:arrow_up: cleanup dependencies (8df1d6bf) · Commits · 钟慕尧 / deepchem

README.md

+8 −4

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		@@ -35,9 +35,11 @@ materials science, quantum chemistry, and biology.
		DeepChem requires these packages on any condition.

		- [joblib](https://pypi.python.org/pypi/joblib)
		- [NumPy](https://numpy.org/)
		- [pandas](http://pandas.pydata.org/)
		- [scikit-learn](https://github.com/scikit-learn/scikit-learn.git)
		- [tensorflow](https://www.tensorflow.org/)
		- [scikit-learn](https://scikit-learn.org/stable/)
		- [SciPy](https://www.scipy.org/)
		- [TensorFlow](https://www.tensorflow.org/)
		- `deepchem>=2.4.0` requires tensorflow v2
		- `deepchem<2.4.0` requires tensorflow v1

		@@ -45,8 +47,10 @@ DeepChem requires these packages on any condition.

		DeepChem has a number of "soft" requirements. These are packages which are needed for various submodules of DeepChem but not for the package as a whole.

		- [BioPython](https://biopython.org/wiki/Documentation)
		- [MDTraj](http://mdtraj.org/)
		- [NetworkX](https://networkx.github.io/documentation/stable/index.html)
		- [OpenMM](http://openmm.org/)
		- [PDBFixer](https://github.com/pandegroup/pdbfixer)
		- [Pillow](https://pypi.org/project/Pillow/)
		- [RDKit](http://www.rdkit.org/docs/Install.html)
		@@ -87,13 +91,13 @@ Coming soon...
		`deepchem<2.4.0`

		```bash
		pip install joblib pandas pillow scikit-learn==0.22 tensorflow==1.15 deepchem==2.2.1.dev54
		pip install pandas pillow scikit-learn==0.22 tensorflow==1.15 deepchem==2.2.1.dev54
		```

		If you want GPU support:

		```bash
		pip install joblib pandas pillow scikit-learn==0.22 tensorflow-gpu==1.15 deepchem==2.2.1.dev54
		pip install pandas pillow scikit-learn==0.22 tensorflow-gpu==1.15 deepchem==2.2.1.dev54
		```

		### Install from source

scripts/install_deepchem_conda.sh

+11 −13

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		@@ -24,22 +24,20 @@ fi

		yes \| pip install --upgrade pip
		conda install -y -q -c deepchem -c rdkit -c conda-forge -c omnia \
		mdtraj \
		pdbfixer \
		rdkit \
		joblib \
		pandas \
		scikit-learn \
		# soft dependencies
		biopython \
		mdtraj \
		networkx \
		openmm \
		pdbfixer \
		pillow \
		pandas \
		rdkit \
		simdna \
		py-xgboost \
		# test dependencies
		nose \
		nose-timer \
		flaky \
		zlib \
		requests \
		py-xgboost \
		simdna \
		setuptools \
		biopython \
		numpy
		flaky
		yes \| pip install -U tensorflow tensorflow-probability

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