Merge pull request #1134 from lilleswing/version-bumps (58d6b17b) · Commits · 钟慕尧 / deepchem

Dockerfile

+8 −17

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		FROM nvidia/cuda
		FROM nvidia/cuda:9.0-cudnn7-runtime

		# Install some utilities
		RUN apt-get update && \
		apt-get install -y -q wget git libxrender1 libsm6 && \
		apt-get install -y -q wget git libxrender1 libsm6 bzip2 && \
		apt-get clean

		# Install miniconda
		RUN MINICONDA="Miniconda2-latest-Linux-x86_64.sh" && \
		RUN MINICONDA="Miniconda3-latest-Linux-x86_64.sh" && \
		wget --quiet https://repo.continuum.io/miniconda/$MINICONDA && \
		bash $MINICONDA -b -p /miniconda && \
		rm -f $MINICONDA
		ENV PATH /miniconda/bin:$PATH

		# Install deepchem conda package from omnia
		# TODO: Uncomment this when there is a stable release of deepchem.
		#RUN conda config --add channels omnia
		#RUN conda install --yes deepchem

		# Install deepchem with GPU support from github using Tue 14 Mar 2017 git head
		# TODO: Get rid of this when there is a stable release of deepchem.
		RUN git clone https://github.com/deepchem/deepchem.git && \
		RUN conda update -n base conda
		RUN export LANG=en_US.UTF-8 && \
		git clone https://github.com/deepchem/deepchem.git && \
		cd deepchem && \
		git checkout tags/1.3.1 && \
		git checkout 2.0.0 && \
		sed -i -- 's/tensorflow$/tensorflow-gpu/g' scripts/install_deepchem_conda.sh && \
		bash scripts/install_deepchem_conda.sh root && \
		bash scripts/install_deepchem_conda.sh && \
		python setup.py develop

		# Clean up
		RUN cd deepchem && \
		git clean -fX

		# Run tests
		#RUN pip install nose && \
		# nosetests -v deepchem --nologcapture

+2 −2

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		@@ -72,7 +72,7 @@ via this installation procedure.
		### Easy Install via Conda

		```bash
		conda install -c deepchem -c rdkit -c conda-forge -c omnia deepchem=1.3.1
		conda install -c deepchem -c rdkit -c conda-forge -c omnia deepchem=2.0.0
		```
		Note: `Easy Install` installs the latest stable version of `deepchem` and _does not install from source_. If you need to install from source make sure you follow the steps [here](#using-a-conda-environment).

		@@ -182,4 +182,4 @@ DeepChem is supported by a number of corporate partners who use DeepChem to solv


		## Version
		1.3.1
		2.0.0

+12 −17

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		package:
		name: {{ environ.get('package_name', 'deepchem') }}
		version: "1.3.1"
		version: "2.0.0"

		source:
		git_url: https://github.com/deepchem/deepchem.git
		git_tag: 1.3.0
		git_tag: 2.0.0

		build:
		number: 0
		skip: True # [osx or win]
		skip: True # [win]


		requirements:
		@@ -21,27 +21,22 @@ requirements:
		run:
		- python {{ environ.get('python_version', '3.5') }}
		- pdbfixer ==1.4
		- rdkit ==2017.03.1
		- icu ==56.1
		- mdtraj ==1.8.0
		- mdtraj ==1.9.1
		- joblib ==0.11
		- scikit-learn ==0.18.1
		- keras ==1.2.2
		- scikit-learn ==0.19.1
		- networkx ==1.11
		- xgboost ==0.6a2
		- pillow ==4.2.1
		- pandas ==0.19.2
		- {{ environ.get('tensorflow_enabled','tensorflow') }} ==1.3.0
		- pillow ==4.3.0
		- pandas ==0.22.0
		- {{ environ.get('tensorflow_enabled','tensorflow') }} ==1.5.0
		- nose ==1.3.7
		- nose-timer ==0.7.0
		- flaky ==3.3.0
		- zlib ==1.2.11


		test:

		imports:
		- deepchem
		- requests ==2.18.4
		- simdna ==0.4.2
		- jupyter=1.0.0
		- rdkit ==2017.09.1


		about:

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		@@ -8,14 +8,14 @@ export python_version=2.7
		conda build deepchem -c defaults -c rdkit -c omnia -c conda-forge
		export python_version=3.5
		conda build deepchem -c defaults -c rdkit -c omnia -c conda-forge
		export python_version=3.6
		conda build deepchem -c defaults -c rdkit -c omnia -c conda-forge
		#export python_version=3.6
		#conda build deepchem -c defaults -c rdkit -c omnia -c conda-forge

		export package_name=deepchem-gpu
		export tensorflow_enabled=tensorflow-gpu
		export python_version=2.7
		conda build deepchem -c defaults -c rdkit -c omnia -c conda-forge
		export python_version=3.5
		conda build deepchem -c defaults -c rdkit -c omnia -c conda-forge
		export python_version=3.6
		conda build deepchem -c defaults -c rdkit -c omnia -c conda-forge
		#export package_name=deepchem-gpu
		#export tensorflow_enabled=tensorflow-gpu
		#export python_version=2.7
		#conda build deepchem -c defaults -c rdkit -c omnia -c conda-forge
		#export python_version=3.5
		#conda build deepchem -c defaults -c rdkit -c omnia -c conda-forge
		#export python_version=3.6
		#conda build deepchem -c defaults -c rdkit -c omnia -c conda-forge

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		@@ -6,33 +6,33 @@
		export tensorflow=tensorflow


		if [ -z "$1" ]
		then
		echo "Must Specify Conda Environment Name"
		fi

		if [ -z "$python_version" ]
		then
		echo "Using python 3.5 by default"
		export python_version=3.5
		fi

		if [ -z "$1" ];
		then
		echo "Installing DeepChem in current env"
		else
		export envname=$1
		conda create -y --name $envname python=$python_version
		source activate $envname
		fi

		unamestr=`uname`
		if [[ "$unamestr" == 'Darwin' ]]; then
		source activate root
		conda install -y -q conda=4.3.25
		fi

		export envname=$1
		conda create -y --name $envname python=$python_version
		source activate $envname
		conda install -y -q -c omnia pdbfixer=1.4
		conda install -y -q -c conda-forge joblib=0.11
		conda install -y -q -c conda-forge six=1.10.0
		conda install -y -q -c deepchem mdtraj=1.9.1
		conda install -y -q -c conda-forge scikit-learn=0.19.1
		conda install -y -q -c conda-forge setuptools=36.2.2
		conda install -y -q -c conda-forge keras=1.2.2
		conda install -y -q -c conda-forge networkx=1.11
		conda install -y -q -c conda-forge pillow=4.3.0
		conda install -y -q -c conda-forge pandas=0.22.0