Docs (#200)

* docs start

* new start

* add .readthedocs.yml

* update .readthedoc.yml

* update

* 1

* 2

* update requirement for docs

* rst to md

* add mds

* update requirements installation tutorial

* update docs

* add task/model docs (#195)

task&model docs

* add docs for task and model

* update model and task

* update

* update

* add doc (#197)

Co-authored-by: nobody <nobody>

* add utils and update

* init docs of interface (#198)

* update train-predict

* update doc of Data

* add data

* update predict

* update readme

* update readme

---------

Co-authored-by: cuiyaning <[email protected]>
Co-authored-by: Cody Zhao <[email protected]>
Co-authored-by: robotcator <[email protected]>
Co-authored-by: Zhifeng Gao <[email protected]>
Co-authored-by: hswang <[email protected]>

.readthedocs.yml

@@ -0,0 +1,28 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+   - requirements: docs/requirements.txt

README.md

@@ -48,6 +48,8 @@ Uni-Mol tools is a easy-use wrappers for property prediction,representation and
 
 Check this [subfolder](./unimol_tools/) for more detalis.
 
+Documentation of Uni-Mol tools is available at https://unimol.readthedocs.io/en/latest/
+
 News
 ----
 **Jul 7 2023**: We update a new version of Uni-Mol+, including the model setting for OC20 and a better performance on PCQM4MV2. 

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# 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)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/requirements.txt

@@ -0,0 +1,27 @@
+# Packages required to build docs, independent of application dependencies
+
+-e ./unimol_tools
+
+sphinx
+
+sphinx_rtd_theme==2.0.0rc2
+sphinx-tabs
+sphinx-intl
+sphinx-design
+sphinx-multiproject
+
+# RTD deps :)
+readthedocs-sphinx-search
+sphinx-hoverxref
+sphinx-notfound-page
+
+# Docs
+sphinxemoji
+sphinxcontrib-httpdomain
+sphinx-prompt
+sphinx-autobuild
+sphinxext-opengraph
+sphinx-copybutton
+
+# Markdown
+myst_parser

docs/source/conf.py

@@ -0,0 +1,60 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'Uni-Mol tools'
+copyright = '2023, cuiyaning'
+author = 'cuiyaning'
+release = '0.1.0'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.viewcode',
+    'myst_parser',
+    ]
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+highlight_language = 'python'
+
+
+# List of modules to be mocked up. This is useful when some external
+# dependencies are not met at build time and break the building process.
+autodoc_mock_imports = [
+    'rdkit',
+    'unicore',
+    'torch',
+    'sklearn',
+]
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']
+
+# -- Autodoc configuration ---------------------------------------------------
+
+autoclass_content = 'class'
+
+# 显式地设置成员的顺序，确保构造函数的参数首先显示
+autodoc_member_order = 'bysource'
+
+# 设置构造函数的默认选项，包括显示参数
+
+autodoc_default_options = {
+    'members': True,
+    'special-members': '__init__',
+    #'undoc-members': False,
+    'private-members': True,
+    #'show-inheritance': False,
+}

docs/source/data.rst

@@ -0,0 +1,36 @@
+Data
+====
+
+`unimol_tools.data <https://github.com/dptech-corp/Uni-Mol/tree/docs/unimol_tools/unimol_tools/data>`_ contains functions and classes for loading, containing, and scaler data, feature.
+
+DataHub
+-------
+
+Classes and functions from  `unimol_tools.data.datahub.py <https://github.com/dptech-corp/Uni-Mol/tree/docs/unimol_tools/unimol_tools/data/datahub.py>`_. 
+
+.. automodule:: unimol_tools.data.datahub
+   :members:
+
+Datareader
+----------
+
+Classes and functions from `unimol_tools.data.datareader.py <https://github.com/dptech-corp/Uni-Mol/tree/docs/unimol_tools/unimol_tools/data/datareader.py>`_.
+
+.. automodule:: unimol_tools.data.datareader
+   :members:
+
+Datascaler
+-----------
+
+Classes and functions from `unimol_tools.data.datascaler.py <https://github.com/dptech-corp/Uni-Mol/tree/docs/unimol_tools/unimol_tools/data/datascaler.py>`_.
+
+.. automodule:: unimol_tools.data.datascaler
+   :members:
+
+Conformer
+---------
+
+Classes and functions from `unimol_tools.data.conformer.py <https://github.com/dptech-corp/Uni-Mol/tree/docs/unimol_tools/unimol_tools/data/conformer.py>`_.
+
+.. automodule:: unimol_tools.data.conformer
+   :members:

docs/source/features.md

@@ -0,0 +1,3 @@
+# New Features
+
+## Coming Soon...

docs/source/index.rst

@@ -0,0 +1,34 @@
+.. UniMol documentation master file, created by
+   sphinx-quickstart on Wed Nov 29 03:53:18 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to Uni-Mol tools' documentation!
+==========================================
+
+Uni-Mol tools is a easy-use wrappers for property prediction,representation and downstreams with Uni-Mol. It includes the following tools:
+
+* molecular property prediction with Uni-Mol.
+* molecular representation with Uni-Mol.
+* other downstreams with Uni-Mol.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   requirements
+   installation
+   tutorial
+   train
+   data
+   models
+   task
+   utils
+   features
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/installation.md

@@ -0,0 +1,33 @@
+# Installation
+
+## Overview
+
+[Uni-Mol](https://github.com/dptech-corp/Uni-Mol/tree/main)
+ now can be installed from source. 
+```shell
+## unicore and other dependencies installation
+pip install -r requirements.txt
+## clone repo
+git clone https://github.com/dptech-corp/Uni-Mol.git
+cd Uni-Mol/unimol_tools/unimol_tools
+
+## download pretrained weights
+wget https://github.com/dptech-corp/Uni-Mol/releases/download/v0.1/mol_pre_all_h_220816.pt
+wget https://github.com/dptech-corp/Uni-Mol/releases/download/v0.1/mol_pre_no_h_220816.pt
+wget https://github.com/dptech-corp/Uni-Mol/releases/download/v0.1/pocket_pre_220816.pt
+wget https://github.com/dptech-corp/Uni-Mol/releases/download/v0.1/mof_pre_no_h_CORE_MAP_20230505.pt
+wget https://github.com/dptech-corp/Uni-Mol/releases/download/v0.1/mp_all_h_230313.pt
+wget https://github.com/dptech-corp/Uni-Mol/releases/download/v0.1/oled_pre_no_h_230101.pt
+
+mkdir -p weights
+mv *.pt weights/
+
+## install
+cd ..
+python setup.py install
+```
+
+## Bohrium notebook
+
+Uni-Mol images can be avaliable on the online notebook platform [Bohirum notebook](https://nb.bohrium.dp.tech/).
+

docs/source/models.rst

@@ -0,0 +1,39 @@
+.. _models:
+
+Models
+======
+
+`unimol_tools.models <https://github.com/dptech-corp/Uni-Mol/blob/docs/unimol_tools/unimol_tools/models>`_ contains the models of Uni-Mol.
+
+
+Uni-Mol
+-------
+
+`unimol_tools.models.unimol.py <https://github.com/dptech-corp/Uni-Mol/blob/docs/unimol_tools/unimol_tools/models/unimol.py>`_ contains the :class:`~unimol_tools.models.UniMolModel`, which is the backbone of Uni-Mol model.
+
+.. automodule:: unimol_tools.models.unimol
+   :members:
+
+Model
+-----
+
+`unimol_tools.models.nnmodel.py <https://github.com/dptech-corp/Uni-Mol/blob/docs/unimol_tools/unimol_tools/models/unimol.py>`_ contains the :class:`~unimol_tools.models.NNModel`, which is responsible for initializing the model.
+
+.. automodule:: unimol_tools.models.nnmodel
+   :members:
+
+Loss
+-----
+
+`unimol_tools.models.loss.py <https://github.com/dptech-corp/Uni-Mol/blob/docs/unimol_tools/unimol_tools/models/loss.py>`_ contains different loss functions.
+
+.. automodule:: unimol_tools.models.loss
+   :members:
+
+Transformers
+------------
+
+`unimol_tools.models.transformers.py <https://github.com/dptech-corp/Uni-Mol/blob/docs/unimol_tools/unimol_tools/models/transformers.py>`_ contains a custom Transformer Encoder module that extends `PyTorch's nn.Module <https://pytorch.org/docs/stable/generated/torch.nn.Module.html>`_.
+
+.. automodule:: unimol_tools.models.transformers
+   :members:

docs/source/requirements.md

@@ -0,0 +1,8 @@
+# Requirements
+
+For small datasets (~1000 molecules), it is possible to train models within a few minutes on a standard laptop with CPUs only. However, for larger datasets and larger Uni-Mol models, we recommend using a GPU for significantly faster training.
+
+Notice: [Uni-Core](https://github.com/dptech-corp/Uni-Core) is needed, please install it first. Current Uni-Core requires torch>=2.0.0 by default, if you want to install other version, please check its [Installation Documentation](https://github.com/dptech-corp/Uni-Core#installation).
+
+
+Uni-Mol is uses Python 3.8+ and all models are built with [PyTorch](https://pytorch.org/). See [Installation](#installation) for details on how to install Uni-Mol and its dependencies.

docs/source/task.rst

@@ -0,0 +1,23 @@
+.. _tasks:
+
+Task
+======
+
+`unimol_tools.tasks <https://github.com/dptech-corp/Uni-Mol/blob/docs/unimol_tools/unimol_tools/tasks>`_ oversees the tasks related to the model, such as training and prediction.
+
+
+Trainer
+-------
+
+`unimol_tools.tasks.trainer.py <https://github.com/dptech-corp/Uni-Mol/blob/docs/unimol_tools/unimol_tools/tasks/trainer.py>`_ contains the :class:`~unimol_tools.unimol_tools.models.tasks.Trainer`, managing the training, validation, and testing phases.
+
+.. automodule:: unimol_tools.tasks.trainer
+   :members:
+
+Split
+-------
+
+`unimol_tools.tasks.split.py <https://github.com/dptech-corp/Uni-Mol/blob/docs/unimol_tools/unimol_tools/tasks/split.py>`_ manages the split methods in the dataset.
+
+.. automodule:: unimol_tools.tasks.split
+   :members: