dayhoff-tools 1.6.3__tar.gz → 1.6.4__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 dayhoff-tools might be problematic. Click here for more details.

Files changed (32) hide show
  1. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/PKG-INFO +1 -1
  2. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/cli/engine_commands.py +9 -7
  3. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/pyproject.toml +1 -1
  4. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/README.md +0 -0
  5. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/__init__.py +0 -0
  6. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/chemistry/standardizer.py +0 -0
  7. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/chemistry/utils.py +0 -0
  8. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/cli/__init__.py +0 -0
  9. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/cli/cloud_commands.py +0 -0
  10. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/cli/main.py +0 -0
  11. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/cli/swarm_commands.py +0 -0
  12. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/cli/utility_commands.py +0 -0
  13. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/deployment/base.py +0 -0
  14. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/deployment/deploy_aws.py +0 -0
  15. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/deployment/deploy_gcp.py +0 -0
  16. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/deployment/deploy_utils.py +0 -0
  17. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/deployment/job_runner.py +0 -0
  18. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/deployment/processors.py +0 -0
  19. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/deployment/swarm.py +0 -0
  20. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/embedders.py +0 -0
  21. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/fasta.py +0 -0
  22. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/file_ops.py +0 -0
  23. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/h5.py +0 -0
  24. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/intake/gcp.py +0 -0
  25. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/intake/gtdb.py +0 -0
  26. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/intake/kegg.py +0 -0
  27. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/intake/mmseqs.py +0 -0
  28. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/intake/structure.py +0 -0
  29. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/intake/uniprot.py +0 -0
  30. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/logs.py +0 -0
  31. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/sqlite.py +0 -0
  32. {dayhoff_tools-1.6.3 → dayhoff_tools-1.6.4}/dayhoff_tools/warehouse.py +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.3
2
2
  Name: dayhoff-tools
3
- Version: 1.6.3
3
+ Version: 1.6.4
4
4
  Summary: Common tools for all the repos at Dayhoff Labs
5
5
  Author: Daniel Martin-Alarcon
6
6
  Author-email: dma@dayhofflabs.com
@@ -1860,13 +1860,13 @@ def _attempt_studio_attach(studio, engine, target_user, public_key):
1860
1860
 
1861
1861
 
1862
1862
  def _poll_operation(operation_id: str, timeout: int = 600) -> Tuple[bool, str]:
1863
- """Poll the /operations/<id> endpoint until it completes or fails.
1863
+ """Poll /operations/<id> until COMPLETED or FAILED.
1864
1864
 
1865
- Returns (True, "") on success, or (False, error_message) on failure/timeout.
1865
+ Returns (True, "") on success or (False, error_message) on failure / timeout.
1866
+ Uses a simple status spinner to avoid nested Live displays.
1866
1867
  """
1867
1868
  start_ts = time.time()
1868
- with Progress(SpinnerColumn(), TimeElapsedColumn(), TextColumn("[progress.description]{task.description}"), transient=True) as prog:
1869
- task = prog.add_task("Waiting for studio attach to complete…", total=None)
1869
+ with console.status("[cyan]Waiting for studio attach to complete…", spinner="dots") as status:
1870
1870
  while True:
1871
1871
  if time.time() - start_ts > timeout:
1872
1872
  return False, "Timed out waiting for attach operation to complete"
@@ -1874,11 +1874,13 @@ def _poll_operation(operation_id: str, timeout: int = 600) -> Tuple[bool, str]:
1874
1874
  if op_resp.status_code != 200:
1875
1875
  return False, f"Failed to fetch operation status (HTTP {op_resp.status_code})"
1876
1876
  data = op_resp.json()
1877
- status = data.get("status")
1878
- if status == "COMPLETED":
1877
+ op_status = data.get("status")
1878
+ if op_status == "COMPLETED":
1879
1879
  return True, ""
1880
- if status == "FAILED":
1880
+ if op_status == "FAILED":
1881
1881
  return False, data.get("error", "Operation failed")
1882
+ # update spinner text occasionally
1883
+ status.update(f"[cyan]Waiting… ({op_status.lower()})")
1882
1884
  time.sleep(3)
1883
1885
 
1884
1886
 
@@ -5,7 +5,7 @@ build-backend = "poetry.core.masonry.api"
5
5
 
6
6
  [project]
7
7
  name = "dayhoff-tools"
8
- version = "1.6.3"
8
+ version = "1.6.4"
9
9
  description = "Common tools for all the repos at Dayhoff Labs"
10
10
  authors = [
11
11
  {name = "Daniel Martin-Alarcon", email = "dma@dayhofflabs.com"}
File without changes