Merge remote-tracking branch 'origin/remove-torch-dependency' into tm…

…qm_add

README.md

@@ -2,16 +2,15 @@
 
 Open Quantum Data Commons
 
-## Setup Datasets
-
-Use the scripts in `setup/` to download the datasets. For more information, see the [README](setup/README.md) in the `setup/` directory.
-
-# Install the library in dev mode
+### Installing openQDC
+```bash
+git clone git@github.com:OpenDrugDiscovery/openQDC.git
+cd openQDC
+# use mamba/conda
+mamba env create -n openqdc -f env.yml
 pip install -e .
 ```
 
-## Development lifecycle
-
 ### Tests
 
 You can run tests locally with:

env.yml

@@ -8,39 +8,22 @@ dependencies:
   - tqdm
   - loguru
   - fsspec
-  - s3fs
   - gcsfs
-  - joblib
-  - prettytable
-  - pyrootutils
 
   # Scientific
   - pandas
   - numpy
-  - scipy
-  - sympy
 
   # Chem
-  - ipdb
   - datamol #==0.9.0
   - rdkit #-pypi #==2022.9.3
   - ase
-
-  # ML
-  #- einops =0.6.0
-  - pytorch
   - dscribe
 
   # other stuffs
   - h5py >=3.8.0
   - gdown #==4.6.4
 
-  # Viz
-  - matplotlib
-  - seaborn
-  - ipywidgets
-  - nglview
-
   # Dev
   - pytest >=6.0
   - pytest-cov
@@ -49,8 +32,6 @@ dependencies:
   - jupyterlab
   - pre-commit
   - ruff
-  - ipykernel
-  - isort
 
   # Doc
   - mkdocs

src/openqdc/datasets/base.py

@@ -6,7 +6,6 @@
 
 import numpy as np
 import pandas as pd
-import torch
 from ase.io.extxyz import write_extxyz
 from loguru import logger
 from sklearn.utils import Bunch
@@ -82,7 +81,7 @@ def read_qc_archive_h5(
     return samples
 
 
-class BaseDataset(torch.utils.data.Dataset):
+class BaseDataset:
     __energy_methods__ = []
     __force_methods__ = []
     energy_target_names = []

src/openqdc/utils/__init__.py

@@ -6,7 +6,6 @@
     load_hdf5_file,
     load_json,
     load_pkl,
-    load_torch,
     makedirs,
     save_pkl,
     set_cache_dir,
@@ -19,7 +18,6 @@
     "makedirs",
     "load_hdf5_file",
     "load_json",
-    "load_torch",
     "create_hdf5_file",
     "check_file",
     "set_cache_dir",

src/openqdc/utils/io.py

@@ -5,7 +5,6 @@
 
 import fsspec
 import h5py
-import torch
 from ase.atoms import Atoms
 from fsspec.implementations.local import LocalFileSystem
 from gcsfs import GCSFileSystem
@@ -70,21 +69,6 @@ def copy_exists(local_path):
     return os.path.exists(local_path) or gcp_filesys.exists(remote_path)
 
 
-def load_torch_gcs(path):
-    """Loads torch file"""
-    # get file system
-    fs: GCSFileSystem = fsspec.filesystem("gs")
-
-    # load from GCS
-    with fs.open(path, "rb") as fp:
-        return torch.load(fp)
-
-
-def load_torch(path):
-    """Loads torch file"""
-    return torch.load(path)
-
-
 def makedirs_gcs(path, exist_ok=True):
     """Creates directory"""
     fs: GCSFileSystem = fsspec.filesystem("gs")