dayhoff-tools 1.14.5__py3-none-any.whl → 1.14.6__py3-none-any.whl

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Files changed (6) hide show
  1. dayhoff_tools/batch/workers/base.py +3 -1
  2. dayhoff_tools/cli/batch/commands/finalize.py +3 -2
  3. {dayhoff_tools-1.14.5.dist-info → dayhoff_tools-1.14.6.dist-info}/METADATA +1 -1
  4. {dayhoff_tools-1.14.5.dist-info → dayhoff_tools-1.14.6.dist-info}/RECORD +6 -6
  5. {dayhoff_tools-1.14.5.dist-info → dayhoff_tools-1.14.6.dist-info}/WHEEL +0 -0
  6. {dayhoff_tools-1.14.5.dist-info → dayhoff_tools-1.14.6.dist-info}/entry_points.txt +0 -0
dayhoff_tools/batch/workers/base.py CHANGED
@@ -83,7 +83,9 @@ def get_input_file(index: int, job_dir: Path, prefix: str = "chunk") -> Path:
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  return job_dir / "input" / f"{prefix}_{index:03d}.fasta"
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- def get_output_file(index: int, job_dir: Path, prefix: str = "embed", suffix: str = ".h5") -> Path:
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+ def get_output_file(
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+ index: int, job_dir: Path, prefix: str = "embed", suffix: str = ".h5"
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+ ) -> Path:
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  """Get the output file path for a given index.
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  Args:
dayhoff_tools/cli/batch/commands/finalize.py CHANGED
@@ -136,10 +136,11 @@ def _finalize_embeddings(output_dir: Path, output_path: Path):
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  # Combine H5 files
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  click.echo("Combining H5 files...")
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+ # Get list of h5 file paths as strings
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+ h5_file_paths = [str(f) for f in h5_files]
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  combine_h5_files(
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- input_folder=str(output_dir),
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+ input_files=h5_file_paths,
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  output_file=str(output_path),
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- glob_pattern="embed_*.h5",
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  )
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  # Deduplicate
{dayhoff_tools-1.14.5.dist-info → dayhoff_tools-1.14.6.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: dayhoff-tools
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- Version: 1.14.5
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+ Version: 1.14.6
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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-1.14.5.dist-info → dayhoff_tools-1.14.6.dist-info}/RECORD RENAMED
@@ -1,7 +1,7 @@
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  dayhoff_tools/__init__.py,sha256=M5zThPyEBRYa5CfwlzKhcqTevWn3OKu62cjV6Zqie2A,469
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  dayhoff_tools/batch/__init__.py,sha256=N7v1pUg3rp68W6J7cX2Gssxdfp57Z7G0WeFJh7gKeiM,163
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  dayhoff_tools/batch/workers/__init__.py,sha256=DJTtiBSE5k9J6qwG_MsXDn8hgz_lvEdaMwqKa6YyqXo,369
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- dayhoff_tools/batch/workers/base.py,sha256=NwvmhUqfN82uyFbf-UyAw7Tddu9kNHnM_nIdCEbZUFc,4263
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+ dayhoff_tools/batch/workers/base.py,sha256=Jie5ScJrPSRkmLQdcM2hPJTmk3pIeLL0oA8Y9pkP0HA,4269
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  dayhoff_tools/batch/workers/boltz.py,sha256=QTIqMWuV_o3v1tYaZhvjyCl5F65ZlPcc0-TXtitMaFQ,14663
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  dayhoff_tools/batch/workers/embed_t5.py,sha256=A5WqsQa1WZ7_la5X5wt0XUP-VwOglH04WyEINhwipeY,2750
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  dayhoff_tools/chemistry/standardizer.py,sha256=uMn7VwHnx02nc404eO6fRuS4rsl4dvSPf2ElfZDXEpY,11188
@@ -13,7 +13,7 @@ dayhoff_tools/cli/batch/commands/__init__.py,sha256=1xRzzL_mc1hz1Pv0OWNr-g6fkL5X
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  dayhoff_tools/cli/batch/commands/boltz.py,sha256=WARoklK5QTo71echUkm-anyj2AlEI9AEtWaiD_ds-EU,11759
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  dayhoff_tools/cli/batch/commands/cancel.py,sha256=5FHLRoq8nvOr8HuKxXUZqAyAdjQP8seaNSaeAdhOoE8,2890
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  dayhoff_tools/cli/batch/commands/embed_t5.py,sha256=UtF8ulJcz15sdd1QzvPVPeioN_AMks1DZ7c6vKtwhDE,11052
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- dayhoff_tools/cli/batch/commands/finalize.py,sha256=2kQTtHxdW52s0lrLUlc7tx7Ab092sxs8uSc9-f2utUg,7198
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+ dayhoff_tools/cli/batch/commands/finalize.py,sha256=i9In09vrzc9jQlCA6F82ceuZB9mHUXeOaYYyRUrHQCc,7254
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  dayhoff_tools/cli/batch/commands/list_jobs.py,sha256=y90_XqFI2qcvV2XUC01P3P2aIdtl5hXP3cBDEofsRtU,2432
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  dayhoff_tools/cli/batch/commands/local.py,sha256=vOTojTAp4YZXIMLKNqc76oIE0oWMjB1mtTe6r19LrEc,3075
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  dayhoff_tools/cli/batch/commands/logs.py,sha256=FOYpANQCsQTJKigq77k1xbhgOqtRPw9hyHkljILWlmo,5241
@@ -70,7 +70,7 @@ dayhoff_tools/intake/uniprot.py,sha256=BZYJQF63OtPcBBnQ7_P9gulxzJtqyorgyuDiPeOJq
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  dayhoff_tools/logs.py,sha256=DKdeP0k0kliRcilwvX0mUB2eipO5BdWUeHwh-VnsICs,838
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  dayhoff_tools/sqlite.py,sha256=jV55ikF8VpTfeQqqlHSbY8OgfyfHj8zgHNpZjBLos_E,18672
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  dayhoff_tools/warehouse.py,sha256=UETBtZD3r7WgvURqfGbyHlT7cxoiVq8isjzMuerKw8I,24475
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- dayhoff_tools-1.14.5.dist-info/METADATA,sha256=D9qnPVpWLC_lEVvpBSloIDCWE28Bhi7XvC-WvLpRQpE,3184
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- dayhoff_tools-1.14.5.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
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- dayhoff_tools-1.14.5.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
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- dayhoff_tools-1.14.5.dist-info/RECORD,,
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+ dayhoff_tools-1.14.6.dist-info/METADATA,sha256=3rnOAUIQQN2JYIy6MtfSgAraglhmDY64Aq7fQWs-iRo,3184
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+ dayhoff_tools-1.14.6.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
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+ dayhoff_tools-1.14.6.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
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+ dayhoff_tools-1.14.6.dist-info/RECORD,,