Update documentation (#757)

github-actions[bot] · github-actions · web-flow · commit 12516c8a75a1 · 2026-05-13T08:23:37.000+02:00
Co-authored-by: github-actions &lt;github-actions@github.com&gt;
diff --git a/colrev/package_manager/package_endpoints.json b/colrev/package_manager/package_endpoints.json
@@ -549,11 +549,6 @@
         }
     ],
     "pdf_get": [
-        {
-            "package_endpoint_identifier": "colrev-scidb",
-            "status": "|EXPERIMENTAL|",
-            "short_description": "TODO (:doc:`instructions </manual/packages/colrev-scidb>`)"
-        },
         {
             "package_endpoint_identifier": "colrev.download_from_website",
             "status": "|MATURING|",
diff --git a/docs/source/manual/package_endpoints.json b/docs/source/manual/package_endpoints.json
@@ -549,11 +549,6 @@
         }
     ],
     "pdf_get": [
-        {
-            "package_endpoint_identifier": "colrev-scidb",
-            "status": "|EXPERIMENTAL|",
-            "short_description": "TODO (:doc:`instructions </manual/packages/colrev-scidb>`)"
-        },
         {
             "package_endpoint_identifier": "colrev.download_from_website",
             "status": "|MATURING|",
diff --git a/docs/source/manual/packages.rst b/docs/source/manual/packages.rst
@@ -140,7 +140,6 @@ Packages
    packages/colrev.scope_prescreen.rst
 
 
-   packages/colrev-scidb.rst
    packages/colrev.download_from_website.rst
    packages/colrev.local_index.rst
    packages/colrev.unpaywall.rst
diff --git a/docs/source/manual/packages/colrev.critical_review.rst b/docs/source/manual/packages/colrev.critical_review.rst
@@ -53,7 +53,7 @@ Summary
 
 A critical review is a form of research synthesis that rigorously evaluates existing literature to identify weaknesses, contradictions, and inconsistencies. It assesses each piece of literature against specific criteria to gauge its adequacy, thereby highlighting areas where current knowledge may be unreliable. This approach aids in directing future research by pinpointing specific problems and discrepancies that need to be addressed. Critical reviews are typically either selective or representative in nature, often omitting a comprehensive literature search, and may use various data synthesis methods rooted in either positivist or interpretivist epistemological positions.
 
-If the focus is on research methods, a  :doc:`critical methodological review <colrev.methodological_review>` may be appropriate.
+If the focus is on research methods, a `critical methodological review <colrev.methodological_review.html>`_ may be appropriate.
 
 Characteristics
 ---------------
@@ -78,8 +78,8 @@ Data extraction, analysis, and synthesis
 The following packages are automatically set up in a critical review:
 
 
-*  :doc:`colrev.prisma <colrev.prisma>`
-*  :doc:`colrev.paper_md <colrev.paper_md>`
+* `colrev.prisma <colrev.prisma.html>`_
+* `colrev.paper_md <colrev.paper_md.html>`_
 
 Examples
 --------
diff --git a/docs/source/manual/packages/colrev.crossref.rst b/docs/source/manual/packages/colrev.crossref.rst
@@ -143,6 +143,6 @@ Links
 
 
 * `Crossref <https://www.crossref.org/>`_
-* `License <https://www.crossref.org/documentation/retrieve-metadata/rest-api/tips-for-using-the-crossref-rest-api/>`_
+* `License <https://www.crossref.org/documentation/retrieve-metadata/rest-api/rest-api-metadata-license-information/>`_
 * `Crossref types <https://api.crossref.org/types>`_
 * `Issue: AND Operators not yet supported <https://github.com/fabiobatalha/crossrefapi/issues/20>`_
diff --git a/docs/source/manual/packages/colrev.dedupe.rst b/docs/source/manual/packages/colrev.dedupe.rst
@@ -54,8 +54,8 @@ Summary
 BibDedupe is an open-source Python library for deduplication of bibliographic records, tailored for literature reviews. Unlike traditional deduplication methods, BibDedupe focuses on entity resolution, linking duplicate records instead of simply deleting them.
 
 
-.. image:: https://joss.theoj.org/papers/10.21105/joss.06318/status.svg
-   :target: https://joss.theoj.org/papers/10.21105/joss.06318
+.. image:: https://joss.theoj.org/papers/b954027d06d602c106430e275fe72130/status.svg
+   :target: https://joss.theoj.org/papers/b954027d06d602c106430e275fe72130
    :alt: status
 
 
@@ -100,4 +100,4 @@ Links
 
 * `bib-dedupe <https://github.com/CoLRev-Environment/bib-dedupe>`_
 * `Documentation <https://colrev-environment.github.io/bib-dedupe/>`_
-* `Evaluation <https://github.com/CoLRev-Environment/bib-dedupe#evaluation>`_
+* `Evaluation <https://colrev-environment.github.io/bib-dedupe/evaluation.html>`_
diff --git a/docs/source/manual/packages/colrev.descriptive_review.rst b/docs/source/manual/packages/colrev.descriptive_review.rst
@@ -76,10 +76,10 @@ Data extraction, analysis, and synthesis
 The following packages are automatically set up in a descriptive review:
 
 
-*  :doc:`colrev.prisma <colrev.prisma>`
-*  :doc:`colrev.profile <colrev.profile>`
-*  :doc:`colrev.structured <colrev.structured>`
-*  :doc:`colrev.paper_md <colrev.paper_md>`
+* `colrev.prisma <colrev.prisma.html>`_
+* `colrev.profile <colrev.profile.html>`_
+* `colrev.structured <colrev.structured.html>`_
+* `colrev.paper_md <colrev.paper_md.html>`_
 
 Examples
 --------
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 APIs <https://developer.ebsco.com/home/docs/available-apis-and-requirements>`_
+* `EBSCOHost <https://search.ebscohost.com/>`_
+* `EBSCOHost APIs <https://developer.ebsco.com/getting-started/available-apis>`_
diff --git a/docs/source/manual/packages/colrev.enlit.rst b/docs/source/manual/packages/colrev.enlit.rst
@@ -79,9 +79,9 @@ Cite
 
 Wagner, G., Empl, P., & Schryen, G. (2020, May). Designing a novel strategy for exploring literature corpora. In *Proceedings of the European Conference on Information Systems*. https://aisel.aisnet.org/ecis2020_rp/44/
 
-Original repository: `link <https://github.com/fs-ise/enlit>`_
+Original repository: `link <https://github.com/digital-work-lab/enlit>`_
 
 License
 -------
 
-This project is licensed under the MIT License - see the `LICENSE <https://github.com/CoLRev-Environment/colrev/blob/main/LICENSE>`_ file for details.
+This project is licensed under the MIT License - see the `LICENSE <LICENSE>`_ file for details.
diff --git a/docs/source/manual/packages/colrev.files_dir.rst b/docs/source/manual/packages/colrev.files_dir.rst
@@ -63,7 +63,7 @@ FILES  search
 
 
 * PDF metadata extracted based on PDF hashes and the local_index (clone curations and run ``colrev env --index``\ ).
-* PDF metadata extracted based on `GROBID <https://github.com/grobidOrg/grobid>`_
+* PDF metadata extracted based on `GROBID <https://github.com/kermitt2/grobid>`_
 
 For metadata curations, i.e., repositories containing all PDFs organized in directories for volumes/issues, it is possible to set the ``scope`` parameter in the ``settings.json``\ , ensuring that the journal name, entrytype, and volume/issue is set automatically.
 
diff --git a/docs/source/manual/packages/colrev.github_pages.rst b/docs/source/manual/packages/colrev.github_pages.rst
@@ -62,5 +62,5 @@ Links
 -----
 
 
-* Example: `literature-search-resources <https://github.com/fs-ise/literature-search-resources>`_ and the `GitHub page of literature-search-resources <https://fs-ise.github.io/literature-search-resources/>`_
+* Example: `literature-search-resources <https://github.com/digital-work-lab/literature-search-resources>`_ and the `GitHub page of literature-search-resources <https://digital-work-lab.github.io/literature-search-resources/>`_
 * `GitHub pages <https://pages.github.com/>`_
diff --git a/docs/source/manual/packages/colrev.grobid_tei.rst b/docs/source/manual/packages/colrev.grobid_tei.rst
@@ -68,10 +68,10 @@ Links
 -----
 
 
-.. image:: https://img.shields.io/github/commit-activity/y/grobidOrg/grobid?color=green&style=plastic
-   :target: https://img.shields.io/github/commit-activity/y/grobidOrg/grobid?color=green&style=plastic
+.. image:: https://img.shields.io/github/commit-activity/y/kermitt2/grobid?color=green&style=plastic
+   :target: https://img.shields.io/github/commit-activity/y/kermitt2/grobid?color=green&style=plastic
    :alt: grobidactivity
 
 
 
-* `GROBID <https://github.com/grobidOrg/grobid>`_\ : parsing annotated PDF content (License: `Apache 2.0 <https://github.com/grobidOrg/grobid/blob/master/LICENSE>`_\ )
+* `GRBOBID <https://github.com/kermitt2/grobid>`_\ : parsing annotated PDF content (License: `Apache 2.0 <https://github.com/kermitt2/grobid/blob/master/LICENSE>`_\ )
diff --git a/docs/source/manual/packages/colrev.literature_review.rst b/docs/source/manual/packages/colrev.literature_review.rst
@@ -53,7 +53,7 @@ Summary
 
 This ReviewType contains a basic setup for literature reviews. It is a good choice to try the CoLRev system. Similar to the other packages for review types, it can be used to complete a review project and report each step for a standalone review paper.
 
-For standalone review papers, it is recommended to use a specific review type, such as a  :doc:`scoping review <colrev.scoping_review>` or a  :doc:`qualitative systematic review <colrev.qualitative_systematic_review>`.
+For standalone review papers, it is recommended to use a specific review type, such as a `scoping review <colrev.scoping_review.html>`_ or a `qualitative systematic review <colrev.qualitative_systematic_review.html>`_.
 
 Characteristics
 ---------------
@@ -65,7 +65,7 @@ Data extraction, analysis, and synthesis
 ----------------------------------------
 
 
-* For the synthesis, the  :doc:`colrev.paper_md <colrev.paper_md>` is activated, which creates the ``data/data/paper.md`` file. This file can be used to keep notes, draft a review protocol, and to write a synthesis. Based on the ``paper.md``\ , the ``output/paper.docx`` is generated automatically.
+* For the synthesis, the `colrev.paper_md <colrev.paper_md.html>`_ is activated, which creates the ``data/data/paper.md`` file. This file can be used to keep notes, draft a review protocol, and to write a synthesis. Based on the ``paper.md``\ , the ``output/paper.docx`` is generated automatically.
 * To extract structured data, or conduct other forms of analysis and synthesis, other `data packages <https://colrev-environment.github.io/colrev/manual/data/data.html>`_ can be activated.
 
 Textbooks
diff --git a/docs/source/manual/packages/colrev.meta_analysis.rst b/docs/source/manual/packages/colrev.meta_analysis.rst
@@ -62,7 +62,7 @@ Short summary
 * dimensions
 * differences between disciplines
 
-For the data extraction, risk-of-bias assessment, and meta-analysis, established software packages like `RevMan <https://www.cochrane.org/learn>`_ are recommended.
+For the data extraction, risk-of-bias assessment, and meta-analysis, established software packages like `RevMan <https://training.cochrane.org/online-learning/core-software/revman>`_ are recommended.
 
 For the analysis, R packages are recommended.
 
diff --git a/docs/source/manual/packages/colrev.methodological_review.rst b/docs/source/manual/packages/colrev.methodological_review.rst
@@ -61,4 +61,4 @@ Balijepally, V., Mangalaraj, G., & Iyengar, K. (2011). Are we wielding this hamm
 Methods papers
 --------------
 
-Aguinis, H., Ramani, R. S., & Alabduljader, N. (2023). Best-practice recommendations for producers, evaluators, and users of methodological literature reviews. Organizational Research Methods, 26(1), 46-76. doi:\ `10.1177/109442812094328 <https://doi.org/10.1177/1094428120943285>`_
+Aguinis, H., Ramani, R. S., & Alabduljader, N. (2023). Best-practice recommendations for producers, evaluators, and users of methodological literature reviews. Organizational Research Methods, 26(1), 46-76. doi:\ `10.1177/109442812094328 <https://doi.org/10.1177/109442812094328>`_
diff --git a/docs/source/manual/packages/colrev.narrative_review.rst b/docs/source/manual/packages/colrev.narrative_review.rst
@@ -79,7 +79,7 @@ Data extraction, analysis, and synthesis
 The following packages are automatically set up in a scoping review:
 
 
-*  :doc:`colrev.paper_md <colrev.paper_md>`
+* `colrev.paper_md <colrev.paper_md.html>`_
 
 Examples
 --------
@@ -91,4 +91,4 @@ Methods papers
 
 Davies, P. (2000). The relevance of systematic reviews to educational policy and practice. *Oxford Review of Education*\ , 26(3-4), 365-378. doi:\ `10.1080/713688543 <https://doi.org/10.1080/713688543>`_
 
-Green, B. N., Johnson, C. D., & Adams, A. (2006). Writing narrative literature reviews for peer-reviewed journals: secrets of the trade. *Journal of Chiropractic Medicine*\ , 5(3), 101-117. doi:\ `10.1016/S0899-3467(07)60142-6 <https://doi.org/10.1016/S0899-3467(07)60142-6>`_
+Green, B. N., Johnson, C. D., & Adams, A. (2006). Writing narrative literature reviews for peer-reviewed journals: secrets of the trade. *Journal of Chiropractic Medicine*\ , 5(3), 101-117. doi:\ `10.1016/S0899-3467(07)60142-6 <https://doi.org/10.1016/S0899-3467(07>`_\ 60142-6)
diff --git a/docs/source/manual/packages/colrev.pdf_backward_search.rst b/docs/source/manual/packages/colrev.pdf_backward_search.rst
@@ -62,7 +62,7 @@ colrev search --add colrev.pdf_backward_search:min_intext_citations=2
 
 Citation data is automatically consolidated with open-citations data to improve data quality.
 
-based on `GROBID <https://github.com/grobidOrg/grobid>`_
+based on `GROBID <https://github.com/kermitt2/grobid>`_
 
 .. code-block::
 
diff --git a/docs/source/manual/packages/colrev.plos.rst b/docs/source/manual/packages/colrev.plos.rst
@@ -108,7 +108,7 @@ In order to test the metada provided for a specific ``DOI`` it can be used the f
 License
 -------
 
-This project is licensed under the MIT License - see the `LICENSE <https://github.com/CoLRev-Environment/colrev/blob/main/LICENSE>`_ file for details.
+This project is licensed under the MIT License - see the `LICENSE <LICENSE>`_ file for details.
 
 Links
 -----
diff --git a/docs/source/manual/packages/colrev.prospero.rst b/docs/source/manual/packages/colrev.prospero.rst
@@ -51,7 +51,7 @@ colrev.prospero
 Summary
 -------
 
-`PROSPERO <https://www.crd.york.ac.uk/prospero/>`_ is an international database of prospectively registered systematic reviews in health and social care, welfare, public health, education, crime, justice, and international development, where there is a health related outcome.
+`PROSPERO <https://www.crd.york.ac.uk/prospero/#searchadvanced>`_ is an international database of prospectively registered systematic reviews in health and social care, welfare, public health, education, crime, justice, and international development, where there is a health related outcome.
 
 Installation
 ^^^^^^^^^^^^
@@ -89,4 +89,4 @@ Links
 License
 -------
 
-This project is licensed under the MIT License - see the `LICENSE <https://github.com/CoLRev-Environment/colrev/blob/main/LICENSE>`_ file for details.
+This project is licensed under the MIT License - see the `LICENSE <LICENSE>`_ file for details.
diff --git a/docs/source/manual/packages/colrev.pubmed.rst b/docs/source/manual/packages/colrev.pubmed.rst
@@ -98,5 +98,5 @@ Links
 -----
 
 
-* `Data field descriptions <https://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html>`_
+* `Data field descriptions <https://www.nlm.nih.gov/bsd/mms/medlineelements.html>`_
 * `Pubmed <https://pubmed.ncbi.nlm.nih.gov/>`_
diff --git a/docs/source/manual/packages/colrev.scoping_review.rst b/docs/source/manual/packages/colrev.scoping_review.rst
@@ -84,9 +84,9 @@ Data extraction, analysis, and synthesis
 The following packages are automatically set up in a scoping review:
 
 
-*  :doc:`colrev.prisma <colrev.prisma>`
-*  :doc:`colrev.structured <colrev.structured>`
-*  :doc:`colrev.paper_md <colrev.paper_md>`
+* `colrev.prisma <colrev.prisma.html>`_
+* `colrev.structured <colrev.structured.html>`_
+* `colrev.paper_md <colrev.paper_md.html>`_
 
 Examples
 --------
diff --git a/docs/source/manual/packages/colrev.springer_link.rst b/docs/source/manual/packages/colrev.springer_link.rst
@@ -222,4 +222,4 @@ Links
 
 * `SpringerLink <https://link.springer.com/>`_
 * `SpringerLink API <https://dev.springernature.com/>`_
-* `SpringerLink API Documentation <https://dev.springernature.com/docs/introduction/>`_
+* `SpringerLink API Documentation <https://docs-dev.springernature.com/docs/>`_
diff --git a/docs/source/manual/packages_overview.json b/docs/source/manual/packages_overview.json
@@ -619,12 +619,6 @@
         "short_description": "Scope-based Prescreen (:doc:`instructions </manual/packages/colrev.scope_prescreen>`)",
         "endpoint_type": "prescreen"
     },
-    {
-        "package_endpoint_identifier": "colrev-scidb",
-        "status": "|EXPERIMENTAL|",
-        "short_description": "TODO (:doc:`instructions </manual/packages/colrev-scidb>`)",
-        "endpoint_type": "pdf_get"
-    },
     {
         "package_endpoint_identifier": "colrev.download_from_website",
         "status": "|MATURING|",
diff --git a/uv.lock b/uv.lock

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`@@ -549,11 +549,6 @@`
`549`	`549`	`}`
`550`	`550`	`],`
`551`	`551`	`"pdf_get": [`
`552`		`- {`
`553`		`- "package_endpoint_identifier": "colrev-scidb",`
`554`		`- "status": "\|EXPERIMENTAL\|",`
`555`		- "short_description": "TODO (:doc:`instructions </manual/packages/colrev-scidb>`)"
`556`		`- },`
`557`	`552`	`{`
`558`	`553`	`"package_endpoint_identifier": "colrev.download_from_website",`
`559`	`554`	`"status": "\|MATURING\|",`