Merge remote-tracking branch 'origin/main' into custom_dataset

.github/workflows/CI.yml

@@ -44,3 +44,7 @@ jobs:
 
       - name: Run tests
         run: pytest -v -s
+
+      - name: Test torchmd-train utility
+        run: torchmd-train --help
+

.github/workflows/docs_build.yaml

@@ -0,0 +1,36 @@
+name: Build Documentation
+
+on:
+  push:
+    branches:
+      - "main"
+  pull_request:
+    branches:
+      - "main"
+
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Env
+      uses: mamba-org/setup-micromamba@v1
+      with:
+        environment-file: environment.yml
+        init-shell: bash
+        generate-run-shell: true
+
+    - name: Install docs dependencies
+      run: |
+        pip install -vv .
+        pip install -r docs/requirements.txt
+      shell: bash -el {0}
+
+    - name: Build Sphinx Documentation
+      run: |
+        cd docs
+        make html
+      shell: bash -el {0}

.gitignore

@@ -133,3 +133,11 @@ dmypy.json
 
 # temp directories
 logs/
+
+# Docs
+docs/build/
+docs/source/generated
+
+# Extra
+
+*~

.readthedocs.yaml

@@ -0,0 +1,17 @@
+version: "2"
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+     python: "mambaforge-22.9"
+  jobs:
+     post_create_environment:
+       - pip install -r docs/requirements.txt
+       - pip install .
+
+conda:
+  environment: environment.yml
+
+
+sphinx:
+  configuration: docs/source/conf.py

README.md

@@ -1,10 +1,16 @@
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![CI](https://github.com/torchmd/torchmd-net/actions/workflows/CI.yml/badge.svg)](https://github.com/torchmd/torchmd-net/actions/workflows/CI.yml)
+[![Documentation Status](https://readthedocs.org/projects/torchmd-net/badge/?version=latest)](https://torchmd-net.readthedocs.io/en/latest/?badge=latest)  
 
 # TorchMD-NET
 
 TorchMD-NET provides state-of-the-art neural networks potentials (NNPs) and a mechanism to train them. It offers efficient and fast implementations if several NNPs and it is integrated in GPU-accelerated molecular dynamics code like [ACEMD](https://www.acellera.com/products/molecular-dynamics-software-gpu-acemd/), [OpenMM](https://www.openmm.org) and [TorchMD](https://github.com/torchmd/torchmd). TorchMD-NET exposes its NNPs as [PyTorch](https://pytorch.org) modules.
 
+
+## Documentation
+
+Documentation is available at https://torchmd-net.readthedocs.io  
+
 ## Available architectures
 
 - [Equivariant Transformer (ET)](https://arxiv.org/abs/2202.02541)
@@ -13,15 +19,23 @@ TorchMD-NET provides state-of-the-art neural networks potentials (NNPs) and a me
 - [TensorNet](https://arxiv.org/abs/2306.06482)
 
 
-## Installation
+
+## Installation  
+TorchMD-Net is available in [conda-forge](https://conda-forge.org/) and can be installed with:  
+```shell
+mamba install torchmd-net
+```
+We recommend using [Mamba](https://github.com/conda-forge/miniforge/#mambaforge) instead of conda.  
+
+### Install from source  
 
 1. Clone the repository:
     ```shell
     git clone https://github.com/torchmd/torchmd-net.git
     cd torchmd-net
     ```
 
-2. Install [Mambaforge](https://github.com/conda-forge/miniforge/#mambaforge). We recommend to use `mamba` rather than `conda`.
+2. Install the dependencies in environment.yml. You can do it via pip, but we recommend [Mambaforge](https://github.com/conda-forge/miniforge/#mambaforge) instead.
 
 3. Create an environment and activate it:
     ```shell
@@ -36,6 +50,23 @@ TorchMD-NET provides state-of-the-art neural networks potentials (NNPs) and a me
 This will install TorchMD-NET in editable mode, so that changes to the source code are immediately available.
 Besides making all python utilities available environment-wide, this will also install the `torchmd-train` command line utility.
 
+
+#### CUDA enabled installation
+
+Besides the dependencies listed in the environment file, you will also need the CUDA `nvcc` compiler suite to build TorchMD-Net.   
+If your system lacks nvcc you may install it via conda-forge:
+	```shell
+	mamba install cudatoolkit-dev
+	```
+Or from the nvidia channel:
+```shell
+mamba install -c nvidia cuda-nvcc cuda-cudart-dev cuda-libraries-dev
+```
+Make sure you install a major version compatible with your torch installation, which you can check with:
+```shell
+python -c "import torch; print(torch.version.cuda)"
+```
+
 ## Usage
 Specifying training arguments can either be done via a configuration yaml file or through command line arguments directly. Several examples of architectural and training specifications for some models and datasets can be found in [examples/](https://github.com/torchmd/torchmd-net/tree/main/examples). Note that if a parameter is present both in the yaml file and the command line, the command line version takes precedence.
 GPUs can be selected by setting the `CUDA_VISIBLE_DEVICES` environment variable. Otherwise, the argument `--ngpus` can be used to select the number of GPUs to train on (-1, the default, uses all available GPUs or the ones specified in `CUDA_VISIBLE_DEVICES`). Keep in mind that the [GPU ID reported by nvidia-smi might not be the same as the one `CUDA_VISIBLE_DEVICES` uses](https://stackoverflow.com/questions/26123252/inconsistency-of-ids-between-nvidia-smi-l-and-cudevicegetname).  

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/_static/style.css

@@ -0,0 +1,59 @@
+@import 'theme.css';
+
+.rst-content dl:not(.docutils) dt:first-child {
+  margin-top: 0;
+}
+
+.rst-content dl:not(.docutils) dl dt {
+    margin-bottom: 4px;
+    border: none;
+    border-left: solid 3px #ccc;
+    background: #f0f0f0;
+    color: #555;
+}
+
+.rst-content dl table,
+.rst-content dl ul,
+.rst-content dl ol,
+.rst-content dl p {
+    margin-bottom: 8px !important;
+}
+
+.rst-content dl:not(.docutils) dt {
+    display: table;
+    margin: 6px 0;
+    font-size: 90%;
+    line-height: normal;
+    background: #e7f2fa;
+    color: #2980B9;
+    border-top: solid 3px #6ab0de;
+    padding: 6px;
+    position: relative;
+}
+
+html.writer-html5 .rst-content dl.field-list {
+    display: initial;
+}
+
+html.writer-html5 .rst-content dl.field-list>dd,
+html.writer-html5 .rst-content dl.field-list>dt {
+    margin-bottom: 4px;
+    padding-left: 6px;
+}
+
+p {
+    line-height: 20px;
+    font-size: 14px;
+}
+
+html.writer-html5 .rst-content dl.field-list>dt:after {
+    content: initial;
+}
+
+dt.field-even {
+    text-transform: uppercase;
+}
+
+dt.field-odd {
+    text-transform: uppercase;
+}

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
+
+if "%1" == "" goto help
+
+%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.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/requirements.txt

@@ -0,0 +1,5 @@
+sphinx==7.2.6
+sphinx-rtd-theme==1.3.0
+sphinxcontrib-autoprogram==0.1.8
+sphinxcontrib-napoleon==0.7
+gitpython

docs/source/api.rst

@@ -0,0 +1,10 @@
+API Reference
+=============
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   torchmdnet
+
+

docs/source/conf.py

@@ -0,0 +1,88 @@
+# Configuration file for the Sphinx documentation builder.
+
+# -- Project information
+project = "TorchMD-Net"
+author = "RaulPPelaez"
+
+import git
+
+
+def get_latest_git_tag(repo_path="."):
+    repo = git.Repo(repo_path)
+    tags = sorted(repo.tags, key=lambda t: t.commit.committed_datetime)
+    return tags[-1].name if tags else None
+
+
+current_tag = get_latest_git_tag("../../")
+if current_tag is None:
+    current_tag = "master"
+release = current_tag
+version = current_tag
+
+# -- General configuration
+extensions = [
+    "sphinx.ext.duration",
+    "sphinx.ext.doctest",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+    "sphinxcontrib.autoprogram",
+]
+napoleon_google_docstring = True
+napoleon_numpy_docstring = True
+napoleon_include_init_with_doc = False
+napoleon_include_private_with_doc = False
+napoleon_include_special_with_doc = True
+napoleon_use_admonition_for_examples = True
+napoleon_use_admonition_for_notes = True
+napoleon_use_admonition_for_references = True
+napoleon_use_ivar = False
+napoleon_use_param = True
+napoleon_use_rtype = True
+napoleon_preprocess_types = True
+napoleon_type_aliases = None
+napoleon_attr_annotations = True
+autosummary_ignore_module_all = False
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3/", None),
+    "torch": ("https://pytorch.org/docs/stable/", None),
+    "sphinx": ("https://www.sphinx-doc.org/en/master/", None),
+}
+intersphinx_disabled_domains = ["std"]
+
+templates_path = ["_templates"]
+
+# -- Options for HTML output
+
+html_theme = "sphinx_rtd_theme"
+
+# -- Options for EPUB output
+epub_show_urls = "footnote"
+
+autoclass_content = "both"
+autodoc_typehints = "none"
+autodoc_inherit_docstrings = False
+sphinx_autodoc_typehints = True
+html_show_sourcelink = True
+autodoc_default_options = {
+    "members": True,
+    "member-order": "bysource",
+    "exclude-members": "__weakref__",
+    "undoc-members": False,
+    "show-inheritance": True,
+    "inherited-members": False,
+}
+# Exclude all torchmdnet.datasets.*.rst files in source/generated/
+exclude_patterns = [
+    "generated/torchmdnet.datasets.*.rst",
+    "generated/torchmdnet.scripts.*rst",
+]
+html_static_path = ["../_static"]
+html_css_files = [
+    "style.css",
+]
+
+autodoc_mock_imports = ["torchmdnet.extensions.torchmdnet_extensions"]