dayhoff-tools 1.0.17__tar.gz → 1.0.18__tar.gz

{dayhoff_tools-1.0.17 → dayhoff_tools-1.0.18}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: dayhoff-tools
-Version: 1.0.17
+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-1.0.17 → dayhoff_tools-1.0.18}/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,
         )
 
@@ -364,8 +370,9 @@ def update_dayhoff_tools():
     """
     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)
+        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 attempting update: {e}")
@@ -374,21 +381,30 @@ def update_dayhoff_tools():
         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-1.0.17 → dayhoff_tools-1.0.18}/pyproject.toml

@@ -4,24 +4,15 @@ build-backend = "poetry.core.masonry.api"
 
 [project]
 name = "dayhoff-tools"
-version = "1.0.17"
+version = "1.0.18"
 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 = [
+# Default dependencies now include the formerly "full" set
+dependencies = [
     "biopython>=1.84",
     "boto3>=1.36.8",
     "docker>=7.1.0",
@@ -32,9 +23,27 @@ 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]
+# Minimal base dependencies
+base = [
+    "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 = [
@@ -57,6 +66,8 @@ 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]