dayhoff-tools 1.11.5__tar.gz → 1.11.7__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-1.11.5 → dayhoff_tools-1.11.7}/PKG-INFO +1 -1
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/utility_commands.py +72 -14
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/pyproject.toml +1 -1
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/README.md +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/__init__.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/chemistry/standardizer.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/chemistry/utils.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/__init__.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/cloud_commands.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/engine/__init__.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/engine/engine_core.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/engine/engine_lifecycle.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/engine/engine_maintenance.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/engine/engine_management.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/engine/shared.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/engine/studio_commands.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/main.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/swarm_commands.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/deployment/base.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/deployment/deploy_aws.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/deployment/deploy_gcp.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/deployment/deploy_utils.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/deployment/job_runner.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/deployment/processors.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/deployment/swarm.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/embedders.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/fasta.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/file_ops.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/h5.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/intake/gcp.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/intake/gtdb.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/intake/kegg.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/intake/mmseqs.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/intake/structure.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/intake/uniprot.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/logs.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/sqlite.py +0 -0
 - {dayhoff_tools-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/warehouse.py +0 -0
 
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         @@ -559,16 +559,44 @@ def sync_with_toml( 
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                        # Sync into the active environment
         
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                        if install_project:
         
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                            print(
         
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                                "Syncing dependencies into ACTIVE env  
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                                "Syncing dependencies into ACTIVE env (project installed separately)…"
         
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                            )
         
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                            sync_cmd = [ 
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                            sync_cmd = [
         
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                                "uv",
         
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                                "sync",
         
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                                "--all-groups",
         
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                                "--no-install-project",
         
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                                "--active",
         
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                            ]
         
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                            print(f"Running command: {BLUE}{' '.join(sync_cmd)}{RESET}")
         
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                            subprocess.run(sync_cmd, check=True, cwd=str(mac_uv_dir))
         
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                            # Install project from repo root (where source code actually is)
         
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                            # Temporarily create pyproject.toml at repo root for UV
         
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                            print("Installing project with 'full' extras from repo root…")
         
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                            temp_pyproject = False
         
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                            backup_created = False
         
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                            try:
         
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                                if not Path("pyproject.toml").exists():
         
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                                    # Create temp pyproject.toml from platform manifest
         
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                                    Path("pyproject.toml").write_text(mac_manifest.read_text())
         
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                                    temp_pyproject = True
         
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                                elif Path("pyproject.toml").is_symlink():
         
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                                    # Backup existing symlink
         
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                                    Path("pyproject.toml").rename("pyproject.toml.sync.bak")
         
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                                    Path("pyproject.toml").write_text(mac_manifest.read_text())
         
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                                    backup_created = True
         
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                                pip_install_cmd = ["uv", "pip", "install", "-e", ".[full]"]
         
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                                print(f"Running command: {BLUE}{' '.join(pip_install_cmd)}{RESET}")
         
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                                subprocess.run(pip_install_cmd, check=True)
         
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                                print("Project installed with 'full' extras successfully.")
         
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                            finally:
         
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                                # Clean up temp pyproject.toml
         
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                                if temp_pyproject and Path("pyproject.toml").exists():
         
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                                    Path("pyproject.toml").unlink()
         
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                                if backup_created and Path("pyproject.toml.sync.bak").exists():
         
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                                    Path("pyproject.toml.sync.bak").rename("pyproject.toml")
         
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                        else:
         
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                            print("Syncing dependencies into ACTIVE env (project not installed)…")
         
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                            sync_cmd = [
         
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                            # Sync into the active environment
         
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                            if install_project:
         
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                                print(
         
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                                    "Syncing dependencies into ACTIVE env  
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                                    "Syncing dependencies into ACTIVE env (project installed separately)…"
         
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                                )
         
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                                sync_cmd = [ 
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                                sync_cmd = [
         
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                                    "uv",
         
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                                    "sync",
         
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                                    "--all-groups",
         
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                                    "--no-install-project",
         
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                                    "--active",
         
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                                ]
         
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                                print(f"Running command: {BLUE}{' '.join(sync_cmd)}{RESET}")
         
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                                subprocess.run(sync_cmd, check=True, cwd=str(aws_uv_dir))
         
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                                # Install project from repo root (where source code actually is)
         
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            +
                                # Temporarily create pyproject.toml at repo root for UV
         
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                                print("Installing project with 'full' extras from repo root…")
         
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                                temp_pyproject = False
         
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                                backup_created = False
         
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                                try:
         
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                                    if not Path("pyproject.toml").exists():
         
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                                        # Create temp pyproject.toml from platform manifest
         
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                                        Path("pyproject.toml").write_text(aws_manifest.read_text())
         
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                                        temp_pyproject = True
         
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                                    elif Path("pyproject.toml").is_symlink():
         
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                                        # Backup existing symlink
         
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                                        Path("pyproject.toml").rename("pyproject.toml.sync.bak")
         
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                                        Path("pyproject.toml").write_text(aws_manifest.read_text())
         
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                                        backup_created = True
         
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                                    pip_install_cmd = ["uv", "pip", "install", "-e", ".[full]"]
         
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                                    print(
         
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                                        f"Running command: {BLUE}{' '.join(pip_install_cmd)}{RESET}"
         
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                                    )
         
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                                    subprocess.run(pip_install_cmd, check=True)
         
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                                    print("Project installed with 'full' extras successfully.")
         
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                                finally:
         
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                                    # Clean up temp pyproject.toml
         
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                                    if temp_pyproject and Path("pyproject.toml").exists():
         
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                                        Path("pyproject.toml").unlink()
         
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                                    if backup_created and Path("pyproject.toml.sync.bak").exists():
         
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                                        Path("pyproject.toml.sync.bak").rename("pyproject.toml")
         
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                            else:
         
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                                print(
         
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                                    "Syncing dependencies into ACTIVE env (project not installed)…"
         
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            [project]
         
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            name = "dayhoff-tools"
         
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            version = "1.11. 
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            version = "1.11.7"
         
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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-1.11.5 → dayhoff_tools-1.11.7}/dayhoff_tools/cli/engine/engine_maintenance.py
    RENAMED
    
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