Loading docker/master/Dockerfile +1 −1 Original line number Diff line number Diff line Loading @@ -18,7 +18,7 @@ RUN conda update -n base conda && \ git clone --depth 1 https://github.com/deepchem/deepchem.git && \ cd deepchem && \ . /miniconda/etc/profile.d/conda.sh && \ bash scripts/install_deepchem_conda.sh deepchem && \ bash scripts/install_deepchem_conda.sh deepchem gpu && \ conda activate deepchem && \ python setup.py install && \ conda clean -afy && \ Loading docs/installation.rst +7 −0 Original line number Diff line number Diff line Loading @@ -141,6 +141,13 @@ Then, execute the shell script. bash scripts/install_deepchem_conda.sh deepchem If you want GPU support: .. code-block:: bash bash scripts/install_deepchem_conda.sh deepchem gpu If you are using the Windows and the PowerShell: .. code-block:: ps1 Loading docs/requirements.rst +13 −13 Original line number Diff line number Diff line Loading @@ -26,7 +26,7 @@ DeepChem has a number of "soft" requirements. | Package name | Version | Location where this package is imported | | | | (dc: deepchem) | +================================+===============+===================================================+ | `BioPython`_ | 1.77 | :code:`dc.utlis.genomics_utils` | | `BioPython`_ | latest | :code:`dc.utlis.genomics_utils` | | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ Loading @@ -38,35 +38,35 @@ DeepChem has a number of "soft" requirements. | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `matminer`_ | 0.6.3 | :code:`dc.feat.materials_featurizers` | | `matminer`_ | latest | :code:`dc.feat.materials_featurizers` | | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `MDTraj`_ | 1.9.4 | :code:`dc.utils.pdbqt_utils` | | `MDTraj`_ | latest | :code:`dc.utils.pdbqt_utils` | | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `NetworkX`_ | 2.4 | :code:`dc.utils.rdkit_utils` | | `NetworkX`_ | latest | :code:`dc.utils.rdkit_utils` | | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `OpenMM`_ | 7.4.2 | :code:`dc.utils.rdkit_utils` | | `OpenMM`_ | latest | :code:`dc.utils.rdkit_utils` | | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `PDBFixer`_ | 1.6 | :code:`dc.utils.rdkit_utils` | | `PDBFixer`_ | latest | :code:`dc.utils.rdkit_utils` | | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `Pillow`_ | 7.1.2 | :code:`dc.data.data_loader`, | | `Pillow`_ | latest | :code:`dc.data.data_loader`, | | | | :code:`dc.trans.transformers` | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `pyGPGO`_ | 0.4.0.dev1 | :code:`dc.hyper.gaussian_process` | | `pyGPGO`_ | latest | :code:`dc.hyper.gaussian_process` | | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `Pymatgen`_ | 2020.7.18 | :code:`dc.feat.materials_featurizers` | | `Pymatgen`_ | latest | :code:`dc.feat.materials_featurizers` | | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ Loading @@ -78,19 +78,19 @@ DeepChem has a number of "soft" requirements. | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `RDKit`_ | 2020.03.4 | Many modules | | `RDKit`_ | latest | Many modules | | | | (we recommend you to instal) | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `simdna`_ | 0.4.3.2 | :code:`dc.metrics.genomic_metrics`, | | `simdna`_ | latest | :code:`dc.metrics.genomic_metrics`, | | | | :code:`dc.molnet.dnasim` | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `Tensorflow Probability`_ | 0.10 | :code:`dc.rl` | | `Tensorflow Probability`_ | 0.10.1 | :code:`dc.rl` | | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `XGBoost`_ | 1.1.1 | :code:`dc.models.xgboost_models` | | `XGBoost`_ | latest | :code:`dc.models.xgboost_models` | | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ Loading requirements-pyg.txtdeleted 100644 → 0 +0 −5 Original line number Diff line number Diff line 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 requirements-torch.txtdeleted 100644 → 0 +0 −2 Original line number Diff line number Diff line torch==1.5.1 torchvision==0.6.1 Loading
docker/master/Dockerfile +1 −1 Original line number Diff line number Diff line Loading @@ -18,7 +18,7 @@ RUN conda update -n base conda && \ git clone --depth 1 https://github.com/deepchem/deepchem.git && \ cd deepchem && \ . /miniconda/etc/profile.d/conda.sh && \ bash scripts/install_deepchem_conda.sh deepchem && \ bash scripts/install_deepchem_conda.sh deepchem gpu && \ conda activate deepchem && \ python setup.py install && \ conda clean -afy && \ Loading
docs/installation.rst +7 −0 Original line number Diff line number Diff line Loading @@ -141,6 +141,13 @@ Then, execute the shell script. bash scripts/install_deepchem_conda.sh deepchem If you want GPU support: .. code-block:: bash bash scripts/install_deepchem_conda.sh deepchem gpu If you are using the Windows and the PowerShell: .. code-block:: ps1 Loading
docs/requirements.rst +13 −13 Original line number Diff line number Diff line Loading @@ -26,7 +26,7 @@ DeepChem has a number of "soft" requirements. | Package name | Version | Location where this package is imported | | | | (dc: deepchem) | +================================+===============+===================================================+ | `BioPython`_ | 1.77 | :code:`dc.utlis.genomics_utils` | | `BioPython`_ | latest | :code:`dc.utlis.genomics_utils` | | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ Loading @@ -38,35 +38,35 @@ DeepChem has a number of "soft" requirements. | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `matminer`_ | 0.6.3 | :code:`dc.feat.materials_featurizers` | | `matminer`_ | latest | :code:`dc.feat.materials_featurizers` | | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `MDTraj`_ | 1.9.4 | :code:`dc.utils.pdbqt_utils` | | `MDTraj`_ | latest | :code:`dc.utils.pdbqt_utils` | | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `NetworkX`_ | 2.4 | :code:`dc.utils.rdkit_utils` | | `NetworkX`_ | latest | :code:`dc.utils.rdkit_utils` | | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `OpenMM`_ | 7.4.2 | :code:`dc.utils.rdkit_utils` | | `OpenMM`_ | latest | :code:`dc.utils.rdkit_utils` | | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `PDBFixer`_ | 1.6 | :code:`dc.utils.rdkit_utils` | | `PDBFixer`_ | latest | :code:`dc.utils.rdkit_utils` | | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `Pillow`_ | 7.1.2 | :code:`dc.data.data_loader`, | | `Pillow`_ | latest | :code:`dc.data.data_loader`, | | | | :code:`dc.trans.transformers` | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `pyGPGO`_ | 0.4.0.dev1 | :code:`dc.hyper.gaussian_process` | | `pyGPGO`_ | latest | :code:`dc.hyper.gaussian_process` | | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `Pymatgen`_ | 2020.7.18 | :code:`dc.feat.materials_featurizers` | | `Pymatgen`_ | latest | :code:`dc.feat.materials_featurizers` | | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ Loading @@ -78,19 +78,19 @@ DeepChem has a number of "soft" requirements. | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `RDKit`_ | 2020.03.4 | Many modules | | `RDKit`_ | latest | Many modules | | | | (we recommend you to instal) | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `simdna`_ | 0.4.3.2 | :code:`dc.metrics.genomic_metrics`, | | `simdna`_ | latest | :code:`dc.metrics.genomic_metrics`, | | | | :code:`dc.molnet.dnasim` | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `Tensorflow Probability`_ | 0.10 | :code:`dc.rl` | | `Tensorflow Probability`_ | 0.10.1 | :code:`dc.rl` | | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ | `XGBoost`_ | 1.1.1 | :code:`dc.models.xgboost_models` | | `XGBoost`_ | latest | :code:`dc.models.xgboost_models` | | | | | | | | | +--------------------------------+---------------+---------------------------------------------------+ Loading
requirements-pyg.txtdeleted 100644 → 0 +0 −5 Original line number Diff line number Diff line 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
requirements-torch.txtdeleted 100644 → 0 +0 −2 Original line number Diff line number Diff line torch==1.5.1 torchvision==0.6.1
