dayhoff-tools 1.0.9__tar.gz → 1.0.14__tar.gz

{dayhoff_tools-1.0.9 → dayhoff_tools-1.0.14}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: dayhoff-tools
-Version: 1.0.9
+Version: 1.0.14
 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 (==2.4.0+cu121) ; extra == "full"
+Requires-Dist: torchvision (==0.19.0+cu121) ; 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 → dayhoff_tools-1.0.14}/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-1.0.9 → dayhoff_tools-1.0.14}/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-1.0.14/pyproject.toml

@@ -0,0 +1,73 @@
+[build-system]
+requires = ["poetry-core>=2.0"]
+build-backend = "poetry.core.masonry.api"
+
+[project]
+name = "dayhoff-tools"
+version = "1.0.14"
+description = "Common tools for all the repos at Dayhoff Labs"
+authors = [
+    {name = "Daniel Martin-Alarcon", email = "dma@dayhofflabs.com"}
+]
+readme = "README.md"
+# Just enough deps to use the job_runner
+dependencies = [
+    "firebase-admin>=6.5.0",
+    "pyyaml>=6.0",
+    "requests>=2.31.0",
+    "typer>=0.9.0",
+]
+requires-python = ">=3.10,<4.0"
+
+[project.optional-dependencies]
+# Deps we expect to need to bring to new repos
+full = [
+    "biopython>=1.84",
+    "boto3>=1.36.8",
+    "docker>=7.1.0",
+    "fair-esm>=2.0.0",
+    "h5py>=3.11.0",
+    "pandas>=2.2.3",
+    "questionary>=2.0.1",
+    "rdkit-pypi>=2022.9.5",
+    "sqlalchemy (>=2.0.40,<3.0.0)",
+    "transformers==4.36.2",
+    "torch==2.4.0+cu121",
+    "torchvision==0.19.0+cu121",
+]
+
+# Specific configuration for PyTorch source
+[[tool.uv.index]]
+name = "torch-cuda"
+url = "https://download.pytorch.org/whl/cu121"
+explicit = true
+
+[tool.uv.sources]
+torch = { index = "torch-cuda" }
+torchvision = { index = "torch-cuda" }
+
+[dependency-groups] # Top-level table for groups
+common = [
+    "black>=25.1.0,<26",
+    "boto3>=1.36.8",
+    "colorlog>=6.8.2,<7",
+    "docker>=7.1.0",
+    "dvc>=3.48.2,<4",
+    "dvc-gs>=3.0.1,<4",
+    "flake8>=7.0.0,<8",
+    "google-cloud-storage>=2.14.0",
+    "ipykernel>=6.29.5,<7",
+    "ipywidgets>=8.1.3,<9",
+    "isort>=5.13.2,<6",
+    "nbformat>=5.10.4",
+    "numpy<2.0.0",
+    "pandas (>=2.2.3,<3.0.0)",
+    "pylance>=0.10.2,<1",
+    "pylint>=3.1.0,<4",
+    "pytest>=8.0.2,<9",
+    "pytest-cov>=4.1.0,<5",
+    "pytest-mock>=3.12.0,<4",
+]
+
+[project.scripts]
+dh = "dayhoff_tools.cli.main:app"

dayhoff_tools-1.0.9/pyproject.toml

@@ -1,53 +0,0 @@
-[build-system]
-requires = ["poetry-core>=2.0"]
-build-backend = "poetry.core.masonry.api"
-
-[project]
-name = "dayhoff-tools"
-version = "1.0.9"
-description = "Common tools for all the repos at Dayhoff Labs"
-authors = [
-    {name = "Daniel Martin-Alarcon", email = "dma@dayhofflabs.com"}
-]
-readme = "README.md"
-# Just enough deps to use the job_runner
-dependencies = [
-    "firebase-admin>=6.5.0",
-    "pyyaml>=6.0",
-    "requests>=2.31.0",
-    "typer>=0.9.0",
-]
-
-[project.optional-dependencies]
-# Deps we expect to need to bring to new repos
-core = [
-    "biopython>=1.84",
-    "boto3>=1.36.8",
-    "docker>=7.1.0",
-    "fair-esm>=2.0.0",
-    "h5py>=3.11.0",
-    "questionary>=2.0.1",
-]
-
-[tool.poetry.group.dev.dependencies]
-black = "^25.1.0"
-colorlog = "^6.8.2"
-dvc = "^3.48.2"
-dvc-gs = "^3.0.1"
-flake8 = "^7.0.0"
-isort = "^5.13.2"
-pylance = "^0.10.2"
-pylint = "^3.1.0"
-pytest = "^8.0.2"
-pytest-cov = "^4.1.0"
-pytest-mock = "^3.12.0"
-ipykernel = "^6.29.5"
-
-[project.scripts]
-dh = "dayhoff_tools.cli.main:app"
-
-[tool.poetry]
-package-mode = true
-
-[tool.poetry.dependencies]
-python = ">=3.10,<4.0"