
+
 from __future__ import annotations
 
 import re