dayhoff-tools 1.0.16__py3-none-any.whl → 1.0.18__py3-none-any.whl

dayhoff_tools/cli/utility_commands.py

@@ -7,6 +7,7 @@ import subprocess
 import sys
 from pathlib import Path
 
+import typer
 import yaml
 
 
@@ -211,6 +212,8 @@ def build_and_upload_wheel(bump_part: str = "patch"):
         return
 
     # Build the command with token authentication
+    # IMPORTANT: Mask token for printing
+    publish_cmd_safe_print = ["uv", "publish", "--token", "*****"]
     publish_cmd = ["uv", "publish", "--token", token]
     print("Using UV_PUBLISH_TOKEN for authentication.")
 
@@ -279,13 +282,16 @@ def build_and_upload_wheel(bump_part: str = "patch"):
         # --- End Version Bumping Logic ---
 
         # Build wheel and sdist
-        print("Building wheel and sdist using uv build...")
-        subprocess.run(["uv", "build"], check=True)
+        build_cmd = ["uv", "build"]
+        print(f"Running command: {' '.join(build_cmd)}")
+        subprocess.run(build_cmd, check=True)
 
         # Upload using uv publish with explicit arguments
-        print("Uploading to PyPI using uv publish...")
+        print(
+            f"Running command: {' '.join(publish_cmd_safe_print)}"
+        )  # Print masked command
         subprocess.run(
-            publish_cmd,  # Use the command list built earlier
+            publish_cmd,  # Use the actual command with token
             check=True,
         )
 
@@ -357,39 +363,48 @@ def build_and_upload_wheel(bump_part: str = "patch"):
 def update_dayhoff_tools():
     """Update the dayhoff-tools package to the latest version using uv.
 
-    Runs `uv add dayhoff-tools@latest --group common` which attempts to update
-    dayhoff-tools within the 'common' dependency group.
+    Runs `uv add dayhoff-tools@latest`. Note: This command might not correctly
+    update dayhoff-tools if it's only listed in a top-level [dependency-groups]
+    table in the target project's pyproject.toml. It works best for dependencies
+    in [project.dependencies] or [project.optional-dependencies].
     """
     try:
-        print(
-            "Updating dayhoff-tools to the latest version in 'common' group using uv..."
-        )
-        # Use uv add with --group common to explicitly target the dependency
-        subprocess.run(
-            ["uv", "add", "dayhoff-tools@latest", "--group", "common"], check=True
-        )
-        print(
-            "Update complete! Run 'uv sync --group common' or relevant sync command if needed."
-        )
+        print("Attempting to update dayhoff-tools to the latest version using uv...")
+        update_cmd = ["uv", "add", "dayhoff-tools@latest"]
+        print(f"Running command: {' '.join(update_cmd)}")
+        subprocess.run(update_cmd, check=True)
+        print("Update attempt complete! Check pyproject.toml and run sync if needed.")
     except subprocess.CalledProcessError as e:
-        print(f"Error occurred while updating: {e}")
+        print(f"Error occurred while attempting update: {e}")
+    except FileNotFoundError:
+        print("Error: 'uv' command not found. Is uv installed and in PATH?")
+        sys.exit(1)
 
 
-def sync_dependencies():
+def sync_dependencies(
+    install_project: bool = typer.Option(
+        False,
+        "--install-project",
+        help="Install the local project package itself into the environment.",
+    )
+):
     """Update uv.lock and sync dependencies based on pyproject.toml.
 
-    Runs `uv lock` followed by `uv sync --all-groups --no-install-project`.
-    This ensures the lock file is up-to-date and installs all declared
-    dependencies without building/installing the local project itself.
+    By default, installs all declared dependencies without building/installing
+    the local project itself (--no-install-project). Use --install-project to
+    include the local project.
     """
     try:
-        print("Updating lock file (uv lock)...")
-        subprocess.run(["uv", "lock"], check=True)
+        lock_cmd = ["uv", "lock"]
+        print(f"Running command: {' '.join(lock_cmd)}")
+        subprocess.run(lock_cmd, check=True)
 
-        print("Syncing dependencies (uv sync --all-groups --no-install-project)...")
-        subprocess.run(
-            ["uv", "sync", "--all-groups", "--no-install-project"], check=True
-        )
+        sync_cmd = ["uv", "sync", "--all-groups"]
+        if not install_project:
+            sync_cmd.append("--no-install-project")
+
+        print(f"Running command: {' '.join(sync_cmd)}")
+        subprocess.run(sync_cmd, check=True)
 
         print("Dependencies synced successfully.")
     except subprocess.CalledProcessError as e:

{dayhoff_tools-1.0.16.dist-info → dayhoff_tools-1.0.18.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: dayhoff-tools
-Version: 1.0.16
+Version: 1.0.18
 Summary: Common tools for all the repos at Dayhoff Labs
 Author: Daniel Martin-Alarcon
 Author-email: dma@dayhofflabs.com
@@ -10,23 +10,21 @@ 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: full
-Requires-Dist: biopython (>=1.84) ; extra == "full"
-Requires-Dist: boto3 (>=1.36.8) ; extra == "full"
-Requires-Dist: docker (>=7.1.0) ; extra == "full"
-Requires-Dist: fair-esm (>=2.0.0) ; extra == "full"
-Requires-Dist: firebase-admin (>=6.5.0)
-Requires-Dist: h5py (>=3.11.0) ; extra == "full"
-Requires-Dist: pandas (>=2.2.3) ; extra == "full"
-Requires-Dist: pyyaml (>=6.0)
-Requires-Dist: questionary (>=2.0.1) ; extra == "full"
-Requires-Dist: rdkit-pypi (>=2022.9.5) ; extra == "full"
-Requires-Dist: requests (>=2.31.0)
-Requires-Dist: sqlalchemy (>=2.0.40,<3.0.0) ; extra == "full"
-Requires-Dist: torch (>=2.1.0) ; extra == "full"
-Requires-Dist: torchvision (>=0.16.0) ; extra == "full"
-Requires-Dist: transformers (==4.36.2) ; extra == "full"
-Requires-Dist: typer (>=0.9.0)
+Provides-Extra: base
+Requires-Dist: biopython (>=1.84)
+Requires-Dist: boto3 (>=1.36.8)
+Requires-Dist: docker (>=7.1.0)
+Requires-Dist: fair-esm (>=2.0.0)
+Requires-Dist: firebase-admin (>=6.5.0) ; extra == "base"
+Requires-Dist: h5py (>=3.11.0)
+Requires-Dist: pandas (>=2.2.3)
+Requires-Dist: pyyaml (>=6.0) ; extra == "base"
+Requires-Dist: questionary (>=2.0.1)
+Requires-Dist: rdkit-pypi (>=2022.9.5)
+Requires-Dist: requests (>=2.31.0) ; extra == "base"
+Requires-Dist: sqlalchemy (>=2.0.40,<3.0.0)
+Requires-Dist: transformers (==4.36.2)
+Requires-Dist: typer (>=0.9.0) ; extra == "base"
 Description-Content-Type: text/markdown
 
 # dayhoff-tools

{dayhoff_tools-1.0.16.dist-info → dayhoff_tools-1.0.18.dist-info}/RECORD

@@ -5,7 +5,7 @@ dayhoff_tools/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU
 dayhoff_tools/cli/cloud_commands.py,sha256=KiYEuD3nSg8QPWBYfrhdze2La_CJe4iqK-8uOAHyS8U,35827
 dayhoff_tools/cli/main.py,sha256=yorL117hknzhNybt7CTz4oKXVuQRIDXPl7huIEWga-M,3666
 dayhoff_tools/cli/swarm_commands.py,sha256=5EyKj8yietvT5lfoz8Zx0iQvVaNgc3SJX1z2zQR6o6M,5614
-dayhoff_tools/cli/utility_commands.py,sha256=vnHhYzAOLOGYqjLSCRInbSOEyRC3iXKnuYMW6hezkrc,14948
+dayhoff_tools/cli/utility_commands.py,sha256=217qbmt4qVoaPwStvwONoAj9NP9k9UkExs5WyKNCQt8,15586
 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-1.0.16.dist-info/METADATA,sha256=LBjBUaTBwD0mOjKSFwdKdK2dD0UPaAgbEwoim8tfDkM,2262
-dayhoff_tools-1.0.16.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-dayhoff_tools-1.0.16.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
-dayhoff_tools-1.0.16.dist-info/RECORD,,
+dayhoff_tools-1.0.18.dist-info/METADATA,sha256=lbn5KAcT-XrkbrPfcPL6mQQrK9PoP0BUyV2Kjv4SIDc,2049
+dayhoff_tools-1.0.18.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+dayhoff_tools-1.0.18.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
+dayhoff_tools-1.0.18.dist-info/RECORD,,