dayhoff-tools 1.0.3__py3-none-any.whl → 1.0.5__py3-none-any.whl

dayhoff_tools/cli/cloud_commands.py

@@ -585,7 +585,8 @@ def aws_interactive():
                 )
 
         elif choice == "Show status":
-            aws_status()
+            # Fix: Explicitly pass None for the profile parameter
+            aws_status(profile=None)
 
         elif choice == "Exit":
             print(f"To activate profile {current_profile} in your current shell, run:")

dayhoff_tools/cli/main.py

@@ -10,6 +10,7 @@ from dayhoff_tools.cli.utility_commands import (
     import_from_warehouse_typer,
     rebuild_devcontainer_file,
     test_github_actions_locally,
+    update_dayhoff_tools,
 )
 
 app = typer.Typer()
@@ -18,6 +19,7 @@ app = typer.Typer()
 app.command("clean")(delete_local_branch)
 app.command("gha")(test_github_actions_locally)
 app.command("rebuild")(rebuild_devcontainer_file)
+app.command("update")(update_dayhoff_tools)
 app.command("wadd")(add_to_warehouse_typer)
 app.command("wancestry")(get_ancestry)
 app.command("wimport")(import_from_warehouse_typer)

dayhoff_tools/cli/utility_commands.py

@@ -251,3 +251,17 @@ def build_and_upload_wheel(bump_part: str = "patch"):
         print(f"Error during build/upload: {e}")
     except Exception as e:
         print(f"An unexpected error occurred: {e}")
+
+
+def update_dayhoff_tools():
+    """Update the dayhoff-tools package to the latest version using poetry."""
+    try:
+        print("Updating dayhoff-tools to the latest version...")
+        subprocess.run(["poetry", "update", "dayhoff-tools"], check=True)
+        print("Update complete!")
+    except subprocess.CalledProcessError as e:
+        print(f"Error occurred while updating: {e}")
+        sys.exit(1)
+    except FileNotFoundError:
+        print("Error: 'poetry' command not found. Make sure Poetry is installed.")
+        sys.exit(1)

dayhoff_tools-1.0.5.dist-info/METADATA

@@ -0,0 +1,58 @@
+Metadata-Version: 2.3
+Name: dayhoff-tools
+Version: 1.0.5
+Summary: Common tools for all the repos at Dayhoff Labs
+Author: Daniel Martin-Alarcon
+Author-email: dma@dayhofflabs.com
+Requires-Python: >=3.10,<4.0
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Provides-Extra: core
+Requires-Dist: biopython (>=1.84) ; extra == "core"
+Requires-Dist: boto3 (>=1.36.8) ; extra == "core"
+Requires-Dist: docker (>=7.1.0) ; extra == "core"
+Requires-Dist: fair-esm (>=2.0.0) ; extra == "core"
+Requires-Dist: firebase-admin (>=6.5.0)
+Requires-Dist: h5py (>=3.11.0) ; extra == "core"
+Requires-Dist: pyyaml (>=6.0)
+Requires-Dist: questionary (>=2.0.1) ; extra == "core"
+Requires-Dist: requests (>=2.31.0)
+Requires-Dist: typer (>=0.9.0)
+Description-Content-Type: text/markdown
+
+# dayhoff-tools
+
+A set of small, sharp tools for everyone at Dayhoff. Hosted on PyPi, so you can Poetry or pip install like everything else.
+
+## Installation
+
+The base package includes minimal dependencies required for core CLI functionality (like job running):
+
+```bash
+pip install dayhoff-tools
+# or
+poetry add dayhoff-tools
+```
+
+### Optional Dependencies
+
+You can install extra sets of dependencies using brackets. Available groups are:
+
+* `core`: Includes common data science and bioinformatics tools (`biopython`, `boto3`, `docker`, `fair-esm`, `h5py`, `questionary`).
+* `dev`: Includes development and testing tools (`black`, `pytest`, `pandas`, `numpy`, `torch`, etc.).
+* `all`: Includes all dependencies from both `core` and `dev`.
+
+**Examples:**
+
+```bash
+# Install with core dependencies
+pip install 'dayhoff-tools[core]'
+poetry add 'dayhoff-tools[core]'
+
+# Install with all dependencies
+pip install 'dayhoff-tools[all]'
+poetry add 'dayhoff-tools[all]'
+```

{dayhoff_tools-1.0.3.dist-info → dayhoff_tools-1.0.5.dist-info}/RECORD

@@ -2,10 +2,10 @@ dayhoff_tools/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dayhoff_tools/chemistry/standardizer.py,sha256=uMn7VwHnx02nc404eO6fRuS4rsl4dvSPf2ElfZDXEpY,11188
 dayhoff_tools/chemistry/utils.py,sha256=jt-7JgF-GeeVC421acX-bobKbLU_X94KNOW24p_P-_M,2257
 dayhoff_tools/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-dayhoff_tools/cli/cloud_commands.py,sha256=XTHylqeZ-CLly_wl--7xQq9Ure_wJbzRZjUIzWhHKiI,20811
-dayhoff_tools/cli/main.py,sha256=DJwtU-D-UDzlj_SOZXzw61a2Jg7hvOQLfwBZCcV3eig,3534
+dayhoff_tools/cli/cloud_commands.py,sha256=rt8bcNo73zhCwNwcb8zTGmx2xxcGejhKEEl-d9HH2yM,20889
+dayhoff_tools/cli/main.py,sha256=E1-3rZ26LMgJVKBz6CdJwsHs9fJsSGa2_9tot3hNgz4,3604
 dayhoff_tools/cli/swarm_commands.py,sha256=5EyKj8yietvT5lfoz8Zx0iQvVaNgc3SJX1z2zQR6o6M,5614
-dayhoff_tools/cli/utility_commands.py,sha256=Q6FyQjJ-Zyj1Qw_jkBZm4xrvtX0NF4_v5_nhcdtNdco,9058
+dayhoff_tools/cli/utility_commands.py,sha256=AsZMpvUNP2xjn5cZ9_BrBNHggfuy6PLwlHw1WP0d7o0,9602
 dayhoff_tools/deployment/base.py,sha256=u-AjbtHnFLoLt33dhYXHIpV-6jcieMEHHGBGN_U9Hm0,15626
 dayhoff_tools/deployment/deploy_aws.py,sha256=O0gQxHioSU_sNU8T8MD4wSOPvWc--V8eRRZzlRu035I,16446
 dayhoff_tools/deployment/deploy_gcp.py,sha256=DxBM4sUzwPK9RWLP9bSfr38n1HHl-TVrp4TsbdN8pUA,5795
@@ -25,7 +25,7 @@ dayhoff_tools/sqlite.py,sha256=jV55ikF8VpTfeQqqlHSbY8OgfyfHj8zgHNpZjBLos_E,18672
 dayhoff_tools/structure.py,sha256=ufN3gAodQxhnt7psK1VTQeu9rKERmo_PhoxIbB4QKMw,27660
 dayhoff_tools/uniprot.py,sha256=BZYJQF63OtPcBBnQ7_P9gulxzJtqyorgyuDiPeOJqE4,16456
 dayhoff_tools/warehouse.py,sha256=TqV8nex1AluNaL4JuXH5zuu9P7qmE89lSo6f_oViy6U,14965
-dayhoff_tools-1.0.3.dist-info/METADATA,sha256=2RVN1BBfQkoMzU97u5LgG0IXhZOzbLNQPp2LcEhiOA0,3949
-dayhoff_tools-1.0.3.dist-info/WHEEL,sha256=IYZQI976HJqqOpQU6PHkJ8fb3tMNBFjg-Cn-pwAbaFM,88
-dayhoff_tools-1.0.3.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
-dayhoff_tools-1.0.3.dist-info/RECORD,,
+dayhoff_tools-1.0.5.dist-info/METADATA,sha256=LE_AxsDAgFzG6oW_i2YL3sZOfbC0V1JDpAidC40Yfek,1930
+dayhoff_tools-1.0.5.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
+dayhoff_tools-1.0.5.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
+dayhoff_tools-1.0.5.dist-info/RECORD,,

{dayhoff_tools-1.0.3.dist-info → dayhoff_tools-1.0.5.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.0.1
+Generator: poetry-core 2.1.2
 Root-Is-Purelib: true
 Tag: py3-none-any

dayhoff_tools-1.0.3.dist-info/METADATA

@@ -1,99 +0,0 @@
-Metadata-Version: 2.3
-Name: dayhoff-tools
-Version: 1.0.3
-Summary: Common tools for all the repos at Dayhoff Labs
-Author: Daniel Martin-Alarcon
-Author-email: dma@dayhofflabs.com
-Requires-Python: >=3.10,<4.0
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-Provides-Extra: all
-Provides-Extra: core
-Provides-Extra: dev
-Requires-Dist: biopython (>=1.84) ; extra == "all"
-Requires-Dist: biopython (>=1.84) ; extra == "core"
-Requires-Dist: black (>=25.1.0) ; extra == "all"
-Requires-Dist: black (>=25.1.0) ; extra == "dev"
-Requires-Dist: boto3 (>=1.36.8) ; extra == "all"
-Requires-Dist: boto3 (>=1.36.8) ; extra == "core"
-Requires-Dist: colorlog (>=6.8.2) ; extra == "all"
-Requires-Dist: colorlog (>=6.8.2) ; extra == "dev"
-Requires-Dist: docker (>=7.1.0) ; extra == "all"
-Requires-Dist: docker (>=7.1.0) ; extra == "core"
-Requires-Dist: dvc (>=3.48.2) ; extra == "all"
-Requires-Dist: dvc (>=3.48.2) ; extra == "dev"
-Requires-Dist: dvc-gs (>=3.0.1) ; extra == "all"
-Requires-Dist: dvc-gs (>=3.0.1) ; extra == "dev"
-Requires-Dist: fair-esm (>=2.0.0) ; extra == "all"
-Requires-Dist: fair-esm (>=2.0.0) ; extra == "core"
-Requires-Dist: firebase-admin (>=6.5.0)
-Requires-Dist: flake8 (>=7.0.0) ; extra == "all"
-Requires-Dist: flake8 (>=7.0.0) ; extra == "dev"
-Requires-Dist: h5py (>=3.11.0) ; extra == "all"
-Requires-Dist: h5py (>=3.11.0) ; extra == "core"
-Requires-Dist: isort (>=5.13.2) ; extra == "all"
-Requires-Dist: isort (>=5.13.2) ; extra == "dev"
-Requires-Dist: numpy (<2.0.0) ; extra == "all"
-Requires-Dist: numpy (<2.0.0) ; extra == "dev"
-Requires-Dist: pandas (>=2.2.3) ; extra == "dev"
-Requires-Dist: pylance (>=0.10.2) ; extra == "all"
-Requires-Dist: pylance (>=0.10.2) ; extra == "dev"
-Requires-Dist: pylint (>=3.1.0) ; extra == "all"
-Requires-Dist: pylint (>=3.1.0) ; extra == "dev"
-Requires-Dist: pytest (>=8.0.2) ; extra == "all"
-Requires-Dist: pytest (>=8.0.2) ; extra == "dev"
-Requires-Dist: pytest-cov (>=4.1.0) ; extra == "all"
-Requires-Dist: pytest-cov (>=4.1.0) ; extra == "dev"
-Requires-Dist: pytest-mock (>=3.12.0) ; extra == "all"
-Requires-Dist: pytest-mock (>=3.12.0) ; extra == "dev"
-Requires-Dist: pyyaml (>=6.0)
-Requires-Dist: questionary (>=2.0.1) ; extra == "all"
-Requires-Dist: questionary (>=2.0.1) ; extra == "core"
-Requires-Dist: rdkit-pypi (>=2022.9.5) ; extra == "all"
-Requires-Dist: rdkit-pypi (>=2022.9.5) ; extra == "dev"
-Requires-Dist: requests (>=2.31.0)
-Requires-Dist: torch (>=1.10.0) ; extra == "all"
-Requires-Dist: torch (>=1.10.0) ; extra == "dev"
-Requires-Dist: torchvision (>=0.11.0) ; extra == "all"
-Requires-Dist: torchvision (>=0.11.0) ; extra == "dev"
-Requires-Dist: transformers (>=4.20.0) ; extra == "all"
-Requires-Dist: transformers (>=4.36.2) ; extra == "dev"
-Requires-Dist: typer (>=0.9.0)
-Description-Content-Type: text/markdown
-
-# dayhoff-tools
-
-A set of small, sharp tools for everyone at Dayhoff. Hosted on PyPi, so you can Poetry or pip install like everything else.
-
-## Installation
-
-The base package includes minimal dependencies required for core CLI functionality (like job running):
-
-```bash
-pip install dayhoff-tools
-# or
-poetry add dayhoff-tools
-```
-
-### Optional Dependencies
-
-You can install extra sets of dependencies using brackets. Available groups are:
-
-* `core`: Includes common data science and bioinformatics tools (`biopython`, `boto3`, `docker`, `fair-esm`, `h5py`, `questionary`).
-* `dev`: Includes development and testing tools (`black`, `pytest`, `pandas`, `numpy`, `torch`, etc.).
-* `all`: Includes all dependencies from both `core` and `dev`.
-
-**Examples:**
-
-```bash
-# Install with core dependencies
-pip install 'dayhoff-tools[core]'
-poetry add 'dayhoff-tools[core]'
-
-# Install with all dependencies
-pip install 'dayhoff-tools[all]'
-poetry add 'dayhoff-tools[all]'
-```