diff --git a/README.md b/README.md index 857a06e..c6119cd 100644 --- a/README.md +++ b/README.md @@ -6,9 +6,10 @@ -[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1Tbnr1Fog_YjkqU1MOhcVLuxqZ4DC-c8-#forceEdit=true&sandboxMode=true) +[![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1Tbnr1Fog_YjkqU1MOhcVLuxqZ4DC-c8-#forceEdit=true&sandboxMode=true) [![Contributions](https://img.shields.io/badge/contributions-welcome-blue)](https://github.com/DeepGraphLearning/torchdrug/blob/master/CONTRIBUTING.md) [![License Apache-2.0](https://img.shields.io/github/license/DeepGraphLearning/torchdrug?color=blue)](https://github.com/DeepGraphLearning/torchdrug/blob/master/LICENSE) +[![PyPI downloads](https://static.pepy.tech/personalized-badge/torchdrug?period=total&units=international_system&left_color=grey&right_color=blue&left_text=downloads)](https://pypi.org/project/torchdrug/) [![TorchDrug Twitter](https://img.shields.io/twitter/url?label=TorchDrug&style=social&url=https%3A%2F%2Ftwitter.com%2FDrugTorch)](https://twitter.com/DrugTorch) [Docs] | [Tutorials] | [Benchmarks] | [Papers Implemented] @@ -42,7 +43,7 @@ conda install torchdrug -c milagraph -c conda-forge -c pytorch -c pyg ```bash pip3 install torch==1.9.0 -pip3 install torch-scatter -f https://pytorch-geometric.com/whl/torch-1.9.0+cu102.html +pip3 install torch-scatter torch-cluster -f https://pytorch-geometric.com/whl/torch-1.9.0+cu102.html pip3 install torchdrug ``` diff --git a/asset/graph/residues.png b/asset/graph/residues.png new file mode 100644 index 0000000..653c2b9 Binary files /dev/null and b/asset/graph/residues.png differ diff --git a/conda/torchdrug/meta.yaml b/conda/torchdrug/meta.yaml index b48a11a..9dd6ab0 100644 --- a/conda/torchdrug/meta.yaml +++ b/conda/torchdrug/meta.yaml @@ -1,6 +1,6 @@ package: name: torchdrug - version: 0.1.3 + version: 0.2.0 source: path: ../.. @@ -13,6 +13,7 @@ requirements: - python >=3.7,<3.10 - pytorch >=1.8.0 - pytorch-scatter >=2.0.8 + - pytorch-cluster >=1.5.9 - decorator - numpy >=1.11 - rdkit >=2020.09 @@ -21,6 +22,8 @@ requirements: - networkx - ninja - jinja2 + - python-lmdb + - bio-embeddings-esm build: noarch: python diff --git a/doc/source/installation.rst b/doc/source/installation.rst index 5d6a2a3..7101cf8 100644 --- a/doc/source/installation.rst +++ b/doc/source/installation.rst @@ -30,7 +30,7 @@ and CUDA is ``10.2``, the command should be .. code:: bash - pip3 install torch-scatter -f https://pytorch-geometric.com/whl/torch-1.8.0+cu102.html + pip3 install torch-scatter torch-cluster -f https://pytorch-geometric.com/whl/torch-1.8.0+cu102.html Replace the versions in the above url according to your case. If you don't have GPUs or CUDA installed, treat the CUDA version in the url as ``cpu``. See diff --git a/docker/Dockerfile b/docker/Dockerfile index 952009a..3b22f84 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -1,7 +1,7 @@ FROM pytorch/pytorch:1.8.1-cuda11.1-cudnn8-devel # metainformation -LABEL org.opencontainers.image.version = "0.1.3" +LABEL org.opencontainers.image.version = "0.2.0" LABEL org.opencontainers.image.authors = "TorchDrug Team" LABEL org.opencontainers.image.source = "https://github.com/DeepGraphLearning/torchdrug" LABEL org.opencontainers.image.licenses = "Apache License 2.0" @@ -11,5 +11,5 @@ RUN apt-get update && \ apt-get install -y libxrender1 && \ rm -rf /var/lib/apt/lists/* -RUN pip install torch-scatter -f https://pytorch-geometric.com/whl/torch-1.8.1+cu111.html && \ +RUN pip install torch-scatter torch-cluster -f https://pytorch-geometric.com/whl/torch-1.8.1+cu111.html && \ pip install torchdrug diff --git a/requirements.txt b/requirements.txt index 683eb65..c44f2c1 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,10 +1,13 @@ torch>=1.8.0 torch-scatter>=2.0.8 +torch-cluster>=1.5.9 decorator numpy>=1.11 -rdkit-pypi +rdkit-pypi>=2020.9 matplotlib tqdm networkx ninja -jinja2 \ No newline at end of file +jinja2 +lmdb +fair-esm \ No newline at end of file diff --git a/setup.py b/setup.py index c72475c..afa59de 100644 --- a/setup.py +++ b/setup.py @@ -13,7 +13,7 @@ long_description_content_type="text/markdown", url="https://torchdrug.ai/", author="TorchDrug Team", - version="0.1.3", + version="0.2.0", license="Apache-2.0", keywords=["deep-learning", "pytorch", "drug-discovery"], packages=setuptools.find_packages(), @@ -31,6 +31,7 @@ install_requires=[ "torch>=1.8.0", "torch-scatter>=2.0.8", + "torch-cluster>=1.5.9", "decorator", "numpy>=1.11", "rdkit-pypi>=2020.9", @@ -39,6 +40,8 @@ "networkx", "ninja", "jinja2", + "lmdb", + "fair-esm", ], python_requires=">=3.7,<3.10", classifiers=[ diff --git a/torchdrug/__init__.py b/torchdrug/__init__.py index b0989c3..3ece07b 100644 --- a/torchdrug/__init__.py +++ b/torchdrug/__init__.py @@ -12,4 +12,4 @@ handler.setFormatter(format) logger.addHandler(handler) -__version__ = "0.1.3" \ No newline at end of file +__version__ = "0.2.0" \ No newline at end of file diff --git a/torchdrug/layers/common.py b/torchdrug/layers/common.py index 98d06d7..f2b4582 100644 --- a/torchdrug/layers/common.py +++ b/torchdrug/layers/common.py @@ -74,7 +74,7 @@ def forward(self, input): class GaussianSmearing(nn.Module): r""" Gaussian smearing from - `SchNet: A continuous-filter convolutional neural network for modeling quantum interactions`_.`` + `SchNet: A continuous-filter convolutional neural network for modeling quantum interactions`_. There are two modes for Gaussian smearing.