From 45efa075daa81370c19b1487da7ab00675c84532 Mon Sep 17 00:00:00 2001
From: Daniel <d.hornung@indiscale.com>
Date: Wed, 10 Apr 2024 10:12:55 +0200
Subject: [PATCH] MAINT: Cleaning up Sphinx documentation.
---
src/caosadvancedtools/cache.py | 17 +++++++++++------
src/caosadvancedtools/json_schema_exporter.py | 4 ++--
src/caosadvancedtools/models/parser.py | 10 +++++-----
.../table_json_conversion/table_generator.py | 2 +-
src/doc/conf.py | 4 ++--
src/doc/crawler.rst | 4 ++--
src/doc/index.rst | 5 +++--
7 files changed, 26 insertions(+), 20 deletions(-)
diff --git a/src/caosadvancedtools/cache.py b/src/caosadvancedtools/cache.py
index cf74e330..bf1287ba 100644
--- a/src/caosadvancedtools/cache.py
+++ b/src/caosadvancedtools/cache.py
@@ -150,13 +150,18 @@ 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.
- Otherwise nothing is returned.
+fetchall: bool, optional
+ When True, run fetchall as last command and return the results.
+ Otherwise nothing is returned.
"""
conn = sqlite3.connect(self.db_file)
c = conn.cursor()
diff --git a/src/caosadvancedtools/json_schema_exporter.py b/src/caosadvancedtools/json_schema_exporter.py
index 11e74369..3ac5247d 100644
--- a/src/caosadvancedtools/json_schema_exporter.py
+++ b/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
diff --git a/src/caosadvancedtools/models/parser.py b/src/caosadvancedtools/models/parser.py
index fa21aa13..f9bea924 100644
--- a/src/caosadvancedtools/models/parser.py
+++ b/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
diff --git a/src/caosadvancedtools/table_json_conversion/table_generator.py b/src/caosadvancedtools/table_json_conversion/table_generator.py
index 5caefc8d..8ca026a8 100644
--- a/src/caosadvancedtools/table_json_conversion/table_generator.py
+++ b/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.
"""
diff --git a/src/doc/conf.py b/src/doc/conf.py
index 590feca4..37397f24 100644
--- a/src/doc/conf.py
+++ b/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),
}
diff --git a/src/doc/crawler.rst b/src/doc/crawler.rst
index aea02319..d7b351bb 100644
--- a/src/doc/crawler.rst
+++ b/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.
diff --git a/src/doc/index.rst b/src/doc/index.rst
index 15a7b7ab..aa5cedca 100644
--- a/src/doc/index.rst
+++ b/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/>
--
GitLab