Commit efe72435 authored by nd-02110114's avatar nd-02110114
Browse files

⬆️ upgrade dependecies

parent 537af984

docs/requirements.rst

+7 −7
Original line number Diff line number Diff line
@@ -13,8 +13,8 @@ DeepChem currently supports Python 3.5 through 3.7 and requires these packages o 
- `SciPy`_

- `TensorFlow`_



  - `deepchem>=2.4.0` requires tensorflow v2

  - `deepchem<2.4.0` requires tensorflow v1

  - `deepchem>=2.4.0` requires tensorflow v2 (2.3.0)

  - `deepchem<2.4.0` requires tensorflow v1 (>=1.14)





Soft requirements
@@ -30,7 +30,7 @@ DeepChem has a number of "soft" requirements. 
|                                |               |                                                   |

|                                |               |                                                   |

+--------------------------------+---------------+---------------------------------------------------+

| `Deep Graph Library`_          | 0.4.3.post2   | :code:`dc.feat.graph_data`                        |

| `Deep Graph Library`_          | latset        | :code:`dc.feat.graph_data`                        |

|                                |               |                                                   |

|                                |               |                                                   |

+--------------------------------+---------------+---------------------------------------------------+
@@ -70,12 +70,12 @@ DeepChem has a number of "soft" requirements. 
|                                |               |                                                   |

|                                |               |                                                   |

+--------------------------------+---------------+---------------------------------------------------+

| `PyTorch`_                     | 1.5.1         | :code:`dc.data.datasets`                          |

| `PyTorch`_                     | 1.6.0         | :code:`dc.data.datasets`                          |

|                                |               |                                                   |

|                                |               |                                                   |

+--------------------------------+---------------+---------------------------------------------------+

| `PyTorch Geometric`_           | 1.6.0         | :code:`dc.feat.graph_data`                        |

|                                |               |                                                   |

| `PyTorch Geometric`_           | latest (with  | :code:`dc.feat.graph_data`                        |

|                                | PyTorch 1.6.0)|                                                   |

|                                |               |                                                   |

+--------------------------------+---------------+---------------------------------------------------+

| `RDKit`_                       | latest        | Many modules                                      |
@@ -86,7 +86,7 @@ DeepChem has a number of "soft" requirements. 
|                                |               | :code:`dc.molnet.dnasim`                          |

|                                |               |                                                   |

+--------------------------------+---------------+---------------------------------------------------+

| `Tensorflow Probability`_      | 0.10.1        | :code:`dc.rl`                                     |

| `Tensorflow Probability`_      | latest        | :code:`dc.rl`                                     |

|                                |               |                                                   |

|                                |               |                                                   |

+--------------------------------+---------------+---------------------------------------------------+

scripts/install_deepchem_conda.ps1

+11 −18
Original line number Diff line number Diff line
@@ -30,28 +30,21 @@ $path = Join-Path $Pwd "requirements-test.txt" 
pip install -r $path



# Fixed packages

$tensorflow=2.2.0

$tensorflow_probability=0.10.1

$torch=1.5.1

$torchvision=0.6.1

$torch_scatter=2.0.5

$torch_sparse=0.6.6

$torch_cluster=1.5.6

$torch_spline_conv=1.2.0

$torch_geometric=1.6.0

$dgl=0.4.3.post2

$tensorflow=2.3.0

$torch=1.6.0

$torchvision=0.7.0

$pyg_torch=1.6.0



# Install Tensorflow dependencies

pip install tensorflow==$tensorflow tensorflow-probability==$tensorflow_probability

pip install tensorflow==$tensorflow tensorflow-probability



# Install PyTorch dependencies

pip install torch==$torch+$cuda torchvision==$torchvision+$cuda -f https://download.pytorch.org/whl/torch_stable.html



# Install PyTorch Geometric and DGL dependencies

$TORCH=1.5.0

pip install torch-scatter==$torch_scatter+$cuda -f https://pytorch-geometric.com/whl/torch-$TORCH.html

pip install torch-sparse==$torch_sparse+$cuda -f https://pytorch-geometric.com/whl/torch-$TORCH.html

pip install torch-cluster==$torch_cluster+$cuda -f https://pytorch-geometric.com/whl/torch-$TORCH.html

pip install torch-spline-conv==$torch_spline_conv+$cuda -f https://pytorch-geometric.com/whl/torch-$TORCH.html

pip install torch-geometric==$torch_geometric

pip install $dgl_pkg==$dgl
 
pip install torch-scatter==latest+$cuda -f https://pytorch-geometric.com/whl/torch-$pyg_torch.html

pip install torch-sparse==latest+$cuda -f https://pytorch-geometric.com/whl/torch-$pyg_torch.html

pip install torch-cluster==latest+$cuda -f https://pytorch-geometric.com/whl/torch-$pyg_torch.html

pip install torch-spline-conv==latest+$cuda -f https://pytorch-geometric.com/whl/torch-$pyg_torch.html

pip install torch-geometric

pip install $dgl_pkg

scripts/install_deepchem_conda.sh

+13 −18
Original line number Diff line number Diff line
@@ -15,6 +15,8 @@ fi 


if [ "$0" = "gpu" ];

then

    # We expect that the CUDA vesion is 10.1.

    # This is because the 

    cuda=cu101

    dgl_pkg=dgl-cu101

    echo "Installing DeepChem in the GPU envirionment"
@@ -31,19 +33,13 @@ conda env update --file $PWD/requirements.yml 
pip install -r $PWD/requirements-test.txt



# Fixed packages

tensorflow=2.2.0

tensorflow_probability=0.10.1

torch=1.5.1

torchvision=0.6.1

torch_scatter=2.0.5

torch_sparse=0.6.6

torch_cluster=1.5.6

torch_spline_conv=1.2.0

torch_geometric=1.6.0

dgl=0.4.3.post2

tensorflow=2.3.0

torch=1.6.0

torchvision=0.7.0

pyg_torch=1.6.0



# Install TensorFlow dependencies

pip install tensorflow==$tensorflow tensorflow-probability==$tensorflow_probability

pip install tensorflow==$tensorflow tensorflow-probability



# Install PyTorch dependencies

if [ "$(uname)" == 'Darwin' ];
@@ -55,10 +51,9 @@ else 
fi



# Install PyTorch Geometric and DGL dependencies

TORCH=1.5.0

pip install torch-scatter==$torch_scatter+$cuda -f https://pytorch-geometric.com/whl/torch-$TORCH.html

pip install torch-sparse==$torch_sparse+$cuda -f https://pytorch-geometric.com/whl/torch-$TORCH.html

pip install torch-cluster==$torch_cluster+$cuda -f https://pytorch-geometric.com/whl/torch-$TORCH.html

pip install torch-spline-conv==$torch_spline_conv+$cuda -f https://pytorch-geometric.com/whl/torch-$TORCH.html

pip install torch-geometric==$torch_geometric

pip install $dgl_pkg==$dgl
 
pip install torch-scatter==latest+$cuda -f https://pytorch-geometric.com/whl/torch-$pyg_torch.html

pip install torch-sparse==latest+$cuda -f https://pytorch-geometric.com/whl/torch-$pyg_torch.html

pip install torch-cluster==latest+$cuda -f https://pytorch-geometric.com/whl/torch-$pyg_torch.html

pip install torch-spline-conv==latest+$cuda -f https://pytorch-geometric.com/whl/torch-$pyg_torch.html

pip install torch-geometric

pip install $dgl_pkg

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