dayhoff-tools 1.0.17__tar.gz → 1.0.19__tar.gz

{dayhoff_tools-1.0.17 → dayhoff_tools-1.0.19}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: dayhoff-tools
-Version: 1.0.17
+Version: 1.0.19
 Summary: Common tools for all the repos at Dayhoff Labs
 Author: Daniel Martin-Alarcon
 Author-email: dma@dayhofflabs.com
@@ -10,23 +10,26 @@ 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"
+Provides-Extra: lite
+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)
-Requires-Dist: h5py (>=3.11.0) ; extra == "full"
-Requires-Dist: pandas (>=2.2.3) ; extra == "full"
+Requires-Dist: firebase-admin (>=6.5.0) ; extra == "lite"
+Requires-Dist: h5py (>=3.11.0)
+Requires-Dist: pandas (>=2.2.3)
 Requires-Dist: pyyaml (>=6.0)
-Requires-Dist: questionary (>=2.0.1) ; extra == "full"
-Requires-Dist: rdkit-pypi (>=2022.9.5) ; extra == "full"
+Requires-Dist: pyyaml (>=6.0) ; extra == "lite"
+Requires-Dist: questionary (>=2.0.1)
+Requires-Dist: rdkit-pypi (>=2022.9.5)
 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: requests (>=2.31.0) ; extra == "lite"
+Requires-Dist: sqlalchemy (>=2.0.40,<3.0.0)
+Requires-Dist: toml (>=0.10)
+Requires-Dist: transformers (==4.36.2)
 Requires-Dist: typer (>=0.9.0)
+Requires-Dist: typer (>=0.9.0) ; extra == "lite"
 Description-Content-Type: text/markdown
 
 # dayhoff-tools

{dayhoff_tools-1.0.17 → dayhoff_tools-1.0.19}/dayhoff_tools/cli/utility_commands.py

@@ -7,6 +7,8 @@ import subprocess
 import sys
 from pathlib import Path
 
+import toml
+import typer
 import yaml
 
 
@@ -200,6 +202,10 @@ def build_and_upload_wheel(bump_part: str = "patch"):
         )
         return
 
+    # ANSI color codes
+    BLUE = "\033[94m"
+    RESET = "\033[0m"
+
     # --- Authentication Setup ---
     token = os.environ.get("UV_PUBLISH_TOKEN")
 
@@ -211,6 +217,8 @@ 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 +287,16 @@ 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 command in blue
+        print(f"Running command: {BLUE}{' '.join(build_cmd)}{RESET}")
+        subprocess.run(build_cmd, check=True)
 
         # Upload using uv publish with explicit arguments
-        print("Uploading to PyPI using uv publish...")
+        # Print masked command in blue
+        print(f"Running command: {BLUE}{' '.join(publish_cmd_safe_print)}{RESET}")
         subprocess.run(
-            publish_cmd,  # Use the command list built earlier
+            publish_cmd,  # Use the actual command with token
             check=True,
         )
 
@@ -355,40 +366,140 @@ def build_and_upload_wheel(bump_part: str = "patch"):
 
 
 def update_dayhoff_tools():
-    """Update the dayhoff-tools package to the latest version using uv.
+    """Update dayhoff-tools to latest, update pyproject.toml, and sync.
 
-    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].
+    1. Runs `uv lock --upgrade-package dayhoff-tools`
+    2. Parses uv.lock to find the new version.
+    3. Updates the version constraint in pyproject.toml to `>=<new_version>`.
+    4. Runs `uv sync --no-install-project`.
     """
+    # ANSI color codes
+    BLUE = "\033[94m"
+    RESET = "\033[0m"
+
+    lock_file_path = Path("uv.lock")
+    pyproject_path = Path("pyproject.toml")
+
     try:
-        print("Attempting to update dayhoff-tools to the latest version using uv...")
-        # Reverted to simple uv add, acknowledging limitations with top-level groups
-        subprocess.run(["uv", "add", "dayhoff-tools@latest"], check=True)
-        print("Update attempt complete! Check pyproject.toml and run sync if needed.")
+        print("Updating dayhoff-tools lock...")
+
+        # Step 1: Update lock file for dayhoff-tools
+        lock_cmd = ["uv", "lock", "--upgrade-package", "dayhoff-tools"]
+        print(f"Running command: {BLUE}{' '.join(lock_cmd)}{RESET}")
+        subprocess.run(lock_cmd, check=True)
+
+        # Step 2: Parse uv.lock to find the new version
+        print(f"Reading {lock_file_path} to find new version...")
+        if not lock_file_path.exists():
+            print(f"Error: {lock_file_path} not found after lock command.")
+            return
+
+        locked_version = None
+        try:
+            lock_data = toml.load(lock_file_path)
+            # Find dayhoff-tools in the lock file packages
+            for package in lock_data.get("package", []):
+                if package.get("name") == "dayhoff-tools":
+                    locked_version = package.get("version")
+                    break
+        except toml.TomlDecodeError as e:
+            print(f"Error parsing {lock_file_path}: {e}")
+            return
+        except Exception as e:
+            print(f"Error reading lock file: {e}")
+            return
+
+        if not locked_version:
+            print(f"Error: Could not find dayhoff-tools version in {lock_file_path}.")
+            return
+
+        print(f"Found dayhoff-tools version {locked_version} in lock file.")
+
+        # Step 3: Update pyproject.toml
+        print(f"Updating {pyproject_path} version constraint...")
+        try:
+            content = pyproject_path.read_text()
+            # Regex to find the dayhoff-tools dependency line, capturing name+extra
+            # Matches 'dayhoff-tools' or \"dayhoff-tools\", optional [extra], >= constraints etc.
+            pattern = re.compile(
+                r"(^[\'\"](dayhoff-tools(?:\[[^\\\]]+\\])?)[\'\"]\s*)[\\>\\<\\=\\~\\^\\(\\)\\s,0-9\\.\\*\'\"]+",
+                re.MULTILINE,
+            )
+            new_constraint = f">= {locked_version}"
+            new_content, num_replacements = pattern.subn(
+                rf"\1{new_constraint}", content
+            )
+
+            if num_replacements > 0:
+                pyproject_path.write_text(new_content)
+                print(
+                    f"Updated dayhoff-tools constraint in {pyproject_path} to '{new_constraint}'"
+                )
+            else:
+                print(
+                    f"Warning: Could not find dayhoff-tools dependency line in {pyproject_path} to update constraint."
+                )
+
+        except FileNotFoundError:
+            print(f"Error: {pyproject_path} not found.")
+            return
+        except Exception as e:
+            print(f"Error updating {pyproject_path}: {e}")
+            # Continue to sync step even if pyproject update fails?
+            # For now, let's proceed to sync.
+            print("Proceeding with sync despite pyproject.toml update error.")
+
+        # Step 4: Sync environment based on updated lock file
+        print("Syncing environment...")
+        sync_cmd = ["uv", "sync", "--no-install-project"]
+        print(f"Running command: {BLUE}{' '.join(sync_cmd)}{RESET}")
+        subprocess.run(sync_cmd, check=True)
+
+        print(
+            "dayhoff-tools updated, pyproject.toml modified, and environment synced successfully."
+        )
+
     except subprocess.CalledProcessError as e:
-        print(f"Error occurred while attempting update: {e}")
+        print(f"Error occurred during update/sync process: {e}")
     except FileNotFoundError:
+        # This catches if uv command itself is not found
         print("Error: 'uv' command not found. Is uv installed and in PATH?")
         sys.exit(1)
+    except Exception as e:
+        # Catch any other unexpected errors
+        print(f"An unexpected error occurred: {e}")
 
 
-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)
+    # ANSI color codes
+    BLUE = "\033[94m"
+    RESET = "\033[0m"
 
-        print("Syncing dependencies (uv sync --all-groups --no-install-project)...")
-        subprocess.run(
-            ["uv", "sync", "--all-groups", "--no-install-project"], check=True
-        )
+    try:
+        lock_cmd = ["uv", "lock"]
+        # Print command in blue
+        print(f"Running command: {BLUE}{' '.join(lock_cmd)}{RESET}")
+        subprocess.run(lock_cmd, check=True)
+
+        sync_cmd = ["uv", "sync", "--all-groups"]
+        if not install_project:
+            sync_cmd.append("--no-install-project")
+
+        # Print command in blue
+        print(f"Running command: {BLUE}{' '.join(sync_cmd)}{RESET}")
+        subprocess.run(sync_cmd, check=True)
 
         print("Dependencies synced successfully.")
     except subprocess.CalledProcessError as e:

{dayhoff_tools-1.0.17 → dayhoff_tools-1.0.19}/pyproject.toml

@@ -4,24 +4,20 @@ build-backend = "poetry.core.masonry.api"
 
 [project]
 name = "dayhoff-tools"
-version = "1.0.17"
+version = "1.0.19"
 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
+
+# Default dependencies now include the formerly "full" set + base set
 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 = [
+    "toml>=0.10",
     "biopython>=1.84",
     "boto3>=1.36.8",
     "docker>=7.1.0",
@@ -32,12 +28,29 @@ full = [
     "rdkit-pypi>=2022.9.5",
     "sqlalchemy (>=2.0.40,<3.0.0)",
     "transformers==4.36.2",
-    "torch>=2.1.0",
-    "torchvision>=0.16.0",
 ]
+requires-python = ">=3.10,<4.0"
+
+[project.optional-dependencies]
+lite = [
+    "firebase-admin>=6.5.0",
+    "pyyaml>=6.0",
+    "requests>=2.31.0",
+    "typer>=0.9.0",
+]
+
+# Added UV-specific configuration for PyTorch source (for dev/test env)
+[[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]
-common = [
+dev = [
     "black>=25.1.0,<26",
     "boto3>=1.36.8",
     "colorlog>=6.8.2,<7",
@@ -57,6 +70,8 @@ common = [
     "pytest>=8.0.2,<9",
     "pytest-cov>=4.1.0,<5",
     "pytest-mock>=3.12.0,<4",
+    "torch==2.4.0+cu121",
+    "torchvision==0.19.0+cu121",
 ]
 
 [project.scripts]