Update docs

.gitignore

@@ -78,6 +78,8 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/_static/
+docs/_templates/
 
 # PyBuilder
 target/

docs/Configuration.rst

@@ -0,0 +1,5 @@
+Configuration
+=============
+
+High-level overview
+-------------------

docs/GettingStarted.rst

@@ -0,0 +1,20 @@
+Getting started
+===============
+
+``lartpc_mlreco3d`` is a machine learning pipeline for LArTPC data.
+
+Basic example
+--------------
+
+.. code-block:: python
+   :linenos:
+
+   # assume that lartpc_mlreco3d folder is on python path
+   from mlreco.main_funcs import process_config, train
+   import yaml
+   # Load configuration file
+   with open('lartpc_mlreco3d/config/test_uresnet.cfg', 'r') as f:
+       cfg = yaml.load(f, Loader=yaml.Loader)
+   process_config(cfg)
+   # train a model based on configuration
+   train(cfg)

docs/conf.py

@@ -24,10 +24,17 @@
 
 # -- General configuration ---------------------------------------------------
 
+import sphinx_rtd_theme
+import sys
+sys.path.append("../")
+
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
+    'sphinx_rtd_theme',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.napoleon'
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -44,9 +51,10 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+# html_theme = 'alabaster'
+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']

docs/index.rst

@@ -5,15 +5,25 @@
 
 Welcome to lartpc_mlreco3d's documentation!
 ===========================================
+This documentation is meant to host technical details related to ``lartpc_mlreco3d``.
 
 .. toctree::
+   :maxdepth: 3
+   :caption: First steps
+
+   GettingStarted
+   Configuration
+
+.. toctree::
+   :caption: Code documentation
    :maxdepth: 2
-   :caption: Contents:
+
+   mlreco
 
 
 
 Indices and tables
-==================
+------------------
 
 * :ref:`genindex`
 * :ref:`modindex`

docs/mlreco.iotools.rst

@@ -0,0 +1,53 @@
+mlreco.iotools package
+======================
+
+Submodules
+----------
+
+mlreco.iotools.collates module
+------------------------------
+
+.. automodule:: mlreco.iotools.collates
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mlreco.iotools.datasets module
+------------------------------
+
+.. automodule:: mlreco.iotools.datasets
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mlreco.iotools.factories module
+-------------------------------
+
+.. automodule:: mlreco.iotools.factories
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mlreco.iotools.parsers module
+-----------------------------
+
+.. automodule:: mlreco.iotools.parsers
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mlreco.iotools.samplers module
+------------------------------
+
+.. automodule:: mlreco.iotools.samplers
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: mlreco.iotools
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/mlreco.models.chain.rst

@@ -0,0 +1,29 @@
+mlreco.models.chain package
+===========================
+
+Submodules
+----------
+
+mlreco.models.chain.full\_cnn module
+------------------------------------
+
+.. automodule:: mlreco.models.chain.full_cnn
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mlreco.models.chain.pooling module
+----------------------------------
+
+.. automodule:: mlreco.models.chain.pooling
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: mlreco.models.chain
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/mlreco.models.cluster_cnn.losses.rst

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+mlreco.models.cluster\_cnn.losses package
+=========================================
+
+Submodules
+----------
+
+mlreco.models.cluster\_cnn.losses.dense\_cluster module
+-------------------------------------------------------
+
+.. automodule:: mlreco.models.cluster_cnn.losses.dense_cluster
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mlreco.models.cluster\_cnn.losses.lovasz module
+-----------------------------------------------
+
+.. automodule:: mlreco.models.cluster_cnn.losses.lovasz
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mlreco.models.cluster\_cnn.losses.misc module
+---------------------------------------------
+
+.. automodule:: mlreco.models.cluster_cnn.losses.misc
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mlreco.models.cluster\_cnn.losses.multi\_layers module
+------------------------------------------------------
+
+.. automodule:: mlreco.models.cluster_cnn.losses.multi_layers
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mlreco.models.cluster\_cnn.losses.occuseg module
+------------------------------------------------
+
+.. automodule:: mlreco.models.cluster_cnn.losses.occuseg
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mlreco.models.cluster\_cnn.losses.radius\_nnloss module
+-------------------------------------------------------
+
+.. automodule:: mlreco.models.cluster_cnn.losses.radius_nnloss
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mlreco.models.cluster\_cnn.losses.single\_layers module
+-------------------------------------------------------
+
+.. automodule:: mlreco.models.cluster_cnn.losses.single_layers
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mlreco.models.cluster\_cnn.losses.spatial\_embeddings module
+------------------------------------------------------------
+
+.. automodule:: mlreco.models.cluster_cnn.losses.spatial_embeddings
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mlreco.models.cluster\_cnn.losses.spatial\_embeddings\_fast module
+------------------------------------------------------------------
+
+.. automodule:: mlreco.models.cluster_cnn.losses.spatial_embeddings_fast
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: mlreco.models.cluster_cnn.losses
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/mlreco.models.cluster_cnn.rst

@@ -0,0 +1,61 @@
+mlreco.models.cluster\_cnn package
+==================================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   mlreco.models.cluster_cnn.losses
+
+Submodules
+----------
+
+mlreco.models.cluster\_cnn.clusternet module
+--------------------------------------------
+
+.. automodule:: mlreco.models.cluster_cnn.clusternet
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mlreco.models.cluster\_cnn.embeddings module
+--------------------------------------------
+
+.. automodule:: mlreco.models.cluster_cnn.embeddings
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mlreco.models.cluster\_cnn.factories module
+-------------------------------------------
+
+.. automodule:: mlreco.models.cluster_cnn.factories
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mlreco.models.cluster\_cnn.spatial\_embeddings module
+-----------------------------------------------------
+
+.. automodule:: mlreco.models.cluster_cnn.spatial_embeddings
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mlreco.models.cluster\_cnn.utils module
+---------------------------------------
+
+.. automodule:: mlreco.models.cluster_cnn.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: mlreco.models.cluster_cnn
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/mlreco.models.gnn.encoders.rst

@@ -0,0 +1,45 @@
+mlreco.models.gnn.encoders package
+==================================
+
+Submodules
+----------
+
+mlreco.models.gnn.encoders.cnn module
+-------------------------------------
+
+.. automodule:: mlreco.models.gnn.encoders.cnn
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mlreco.models.gnn.encoders.geometric module
+-------------------------------------------
+
+.. automodule:: mlreco.models.gnn.encoders.geometric
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mlreco.models.gnn.encoders.gnn module
+-------------------------------------
+
+.. automodule:: mlreco.models.gnn.encoders.gnn
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+mlreco.models.gnn.encoders.mixed module
+---------------------------------------
+
+.. automodule:: mlreco.models.gnn.encoders.mixed
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: mlreco.models.gnn.encoders
+   :members:
+   :undoc-members:
+   :show-inheritance: