release 0.16.0

Gerit Wagner · Gerit Wagner · commit 35fea3c73776 · 2026-01-28T14:26:48.000+01:00
diff --git a/CHANGELOG.md b/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
diff --git a/CITATION.cff b/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"
diff --git a/colrev/dataset.py b/colrev/dataset.py
@@ -31,6 +31,7 @@ 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:
diff --git a/colrev/env/tei_parser.py b/colrev/env/tei_parser.py
@@ -641,7 +641,7 @@ def is_in_excluded_section(p_elem: Element) -> bool:
                 continue
 
             # Collect all text inside <p>, including nested tags like <ref>, <hi>, etc.
-            text_chunks = [t for t in p.itertext()]
+            text_chunks = list(p.itertext())
             paragraph_text = " ".join(text_chunks)
             paragraph_text = " ".join(paragraph_text.split())  # normalize whitespace
 
diff --git a/colrev/ops/dedupe.py b/colrev/ops/dedupe.py
@@ -28,6 +28,7 @@ def same_source_merge(
     main_record: colrev.record.record.Record,
     dupe_record: colrev.record.record.Record,
 ) -> bool:
+    """Same source merge check"""
     main_rec_sources = [x.split("/")[0] for x in main_record.data[Fields.ORIGIN]]
     dupe_rec_sources = [x.split("/")[0] for x in dupe_record.data[Fields.ORIGIN]]
     same_sources = set(main_rec_sources).intersection(set(dupe_rec_sources))
diff --git a/colrev/ops/pdf_get.py b/colrev/ops/pdf_get.py
@@ -31,6 +31,7 @@ def relink_pdfs_in_source(
     pdf_dir: Path,
     logger: logging.Logger,
 ) -> None:
+    """Relink PDFs in the given source based on CPIDs"""
 
     # pylint: disable=too-many-locals
 
diff --git a/colrev/ops/upgrade.py b/colrev/ops/upgrade.py
@@ -215,6 +215,12 @@ def main(self) -> None:
                 "script": self._migrate_0_15_0,
                 "released": True,
             },
+            {
+                "version": CoLRevVersion("0.15.0"),
+                "target_version": CoLRevVersion("0.16.0"),
+                "script": self._migrate_0_16_0,
+                "released": True,
+            },
         ]
         self.review_manager.logger.info(
             "Colrev version installed:           %s", installed_colrev_version
@@ -928,6 +934,9 @@ def _migrate_0_15_0(self) -> bool:
 
         return self.repo.is_dirty()
 
+    def _migrate_0_16_0(self) -> bool:
+        return False
+
 
 # Note: we can ask users to make decisions (when defaults are not clear)
 # via input() or simply cancel the process (raise a CoLrevException)
diff --git a/docs/source/manual/packages/colrev.colrev_cli_prescreen.rst b/docs/source/manual/packages/colrev.colrev_cli_prescreen.rst
@@ -55,3 +55,12 @@ prescreen
 ---------
 
 Interactively prescreen records using the CLI.
+
+Prescreening BibTex
+-------------------
+
+The following cli tool supports pre-screening outside of CoLRev projects:
+
+.. code-block:: sh
+
+   colrev-cli-prescreen
diff --git a/docs/source/manual/packages/colrev.ebsco_host.rst b/docs/source/manual/packages/colrev.ebsco_host.rst
@@ -57,12 +57,12 @@ search
 DB search
 ^^^^^^^^^
 
-Export is available after adding citations to a folder (\ `1 <https://connect.ebsco.com/s/article/How-to-Use-the-Export-Manager-in-EBSCOhost?language=en_US>`_\ ).
+Export is available after adding citations to a folder (\ `1 <https://connect.ebsco.com/s/article/How-to-Use-the-Export-Manager?language=en_US>`_\ ).
 Download search results and store in ``data/search/`` directory. API-access not yet available.
 
 Links
 -----
 
 
-* `EBSCOHost <https://www.ebsco.com/products/research-databases/ebscohost-research-platform>`_
+* `EBSCOHost <https://search.ebscohost.com/>`_
 * `EBSCOHost APIs <https://developer.ebsco.com/getting-started/available-apis>`_
diff --git a/docs/source/manual/packages/colrev.genai.rst b/docs/source/manual/packages/colrev.genai.rst
@@ -80,9 +80,9 @@ To set the open-AI key, run
 
    export OPENAI_API_KEY="your_api_key_here"
 
-For a permanent configuration, append the ``export`` statement to your shell
-profile (for example ``~/.bashrc``) and reload it using
-``source ~/.bashrc`` so the key is available in future sessions.
+To keep the key available in future shell sessions, append the ``export`` line
+to your shell profile (for example ``~/.bashrc``\ ) and reload it with
+``source ~/.bashrc``.
 
 prescreen
 ---------
diff --git a/docs/source/manual/packages/colrev.github.rst b/docs/source/manual/packages/colrev.github.rst
@@ -66,7 +66,7 @@ search
 API search
 ^^^^^^^^^^
 
-ℹ️ Restriction: API searches require an GitHub access token to retrieve all the relevant meta data.
+ℹ️ Restriction: API searches require an GitHub access token to retrieve all the relevant meta data. Store the token in the ``GITHUB_API_TOKEN`` environment variable (for example with ``export GITHUB_API_TOKEN="<your-token>"``\ ). If it is not set you will be prompted to enter the token and it will be stored for the current session.
 
 In your GitHub account, a classic `personal access tokens <https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens>`_ can be created. It is not necessary to select any scopes.
 
diff --git a/docs/source/manual/packages/colrev.ieee.rst b/docs/source/manual/packages/colrev.ieee.rst
@@ -74,7 +74,7 @@ Data from the IEEE database can be retrieved with the URL from the `https://www.
 
 All configured metadata fields, the abstract and the document text are queried.
 
-It is not necessary to pass an API key as a parameter here. In order to keep the key secret, you will be prompted to enter it through user input if it is not already stored in the settings. The api key can be requested via the `IEEE Xplore API Portal <https://developer.ieee.org/member/register>`_.
+It is not necessary to pass an API key as a parameter here. In order to keep the key secret, set it in the ``IEEE_API_KEY`` environment variable (for example with ``export IEEE_API_KEY="<your-api-key>"``\ ). The api key can be requested via the `IEEE Xplore API Portal <https://developer.ieee.org/member/register>`_. If the variable is not defined, colrev will prompt for the key and store it for the current session.
 
 Specific parameters can also be searched for, such as issn, isbn, doi, article_number, author, publication_year. For each of these, append "parameter=value" to the URL.
 
diff --git a/docs/source/manual/packages/colrev.osf.rst b/docs/source/manual/packages/colrev.osf.rst
@@ -69,7 +69,7 @@ Data from the OSF open platform can be retrieved with the URL from the `https://
 
 The retrieved data, including detailed project metadata and resources, is processed and made available for further actions within CoLRev, such as analysis or reporting.
 
-It is not necessary to pass an API key as a parameter here. In order to keep the key secret, you will be prompted to enter it through user input if it is not already stored in the settings. The api key can be requested via the `OSF settings page <https://accounts.osf.io/login?service=https://osf.io/settings/tokens/>`_.
+It is not necessary to pass an API key as a parameter here. In order to keep the key secret, set it in the ``OSF_API_KEY`` environment variable (for example with ``export OSF_API_KEY="<your-api-key>"``\ ). The api key can be requested via the `OSF settings page <https://accounts.osf.io/login?service=https://osf.io/settings/tokens/>`_. If the variable is not defined, colrev will prompt for the key and store it for the current session.
 
 The search can be filtered by changing the filter parameter to one of the following parameters: title, id, type, category, year, description, tags, data_created. For each of these, change "filter[parameter]=value" in the URL.
 
diff --git a/docs/source/manual/packages/colrev.scopus.rst b/docs/source/manual/packages/colrev.scopus.rst
@@ -68,11 +68,10 @@ Get an API key and set it using
 
    export SCOPUS_API_KEY="your-api-key"
 
-.. note::
+..
+
+   **Tip:** To keep the key for future sessions, append the export line to your shell profile (for example ``~/.bashrc``\ ) and reload it with ``source ~/.bashrc``.
 
-   Add the ``export`` command to your shell profile (for example ``~/.bashrc``)
-   and reload it with ``source ~/.bashrc`` to keep the key available across
-   sessions.
 
 Links
 -----
diff --git a/docs/source/manual/packages/colrev.semanticscholar.rst b/docs/source/manual/packages/colrev.semanticscholar.rst
@@ -124,7 +124,7 @@ If the user decides to conduct a search without entering any search parameters,
 API search: API key for SemanticScholar
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-While it is not necessary to enter an API key to conduct a search in SemanticScholar, we highly recommend it. Without an API key, SemanticScholar only allows limited access attempts per minute. This might lead to the site being unavailable for a short time. An API key can be requested via the SemanticScholar API (link below). Once a valid API key was entered, it will be saved in the ``SETTINGS`` file. Subsequent searches of SematicScholar will now include this API key. Every time a new search is conducted, the user will have the opportunity to change or delete the stored API key via the user interface.
+While it is not necessary to enter an API key to conduct a search in SemanticScholar, we highly recommend it. Without an API key, SemanticScholar only allows limited access attempts per minute. This might lead to the site being unavailable for a short time. An API key can be requested via the SemanticScholar API (link below). Store the key in the environment variable ``SEMANTIC_SCHOLAR_API_KEY`` (for example by running ``export SEMANTIC_SCHOLAR_API_KEY="<your-api-key>"``\ ). If the variable is not set, the search interface will prompt for the key and store it for the current session.
 
 API search: Search results
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/docs/source/manual/packages/colrev.springer_link.rst b/docs/source/manual/packages/colrev.springer_link.rst
@@ -118,11 +118,12 @@ Set the API-KEY using
 
    export SPRINGER_API_KEY="your-api-key"
 
-.. note::
+..
+
+   **Tip:** Add the export line to your shell profile (for example ``~/.bashrc``\ )
+   and reload it with ``source ~/.bashrc`` to keep the key available in future
+   sessions.
 
-   To keep the API key available across terminal sessions, append the
-   ``export`` command to your shell profile (for example ``~/.bashrc``) and
-   reload it with ``source ~/.bashrc``.
 
 The user can choose between ``complete_search_string`` for searching with a complex query or ``interactively`` to enter search parameters interactively.
 
diff --git a/docs/source/manual/packages/colrev.trid.rst b/docs/source/manual/packages/colrev.trid.rst
@@ -63,4 +63,4 @@ Links
 -----
 
 
-* `TRID <https://www.trid.trb.org/>`_
+* `TRID <https://trid.trb.org/>`_
diff --git a/docs/source/manual/packages/colrev.unpaywall.rst b/docs/source/manual/packages/colrev.unpaywall.rst
@@ -65,11 +65,11 @@ The search method provides functionality for searching the Unpaywall database. T
 This package primarily supports the retrieval of PDF documents from the `unpaywall <https://unpaywall.org/>`_ API, which provides access to over 40,000,000 free scholarly articles.
 
 An **email address** is required for API calls for the search and retrieval of PDFs.
-By default, the email address used in the git configuration is added to the unpaywall requests. If you would like to use a different email address, use the following command.
+By default, the email address used in the git configuration is added to the unpaywall requests. To use a different email address, set the environment variable ``UNPAYWALL_EMAIL``\ , for example:
 
 .. code-block::
 
-   colrev settings --update-global=packages.pdf_get.colrev.unpaywall.email=<email_address>
+   export UNPAYWALL_EMAIL="your@email.com"
 
 search
 ------
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "colrev"
-version = "0.15.0"
+version = "0.16.0"
 description = "CoLRev: An open-source environment for collaborative reviews"
 authors = [
     { name = "Gerit Wagner", email = "gerit.wagner@uni-bamberg.de" },
diff --git a/tests/review_manager/0_core/review_manager_test.py b/tests/review_manager/0_core/review_manager_test.py
@@ -43,7 +43,7 @@ def test_get_colrev_versions(
     base_repo_review_manager: colrev.review_manager.ReviewManager,
 ) -> None:
     colrev_versions = base_repo_review_manager.get_colrev_versions()
-    assert ["0.15.0", "0.15.0"] == colrev_versions, print(
+    assert ["0.16.0", "0.16.0"] == colrev_versions, print(
         f"To install the current version, run {Colors.ORANGE}pip install -e .{Colors.END}"
     )
 
