Merge branch 'main' into base-causal-test-case

Author: christopher-wild

docs/source/conf.py

@@ -13,29 +13,26 @@
 import os
 import sys
 
-#Include root directory of project
+# Include root directory of project
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "../..")))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'Causal Testing'
-copyright = '2021, Andrew Clark, Michael Foster, Neil Walkinshaw, Rob Hierons, Bob Turner'
-author = 'Andrew Clark, Michael Foster, Neil Walkinshaw, Rob Hierons, Bob Turner'
+project = "Causal Testing"
+copyright = "2021, Andrew Clark, Michael Foster, Neil Walkinshaw, Rob Hierons, Bob Turner"
+author = "Andrew Clark, Michael Foster, Neil Walkinshaw, Rob Hierons, Bob Turner"
 
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [
-    'autoapi.extension',
-    'sphinx.ext.autosectionlabel'
-]
+extensions = ["autoapi.extension", "myst_parser", "sphinx.ext.autosectionlabel"]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -47,12 +44,12 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-#html_static_path = ['_static']
+# html_static_path = ['_static']
 
-#Path to generate documentation from using sphinx AutoAPI
-autoapi_dirs = [os.path.abspath(os.path.join('..', '..', 'causal_testing'))]
+# Path to generate documentation from using sphinx AutoAPI
+autoapi_dirs = [os.path.abspath(os.path.join("..", "..", "causal_testing"))]

docs/source/glossary.md

@@ -0,0 +1,3 @@
+# Glossary
+
+TDB

docs/source/index.rst

@@ -27,6 +27,12 @@ Causal testing is a causal inference-driven framework for functional black-box t
 
    json_front_end
 
+.. toctree::
+   :maxdepth: 1
+   :caption: Glossary
+
+   glossary
+
 Indices and tables
 ==================
 

docs/source/installation.rst

@@ -21,35 +21,28 @@ Alternatively, on Linux systems, this can be done with `sudo apt install graphvi
 Install from source
 -------------------
 
-In future it will be possible to install from PyPI, but for now...
-
-.. code-block:: console
+In future it will be possible to install from PyPI, but for now::
 
     git clone https://github.com/CITCOM-project/CausalTestingFramework
     cd CausalTestingFramework
 
-then, to install a specific release:
+then, to install a specific release::
 
-.. code-block:: console    
     git fetch --all --tags --prune
     git checkout tags/<tag> -b <branch>
     pip install -e .
 
-e.g. version `1.0.0`
+e.g. version `1.0.0`::
 
-.. code-block:: console    
     git fetch --all --tags --prune
     git checkout tags/1.0.0 -b version
     pip install -e .
 
-or to install the latest development version:
+or to install the latest development version::
 
-.. code-block:: console    
     pip install -e .
 
-Use 
-
-.. code-block:: console
+Use::
 
     pip install -e .[dev]
 

docs/source/json_front_end.rst

@@ -33,23 +33,17 @@ Each test requires:
 
 Run Commands
 ------------
-To run the JSON frontend example from the root directory of the project, use
-
-.. code-block:: console
+To run the JSON frontend example from the root directory of the project, use::
 
     python examples/poisson/run_causal_tests.py
 
-A failure flag `-f` can be specified to stop the framework running if a test is failed
-
-.. code-block:: console
+A failure flag `-f` can be specified to stop the framework running if a test is failed::
 
     python examples/poisson/run_causal_tests.py -f
 
 There are two main outputs of this frontend, both are controlled by the logging module. Firstly outputs are printed to stdout (terminal).
 Secondly a log file is produced, by default a file called `json_frontend.log` is produced in the directory the script is called from.
 
-The behaviour of where the log file is produced and named can be altered with the --log_path argument:
-
-.. code-block:: console
+The behaviour of where the log file is produced and named can be altered with the --log_path argument::
 
     python examples\poisson\run_causal_tests.py -f --data_path="examples\poisson\data.csv" --dag_path="examples\poisson\dag.dot" --json_path="examples\poisson\causal_tests.json --log_path="example_directory\logname.log"

docs/source/requirements.txt

@@ -1,3 +1,4 @@
-sphinx==4.2.0
-sphinx-autoapi==1.8.4
-sphinx-rtd-theme==1.0.0
+Sphinx==5.3.0
+myst-parser==0.18.1
+sphinx-autoapi==2.0.1
+sphinx-rtd-theme==1.1.1

setup.py

@@ -15,9 +15,19 @@
 ]
 
 # Additional dependencies for development
-dev_requirements = ["autopep8", "isort", "pytest", "pylint", "black"]
+dev_requirements = [
+    "autopep8",
+    "isort",
+    "pytest",
+    "pylint",
+    "black",
+    "autoapi",
+    "myst-parser",
+    "sphinx-autoapi",
+    "sphinx_rtd_theme",
+]
 
-readme = open("README.md", encoding = "UTF-8").read()
+readme = open("README.md", encoding="UTF-8").read()
 
 setup(
     name="causal_testing_framework",