deepskies · bnord · May 17, 2024 · Apr 15, 2024 · Apr 15, 2024
diff --git a/docs/source/API/client.rst b/docs/source/API/client.rst
@@ -1,5 +1,5 @@
 Client 
 ========
 
-.. autoclass:: DeepDiagnostics.Client
+.. automodule:: client
     :members:
diff --git a/docs/source/API/data.rst b/docs/source/API/data.rst
@@ -1,5 +1,11 @@
 Data 
 ======
 
-.. autoclass:: DeepDiagnostics.data.data.Data
+.. autoclass:: data.data.Data
+    :members:
+
+.. autoclass:: data.H5Data
+    :members:
+
+.. autoclass:: data.PickleData
     :members:
diff --git a/docs/source/API/metrics.rst b/docs/source/API/metrics.rst
@@ -1,5 +1,5 @@
 Metrics 
 ===========
 
-.. autoclass:: DeepDiagnostics.metrics.metrics.Metrics
+.. autoclass:: metrics.metric.Metric
     :members:
diff --git a/docs/source/API/models.rst b/docs/source/API/models.rst
@@ -1,2 +1,8 @@
 Models 
-========
+========
+
+.. autoclass:: models.model.Model
+    :members:
+
+.. autoclass:: models.SBIModel
+    :members:
diff --git a/docs/source/API/plots.rst b/docs/source/API/plots.rst
@@ -1,6 +1,6 @@
 Plots 
 ========
 
-.. autoclass:: DeepDiagnostics.plots.plots.Plots
+.. autoclass:: plots.Plots
     :members:
 
diff --git a/docs/source/API/utils.rst b/docs/source/API/utils.rst
@@ -1,5 +1,6 @@
 Utils 
 =======
 
-.. autoclass:: DeepDiagnostics.utils.config.Config 
-    :members:
+.. autoclass:: utils.config.Config 
+    :members:
+
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -14,6 +14,9 @@
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
+import sys
+sys.path.append("../src")
+
 extensions = [
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",

diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -14,7 +14,12 @@ Welcome to DeepDiagnostics's documentation!
    configuration
    plots
    metrics
-   API 
+   API/client
+   API/utils 
+   API/data
+   API/models 
+   API/plots 
+   API/metrics
 
 Indices and tables
 ==================

diff --git a/docs/source/metrics.rst b/docs/source/metrics.rst
@@ -1,2 +1,4 @@
+.. _metrics:
+
 Metrics
 =========
diff --git a/docs/source/plots.rst b/docs/source/plots.rst
@@ -1,2 +1,4 @@
+.. _plots:
+
 Plots 
 =======
diff --git a/docs/source/quickstart.rst b/docs/source/quickstart.rst
@@ -1,2 +1,60 @@
 Quickstart 
-============
+============
+
+Installation 
+--------------
+
+* From PyPi 
+.. code-block:: console 
+    pip install DeepDiagnostics
+
+
+* From Source 
+.. code-block:: console 
+    git clone https://github.com/deepskies/DeepDiagnostics/ 
+    pip install poetry 
+    poetry shell 
+    poetry install
+
+
+Pipeline 
+---------
+
+`DeepDiagnostics` includes a CLI tool for analysis. 
+* To run the tool using a configuration file: 
+
+.. code-block:: console 
+    diagnose --config {path to yaml}
+
+
+* To use defaults with specific models and data: 
+
+.. code-block:: console 
+    diagnose --model_path {model pkl} --data_path {data pkl} [--simulator {sim name}]
+
+
+Additional arguments can be found using ``diagnose -h``
+
+Standalone 
+----
+
+`DeepDiagnostics` comes with the option to run different plots and metrics independently. 
+This requires setting a configuration file ahead of time, and then running the plots. 
+
+All plots and metrics can be found in :ref:`plots<plots>` and :ref:`metrics<metrics>`. 
+
+
+
+.. code-block:: python 
+
+    from DeepDiagnostics.utils.configuration import Config 
+    from DeepDiagnostics.model import SBIModel 
+    from DeepDiagnostics.data import H5Data
+
+    from DeepDiagnostics.plots import ...
+
+    Config({configuration_path})
+    model = SBIModel({model_path})
+    data = H5Data({data_path})
+
+    {Plot of choice}