Cleanup works + bug fixes

.gitignore

@@ -13,4 +13,7 @@ __pycache__/
 .eggs/
 
 # Jupyter
-.ipynb_checkpoints/
+.ipynb_checkpoints/
+
+# Mac File System
+.DS_Store

devtools/create_env.sh

@@ -1,10 +1,12 @@
-# Developed by Kevin A. Spiekermann
+# Developed by Xiaorui Dong and Kevin A. Spiekermann
 # This script does the following tasks:
 # 	- creates the conda
-# 	- prompts user for desired CUDA version
 # 	- installs PyTorch with specified CUDA version in the environment
 # 	- installs torch torch-geometric in the environment
 
+SCRIPT_DIR=$(dirname $0)
+
+CONDA_ENV_NAME="GeoMol"
 
 # get OS type
 unameOut="$(uname -s)"
@@ -17,66 +19,17 @@ case "${unameOut}" in
 esac
 echo "Running ${machine}..."
 
+if [ "$machine" != "MacOS" ]; then
+    # Prompt the user to input their desired CUDA version or 'cpu'
+    echo "Please input your desired CUDA version in the format xx.xx (e.g., 10.2, 12.3) or 'cpu' for no CUDA available:"
+    read cuda_input
 
-# request user to select one of the supported CUDA versions
-# source: https://pytorch.org/get-started/locally/
-PS3='Please enter 1, 2, 3, or 4 to specify the desired CUDA version from the options above: '
-options=("9.2" "10.1" "10.2" "cpu" "Quit")
-select opt in "${options[@]}"
-do
-    case $opt in
-        "9.2")
-            CUDA="cudatoolkit=9.2"
-            CUDA_VERSION="cu92"
-            break
-            ;;
-        "10.1")
-			CUDA="cudatoolkit=10.1"
-            CUDA_VERSION="cu101"
-            break
-            ;;
-        "10.2")
-			CUDA="cudatoolkit=10.2"
-            CUDA_VERSION="cu102"
-            break
-            ;;
-        "cpu")
-			# "cpuonly" works for Linux and Windows
-			CUDA="cpuonly"
-			# Mac does not use "cpuonly"
-			if [ $machine == "Mac" ]
-			then
-				CUDA=" "
-			fi
-            CUDA_VERSION="cpu"
-            break
-            ;;
-        "Quit")
-            exit
-            ;;
-        *) echo "invalid option $REPLY";;
-    esac
-done
-
-echo "Creating conda environment..."
-echo "Running: conda env create -f environment.yml"
-conda env create -f devtools/environment.yml
+if [ "$machine" == "MacOS" ] && [ "$(uname -m)" == "arm64" ]; then
 
-# activate the environment to install torch-geometric
-source activate GeoMol
+    $SHELL $SCRIPT_DIR/install_pyg_macos_arm64.sh -n $CONDA_ENV_NAME
 
-echo "Installing PyTorch with requested CUDA version..."
-echo "Running: conda install pytorch torchvision $CUDA -c pytorch"
-conda install pytorch torchvision $CUDA -c pytorch
+else
 
-echo "Installing torch-geometric..."
-echo "Using CUDA version: $CUDA_VERSION"
-# get PyTorch version
-TORCH_VERSION=$(python -c "import torch; print(torch.__version__)")
-echo "Using PyTorch version: $TORCH_VERSION"
+    source $SCRIPT_DIR/install_pyg.sh -n $CONDA_ENV_NAME -c $cuda_input
 
-pip install torch-scatter -f https://pytorch-geometric.com/whl/torch-${TORCH_VERSION}+${CUDA_VERSION}.html
-pip install torch-sparse -f https://pytorch-geometric.com/whl/torch-${TORCH_VERSION}+${CUDA_VERSION}.html
-pip install torch-cluster -f https://pytorch-geometric.com/whl/torch-${TORCH_VERSION}+${CUDA_VERSION}.html
-pip install torch-spline-conv -f https://pytorch-geometric.com/whl/torch-${TORCH_VERSION}+${CUDA_VERSION}.html
-pip install torch-geometric
+fi

devtools/environment.yml

@@ -1,146 +1,10 @@
 name: GeoMol
 channels:
-  - rdkit
-  - anaconda
-  - conda-forge
   - defaults
+  - conda-forge
 dependencies:
-  - _libgcc_mutex=0.1=main
-  - _openmp_mutex=4.5=1_gnu
-  - argon2-cffi=20.1.0=py37h5e8e339_2
-  - async_generator=1.10=py_0
-  - attrs=21.2.0=pyhd8ed1ab_0
-  - backcall=0.2.0=pyh9f0ad1d_0
-  - backports=1.0=py_2
-  - backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
-  - blas=1.0=mkl
-  - bleach=3.3.0=pyh44b312d_0
-  - bzip2=1.0.8=h7b6447c_0
-  - ca-certificates=2021.5.30=ha878542_0
-  - cairo=1.16.0=hf32fb01_1
-  - certifi=2021.5.30=py37h89c1867_0
-  - cffi=1.14.5=py37hc58025e_0
-  - cycler=0.10.0=py37_0
-  - dbus=1.13.18=hb2f20db_0
-  - decorator=4.4.2=pyhd3eb1b0_0
-  - defusedxml=0.7.1=pyhd8ed1ab_0
-  - entrypoints=0.3=pyhd8ed1ab_1003
-  - expat=2.4.1=h2531618_2
-  - fontconfig=2.13.1=h6c09931_0
-  - freetype=2.10.4=h5ab3b9f_0
-  - glib=2.68.2=h36276a3_0
-  - gst-plugins-base=1.14.0=h8213a91_2
-  - gstreamer=1.14.0=h28cd5cc_2
-  - icu=58.2=he6710b0_3
-  - importlib-metadata=4.6.0=py37h89c1867_0
-  - intel-openmp=2021.2.0=h06a4308_610
-  - ipykernel=5.5.5=py37h085eea5_0
-  - ipython=7.25.0=py37h085eea5_1
-  - ipython_genutils=0.2.0=py_1
-  - ipywidgets=7.6.3=pyhd3deb0d_0
-  - jedi=0.18.0=py37h89c1867_2
-  - jinja2=3.0.1=pyhd8ed1ab_0
-  - jpeg=9b=h024ee3a_2
-  - jsonschema=3.2.0=pyhd8ed1ab_3
-  - jupyter=1.0.0=py37h89c1867_6
-  - jupyter_client=6.1.12=pyhd8ed1ab_0
-  - jupyter_console=6.4.0=pyhd8ed1ab_0
-  - jupyter_core=4.7.1=py37h89c1867_0
-  - jupyterlab_pygments=0.1.2=pyh9f0ad1d_0
-  - jupyterlab_widgets=1.0.0=pyhd8ed1ab_1
-  - kiwisolver=1.3.1=py37h2531618_0
-  - lcms2=2.12=h3be6417_0
-  - ld_impl_linux-64=2.35.1=h7274673_9
-  - libboost=1.73.0=h3ff78a5_11
-  - libffi=3.3=he6710b0_2
-  - libgcc-ng=9.3.0=h5101ec6_17
-  - libgfortran-ng=7.5.0=ha8ba4b0_17
-  - libgfortran4=7.5.0=ha8ba4b0_17
-  - libgomp=9.3.0=h5101ec6_17
-  - libpng=1.6.37=hbc83047_0
-  - libsodium=1.0.18=h36c2ea0_1
-  - libstdcxx-ng=9.3.0=hd4cf53a_17
-  - libtiff=4.2.0=h85742a9_0
-  - libuuid=1.0.3=h1bed415_2
-  - libwebp-base=1.2.0=h27cfd23_0
-  - libxcb=1.14=h7b6447c_0
-  - libxml2=2.9.12=h03d6c58_0
-  - lz4-c=1.9.3=h2531618_0
-  - markupsafe=2.0.1=py37h5e8e339_0
-  - matplotlib=3.3.4=py37h06a4308_0
-  - matplotlib-base=3.3.4=py37h62a2d02_0
-  - matplotlib-inline=0.1.2=pyhd8ed1ab_2
-  - mistune=0.8.4=py37h5e8e339_1004
-  - mkl=2021.2.0=h06a4308_296
-  - mkl-service=2.3.0=py37h27cfd23_1
-  - mkl_fft=1.3.0=py37h42c9631_2
-  - mkl_random=1.2.1=py37ha9443f7_2
-  - nbclient=0.5.3=pyhd8ed1ab_0
-  - nbconvert=6.1.0=py37h89c1867_0
-  - nbformat=5.1.3=pyhd8ed1ab_0
-  - ncurses=6.2=he6710b0_1
-  - nest-asyncio=1.5.1=pyhd8ed1ab_0
-  - networkx=2.5.1=pyhd3eb1b0_0
-  - notebook=6.4.0=pyha770c72_0
-  - numpy=1.20.2=py37h2d18471_0
-  - numpy-base=1.20.2=py37hfae3a4d_0
-  - olefile=0.46=py37_0
-  - openssl=1.1.1k=h7f98852_0
-  - packaging=20.9=pyh44b312d_0
-  - pandas=1.2.5=py37h295c915_0
-  - pandoc=2.14.0.3=h7f98852_0
-  - pandocfilters=1.4.2=py_1
-  - parso=0.8.2=pyhd8ed1ab_0
-  - pcre=8.45=h295c915_0
-  - pexpect=4.8.0=pyh9f0ad1d_2
-  - pickleshare=0.7.5=py_1003
-  - pillow=8.2.0=py37he98fc37_0
-  - pip=21.1.3=py37h06a4308_0
-  - pixman=0.40.0=h7b6447c_0
-  - pot=0.7.0=py37h3340039_0
-  - prometheus_client=0.11.0=pyhd8ed1ab_0
-  - prompt-toolkit=3.0.19=pyha770c72_0
-  - prompt_toolkit=3.0.19=hd8ed1ab_0
-  - ptyprocess=0.7.0=pyhd3deb0d_0
-  - py-boost=1.73.0=py37ha9443f7_11
-  - py3dmol=0.9.1=pyhd8ed1ab_0
-  - pycparser=2.20=pyh9f0ad1d_2
-  - pygments=2.9.0=pyhd8ed1ab_0
-  - pyparsing=2.4.7=pyhd3eb1b0_0
-  - pyqt=5.9.2=py37h05f1152_2
-  - pyrsistent=0.17.3=py37h5e8e339_2
-  - python=3.7.10=h12debd9_4
-  - python-dateutil=2.8.1=pyhd3eb1b0_0
-  - python_abi=3.7=2_cp37m
-  - pytz=2021.1=pyhd3eb1b0_0
-  - pyyaml=5.3.1=py37h7b6447c_1
-  - pyzmq=22.1.0=py37h336d617_0
-  - qt=5.9.7=h5867ecd_1
-  - qtconsole=5.1.1=pyhd8ed1ab_0
-  - qtpy=1.9.0=py_0
-  - rdkit=2020.09.1.0=py37hd50e099_1
-  - readline=8.1=h27cfd23_0
-  - scipy=1.6.2=py37had2a1c9_1
-  - seaborn=0.11.1=pyhd3eb1b0_0
-  - send2trash=1.7.1=pyhd8ed1ab_0
-  - setuptools=52.0.0=py37h06a4308_0
-  - sip=4.19.8=py37hf484d3e_0
-  - six=1.16.0=pyhd3eb1b0_0
-  - sqlite=3.36.0=hc218d9a_0
-  - terminado=0.10.1=py37h89c1867_0
-  - testpath=0.5.0=pyhd8ed1ab_0
-  - tk=8.6.10=hbc83047_0
-  - tornado=6.1=py37h27cfd23_0
-  - tqdm=4.61.1=pyhd3eb1b0_1
-  - traitlets=5.0.5=py_0
-  - typing_extensions=3.10.0.0=pyha770c72_0
-  - wcwidth=0.2.5=pyh9f0ad1d_2
-  - webencodings=0.5.1=py_1
-  - wheel=0.36.2=pyhd3eb1b0_0
-  - widgetsnbextension=3.5.1=py37h89c1867_4
-  - xz=5.2.5=h7b6447c_0
-  - yaml=0.2.5=h7b6447c_0
-  - zeromq=4.3.4=h9c3ff4c_0
-  - zipp=3.4.1=pyhd8ed1ab_0
-  - zlib=1.2.11=h7b6447c_3
-  - zstd=1.4.9=haebb681_0
+  - rdkit >=2020.03.2
+  - networkx
+  - pot
+  - yaml
+  - pyyaml