Updated Dockerfile and README.md for LatentGAN (molecularsets#70)

* updated Dockerfile for LatentGAN

* updated README

* add rdkit version

* remove rdkit from external installation script

* TF 1.14

* pip instead of conda

Dockerfile

@@ -4,23 +4,22 @@ ENV DEBIAN_FRONTEND noninteractive
 ENV TERM linux
 
 RUN mkdir /moses
-COPY . /moses
 
 RUN set -ex \
     && apt-get update -yqq \
     && apt-get upgrade -yqq \
     && apt-get install -yqq --no-install-recommends \
         git wget curl ssh libxrender1 libxext6 software-properties-common apt-utils \
-    && wget --no-check-certificate https://repo.continuum.io/miniconda/Miniconda3-4.6.14-Linux-x86_64.sh \
-    && /bin/bash Miniconda3-4.6.14-Linux-x86_64.sh -f -b -p /opt/miniconda \
+    && wget --no-check-certificate https://repo.continuum.io/miniconda/Miniconda3-4.7.12.1-Linux-x86_64.sh \
+    && /bin/bash Miniconda3-4.7.12.1-Linux-x86_64.sh -f -b -p /opt/miniconda \
     && add-apt-repository ppa:git-core/ppa \
     && (curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | bash) \
     && apt-get install git-lfs \
     && git lfs install \
     && apt-get clean \ 
-    && /opt/miniconda/bin/conda install conda=4.6.14=py36_0 \
+    && /opt/miniconda/bin/conda install conda=4.8.1=py37_0 \
     && /opt/miniconda/bin/conda clean -yq -a \
-    && rm Miniconda3-4.6.14-Linux-x86_64.sh \ 
+    && rm Miniconda3-4.7.12.1-Linux-x86_64.sh \
     && rm -rf \
         /tmp/* \
         /var/tmp/* \
@@ -29,10 +28,23 @@ RUN set -ex \
         /usr/share/doc-base
 
 ENV PATH /opt/miniconda/bin:$PATH
-RUN conda install -yq numpy=1.16.0 scipy=1.2.0 matplotlib=3.0.1 pandas=0.25 scikit-learn=0.20.3 tqdm>=4.26.0 \
-    && conda install -yq -c rdkit rdkit=2019.03.2 \
+RUN conda install -yq numpy=1.16.0 scipy=1.2.0 matplotlib=3.0.1 \
+        pandas=0.25 scikit-learn=0.20.3 tqdm>=4.26.0 \
+    && conda install -yq -c rdkit rdkit=2019.09.3 \
     && conda install -yq -c pytorch pytorch=1.1.0 torchvision=0.2.1 \
-    && conda clean -yq -a
+    && conda clean -yq -a \
+    && pip install tensorflow-gpu==1.14
+
+RUN git clone https://github.com/pcko1/Deep-Drug-Coder.git --branch moses \
+    && cd Deep-Drug-Coder \
+    && python setup.py install \
+    && cd .. \
+    && git clone https://github.com/EBjerrum/molvecgen.git \
+    && cd molvecgen \
+    && python setup.py install \
+    && cd ..
+
+COPY . /moses
 
 WORKDIR /moses
 RUN python setup.py install && git lfs pull && conda clean -yq -a && rm -rf .git/lfs

README.md

@@ -191,7 +191,7 @@ For comparison of molecular properties, we computed the Frèchet distance betwee
 # Installation
 
 ### PyPi
-The simplest way to install MOSES (models and metrics) is to install [RDKit](https://www.rdkit.org/docs/Install.html): `conda install -yq -c rdkit rdkit` and then install MOSES (`molsets`) from pip (`pip install molsets`).
+The simplest way to install MOSES (models and metrics) is to install [RDKit](https://www.rdkit.org/docs/Install.html): `conda install -yq -c rdkit rdkit` and then install MOSES (`molsets`) from pip (`pip install molsets`). If you want to use LatentGAN, you should also install additional dependencies using `bash install_latentgan_dependencies.sh`.
 
 If you are using Ubuntu, you should also install `sudo apt-get install libxrender1 libxext6` for RDKit.
 
@@ -238,6 +238,11 @@ git clone https://github.com/molecularsets/moses.git
 python setup.py install
 ```
 
+4. (Optional) Install dependencies for LatentGAN:
+```bash
+bash install_latentgan_dependencies.sh
+```
+
 
 # Benchmarking your models
 

install_moses.sh → install_latentgan_dependencies.sh

@@ -1,8 +1,6 @@
 #!/bin/bash
 # A script to install everything needed to run MOSES in a new environment
-conda create -n moses_env python=3.6
-eval "$(conda shell.bash hook)"
-conda activate moses_env
+set -e
 git clone https://github.com/pcko1/Deep-Drug-Coder.git --branch moses
 cd Deep-Drug-Coder
 python setup.py install
@@ -11,6 +9,4 @@ git clone https://github.com/EBjerrum/molvecgen.git
 cd molvecgen
 python setup.py install
 cd ..
-conda install tensorflow-gpu==1.12
-conda install -c conda-forge rdkit
-python setup.py install
+pip install tensorflow-gpu==1.14

moses/__init__.py

@@ -1 +1 @@
-__version__ = '0.2'
+__version__ = '0.2.1'

moses/latentgan/model.py

@@ -1,7 +1,6 @@
 import torch.nn as nn
 import numpy as np
 import torch
-from ddc_pub import ddc_v3 as ddc
 import os
 from rdkit import Chem
 import sys
@@ -120,6 +119,8 @@ def sample(self, n_batch, max_length=100):
 
 
 def load_model(model_version=None):
+    from ddc_pub import ddc_v3 as ddc
+
     # Import model
     currentDirectory = os.getcwd()
 

moses/latentgan/trainer.py

@@ -12,7 +12,6 @@
 from .model import load_model
 from .model import Sampler
 from rdkit import Chem
-from ddc_pub import ddc_v3 as ddc
 
 
 class LatentGANTrainer(MosesTrainer):
@@ -159,7 +158,7 @@ def fit(self,
             model,
             train_data,
             val_data=None):
-
+        from ddc_pub import ddc_v3 as ddc
         self.generator = model.Generator
         self.discriminator = model.Discriminator
         cuda = True if torch.cuda.is_available() else False

scripts/run_all_models.sh

@@ -3,6 +3,7 @@ for MODEL in char_rnn vae aae
 do
     for SEED in 1 2 3
     do
+        mkdir -p checkpoints/$MODEL/$MODEL\_$SEED
         python scripts/run.py \
             --model $MODEL \
             --data data \