dayhoff-tools 1.11.3__tar.gz → 1.11.4__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.
Files changed (38) hide show
  1. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/PKG-INFO +1 -1
  2. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/utility_commands.py +44 -38
  3. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/pyproject.toml +1 -1
  4. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/README.md +0 -0
  5. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/__init__.py +0 -0
  6. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/chemistry/standardizer.py +0 -0
  7. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/chemistry/utils.py +0 -0
  8. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/__init__.py +0 -0
  9. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/cloud_commands.py +0 -0
  10. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/engine/__init__.py +0 -0
  11. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/engine/engine_core.py +0 -0
  12. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/engine/engine_lifecycle.py +0 -0
  13. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/engine/engine_maintenance.py +0 -0
  14. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/engine/engine_management.py +0 -0
  15. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/engine/shared.py +0 -0
  16. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/engine/studio_commands.py +0 -0
  17. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/main.py +0 -0
  18. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/swarm_commands.py +0 -0
  19. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/deployment/base.py +0 -0
  20. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/deployment/deploy_aws.py +0 -0
  21. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/deployment/deploy_gcp.py +0 -0
  22. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/deployment/deploy_utils.py +0 -0
  23. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/deployment/job_runner.py +0 -0
  24. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/deployment/processors.py +0 -0
  25. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/deployment/swarm.py +0 -0
  26. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/embedders.py +0 -0
  27. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/fasta.py +0 -0
  28. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/file_ops.py +0 -0
  29. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/h5.py +0 -0
  30. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/intake/gcp.py +0 -0
  31. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/intake/gtdb.py +0 -0
  32. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/intake/kegg.py +0 -0
  33. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/intake/mmseqs.py +0 -0
  34. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/intake/structure.py +0 -0
  35. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/intake/uniprot.py +0 -0
  36. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/logs.py +0 -0
  37. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/sqlite.py +0 -0
  38. {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/warehouse.py +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: dayhoff-tools
3
- Version: 1.11.3
3
+ Version: 1.11.4
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
@@ -219,6 +219,7 @@ def build_and_upload_wheel(bump_part: str = "patch"):
219
219
  # Build wheel and sdist
220
220
  # UV expects pyproject.toml, so temporarily copy the platform manifest
221
221
  backup_created = False
222
+ temp_pyproject_created = False
222
223
  if pyproject_path != "pyproject.toml":
223
224
  if Path("pyproject.toml").exists():
224
225
  Path("pyproject.toml").rename("pyproject.toml.build.bak")
@@ -226,48 +227,53 @@ def build_and_upload_wheel(bump_part: str = "patch"):
226
227
  Path(pyproject_path).read_text()
227
228
  with open("pyproject.toml", "w") as f:
228
229
  f.write(Path(pyproject_path).read_text())
230
+ temp_pyproject_created = True
229
231
 
230
- build_cmd = ["uv", "build"]
231
- # Print command in blue
232
- print(f"Running command: {BLUE}{' '.join(build_cmd)}{RESET}")
233
- subprocess.run(build_cmd, check=True)
234
-
235
- # Restore original state
236
- if pyproject_path != "pyproject.toml":
237
- Path("pyproject.toml").unlink()
238
- if backup_created:
239
- Path("pyproject.toml.build.bak").rename("pyproject.toml")
240
-
241
- # Upload using uv publish with explicit arguments
242
- # Print masked command in blue
243
- print(f"Running command: {BLUE}{' '.join(publish_cmd_safe_print)}{RESET}")
244
- subprocess.run(
245
- publish_cmd, # Use the actual command with token
246
- check=True,
247
- )
232
+ try:
233
+ build_cmd = ["uv", "build"]
234
+ # Print command in blue
235
+ print(f"Running command: {BLUE}{' '.join(build_cmd)}{RESET}")
236
+ subprocess.run(build_cmd, check=True)
237
+
238
+ # Upload using uv publish with explicit arguments
239
+ # Print masked command in blue
240
+ print(f"Running command: {BLUE}{' '.join(publish_cmd_safe_print)}{RESET}")
241
+ subprocess.run(
242
+ publish_cmd, # Use the actual command with token
243
+ check=True,
244
+ )
248
245
 
249
- print(f"Successfully built and uploaded version {new_version} to PyPI")
246
+ print(f"Successfully built and uploaded version {new_version} to PyPI")
250
247
 
251
- # Re-install DHT in current venv when building from DHT itself
252
- try:
253
- proj_name = None
248
+ # Re-install DHT in current venv when building from DHT itself
249
+ # (Keep temp pyproject.toml until after this step)
254
250
  try:
255
- proj_toml = toml.load(pyproject_path)
256
- proj_name = (
257
- proj_toml.get("project", {}).get("name")
258
- if isinstance(proj_toml, dict)
259
- else None
260
- )
261
- except Exception:
262
- pass
263
- if proj_name == "dayhoff-tools":
264
- print("Re-installing dayhoff-tools into the active environment…")
265
- reinstall_cmd = ["uv", "pip", "install", "-e", ".[full]"]
266
- print(f"Running command: {BLUE}{' '.join(reinstall_cmd)}{RESET}")
267
- subprocess.run(reinstall_cmd, check=True)
268
- print("dayhoff-tools reinstalled in the current environment.")
269
- except subprocess.CalledProcessError as e:
270
- print(f"Warning: Failed to reinstall dayhoff-tools locally: {e}")
251
+ proj_name = None
252
+ try:
253
+ proj_toml = toml.load(pyproject_path)
254
+ proj_name = (
255
+ proj_toml.get("project", {}).get("name")
256
+ if isinstance(proj_toml, dict)
257
+ else None
258
+ )
259
+ except Exception:
260
+ pass
261
+ if proj_name == "dayhoff-tools":
262
+ print("Re-installing dayhoff-tools into the active environment…")
263
+ reinstall_cmd = ["uv", "pip", "install", "-e", ".[full]"]
264
+ print(f"Running command: {BLUE}{' '.join(reinstall_cmd)}{RESET}")
265
+ subprocess.run(reinstall_cmd, check=True)
266
+ print("dayhoff-tools reinstalled in the current environment.")
267
+ except subprocess.CalledProcessError as e:
268
+ print(f"Warning: Failed to reinstall dayhoff-tools locally: {e}")
269
+
270
+ finally:
271
+ # Restore original state (always clean up, even if errors occurred)
272
+ if temp_pyproject_created:
273
+ if Path("pyproject.toml").exists():
274
+ Path("pyproject.toml").unlink()
275
+ if backup_created and Path("pyproject.toml.build.bak").exists():
276
+ Path("pyproject.toml.build.bak").rename("pyproject.toml")
271
277
 
272
278
  except FileNotFoundError:
273
279
  print(f"Error: {pyproject_path} not found.")
@@ -5,7 +5,7 @@ build-backend = "poetry.core.masonry.api"
5
5
 
6
6
  [project]
7
7
  name = "dayhoff-tools"
8
- version = "1.11.3"
8
+ version = "1.11.4"
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