dayhoff-tools 1.0.7__tar.gz → 1.0.8__tar.gz

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Files changed (30) hide show
  1. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/PKG-INFO +1 -1
  2. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/fasta.py +2 -2
  3. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/pyproject.toml +1 -1
  4. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/README.md +0 -0
  5. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/__init__.py +0 -0
  6. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/chemistry/standardizer.py +0 -0
  7. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/chemistry/utils.py +0 -0
  8. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/cli/__init__.py +0 -0
  9. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/cli/cloud_commands.py +0 -0
  10. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/cli/main.py +0 -0
  11. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/cli/swarm_commands.py +0 -0
  12. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/cli/utility_commands.py +0 -0
  13. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/deployment/base.py +0 -0
  14. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/deployment/deploy_aws.py +0 -0
  15. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/deployment/deploy_gcp.py +0 -0
  16. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/deployment/deploy_utils.py +0 -0
  17. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/deployment/job_runner.py +0 -0
  18. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/deployment/processors.py +0 -0
  19. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/deployment/swarm.py +0 -0
  20. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/embedders.py +0 -0
  21. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/file_ops.py +0 -0
  22. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/gcp.py +0 -0
  23. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/h5.py +0 -0
  24. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/kegg.py +0 -0
  25. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/logs.py +0 -0
  26. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/mmseqs.py +0 -0
  27. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/sqlite.py +0 -0
  28. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/structure.py +0 -0
  29. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/uniprot.py +0 -0
  30. {dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/warehouse.py +0 -0
{dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.3
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  Name: dayhoff-tools
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- Version: 1.0.7
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+ Version: 1.0.8
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  Summary: Common tools for all the repos at Dayhoff Labs
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  Author: Daniel Martin-Alarcon
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  Author-email: dma@dayhofflabs.com
{dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/dayhoff_tools/fasta.py RENAMED
@@ -14,7 +14,7 @@ import requests
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  from Bio import SeqIO
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  from Bio.SeqRecord import SeqRecord
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  from tqdm import tqdm
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- from tqdm.notebook import tqdm_notebook
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+ from tqdm.notebook import tqdm as tqdm_notebook
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  logger = logging.getLogger(__name__)
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@@ -923,7 +923,7 @@ def fetch_uniprot_fasta(
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  # Calculate number of batches for progress bar
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  num_batches = math.ceil(len(accession_list) / batch_size)
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- # Process accessions in batches with progress bar
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+ # Process accessions in batches with progress bar (using notebook version)
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  for i in tqdm_notebook(
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  range(0, len(accession_list), batch_size),
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  desc="Downloading sequences",
{dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
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  [project]
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  name = "dayhoff-tools"
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- version = "1.0.7"
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+ version = "1.0.8"
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  description = "Common tools for all the repos at Dayhoff Labs"
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  authors = [
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  {name = "Daniel Martin-Alarcon", email = "dma@dayhofflabs.com"}
{dayhoff_tools-1.0.7 → dayhoff_tools-1.0.8}/README.md RENAMED
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