Tweak run script args, roll back repo to Python 3.7 (for Colab)

openfold/features/templates.py

@@ -11,7 +11,7 @@ from absl import logging
 import numpy as np
 
 from openfold.features import parsers, mmcif_parsing
-from openfold.features.tools import kalign
+from openfold.features.np import kalign
 from openfold.np import residue_constants
 
 

openfold/utils/deepspeed.py

@@ -18,10 +18,10 @@ from torch.utils.checkpoint import checkpoint
 from typing import Any, Tuple, List, Callable
 
 BLOCK_ARG = Any
-BLOCK_ARGS = Tuple[BLOCK_ARG, ...]
+BLOCK_ARGS = List[BLOCK_ARG]
 
 def checkpoint_blocks(
-    blocks: List[Callable[BLOCK_ARGS, BLOCK_ARGS]], 
+    blocks: List[Callable], 
     args: BLOCK_ARGS, 
     blocks_per_ckpt: int,
 ) -> BLOCK_ARGS:

run_pretrained_alphafold.py

@@ -170,7 +170,7 @@ def main(args):
 if __name__ == "__main__":
     parser = argparse.ArgumentParser()
     parser.add_argument(
-        "--fasta_path", type=str, default=None, required=True
+        "--fasta_path", type=str,
     )
     parser.add_argument(
         "--output_dir", type=str, default=os.getcwd(),
@@ -206,13 +206,13 @@ if __name__ == "__main__":
         '--kalign_binary_path', type=str, default='/usr/bin/kalign'
     )
     parser.add_argument(
-        '--uniref90_database_path', type=str, default=None, required=True
+        '--uniref90_database_path', type=str, 
     )
     parser.add_argument(
-        '--mgnify_database_path', type=str, default=None, required=True
+        '--mgnify_database_path', type=str, 
     )
     parser.add_argument(
-        '--bfd_database_path', type=str, default=None, required=True
+        '--bfd_database_path', type=str,
     )
     parser.add_argument(
         '--small_bfd_database_path', type=str, default=None
@@ -221,19 +221,19 @@ if __name__ == "__main__":
         '--uniclust30_database_path', type=str, default=None
     )
     parser.add_argument(
-        '--pdb70_database_path', type=str, default=None, required=True
+        '--pdb70_database_path', type=str,
     )
     parser.add_argument(
-        '--template_mmcif_dir', type=str, default=None, required=True
+        '--template_mmcif_dir', type=str,
     )
     parser.add_argument(
-        '--max_template_date', type=str, default=None, required=True
+        '--max_template_date', type=str,
     )
     parser.add_argument(
         '--obsolete_pdbs_path', type=str, default=None
     )
     parser.add_argument(
-        '--preset', type=str, default='full_dbs', required=True,
+        '--preset', type=str, default='full_dbs',
         choices=('reduced_dbs', 'full_dbs')
     )
     parser.add_argument(

scripts/install_third_party_dependencies.sh

@@ -13,7 +13,7 @@ wget -q -P /tmp \
 # Grab conda-only packages
 PATH=lib/conda/bin:$PATH
 conda update -qy conda \
-    && conda create --name $ENV_NAME -y python==3.9.5 \
+    && conda create --name $ENV_NAME -y python==3.7 \
     && source lib/conda/etc/profile.d/conda.sh \
     && conda activate $ENV_NAME \
     && pip install -r requirements.txt \
@@ -23,7 +23,7 @@ conda update -qy conda \
 
 # Install DeepMind's OpenMM patch
 OPENFOLD_DIR=$PWD
-pushd lib/conda/envs/$ENV_NAME/lib/python3.9/site-packages/ \
+pushd lib/conda/envs/$ENV_NAME/lib/python3.7/site-packages/ \
     && patch -p0 < $OPENFOLD_DIR/lib/openmm.patch \
     && popd
 

setup.py

@@ -37,7 +37,7 @@ setup(
     classifiers=[
         'License :: OSI Approved :: Apache Software License',
         'Operating System :: POSIX :: Linux',
-        'Programming Language :: Python :: 3.9,' 
+        'Programming Language :: Python :: 3.7,' 
         'Topic :: Scientific/Engineering :: Artificial Intelligence',
     ],
 )