integrating changes for work on integrate_lbann_moses back to personal fork, pull request to update master of sams fork with those changes

.dockerignore

@@ -0,0 +1,12 @@
+__pycache__
+*.pyc
+*.pyo
+*.pyd
+.Python
+env.*
+pip-log.txt
+pip-delete-this-directory.txt
+.tox
+.cache
+*.log
+.ipynb_checkpoints/*

.gitattributes

@@ -1 +1,9 @@
 data/*.csv filter=lfs diff=lfs merge=lfs -text
+data/samples/*generated.csv filter=lfs diff=lfs merge=lfs -text
+*.npz filter=lfs diff=lfs merge=lfs -text
+data/11_p0.smi.gz filter=lfs diff=lfs merge=lfs -text
+moses/dataset/data/test_scaffolds_stats.npz filter=lfs diff=lfs merge=lfs -text
+moses/dataset/data/test_stats.npz filter=lfs diff=lfs merge=lfs -text
+moses/dataset/data/test.csv.gz filter=lfs diff=lfs merge=lfs -text
+moses/dataset/data/test_scaffolds.csv.gz filter=lfs diff=lfs merge=lfs -text
+moses/dataset/data/train.csv.gz filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -4,3 +4,4 @@
 build/
 dist/
 moses.egg-info/
+

.travis.yml

@@ -0,0 +1,23 @@
+language: python
+
+python:
+  - "3.6"
+
+before_install:
+  - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+  - bash miniconda.sh -b -p $HOME/conda
+  - export PATH="$HOME/conda/bin:$PATH"
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+  - conda create -n test_env python=$TRAVIS_PYTHON_VERSION pip cmake
+  - source activate test_env
+
+install:
+  - conda install -q -c rdkit rdkit
+  - conda install -q flake8 scipy=1.2.0 pylint
+  - python setup.py install
+
+script:
+  - flake8
+  - pylint --disable=all --enable=no-else-return,unused-variable,wrong-import-order moses/ scripts/
+  - python tests/test_metrics.py

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 \
-    && wget --no-check-certificate https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
-    && /bin/bash Miniconda3-latest-Linux-x86_64.sh -f -b -p /opt/miniconda \
+        git wget curl ssh libxrender1 libxext6 software-properties-common apt-utils \
+    && 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=4.5.12=py36_0 \
+    && /opt/miniconda/bin/conda install conda=4.8.1=py37_0 \
     && /opt/miniconda/bin/conda clean -yq -a \
-    && rm Miniconda3-latest-Linux-x86_64.sh \ 
+    && rm Miniconda3-4.7.12.1-Linux-x86_64.sh \
     && rm -rf \
         /tmp/* \
         /var/tmp/* \
@@ -29,11 +28,23 @@ RUN set -ex \
         /usr/share/doc-base
 
 ENV PATH /opt/miniconda/bin:$PATH
-RUN conda install -yq numpy=1.15.0 scipy=1.1.0 matplotlib=3.0.1 pandas=0.23.3 scikit-learn=0.19.1 tqdm \
-    && pip install tensorflow-gpu==1.12 keras==2.2.4 \
-    && conda install -yq -c rdkit rdkit=2018.09.1.0 \
-    && conda install -yq -c pytorch pytorch=0.4.1 torchvision=0.2.1 \
-    && conda clean -yq -a
+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 \
+    && 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

MANIFEST.in

@@ -0,0 +1,10 @@
+# MANIFEST.in
+include moses/metrics/NP_Score/publicnp.model.gz
+include moses/metrics/SA_Score/fpscores.pkl.gz
+include moses/metrics/wehi_pains.csv
+include moses/metrics/mcf.csv
+include moses/dataset/data/train.csv.gz
+include moses/dataset/data/test.csv.gz
+include moses/dataset/data/test_scaffolds.csv.gz
+include moses/dataset/data/test_stats.npz
+include moses/dataset/data/test_scaffolds_stats.npz