MAINT: Cleaning up Sphinx documentation.

src/caosadvancedtools/cache.py

@@ -150,12 +150,17 @@ class AbstractCache(ABC):
         finally:
             conn.close()
 
-    def run_sql_commands(self, commands, fetchall=False):
-        """
-        Run a list of SQL commands on self.db_file.
+    def run_sql_commands(self, commands, fetchall: bool = False):
+        """Run a list of SQL commands on self.db_file.
+
+Parameters
+----------
+
+commands:
+  List of sql commands (tuples) to execute
 
-        commands: list of sql commands (tuples) to execute
-        fetchall: When True, run fetchall as last command and return the results.
+fetchall: bool, optional
+  When True, run fetchall as last command and return the results.
   Otherwise nothing is returned.
         """
         conn = sqlite3.connect(self.db_file)

src/caosadvancedtools/json_schema_exporter.py

@@ -88,7 +88,7 @@ class JsonSchemaExporter:
             If True, do not attempt to connect to a LinkAhead server at all. Default is False. Note
             that the exporter may fail if this option is activated and the data model is not
             self-sufficient.
-        use_rt_pool : DataModel, optional
+        use_rt_pool : models.data_model.DataModel, optional
             If given, do not attempt to retrieve RecordType information remotely but from this parameter
             instead.
         multiple_choice : list[str], optional
@@ -562,7 +562,7 @@ def recordtype_to_json_schema(rt: db.RecordType, additional_properties: bool = T
         parameter, the behavior is undefined.
     no_remote : bool, optional
         If True, do not attempt to connect to a LinkAhead server at all.  Default is False.
-    use_rt_pool : DataModel, optional
+    use_rt_pool : models.data_model.DataModel, optional
         If given, do not attempt to retrieve RecordType information remotely but from this parameter
         instead.
     multiple_choice : list[str], optional

src/caosadvancedtools/models/parser.py

@@ -248,7 +248,7 @@ debug : bool, optional
 
         Returns
         -------
-        out : DataModel
+        out : data_model.DataModel
           The created DataModel
         """
         with open(filename, 'r') as outfile:
@@ -269,7 +269,7 @@ debug : bool, optional
 
         Returns
         -------
-        out : DataModel
+        out : data_model.DataModel
           The created DataModel
         """
         ymlmodel = yaml.load(string, Loader=SafeLineLoader)
@@ -289,7 +289,7 @@ debug : bool, optional
 
         Returns
         -------
-        out : DataModel
+        out : data_model.DataModel
           The created DataModel
         """
 
@@ -706,7 +706,7 @@ class JsonSchemaParser(Parser):
 
         Returns
         -------
-        out : DataModel
+        out : data_model.DataModel
             The created DataModel
         """
         # @author Florian Spreckelsen
@@ -732,7 +732,7 @@ class JsonSchemaParser(Parser):
 
         Returns
         -------
-        our : DataModel
+        our : data_model.DataModel
             The datamodel defined in `model_dict`
         """
         # @review Timm Fitschen 2023-05-25

src/caosadvancedtools/table_json_conversion/table_generator.py

@@ -282,7 +282,7 @@ class XLSXTemplateGenerator(TableTemplateGenerator):
         foreign_keys: dict
             A configuration that defines which attributes shall be used to create
             additional columns when a list of references exists. See ``foreign_keys``
-            argument of :ref:`TableTemplateGenerator.generate` .
+            argument of :meth:`TableTemplateGenerator.generate` .
         filepath: str
             The XLSX file will be stored under this path.
         """

src/doc/conf.py

@@ -64,7 +64,7 @@ master_doc = 'index'
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -190,7 +190,7 @@ epub_exclude_files = ['search.html']
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
     "python": ("https://docs.python.org/", None),
-    "caosdb-pylib": ("https://caosdb.gitlab.io/caosdb-pylib/", None),
+    "linkahead-pylib": ("https://docs.indiscale.com/caosdb-pylib/", None),
 }
 
 

src/doc/crawler.rst

@@ -77,8 +77,8 @@ problems. The exact behavior depends on your setup. However, you can
 have a look at the example in the
 `tests <https://gitlab.indiscale.com/caosdb/src/caosdb-advanced-user-tools/-/blob/main/integrationtests/crawl.py>`__.
 
-.. Note:: The crawler depends on the CaosDB Python client, so make sure to install :doc:`pycaosdb
-          <caosdb-pylib:getting_started>`.
+.. Note:: The crawler depends on the LinkAhead Python client, so make sure to install :doc:`pylinkahead
+          <linkahead-pylib:README_SETUP>`.
 
 
 Call ``python3 crawl.py --help`` to see what parameters can be provided.

src/doc/index.rst

@@ -4,8 +4,8 @@ Welcome to caosadvancedtools' documentation!
 Welcome to the advanced Python tools for CaosDB!
 
 
-This documentation helps you to :doc:`get started<getting_started>`, explains the most important
-:doc:`concepts<concepts>` and offers a range of :doc:`tutorials<tutorials>`.
+This documentation helps you to :doc:`get started<README_SETUP>`, explains the most important
+:doc:`concepts<concepts>` and offers a range of deep dives into specific sub-topics.
 
 .. toctree::
    :maxdepth: 2
@@ -16,6 +16,7 @@ This documentation helps you to :doc:`get started<getting_started>`, explains th
    The Caosdb Crawler <crawler>
    YAML data model specification <yaml_interface>
    Specifying a datamodel with JSON schema <json_schema_interface>
+   Conversion between XLSX, JSON and LinkAhead Entities <table-json-conversion/specs>
    _apidoc/modules
    Related Projects <related_projects/index>
    Back to overview <https://docs.indiscale.com/>