Update documentation (#603)

* Update documentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: github-actions <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
CoLRev-Environment · Jan 29, 2025 · 2fe35b9 · 2fe35b9
1 parent 6c5e8b5
commit 2fe35b9
Show file tree

Hide file tree

Showing 10 changed files with 42 additions and 31 deletions.
diff --git a/colrev/package_manager/package_endpoints.json b/colrev/package_manager/package_endpoints.json
@@ -250,6 +250,12 @@
                 "BACKWARD_SEARCH"
             ]
         },
+        {
+            "package_endpoint_identifier": "colrev.plos",
+            "status": "|EXPERIMENTAL|",
+            "short_description": "TODO (:doc:`instructions </manual/packages/colrev.plos>`)",
+            "search_types": []
+        },
         {
             "package_endpoint_identifier": "colrev.prospero",
             "status": "|EXPERIMENTAL|",
@@ -258,12 +264,6 @@
                 "API"
             ]
         },
-        {
-            "package_endpoint_identifier": "colrev.plos",
-            "status": "|EXPERIMENTAL|",
-            "short_description": "TODO (:doc:`instructions </manual/packages/colrev.plos>`)",
-            "search_types": []
-        },
         {
             "package_endpoint_identifier": "colrev.psycinfo",
             "status": "|EXPERIMENTAL|",

diff --git a/docs/source/dev_docs/_autosummary/colrev.constants.Fields.rst b/docs/source/dev_docs/_autosummary/colrev.constants.Fields.rst
@@ -62,6 +62,7 @@ colrev.constants.Fields
       ~Fields.PDF_ID
       ~Fields.PMCID
       ~Fields.PRESCREEN_EXCLUSION
+      ~Fields.PROSPERO_ID
       ~Fields.PUBLISHER
       ~Fields.PUBMED_ID
       ~Fields.REFERENCES

diff --git a/docs/source/dev_docs/_autosummary/colrev.hooks.rst b/docs/source/dev_docs/_autosummary/colrev.hooks.rst
@@ -30,4 +30,3 @@ colrev.hooks
    colrev.hooks.format
    colrev.hooks.report
    colrev.hooks.share
-   colrev.hooks.update
diff --git a/docs/source/dev_docs/_autosummary/colrev.ops.search_api_feed.SearchAPIFeed.rst b/docs/source/dev_docs/_autosummary/colrev.ops.search_api_feed.SearchAPIFeed.rst
@@ -21,13 +21,3 @@ colrev.ops.search\_api\_feed.SearchAPIFeed
       ~SearchAPIFeed.get_last_updated
       ~SearchAPIFeed.get_prev_feed_record
       ~SearchAPIFeed.save
-
-
-
-
-
-   .. rubric:: Attributes
-
-   .. autosummary::
-
-      ~SearchAPIFeed.source_identifier
diff --git a/docs/source/dev_docs/_autosummary/colrev.ui_cli.cli.rst b/docs/source/dev_docs/_autosummary/colrev.ui_cli.cli.rst
@@ -18,6 +18,7 @@ colrev.ui\_cli.cli
       catch_exception
       get_review_manager
       get_search_files
+      select_format
 
 
 

diff --git a/docs/source/dev_docs/_autosummary/colrev.ui_cli.cli.select_format.rst b/docs/source/dev_docs/_autosummary/colrev.ui_cli.cli.select_format.rst
@@ -0,0 +1,6 @@
+colrev.ui\_cli.cli.select\_format
+=================================
+
+.. currentmodule:: colrev.ui_cli.cli
+
+.. autofunction:: select_format
diff --git a/docs/source/manual/package_endpoints.json b/docs/source/manual/package_endpoints.json
@@ -250,6 +250,12 @@
                 "BACKWARD_SEARCH"
             ]
         },
+        {
+            "package_endpoint_identifier": "colrev.plos",
+            "status": "|EXPERIMENTAL|",
+            "short_description": "TODO (:doc:`instructions </manual/packages/colrev.plos>`)",
+            "search_types": []
+        },
         {
             "package_endpoint_identifier": "colrev.prospero",
             "status": "|EXPERIMENTAL|",
@@ -258,12 +264,6 @@
                 "API"
             ]
         },
-        {
-            "package_endpoint_identifier": "colrev.plos",
-            "status": "|EXPERIMENTAL|",
-            "short_description": "TODO (:doc:`instructions </manual/packages/colrev.plos>`)",
-            "search_types": []
-        },
         {
             "package_endpoint_identifier": "colrev.psycinfo",
             "status": "|EXPERIMENTAL|",

diff --git a/docs/source/manual/packages.rst b/docs/source/manual/packages.rst
@@ -82,8 +82,8 @@ Packages
    packages/colrev.open_library.rst
    packages/colrev.osf.rst
    packages/colrev.pdf_backward_search.rst
-   packages/colrev.prospero.rst
    packages/colrev.plos.rst
+   packages/colrev.prospero.rst
    packages/colrev.psycinfo.rst
    packages/colrev.pubmed.rst
    packages/colrev.scopus.rst

diff --git a/docs/source/manual/packages/colrev-sync.rst b/docs/source/manual/packages/colrev-sync.rst
@@ -52,3 +52,16 @@ If BibTeX citations keys are used in the paper project, the following command re
 .. code-block::
 
    colrev-sync
+
+CoLRev sync can also be used through pre-commit hooks, when the following is included in the ``.pre-commit-config.yaml``\ :
+
+.. code-block::
+
+   -   repo: local
+       hooks:
+       -   id: colrev-hooks-update
+           name: "CoLRev ReviewManager: update"
+           entry: colrev-hooks-update
+           language: python
+           stages: [commit]
+           files: 'records.bib|paper.md'
diff --git a/docs/source/manual/packages_overview.json b/docs/source/manual/packages_overview.json
@@ -282,19 +282,20 @@
         ],
         "endpoint_type": "search_source"
     },
+    {
+        "package_endpoint_identifier": "colrev.plos",
+        "status": "|EXPERIMENTAL|",
+        "short_description": "TODO (:doc:`instructions </manual/packages/colrev.plos>`)",
+        "search_types": [],
+        "endpoint_type": "search_source"
+    },
     {
         "package_endpoint_identifier": "colrev.prospero",
         "status": "|EXPERIMENTAL|",
         "short_description": "TODO (:doc:`instructions </manual/packages/colrev.prospero>`)",
         "search_types": [
             "API"
-        ]
-    },
-    {
-        "package_endpoint_identifier": "colrev.plos",
-        "status": "|EXPERIMENTAL|",
-        "short_description": "TODO (:doc:`instructions </manual/packages/colrev.plos>`)",
-        "search_types": [],
+        ],
         "endpoint_type": "search_source"
     },
     {