Merge pull request #1988 from nd-02110114/update-dependecies (80552cbb) · Commits · 钟慕尧 / deepchem

.travis.yml

+4 −5

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		@@ -21,15 +21,12 @@ install:
		- if [[ "$TRAVIS_OS_NAME" == "windows" ]]; then choco install miniconda3 --params="'/JustMe
		/AddToPath:1'"; export PATH="/c/tools/miniconda3/:/c/tools/miniconda3/Scripts:/c/tools/miniconda3/Library/bin:$PATH";
		source /c/tools/miniconda3/etc/profile.d/conda.sh; fi
		- hash -r
		- conda config --set always_yes yes --set changeps1 no
		- conda update -q conda
		- conda config --add channels http://conda.binstar.org/omnia
		- bash scripts/install_deepchem_conda.sh deepchem
		- conda activate deepchem
		- pip install yapf==0.22.0
		- pip install coveralls
		- python setup.py install
		- pip install coveralls yapf==0.22.0
		script:
		- pytest -m "not slow" --cov=deepchem deepchem
		- if [ $TRAVIS_PYTHON_VERSION == '3.7' ]; then find ./deepchem \| grep .py$ \| xargs
		@@ -44,3 +41,5 @@ deploy:
		password:
		secure: 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
		edge: true
		on:
		condition: $TRAVIS_OS_NAME = linux && $TRAVIS_PYTHON_VERSION = 3.7

README.md

+8 −22

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		@@ -16,7 +16,7 @@ materials science, quantum chemistry, and biology.
		- [Requirements](#requirements)
		- [Installation](#installation)
		- [Stable version](#stable-version)
		- [Nightly version](#nightly-build-version)
		- [Nightly build version](#nightly-build-version)
		- [Docker](#docker)
		- [From source](#from-source)
		- [Getting Started](#getting-started)
		@@ -42,24 +42,10 @@ DeepChem currently supports Python 3.5 through 3.7 and requires these packages o

		### Soft Requirements

		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)
		- [OpenAI Gym](https://gym.openai.com/)
		- [matminer](https://hackingmaterials.lbl.gov/matminer/)
		- [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/)
		- [pyGPGO](https://pygpgo.readthedocs.io/en/latest/)
		- [Pymatgen](https://pymatgen.org/)
		- [PyTorch](https://pytorch.org/)
		- [RDKit](http://www.rdkit.org/docs/Install.html)
		- [simdna](https://github.com/kundajelab/simdna)
		- [XGBoost](https://xgboost.readthedocs.io/en/latest/)
		- [Weights & Biases](https://docs.wandb.com/)
		- [Tensorflow Probability](https://www.tensorflow.org/probability)
		DeepChem has a number of "soft" requirements.
		If you face `ImportError: No module named XXXX`, you may need to install some packages.

		Please check [the document](https://deepchem.readthedocs.io/en/latest/requirements.html##soft-requirements) about the details of soft requirements.

		## Installation

		@@ -72,14 +58,14 @@ RDKit is a soft requirement package, but many useful methods like molnet depend

		```bash
		pip install tensorflow==1.14
		conda install -y -c rdkit -c conda-forge rdkit deepchem==2.3.0
		conda install -y -c conda-forge rdkit deepchem==2.3.0
		```

		If you want GPU support:

		```bash
		pip install tensorflow-gpu==1.14
		conda install -y -c rdkit -c conda-forge rdkit deepchem==2.3.0
		conda install -y -c conda-forge rdkit deepchem==2.3.0
		```

		### Nightly build version
		@@ -94,7 +80,7 @@ pip install --pre deepchem
		RDKit is a soft requirement package, but many useful methods like molnet depend on it. We recommend installing RDKit with deepchem if you use conda.

		```bash
		conda install -y -c rdkit rdkit
		conda install -y -c conda-forge rdkit
		```

		### Docker

deepchem/init.py

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		"""
		Imports all submodules
		"""
		__version__ = '2.4.0-rc.1'

		# If you push the tag, please remove `.dev`
		__version__ = '2.4.0-rc1.dev'

		import deepchem.data
		import deepchem.feat

deepchem/dock/pose_generation.py

+0 −1

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		@@ -9,7 +9,6 @@ import os
		import tempfile
		import tarfile
		from subprocess import call
		from deepchem.utils.rdkit_util import add_hydrogens_to_mol
		from subprocess import check_output
		from deepchem.utils import rdkit_util
		from deepchem.utils import mol_xyz_util

deepchem/models/layers.py

+4 −6

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		@@ -447,12 +447,10 @@ class AttnLSTMEmbedding(tf.keras.layers.Layer):
		metric that allows a network to modify its internal notion of
		distance.

		References:
		Matching Networks for One Shot Learning
		https://arxiv.org/pdf/1606.04080v1.pdf

		Order Matters: Sequence to sequence for sets
		https://arxiv.org/abs/1511.06391
		References
		----------
		.. [1] Matching Networks for One Shot Learning, https://arxiv.org/abs/1606.04080
		.. [2] Order Matters: Sequence to sequence for sets, https://arxiv.org/abs/1511.06391
		"""

		def __init__(self, n_test, n_support, n_feat, max_depth, **kwargs):

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