dayhoff-tools 1.0.9__py3-none-any.whl → 1.0.15__py3-none-any.whl

dayhoff_tools/cli/main.py

@@ -11,12 +11,14 @@ from dayhoff_tools.cli.utility_commands import (
     rebuild_devcontainer_file,
     test_github_actions_locally,
     update_dayhoff_tools,
+    sync_dependencies,
 )
 
 app = typer.Typer()
 
 # Utility commands
 app.command("clean")(delete_local_branch)
+app.command("deps")(sync_dependencies)
 app.command("gha")(test_github_actions_locally)
 app.command("rebuild")(rebuild_devcontainer_file)
 app.command("update")(update_dayhoff_tools)

dayhoff_tools/cli/utility_commands.py

@@ -2,6 +2,7 @@
 
 import os
 import re
+import shutil
 import subprocess
 import sys
 from pathlib import Path
@@ -182,16 +183,16 @@ def get_current_version_from_toml(file_path="pyproject.toml"):
 
 
 def build_and_upload_wheel(bump_part: str = "patch"):
-    """Build a Python wheel and upload to PyPI.
+    """Build a Python wheel and upload to PyPI using UV.
 
-    Automatically increments the version number in pyproject.toml before building.
-    Use the bump_part argument to specify major, minor, or patch increment.
-    For example: 1.2.3 -> 1.2.4 (patch), 1.3.0 (minor), 2.0.0 (major)
+    Automatically increments the version number in pyproject.toml before building
+    based on the bump_part argument ('major', 'minor', 'patch').
 
-    Expects the PyPI API token to be available in the PYPI_API_TOKEN environment variable.
+    Expects PyPI authentication to be configured via the environment variable:
+    - UV_PUBLISH_TOKEN
 
     Args:
-        bump_part (str): The part of the version to bump: 'major', 'minor', or 'patch'. Defaults to 'patch'.
+        bump_part (str): The part of the version to bump. Defaults to 'patch'.
     """
     if bump_part not in ["major", "minor", "patch"]:
         print(
@@ -199,69 +200,198 @@ def build_and_upload_wheel(bump_part: str = "patch"):
         )
         return
 
-    pypi_token = os.environ.get("PYPI_API_TOKEN")
-    if not pypi_token:
-        print("Error: PYPI_API_TOKEN environment variable not set.")
-        print("Please set it with your PyPI API token before running this command.")
+    # --- Authentication Setup ---
+    token = os.environ.get("UV_PUBLISH_TOKEN")
+
+    if not token:
+        print("Error: PyPI authentication not configured.")
+        print(
+            "Please set the UV_PUBLISH_TOKEN environment variable with your PyPI API token."
+        )
         return
 
+    # Build the command with token authentication
+    publish_cmd = ["uv", "publish", "--token", token]
+    print("Using UV_PUBLISH_TOKEN for authentication.")
+
+    pyproject_path = "pyproject.toml"
+    current_version = None  # Initialize in case the first try block fails
+
     try:
-        # Get the current version before bumping
-        current_version = get_current_version_from_toml()
+        # --- Clean dist directory ---
+        dist_dir = Path("dist")
+        if dist_dir.exists():
+            print(f"Removing existing build directory: {dist_dir}")
+            shutil.rmtree(dist_dir)
+        # --- End Clean dist directory ---
+
+        # --- Version Bumping Logic ---
+        current_version = get_current_version_from_toml(pyproject_path)
         print(f"Current version: {current_version}")
 
-        # Use poetry to bump the version in pyproject.toml
-        print(f"Bumping {bump_part} version using poetry...")
-        subprocess.run(["poetry", "version", bump_part], check=True)
-
-        # Get the new version after bumping
-        new_version = get_current_version_from_toml()
-        print(f"New version: {new_version}")
+        try:
+            major, minor, patch = map(int, current_version.split("."))
+        except ValueError:
+            print(
+                f"Error: Could not parse version '{current_version}'. Expected format X.Y.Z"
+            )
+            return
+
+        if bump_part == "major":
+            major += 1
+            minor = 0
+            patch = 0
+        elif bump_part == "minor":
+            minor += 1
+            patch = 0
+        else:  # patch
+            patch += 1
+
+        new_version = f"{major}.{minor}.{patch}"
+        print(f"Bumping {bump_part} version to: {new_version}")
+
+        # Read pyproject.toml
+        with open(pyproject_path, "r") as f:
+            content = f.read()
 
-        # Disable keyring to avoid issues in containers/CI
-        print("Disabling Poetry keyring...")
-        subprocess.run(
-            ["poetry", "config", "keyring.enabled", "false"],
-            check=True,
-            capture_output=True,
+        # Replace the version string
+        pattern = re.compile(
+            f'^version\s*=\s*"{re.escape(current_version)}"', re.MULTILINE
         )
-
-        # Configure Poetry with the API token
-        print("Configuring Poetry with PyPI token...")
-        subprocess.run(
-            ["poetry", "config", "pypi-token.pypi", pypi_token],
-            check=True,
-            capture_output=True,  # Hide token from output
+        new_content, num_replacements = pattern.subn(
+            f'version = "{new_version}"', content
         )
 
-        # Build and upload
-        print("Building and uploading wheel to PyPI...")
+        if num_replacements == 0:
+            print(
+                f"Error: Could not find 'version = \"{current_version}\"' in {pyproject_path}"
+            )
+            return  # Exit before build/publish if version wasn't updated
+        if num_replacements > 1:
+            print(
+                f"Warning: Found multiple version lines for '{current_version}'. Only the first was updated."
+            )
+
+        # Write the updated content back
+        with open(pyproject_path, "w") as f:
+            f.write(new_content)
+        print(f"Updated {pyproject_path} with version {new_version}")
+        # --- End Version Bumping Logic ---
+
+        # Build wheel and sdist
+        print("Building wheel and sdist using uv build...")
+        subprocess.run(["uv", "build"], check=True)
+
+        # Upload using uv publish with explicit arguments
+        print("Uploading to PyPI using uv publish...")
         subprocess.run(
-            [
-                "poetry",
-                "publish",
-                "--build",
-            ],
+            publish_cmd,  # Use the command list built earlier
             check=True,
         )
 
         print(f"Successfully built and uploaded version {new_version} to PyPI")
 
+    except FileNotFoundError:
+        print(f"Error: {pyproject_path} not found.")
+        # No version change happened, so no rollback needed
     except subprocess.CalledProcessError as e:
         print(f"Error during build/upload: {e}")
+        # Attempt to roll back version change only if it was bumped successfully
+        if current_version and new_version:
+            try:
+                print(
+                    f"Attempting to revert version in {pyproject_path} back to {current_version}..."
+                )
+                with open(pyproject_path, "r") as f:
+                    content_revert = f.read()
+                # Use new_version in pattern for reverting
+                pattern_revert = re.compile(
+                    f'^version\s*=\s*"{re.escape(new_version)}"', re.MULTILINE
+                )
+                reverted_content, num_revert = pattern_revert.subn(
+                    f'version = "{current_version}"', content_revert
+                )
+                if num_revert > 0:
+                    with open(pyproject_path, "w") as f:
+                        f.write(reverted_content)
+                    print(f"Successfully reverted version in {pyproject_path}.")
+                else:
+                    print(
+                        f"Warning: Could not find version {new_version} to revert in {pyproject_path}."
+                    )
+            except Exception as revert_e:
+                print(
+                    f"Warning: Failed to revert version change in {pyproject_path}: {revert_e}"
+                )
     except Exception as e:
         print(f"An unexpected error occurred: {e}")
+        # Also attempt rollback here if version was bumped
+        if current_version and "new_version" in locals() and new_version:
+            try:
+                print(
+                    f"Attempting to revert version in {pyproject_path} back to {current_version} due to unexpected error..."
+                )
+                # (Same revert logic as above)
+                with open(pyproject_path, "r") as f:
+                    content_revert = f.read()
+                pattern_revert = re.compile(
+                    f'^version\s*=\s*"{re.escape(new_version)}"', re.MULTILINE
+                )
+                reverted_content, num_revert = pattern_revert.subn(
+                    f'version = "{current_version}"', content_revert
+                )
+                if num_revert > 0:
+                    with open(pyproject_path, "w") as f:
+                        f.write(reverted_content)
+                    print(f"Successfully reverted version in {pyproject_path}.")
+                else:
+                    print(
+                        f"Warning: Could not find version {new_version} to revert in {pyproject_path}."
+                    )
+            except Exception as revert_e:
+                print(
+                    f"Warning: Failed to revert version change in {pyproject_path}: {revert_e}"
+                )
 
 
 def update_dayhoff_tools():
-    """Update the dayhoff-tools package to the latest version using poetry."""
+    """Update the dayhoff-tools package to the latest version using uv.
+
+    Runs `uv add dayhoff-tools@latest` which updates pyproject.toml and uv.lock.
+    """
     try:
-        print("Updating dayhoff-tools to the latest version...")
-        subprocess.run(["poetry", "update", "dayhoff-tools"], check=True)
+        print("Updating dayhoff-tools to the latest version using uv...")
+        # Use uv add to update the package and lock file
+        subprocess.run(["uv", "add", "dayhoff-tools@latest"], 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.")
+        print("Error: 'uv' command not found. Is uv installed and in PATH?")
+        sys.exit(1)
+
+
+def sync_dependencies():
+    """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.
+    """
+    try:
+        print("Updating lock file (uv lock)...")
+        subprocess.run(["uv", "lock"], check=True)
+
+        print("Syncing dependencies (uv sync --all-groups --no-install-project)...")
+        subprocess.run(
+            ["uv", "sync", "--all-groups", "--no-install-project"], check=True
+        )
+
+        print("Dependencies synced successfully.")
+    except subprocess.CalledProcessError as e:
+        print(f"Error occurred during dependency sync: {e}")
+        sys.exit(1)
+    except FileNotFoundError:
+        print("Error: 'uv' command not found. Is uv installed and in PATH?")
         sys.exit(1)

{dayhoff_tools-1.0.9.dist-info → dayhoff_tools-1.0.15.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: dayhoff-tools
-Version: 1.0.9
+Version: 1.0.15
 Summary: Common tools for all the repos at Dayhoff Labs
 Author: Daniel Martin-Alarcon
 Author-email: dma@dayhofflabs.com
@@ -10,16 +10,22 @@ 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"
+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 == "core"
+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 == "core"
+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)
 Description-Content-Type: text/markdown
 

{dayhoff_tools-1.0.9.dist-info → dayhoff_tools-1.0.15.dist-info}/RECORD

@@ -3,9 +3,9 @@ dayhoff_tools/chemistry/standardizer.py,sha256=uMn7VwHnx02nc404eO6fRuS4rsl4dvSPf
 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=KiYEuD3nSg8QPWBYfrhdze2La_CJe4iqK-8uOAHyS8U,35827
-dayhoff_tools/cli/main.py,sha256=E1-3rZ26LMgJVKBz6CdJwsHs9fJsSGa2_9tot3hNgz4,3604
+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=AsZMpvUNP2xjn5cZ9_BrBNHggfuy6PLwlHw1WP0d7o0,9602
+dayhoff_tools/cli/utility_commands.py,sha256=-Fe7CkcIZ8e7UWlKO-P2Dgm1p3yg-GOsXcnDwxw5uxQ,14851
 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-1.0.9.dist-info/METADATA,sha256=z5v8zbt4z_B5283bqkkFlybQox_tZacU-Z6JPNyg1vc,1930
-dayhoff_tools-1.0.9.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
-dayhoff_tools-1.0.9.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
-dayhoff_tools-1.0.9.dist-info/RECORD,,
+dayhoff_tools-1.0.15.dist-info/METADATA,sha256=4RV3HI5kIxjjuNaKC9FOdXh-_efd4GqaHy_m0RsB3ak,2262
+dayhoff_tools-1.0.15.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
+dayhoff_tools-1.0.15.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
+dayhoff_tools-1.0.15.dist-info/RECORD,,