✨ Add tutorials to the docs

- for now locally - tutorials will be executed on build (can be changed)
RasmussenLab · Nov 3, 2023 · 1097619 · 1097619
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Showing 6 changed files with 31 additions and 9 deletions.
diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@ a paper on fatty liver disease.
 
 ## Installation
 
-Install using pip from [PyPi](https://pypi.org/project/njab) version
+Install using pip from [PyPi](https://pypi.org/project/njab) version.
 
 ```
 pip install njab

diff --git a/docs/conf.py b/docs/conf.py
@@ -35,10 +35,16 @@
     'sphinx.ext.autodoc',
     'sphinx.ext.autodoc.typehints',
     'sphinx.ext.viewcode',
-    'myst_parser',
+    'myst_nb',
     'sphinx.ext.napoleon',
 ]
 
+#  https://myst-nb.readthedocs.io/en/latest/computation/execute.html
+nb_execution_mode = "auto"
+
+myst_enable_extensions = ["dollarmath", "amsmath"]
+
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -9,11 +9,27 @@ functionality used two papers.
 .. include:: ../README.md
    :parser: myst_parser.sphinx_
    :start-line: 1
-.. :end-line: 22
+
+
+Try it yourself
+---------------
+
+The tutorial showcasing most of the basic functionality can be found on the following
+pages
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Tutorials
+
+   tutorial/explorative_analysis
+   tutorial/log_reg
+
+Python Package reference
+------------------------
 
 .. toctree::
    :maxdepth: 2
-   :caption: Python Package Reference:
+   :
 
    reference/modules
 

diff --git a/docs/tutorial/log_reg.ipynb b/docs/tutorial/log_reg.ipynb
@@ -975,7 +975,7 @@
    "id": "53800467",
    "metadata": {},
    "source": [
-    "# Performance evaluations"
+    "## Performance evaluations"
    ]
   },
   {
@@ -1065,7 +1065,7 @@
    "id": "a1326dcd",
    "metadata": {},
    "source": [
-    "# Multiplicative decompositon"
+    "## Multiplicative decompositon"
    ]
   },
   {

diff --git a/docs/tutorial/log_reg.py b/docs/tutorial/log_reg.py
@@ -522,7 +522,7 @@
 # pred_bins_val
 
 # %% [markdown]
-# # Performance evaluations
+# ## Performance evaluations
 
 # %%
 prc = pd.DataFrame(results_model.train.prc,
@@ -567,7 +567,7 @@
 _
 
 # %% [markdown]
-# # Multiplicative decompositon
+# ## Multiplicative decompositon
 
 # %%
 

diff --git a/setup.cfg b/setup.cfg
@@ -38,7 +38,7 @@ install_requires =
 docs =
     sphinx
     sphinx-book-theme
-    myst-parser
+    myst-nb
 
 [options.packages.find]
 where = src