dayhoff-tools 1.11.0__tar.gz → 1.11.2__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-1.11.0 → dayhoff_tools-1.11.2}/PKG-INFO +3 -3
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/cli/main.py +10 -4
 - dayhoff_tools-1.11.2/dayhoff_tools/cli/utility_commands.py +1041 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/pyproject.toml +9 -15
 - dayhoff_tools-1.11.0/dayhoff_tools/cli/utility_commands.py +0 -626
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/README.md +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/__init__.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/chemistry/standardizer.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/chemistry/utils.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/cli/__init__.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/cli/cloud_commands.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/cli/engine/__init__.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/cli/engine/engine_core.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/cli/engine/engine_lifecycle.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/cli/engine/engine_maintenance.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/cli/engine/engine_management.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/cli/engine/shared.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/cli/engine/studio_commands.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/cli/swarm_commands.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/deployment/base.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/deployment/deploy_aws.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/deployment/deploy_gcp.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/deployment/deploy_utils.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/deployment/job_runner.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/deployment/processors.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/deployment/swarm.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/embedders.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/fasta.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/file_ops.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/h5.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/intake/gcp.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/intake/gtdb.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/intake/kegg.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/intake/mmseqs.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/intake/structure.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/intake/uniprot.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/logs.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/dayhoff_tools/sqlite.py +0 -0
 - {dayhoff_tools-1.11.0 → dayhoff_tools-1.11.2}/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 
     | 
    
         
            +
            Version: 1.11.2
         
     | 
| 
       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
         
     | 
| 
         @@ -23,8 +23,8 @@ Requires-Dist: firebase-admin (>=6.5.0) 
     | 
|
| 
       23 
23 
     | 
    
         
             
            Requires-Dist: h5py (>=3.11.0) ; extra == "full"
         
     | 
| 
       24 
24 
     | 
    
         
             
            Requires-Dist: h5py (>=3.13.0) ; extra == "embedders"
         
     | 
| 
       25 
25 
     | 
    
         
             
            Requires-Dist: numpy (>=1.26.4) ; extra == "embedders"
         
     | 
| 
       26 
     | 
    
         
            -
            Requires-Dist: pandas (>=2.2.3) ; extra == "embedders"
         
     | 
| 
       27 
     | 
    
         
            -
            Requires-Dist: pandas (>=2.2.3) ; extra == "full"
         
     | 
| 
      
 26 
     | 
    
         
            +
            Requires-Dist: pandas (>=2.2.0,<2.2.3) ; extra == "embedders"
         
     | 
| 
      
 27 
     | 
    
         
            +
            Requires-Dist: pandas (>=2.2.0,<2.2.3) ; extra == "full"
         
     | 
| 
       28 
28 
     | 
    
         
             
            Requires-Dist: pyyaml (>=6.0)
         
     | 
| 
       29 
29 
     | 
    
         
             
            Requires-Dist: questionary (>=2.0.1)
         
     | 
| 
       30 
30 
     | 
    
         
             
            Requires-Dist: rdkit-pypi (>=2022.9.5) ; extra == "full"
         
     | 
| 
         @@ -4,13 +4,14 @@ import sys 
     | 
|
| 
       4 
4 
     | 
    
         
             
            from importlib.metadata import PackageNotFoundError, version
         
     | 
| 
       5 
5 
     | 
    
         | 
| 
       6 
6 
     | 
    
         
             
            import typer
         
     | 
| 
       7 
     | 
    
         
            -
             
     | 
| 
       8 
7 
     | 
    
         
             
            from dayhoff_tools.cli.cloud_commands import aws_app, gcp_app
         
     | 
| 
       9 
8 
     | 
    
         
             
            from dayhoff_tools.cli.engine import engine_app, studio_app
         
     | 
| 
       10 
9 
     | 
    
         
             
            from dayhoff_tools.cli.utility_commands import (
         
     | 
| 
      
 10 
     | 
    
         
            +
                add_dependency,
         
     | 
| 
       11 
11 
     | 
    
         
             
                build_and_upload_wheel,
         
     | 
| 
       12 
12 
     | 
    
         
             
                delete_local_branch,
         
     | 
| 
       13 
     | 
    
         
            -
                 
     | 
| 
      
 13 
     | 
    
         
            +
                remove_dependency,
         
     | 
| 
      
 14 
     | 
    
         
            +
                sync_with_toml,
         
     | 
| 
       14 
15 
     | 
    
         
             
                test_github_actions_locally,
         
     | 
| 
       15 
16 
     | 
    
         
             
                update_dependencies,
         
     | 
| 
       16 
17 
     | 
    
         
             
            )
         
     | 
| 
         @@ -45,8 +46,13 @@ app.command("clean")(delete_local_branch) 
     | 
|
| 
       45 
46 
     | 
    
         | 
| 
       46 
47 
     | 
    
         
             
            # Dependency Management
         
     | 
| 
       47 
48 
     | 
    
         
             
            app.command(
         
     | 
| 
       48 
     | 
    
         
            -
                " 
     | 
| 
       49 
     | 
    
         
            -
             
     | 
| 
      
 49 
     | 
    
         
            +
                "tomlsync",
         
     | 
| 
      
 50 
     | 
    
         
            +
                help="Sync environment with platform-specific TOML manifest (install/update dependencies).",
         
     | 
| 
      
 51 
     | 
    
         
            +
            )(sync_with_toml)
         
     | 
| 
      
 52 
     | 
    
         
            +
            app.command("add", help="Add a dependency to all platform manifests.")(add_dependency)
         
     | 
| 
      
 53 
     | 
    
         
            +
            app.command("remove", help="Remove a dependency from all platform manifests.")(
         
     | 
| 
      
 54 
     | 
    
         
            +
                remove_dependency
         
     | 
| 
      
 55 
     | 
    
         
            +
            )
         
     | 
| 
       50 
56 
     | 
    
         
             
            app.command("update", help="Update dayhoff-tools (or all deps) and sync environment.")(
         
     | 
| 
       51 
57 
     | 
    
         
             
                update_dependencies
         
     | 
| 
       52 
58 
     | 
    
         
             
            )
         
     |