Merging recent updates from main branch

.gitignore

-.DS_Store
-*.DS_Store
-**/.DS_Store
+.vscode/
 .idea/
-**/__pycache__
-*.pyc
-build/
-dist/
-*.egg-info/
-openfold/resources
-**/stereo_chemical_props.txt
-**/sample_feats.pickle
+__pycache__/
+*.egg-info
+build
+dist
+
+# files from script downloads
+data
+openfold/resources/
+tests/test_data/
+

README.md

@@ -246,7 +246,7 @@ python3 scripts/precompute_alignments.py mmcif_dir/ alignment_dir/ \
     --pdb70_database_path data/pdb70/pdb70 \
     --uniclust30_database_path data/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
     --bfd_database_path data/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
-    --cpus 16 \
+    --cpus_per_task 16 \
     --jackhmmer_binary_path lib/conda/envs/openfold_venv/bin/jackhmmer \
     --hhblits_binary_path lib/conda/envs/openfold_venv/bin/hhblits \
     --hhsearch_binary_path lib/conda/envs/openfold_venv/bin/hhsearch \

scripts/build_deepspeed_config.py

@@ -248,9 +248,10 @@ if(args.scheduler is not None):
         params["warmup_max_lr"] = args.warmup_max_lr
         params["warmup_num_steps"] = args.warmup_num_steps
     elif(args.scheduler == "WarmupDecayLR"):
-        params["total_num_steps"] = args.warmup_decay_total_num_steps
         params["warmup_min_lr"] = args.warmup_decay_min_lr
         params["warmup_max_lr"] = args.warmup_decay_max_lr
+        params["warmup_num_steps"] = args.warmup_decay_num_steps
+        params["total_num_steps"] = args.warmup_decay_total_num_steps
     else:
         raise ValueError("Invalid scheduler")