Merge pull request #43 from choderalab/add-docs

Add docs

.gitignore

@@ -64,6 +64,8 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/_autosummary/
+
 
 # PyBuilder
 target/

.readthedocs.yaml

@@ -0,0 +1,20 @@
+# readthedocs.yml
+
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "mambaforge-22.9"
+
+sphinx:
+   configuration: docs/conf.py
+
+conda:
+  environment: docs/requirements.yaml
+
+python:
+  # Install our python package before building the docs
+  install:
+    - method: pip
+      path: .

README.md

@@ -3,7 +3,7 @@ MTENN
 [//]: # (Badges)
 [![GitHub Actions Build Status](https://github.com/choderalab/mtenn/workflows/CI/badge.svg)](https://github.com/REPLACE_WITH_OWNER_ACCOUNT/mtenn/actions?query=workflow%3ACI)
 [![codecov](https://codecov.io/gh/choderalab/mtenn/branch/master/graph/badge.svg)](https://codecov.io/gh/REPLACE_WITH_OWNER_ACCOUNT/MTENN/branch/master)
-
+[![Documentation Status](https://readthedocs.org/projects/mtenn/badge/?version=latest)](https://mtenn.readthedocs.io/en/latest/?badge=latest)
 
 Modular Training and Evaluation of Neural Networks
 

docs/Makefile

@@ -1,9 +1,10 @@
 # Minimal makefile for Sphinx documentation
 #
 
-# You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
 SPHINXPROJ    = mtenn
 SOURCEDIR     = .
 BUILDDIR      = _build
@@ -17,4 +18,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/_templates/README.md

@@ -1,11 +1,11 @@
 # Templates Doc Directory
 
-Add any paths that contain templates here, relative to  
+Add any paths that contain templates here, relative to
 the `conf.py` file's directory.
 They are copied after the builtin template files,
 so a file named "page.html" will overwrite the builtin "page.html".
 
-The path to this folder is set in the Sphinx `conf.py` file in the line: 
+The path to this folder is set in the Sphinx `conf.py` file in the line:
 ```python
 html_static_path = ['_templates']
 ```

docs/_templates/custom-class-template.rst

@@ -0,0 +1,32 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+   :show-inheritance:
+   :inherited-members:
+
+   {% block methods %}
+   .. automethod:: __init__
+
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
+
+   .. autosummary::
+   {% for item in methods %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}

docs/_templates/custom-module-template.rst

@@ -0,0 +1,66 @@
+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Module Attributes
+
+   .. autosummary::
+      :toctree:
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+      :toctree:
+      :template: custom-class-template.rst
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+{% block modules %}
+{% if modules %}
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :template: custom-module-template.rst
+   :recursive:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}

docs/conf.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # Configuration file for the Sphinx documentation builder.
 #
@@ -23,12 +22,9 @@
 
 # -- Project information -----------------------------------------------------
 
-project = "MTENN"
-copyright = (
-    "2022, Benjamin Kaminow. Project structure based on the "
-    "Computational Molecular Science Python Cookiecutter version 1.6"
-)
-author = "Benjamin Kaminow"
+project = "mtenn"
+copyright = "2024, Chodera Lab"
+author = "Chodera Lab"
 
 # The short X.Y version
 version = ""
@@ -77,7 +73,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -144,15 +140,29 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, "mtenn.tex", "MTENN Documentation", "mtenn", "manual"),
+    (
+        master_doc,
+        "mtenn.tex",
+        "MTENN Documentation",
+        "mtenn",
+        "manual",
+    ),
 ]
 
 
 # -- Options for manual page output ------------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [(master_doc, "mtenn", "MTENN Documentation", [author], 1)]
+man_pages = [
+    (
+        master_doc,
+        "mtenn",
+        "MTENN Documentation",
+        [author],
+        1,
+    )
+]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -167,7 +177,7 @@
         "MTENN Documentation",
         author,
         "mtenn",
-        "Modular Training and Evaluation of Neural Networks",
+        "Modular Training and Evaluation of Neural Networks.",
         "Miscellaneous",
     ),
 ]

docs/index.rst

@@ -1,17 +1,24 @@
 .. mtenn documentation master file, created by
-   sphinx-quickstart on Thu Mar 15 13:55:56 2018.
+   sphinx-quickstart on Wed Jan 31 13:59:42 2024.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to MTENN's documentation!
-=========================================================
+Welcome to mtenn's documentation!
+=================================
 
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
 
    getting_started
-   api
+
+
+.. autosummary::
+   :toctree: _autosummary
+   :template: custom-module-template.rst
+   :recursive:
+
+   mtenn
 
 
 

docs/requirements.yaml

@@ -1,12 +1,20 @@
-name: docs
+name: mtenn
 channels:
+  - conda-forge
 dependencies:
-    # Base depends
-  - python
-  - pip
-
-
-
-    # Pip-only installs
-  #- pip:
+  - pytorch
+  - pytorch_geometric
+  - pytorch_cluster
+  - pytorch_scatter
+  - pytorch_sparse
+  - numpy
+  - h5py
+  - e3nn
+  - dgllife
+  - dgl
+  - rdkit
+  - ase
 
+  # docs
+  - sphinx
+  - sphinx_rtd_theme