Skip to content

Commit 3abb2ce

Browse files
amoreheadamorehead
committed
Make Python version invocations explicit
1 parent 534b5ce commit 3abb2ce

File tree

3 files changed

+22
-22
lines changed

3 files changed

+22
-22
lines changed

‎project/datasets/builder/compile_db5_dataset_on_andes.sh

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -33,17 +33,17 @@ rm "$PROJDIR"/project/datasets/DB5.tar.gz "$PROJDIR"/project/datasets/DB5/.READM
3333
rm -rf "$PROJDIR"/project/datasets/DB5/interim "$PROJDIR"/project/datasets/DB5/processed
3434
mkdir "$PROJDIR"/project/datasets/DB5/interim "$PROJDIR"/project/datasets/DB5/interim/external_feats "$PROJDIR"/project/datasets/DB5/interim/external_feats/PSAIA "$PROJDIR"/project/datasets/DB5/interim/external_feats/PSAIA/DB5 "$PROJDIR"/project/datasets/DB5/final "$PROJDIR"/project/datasets/DB5/final/raw
3535

36-
python "$PROJDIR"/project/datasets/builder/make_dataset.py "$PROJDIR"/project/datasets/DB5/raw "$PROJDIR"/project/datasets/DB5/interim --num_cpus 32 --rank "$1" --size "$2" --source_type db5
36+
python3 "$PROJDIR"/project/datasets/builder/make_dataset.py "$PROJDIR"/project/datasets/DB5/raw "$PROJDIR"/project/datasets/DB5/interim --num_cpus 32 --rank "$1" --size "$2" --source_type db5
3737

38-
python "$PROJDIR"/project/datasets/builder/generate_psaia_features.py "$PSAIADIR" "$PROJDIR"/project/datasets/builder/psaia_config_file_db5.txt "$PROJDIR"/project/datasets/DB5/raw "$PROJDIR"/project/datasets/DB5/interim/parsed "$PROJDIR"/project/datasets/DB5/interim/parsed "$PROJDIR"/project/datasets/DB5/interim/external_feats --source_type db5 --rank "$1" --size "$2"
39-
srun python "$PROJDIR"/project/datasets/builder/generate_hhsuite_features.py "$PROJDIR"/project/datasets/DB5/interim/parsed "$PROJDIR"/project/datasets/DB5/interim/parsed "$HHSUITE_DB" "$PROJDIR"/project/datasets/DB5/interim/external_feats --rank "$1" --size "$2" --num_cpu_jobs 4 --num_cpus_per_job 8 --num_iter 2 --source_type db5 --write_file
38+
python3 "$PROJDIR"/project/datasets/builder/generate_psaia_features.py "$PSAIADIR" "$PROJDIR"/project/datasets/builder/psaia_config_file_db5.txt "$PROJDIR"/project/datasets/DB5/raw "$PROJDIR"/project/datasets/DB5/interim/parsed "$PROJDIR"/project/datasets/DB5/interim/parsed "$PROJDIR"/project/datasets/DB5/interim/external_feats --source_type db5 --rank "$1" --size "$2"
39+
srun python3 "$PROJDIR"/project/datasets/builder/generate_hhsuite_features.py "$PROJDIR"/project/datasets/DB5/interim/parsed "$PROJDIR"/project/datasets/DB5/interim/parsed "$HHSUITE_DB" "$PROJDIR"/project/datasets/DB5/interim/external_feats --rank "$1" --size "$2" --num_cpu_jobs 4 --num_cpus_per_job 8 --num_iter 2 --source_type db5 --write_file
4040

41-
srun python "$PROJDIR"/project/datasets/builder/postprocess_pruned_pairs.py "$PROJDIR"/project/datasets/DB5/raw "$PROJDIR"/project/datasets/DB5/interim/pairs "$PROJDIR"/project/datasets/DB5/interim/external_feats "$PROJDIR"/project/datasets/DB5/final/raw --num_cpus 32 --rank "$1" --size "$2" --source_type db5
41+
srun python3 "$PROJDIR"/project/datasets/builder/postprocess_pruned_pairs.py "$PROJDIR"/project/datasets/DB5/raw "$PROJDIR"/project/datasets/DB5/interim/pairs "$PROJDIR"/project/datasets/DB5/interim/external_feats "$PROJDIR"/project/datasets/DB5/final/raw --num_cpus 32 --rank "$1" --size "$2" --source_type db5
4242

43-
python "$PROJDIR"/project/datasets/builder/partition_dataset_filenames.py "$PROJDIR"/project/datasets/DB5/final/raw --source_type db5 --rank "$1" --size "$2"
44-
python "$PROJDIR"/project/datasets/builder/collect_dataset_statistics.py "$PROJDIR"/project/datasets/DB5/final/raw --rank "$1" --size "$2"
45-
python "$PROJDIR"/project/datasets/builder/log_dataset_statistics.py "$PROJDIR"/project/datasets/DB5/final/raw --rank "$1" --size "$2"
46-
python "$PROJDIR"/project/datasets/builder/impute_missing_feature_values.py "$PROJDIR"/project/datasets/DB5/final/raw --impute_atom_features False --num_cpus 32 --rank "$1" --size "$2"
43+
python3 "$PROJDIR"/project/datasets/builder/partition_dataset_filenames.py "$PROJDIR"/project/datasets/DB5/final/raw --source_type db5 --rank "$1" --size "$2"
44+
python3 "$PROJDIR"/project/datasets/builder/collect_dataset_statistics.py "$PROJDIR"/project/datasets/DB5/final/raw --rank "$1" --size "$2"
45+
python3 "$PROJDIR"/project/datasets/builder/log_dataset_statistics.py "$PROJDIR"/project/datasets/DB5/final/raw --rank "$1" --size "$2"
46+
python3 "$PROJDIR"/project/datasets/builder/impute_missing_feature_values.py "$PROJDIR"/project/datasets/DB5/final/raw --impute_atom_features False --num_cpus 32 --rank "$1" --size "$2"
4747

4848
# Optionally convert each postprocessed (final 'raw') complex into a pair of DGL graphs (final 'processed') with labels
49-
python "$PROJDIR"/project/datasets/builder/convert_complexes_to_graphs.py "$PROJDIR"/project/datasets/DB5/final/raw "$PROJDIR"/project/datasets/DB5/final/processed --num_cpus 32 --edge_dist_cutoff 15.0 --edge_limit 5000 --self_loops True --rank "$1" --size "$2"
49+
python3 "$PROJDIR"/project/datasets/builder/convert_complexes_to_graphs.py "$PROJDIR"/project/datasets/DB5/final/raw "$PROJDIR"/project/datasets/DB5/final/processed --num_cpus 32 --edge_dist_cutoff 15.0 --edge_limit 5000 --self_loops True --rank "$1" --size "$2"

‎project/datasets/builder/compile_dips_dataset_on_andes.sh

Lines changed: 12 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -33,23 +33,23 @@ rm "$PROJDIR"/project/datasets/DIPS/final/raw/pairs-postprocessed.txt "$PROJDIR"
3333
mkdir "$PROJDIR"/project/datasets/DIPS/raw "$PROJDIR"/project/datasets/DIPS/raw/pdb "$PROJDIR"/project/datasets/DIPS/interim "$PROJDIR"/project/datasets/DIPS/interim/external_feats "$PROJDIR"/project/datasets/DIPS/interim/external_feats/PSAIA "$PROJDIR"/project/datasets/DIPS/interim/external_feats/PSAIA/RCSB "$PROJDIR"/project/datasets/DIPS/final "$PROJDIR"/project/datasets/DIPS/final/raw
3434
rsync -rlpt -v -z --delete --port=33444 --include='*.gz' --include='*/' --exclude '*' rsync.rcsb.org::ftp_data/biounit/coordinates/divided/ "$PROJDIR"/project/datasets/DIPS/raw/pdb
3535

36-
python "$PROJDIR"/project/datasets/builder/extract_raw_pdb_gz_archives.py "$PROJDIR"/project/datasets/DIPS/raw/pdb --rank "$1" --size "$2"
36+
python3 "$PROJDIR"/project/datasets/builder/extract_raw_pdb_gz_archives.py "$PROJDIR"/project/datasets/DIPS/raw/pdb --rank "$1" --size "$2"
3737

38-
python "$PROJDIR"/project/datasets/builder/make_dataset.py "$PROJDIR"/project/datasets/DIPS/raw/pdb "$PROJDIR"/project/datasets/DIPS/interim --num_cpus 32 --rank "$1" --size "$2" --source_type rcsb --bound
38+
python3 "$PROJDIR"/project/datasets/builder/make_dataset.py "$PROJDIR"/project/datasets/DIPS/raw/pdb "$PROJDIR"/project/datasets/DIPS/interim --num_cpus 32 --rank "$1" --size "$2" --source_type rcsb --bound
3939

40-
python "$PROJDIR"/project/datasets/builder/prune_pairs.py "$PROJDIR"/project/datasets/DIPS/interim/pairs "$PROJDIR"/project/datasets/DIPS/filters "$PROJDIR"/project/datasets/DIPS/interim/pairs-pruned --num_cpus 32 --rank "$1" --size "$2"
40+
python3 "$PROJDIR"/project/datasets/builder/prune_pairs.py "$PROJDIR"/project/datasets/DIPS/interim/pairs "$PROJDIR"/project/datasets/DIPS/filters "$PROJDIR"/project/datasets/DIPS/interim/pairs-pruned --num_cpus 32 --rank "$1" --size "$2"
4141

42-
python "$PROJDIR"/project/datasets/builder/generate_psaia_features.py "$PSAIADIR" "$PROJDIR"/project/datasets/builder/psaia_config_file_dips.txt "$PROJDIR"/project/datasets/DIPS/raw/pdb "$PROJDIR"/project/datasets/DIPS/interim/parsed "$PROJDIR"/project/datasets/DIPS/interim/pairs-pruned "$PROJDIR"/project/datasets/DIPS/interim/external_feats --source_type rcsb --rank "$1" --size "$2"
43-
srun python "$PROJDIR"/project/datasets/builder/generate_hhsuite_features.py "$PROJDIR"/project/datasets/DIPS/interim/parsed "$PROJDIR"/project/datasets/DIPS/interim/pairs-pruned "$HHSUITE_DB" "$PROJDIR"/project/datasets/DIPS/interim/external_feats --rank "$1" --size "$2" --num_cpu_jobs 4 --num_cpus_per_job 8 --num_iter 2 --source_type rcsb --write_file
42+
python3 "$PROJDIR"/project/datasets/builder/generate_psaia_features.py "$PSAIADIR" "$PROJDIR"/project/datasets/builder/psaia_config_file_dips.txt "$PROJDIR"/project/datasets/DIPS/raw/pdb "$PROJDIR"/project/datasets/DIPS/interim/parsed "$PROJDIR"/project/datasets/DIPS/interim/pairs-pruned "$PROJDIR"/project/datasets/DIPS/interim/external_feats --source_type rcsb --rank "$1" --size "$2"
43+
srun python3 "$PROJDIR"/project/datasets/builder/generate_hhsuite_features.py "$PROJDIR"/project/datasets/DIPS/interim/parsed "$PROJDIR"/project/datasets/DIPS/interim/pairs-pruned "$HHSUITE_DB" "$PROJDIR"/project/datasets/DIPS/interim/external_feats --rank "$1" --size "$2" --num_cpu_jobs 4 --num_cpus_per_job 8 --num_iter 2 --source_type rcsb --write_file
4444

4545
# Retroactively download the PDB files corresponding to complexes that made it through DIPS-Plus' RCSB complex pruning to reduce storage requirements
46-
python "$PROJDIR"/project/datasets/builder/download_missing_pruned_pair_pdbs.py "$PROJDIR"/project/datasets/DIPS/raw/pdb "$PROJDIR"/project/datasets/DIPS/interim/pairs-pruned --num_cpus 32 --rank "$1" --size "$2"
47-
srun python "$PROJDIR"/project/datasets/builder/postprocess_pruned_pairs.py "$PROJDIR"/project/datasets/DIPS/raw/pdb "$PROJDIR"/project/datasets/DIPS/interim/pairs-pruned "$PROJDIR"/project/datasets/DIPS/interim/external_feats "$PROJDIR"/project/datasets/DIPS/final/raw --num_cpus 32 --rank "$1" --size "$2"
46+
python3 "$PROJDIR"/project/datasets/builder/download_missing_pruned_pair_pdbs.py "$PROJDIR"/project/datasets/DIPS/raw/pdb "$PROJDIR"/project/datasets/DIPS/interim/pairs-pruned --num_cpus 32 --rank "$1" --size "$2"
47+
srun python3 "$PROJDIR"/project/datasets/builder/postprocess_pruned_pairs.py "$PROJDIR"/project/datasets/DIPS/raw/pdb "$PROJDIR"/project/datasets/DIPS/interim/pairs-pruned "$PROJDIR"/project/datasets/DIPS/interim/external_feats "$PROJDIR"/project/datasets/DIPS/final/raw --num_cpus 32 --rank "$1" --size "$2"
4848

49-
python "$PROJDIR"/project/datasets/builder/partition_dataset_filenames.py "$PROJDIR"/project/datasets/DIPS/final/raw --source_type rcsb --filter_by_atom_count True --max_atom_count 17500 --rank "$1" --size "$2"
50-
python "$PROJDIR"/project/datasets/builder/collect_dataset_statistics.py "$PROJDIR"/project/datasets/DIPS/final/raw --rank "$1" --size "$2"
51-
python "$PROJDIR"/project/datasets/builder/log_dataset_statistics.py "$PROJDIR"/project/datasets/DIPS/final/raw --rank "$1" --size "$2"
52-
python "$PROJDIR"/project/datasets/builder/impute_missing_feature_values.py "$PROJDIR"/project/datasets/DIPS/final/raw --impute_atom_features False --num_cpus 32 --rank "$1" --size "$2"
49+
python3 "$PROJDIR"/project/datasets/builder/partition_dataset_filenames.py "$PROJDIR"/project/datasets/DIPS/final/raw --source_type rcsb --filter_by_atom_count True --max_atom_count 17500 --rank "$1" --size "$2"
50+
python3 "$PROJDIR"/project/datasets/builder/collect_dataset_statistics.py "$PROJDIR"/project/datasets/DIPS/final/raw --rank "$1" --size "$2"
51+
python3 "$PROJDIR"/project/datasets/builder/log_dataset_statistics.py "$PROJDIR"/project/datasets/DIPS/final/raw --rank "$1" --size "$2"
52+
python3 "$PROJDIR"/project/datasets/builder/impute_missing_feature_values.py "$PROJDIR"/project/datasets/DIPS/final/raw --impute_atom_features False --num_cpus 32 --rank "$1" --size "$2"
5353

5454
# Optionally convert each postprocessed (final 'raw') complex into a pair of DGL graphs (final 'processed') with labels
55-
python "$PROJDIR"/project/datasets/builder/convert_complexes_to_graphs.py "$PROJDIR"/project/datasets/DIPS/final/raw "$PROJDIR"/project/datasets/DIPS/final/processed --num_cpus 32 --edge_dist_cutoff 15.0 --edge_limit 5000 --self_loops True --rank "$1" --size "$2"
55+
python3 "$PROJDIR"/project/datasets/builder/convert_complexes_to_graphs.py "$PROJDIR"/project/datasets/DIPS/final/raw "$PROJDIR"/project/datasets/DIPS/final/processed --num_cpus 32 --edge_dist_cutoff 15.0 --edge_limit 5000 --self_loops True --rank "$1" --size "$2"

‎setup.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
#!/usr/bin/env python
1+
#!/usr/bin/env python3
22

33
from setuptools import setup, find_packages
44

0 commit comments

Comments
 (0)