docs: update

jjjermiah · Feb 25, 2024 · 4a7e891 · 4a7e891
1 parent f0f8824
commit 4a7e891
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Showing 7 changed files with 79 additions and 75 deletions.
diff --git a/docs/_html_notebooks/test_setup.ipynb b/docs/_html_notebooks/test_setup.ipynb
diff --git a/docs/_static/css/custom.css b/docs/_static/css/custom.css
@@ -0,0 +1,20 @@
+.sphinx-tabs-panel {
+    background: none;
+    border: none;
+    color:aliceblue;
+}
+
+.sphinx-tabs-tab{
+    color: #1D5C87;
+    /* font color */
+    background: none;
+
+}
+
+
+
+.sphinx-tabs-tab[aria-selected="false"]{
+    color: white;
+    /* font color */
+    background: none;
+}
diff --git a/docs/conf.py b/docs/conf.py
@@ -4,6 +4,7 @@
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
+import html
 import os
 import sys
 
@@ -22,9 +23,11 @@
 extensions = [
     "myst_nb",
     "autoapi.extension",
+    "sphinx.ext.autodoc",
     "sphinx.ext.napoleon",
     "sphinx.ext.viewcode",
     "sphinx_tabs.tabs",
+    "sphinx_exec_code",
 ]
 autoapi_dirs = ["../src/nbiatoolkit"]
 
@@ -33,11 +36,26 @@
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "_html_notebooks"]
 
+
+exec_code_working_dir = ".."
+exec_code_source_folders = ["../src"]
+
+
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
+# html_theme = "piccolo_theme"
 html_theme = "sphinx_rtd_theme"
 
+# # user starts in dark mode
+# default_dark_mode = True
+
 html_static_path = ["_static"]
+
+# html_css_files = [
+#     "css/custom.css",
+# ]
+# def setup(app):
+#     app.add_css_file("css/custom.css")
diff --git a/docs/index.md b/docs/index.md
@@ -7,10 +7,12 @@
 
 markdowns/NBIA.md
 markdowns/Installation.md
-InitializeClient.rst
-Tutorial.ipynb
+tutorial_files/1_InitializeClient.rst
+tutorial_files/2_ExploreCollections.rst
 markdowns/CHANGELOG.md
 markdowns/CONTRIBUTING.md
 markdowns/CONDUCT.md
 autoapi/index
 ```
+
+<!-- Tutorial.ipynb -->
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -2,3 +2,6 @@ myst-nb
 sphinx-autoapi
 sphinx-rtd-theme
 sphinx-tabs
+sphinx_exec_code==0.12
+piccolo_theme
+sphinx-rtd-dark-mode
diff --git a/docs/InitializeClient.rst → docs/tutorial_files/1_InitializeClient.rst b/docs/InitializeClient.rst → docs/tutorial_files/1_InitializeClient.rst
@@ -8,6 +8,8 @@ By default, the `NBIAClient` uses the guest account to access all collections in
 If you have a user account that has been granted specific access to a collection, you can use your credentials to
 initialize the client when performing a query.
 
+
+
 .. tabs::
 
    .. tab:: Python
@@ -19,12 +21,14 @@ initialize the client when performing a query.
 
          .. tab:: Guest Account
 
-            .. code-block:: python
+            .. exec_code::
 
                from nbiatoolkit import NBIAClient
 
                client = NBIAClient()
-               client.getCollections(prefix='TCGA')
+               collections = client.getCollections(prefix='TCGA')
+
+               print(collections[0:5])
 
          .. tab:: Your Account
 
@@ -33,7 +37,8 @@ initialize the client when performing a query.
                from nbiatoolkit import NBIAClient
 
                client = NBIAClient(username = "<USERNAME>", password = "<PASSWORD>")
-               client.getCollections(prefix='TCGA')
+               collections = client.getCollections(prefix='TCGA')
+
 
    .. tab:: Command Line
 
@@ -64,12 +69,14 @@ This is especially useful when using the client in a script with a predefined sc
 
    .. tab:: Python
 
-      .. code-block:: python
+      .. exec_code::
 
          from nbiatoolkit import NBIAClient
 
          with NBIAClient() as client:
-            client.getCollections(prefix='TCGA')
+            collections = client.getCollections(prefix='TCGA')
+
+         print(collections[0:5])
 
    .. tab:: Command Line
 
@@ -88,15 +95,21 @@ If you would like to return the data as a pandas DataFrame, you can pass the
 
    .. tab:: Python
 
-      .. code-block:: python
+      .. exec_code::
 
          from nbiatoolkit import NBIAClient
          from nbiatoolkit.utils import ReturnType
 
          client = NBIAClient()
-         client.getCollections(prefix='TCGA', return_type='dataframe')
+         collections_df = client.getCollections(
+            prefix='TCGA', return_type='dataframe'
+         )
          # equivalent to
-         client.getCollections(prefix='TCGA', return_type=ReturnType.DATAFRAME)
+         collections_df = client.getCollections(
+            prefix='TCGA', return_type=ReturnType.DATAFRAME
+         )
+
+         print(collections_df.head())
 
    .. tab:: Command Line
 
@@ -110,12 +123,14 @@ Alternatively, you can set the return type for all methods by passing the `retur
 
    .. tab:: Python
 
-      .. code-block:: python
+      .. exec_code::
 
          from nbiatoolkit import NBIAClient
 
          client = NBIAClient(return_type='dataframe')
-         client.getCollections(prefix='TCGA')
+         collections_df = client.getCollections(prefix='TCGA')
+
+         print(collections_df.head())
 
    .. tab:: Command Line
 

diff --git a/docs/tutorial_files/2_ExploreCollections.rst b/docs/tutorial_files/2_ExploreCollections.rst
@@ -0,0 +1,9 @@
+Metadata Query Methods
+----------------------
+
+
+Collection Methods
+^^^^^^^^^^^^^^^^^^
+
+.. autoclass:: nbiatoolkit.NBIAClient
+    :members: