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.
- {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/PKG-INFO +1 -1
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/utility_commands.py +44 -38
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/pyproject.toml +1 -1
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/README.md +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/__init__.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/chemistry/standardizer.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/chemistry/utils.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/__init__.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/cloud_commands.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/engine/__init__.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/engine/engine_core.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/engine/engine_lifecycle.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/engine/engine_maintenance.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/engine/engine_management.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/engine/shared.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/engine/studio_commands.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/main.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/swarm_commands.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/deployment/base.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/deployment/deploy_aws.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/deployment/deploy_gcp.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/deployment/deploy_utils.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/deployment/job_runner.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/deployment/processors.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/deployment/swarm.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/embedders.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/fasta.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/file_ops.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/h5.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/intake/gcp.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/intake/gtdb.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/intake/kegg.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/intake/mmseqs.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/intake/structure.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/intake/uniprot.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/logs.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/sqlite.py +0 -0
 - {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/warehouse.py +0 -0
 
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         @@ -219,6 +219,7 @@ def build_and_upload_wheel(bump_part: str = "patch"): 
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                    # Build wheel and sdist
         
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                    # UV expects pyproject.toml, so temporarily copy the platform manifest
         
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                    backup_created = False
         
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                    temp_pyproject_created = False
         
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                    if pyproject_path != "pyproject.toml":
         
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                        if Path("pyproject.toml").exists():
         
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                            Path("pyproject.toml").rename("pyproject.toml.build.bak")
         
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         @@ -226,48 +227,53 @@ def build_and_upload_wheel(bump_part: str = "patch"): 
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                        Path(pyproject_path).read_text()
         
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                        with open("pyproject.toml", "w") as f:
         
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                            f.write(Path(pyproject_path).read_text())
         
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                        temp_pyproject_created = True
         
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                    print(f"Running command: {BLUE}{' '.join(publish_cmd_safe_print)}{RESET}")
         
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                    subprocess.run(
         
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                        publish_cmd,  # Use the actual command with token
         
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                        check=True,
         
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                    )
         
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                    try:
         
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                        build_cmd = ["uv", "build"]
         
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                        # Print command in blue
         
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                        print(f"Running command: {BLUE}{' '.join(build_cmd)}{RESET}")
         
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                        subprocess.run(build_cmd, check=True)
         
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                        # Upload using uv publish with explicit arguments
         
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                        # Print masked command in blue
         
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                        print(f"Running command: {BLUE}{' '.join(publish_cmd_safe_print)}{RESET}")
         
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                        subprocess.run(
         
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                            publish_cmd,  # Use the actual command with token
         
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                            check=True,
         
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                        )
         
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                        print(f"Successfully built and uploaded version {new_version} to PyPI")
         
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                        proj_name = None
         
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                        # Re-install DHT in current venv when building from DHT itself
         
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                        # (Keep temp pyproject.toml until after this step)
         
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                        try:
         
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                                proj_toml 
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                            proj_name = None
         
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                            try:
         
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                                proj_toml = toml.load(pyproject_path)
         
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                                proj_name = (
         
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                                    proj_toml.get("project", {}).get("name")
         
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                                    if isinstance(proj_toml, dict)
         
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                                    else None
         
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                                )
         
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                            except Exception:
         
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                                pass
         
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                            if proj_name == "dayhoff-tools":
         
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                                print("Re-installing dayhoff-tools into the active environment…")
         
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                                reinstall_cmd = ["uv", "pip", "install", "-e", ".[full]"]
         
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                                print(f"Running command: {BLUE}{' '.join(reinstall_cmd)}{RESET}")
         
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                                subprocess.run(reinstall_cmd, check=True)
         
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                                print("dayhoff-tools reinstalled in the current environment.")
         
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                        except subprocess.CalledProcessError as e:
         
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                            print(f"Warning: Failed to reinstall dayhoff-tools locally: {e}")
         
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                    finally:
         
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                        # Restore original state (always clean up, even if errors occurred)
         
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                        if temp_pyproject_created:
         
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                            if Path("pyproject.toml").exists():
         
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                                Path("pyproject.toml").unlink()
         
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                            if backup_created and Path("pyproject.toml.build.bak").exists():
         
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                                Path("pyproject.toml.build.bak").rename("pyproject.toml")
         
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                except FileNotFoundError:
         
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                    print(f"Error: {pyproject_path} not found.")
         
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            [project]
         
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            name = "dayhoff-tools"
         
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            version = "1.11. 
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            version = "1.11.4"
         
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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"}
         
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        {dayhoff_tools-1.11.3 → dayhoff_tools-1.11.4}/dayhoff_tools/cli/engine/engine_maintenance.py
    RENAMED
    
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