rcsb-embedding-model 0.0.30__tar.gz → 0.0.31__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.


This version of rcsb-embedding-model might be problematic. Click here for more details.

Files changed (51) hide show
  1. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/PKG-INFO +2 -1
  2. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/pyproject.toml +2 -1
  3. rcsb_embedding_model-0.0.31/src/rcsb_embedding_model/__init__.py +9 -0
  4. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/cli/inference.py +18 -0
  5. rcsb_embedding_model-0.0.30/src/rcsb_embedding_model/__init__.py +0 -4
  6. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/.dockerignore +0 -0
  7. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/.github/workflows/_workflow-docker.yaml +0 -0
  8. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/.github/workflows/publish.yaml +0 -0
  9. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/.gitignore +0 -0
  10. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/Dockerfile +0 -0
  11. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/LICENSE.md +0 -0
  12. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/README.md +0 -0
  13. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/assets/embedding-model-architecture.png +0 -0
  14. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/examples/esm_embeddings.py +0 -0
  15. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/cli/args_utils.py +0 -0
  16. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/dataset/esm_prot_from_chain.py +0 -0
  17. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/dataset/esm_prot_from_structure.py +0 -0
  18. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/dataset/resdiue_assembly_embedding_from_structure.py +0 -0
  19. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/dataset/residue_assembly_embedding_from_tensor_file.py +0 -0
  20. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/dataset/residue_embedding_from_structure.py +0 -0
  21. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/dataset/residue_embedding_from_tensor_file.py +0 -0
  22. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/inference/assembly_inferece.py +0 -0
  23. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/inference/chain_inference.py +0 -0
  24. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/inference/esm_inference.py +0 -0
  25. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/inference/structure_inference.py +0 -0
  26. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/model/layers.py +0 -0
  27. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/model/residue_embedding_aggregator.py +0 -0
  28. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/modules/chain_module.py +0 -0
  29. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/modules/esm_module.py +0 -0
  30. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/modules/structure_module.py +0 -0
  31. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/rcsb_structure_embedding.py +0 -0
  32. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/types/api_types.py +0 -0
  33. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/utils/data.py +0 -0
  34. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/utils/model.py +0 -0
  35. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/utils/structure_parser.py +0 -0
  36. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/utils/structure_provider.py +0 -0
  37. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/src/rcsb_embedding_model/writer/batch_writer.py +0 -0
  38. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/resources/embeddings/1acb.A.pt +0 -0
  39. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/resources/embeddings/1acb.B.pt +0 -0
  40. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/resources/embeddings/2uzi.A.pt +0 -0
  41. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/resources/embeddings/2uzi.B.pt +0 -0
  42. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/resources/embeddings/2uzi.C.pt +0 -0
  43. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/resources/pdb/1acb.cif +0 -0
  44. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/resources/pdb/2uzi.cif +0 -0
  45. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/resources/src_stream/assembly-complete-test.csv +0 -0
  46. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/resources/src_stream/instance-complete-test.csv +0 -0
  47. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/resources/src_stream/instance.csv +0 -0
  48. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/test_cli_inference.py +0 -0
  49. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/test_embedding_model.py +0 -0
  50. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/test_inference.py +0 -0
  51. {rcsb_embedding_model-0.0.30 → rcsb_embedding_model-0.0.31}/tests/test_remote_inference.py +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: rcsb-embedding-model
3
- Version: 0.0.30
3
+ Version: 0.0.31
4
4
  Summary: Protein Embedding Model for Structure Search
5
5
  Project-URL: Homepage, https://github.com/rcsb/rcsb-embedding-model
6
6
  Project-URL: Issues, https://github.com/rcsb/rcsb-embedding-model/issues
@@ -11,6 +11,7 @@ Classifier: Operating System :: OS Independent
11
11
  Classifier: Programming Language :: Python :: 3
12
12
  Requires-Python: >=3.10
13
13
  Requires-Dist: esm>=3.2.0
14
+ Requires-Dist: importlib-metadata>=8.7.0
14
15
  Requires-Dist: lightning>=2.5.0
15
16
  Requires-Dist: typer>=0.15.0
16
17
  Description-Content-Type: text/markdown
@@ -1,6 +1,6 @@
1
1
  [project]
2
2
  name = "rcsb-embedding-model"
3
- version = "0.0.30"
3
+ version = "0.0.31"
4
4
  authors = [
5
5
  { name="Joan Segura", email="joan.segura@rcsb.org" },
6
6
  ]
@@ -14,6 +14,7 @@ classifiers = [
14
14
  license = "BSD-3-Clause"
15
15
  license-files = ["LICEN[CS]E*"]
16
16
  dependencies=[
17
+ "importlib-metadata >= 8.7.0",
17
18
  "esm >= 3.2.0",
18
19
  "lightning >= 2.5.0",
19
20
  "typer >= 0.15.0"
@@ -0,0 +1,9 @@
1
+ from importlib_metadata import version, PackageNotFoundError
2
+ from rcsb_embedding_model.rcsb_structure_embedding import RcsbStructureEmbedding
3
+
4
+ try:
5
+ __version__ = version("rcsb-embedding-model")
6
+ except PackageNotFoundError:
7
+ __version__ = "0.0.0"
8
+
9
+ __all__ = ["RcsbStructureEmbedding", "__version__"]
@@ -3,6 +3,7 @@ from typing import Annotated, List
3
3
 
4
4
  import typer
5
5
 
6
+ from rcsb_embedding_model import __version__
6
7
  from rcsb_embedding_model.cli.args_utils import arg_devices
7
8
  from rcsb_embedding_model.types.api_types import StructureFormat, Accelerator, SrcLocation, SrcProteinFrom, \
8
9
  StructureLocation, SrcAssemblyFrom, SrcTensorFrom, OutFormat
@@ -437,5 +438,22 @@ def complete_embedding(
437
438
  )
438
439
 
439
440
 
441
+ def version_callback(value: bool):
442
+ if value:
443
+ typer.echo(f"{__version__}")
444
+ raise typer.Exit()
445
+
446
+ @app.callback()
447
+ def main(
448
+ version: bool = typer.Option(
449
+ None,
450
+ "--version",
451
+ callback=version_callback,
452
+ is_eager=True,
453
+ help="Show the version and exit",
454
+ )
455
+ ):
456
+ pass
457
+
440
458
  if __name__ == "__main__":
441
459
  app()
@@ -1,4 +0,0 @@
1
-
2
- from rcsb_embedding_model.rcsb_structure_embedding import RcsbStructureEmbedding
3
-
4
- __all__ = ["RcsbStructureEmbedding"]