dayhoff-tools 1.11.6__py3-none-any.whl → 1.11.8__py3-none-any.whl

dayhoff_tools/cli/utility_commands.py

@@ -570,12 +570,33 @@ def sync_with_toml(
                 ]
                 print(f"Running command: {BLUE}{' '.join(sync_cmd)}{RESET}")
                 subprocess.run(sync_cmd, check=True, cwd=str(mac_uv_dir))
+
                 # Install project from repo root (where source code actually is)
+                # Temporarily create pyproject.toml at repo root for UV
                 print("Installing project with 'full' extras from repo root…")
-                pip_install_cmd = ["uv", "pip", "install", "-e", ".[full]"]
-                print(f"Running command: {BLUE}{' '.join(pip_install_cmd)}{RESET}")
-                subprocess.run(pip_install_cmd, check=True)
-                print("Project installed with 'full' extras successfully.")
+                temp_pyproject = False
+                backup_created = False
+                try:
+                    if not Path("pyproject.toml").exists():
+                        # Create temp pyproject.toml from platform manifest
+                        Path("pyproject.toml").write_text(mac_manifest.read_text())
+                        temp_pyproject = True
+                    elif Path("pyproject.toml").is_symlink():
+                        # Backup existing symlink
+                        Path("pyproject.toml").rename("pyproject.toml.sync.bak")
+                        Path("pyproject.toml").write_text(mac_manifest.read_text())
+                        backup_created = True
+
+                    pip_install_cmd = ["uv", "pip", "install", "-e", ".[full]"]
+                    print(f"Running command: {BLUE}{' '.join(pip_install_cmd)}{RESET}")
+                    subprocess.run(pip_install_cmd, check=True)
+                    print("Project installed with 'full' extras successfully.")
+                finally:
+                    # Clean up temp pyproject.toml
+                    if temp_pyproject and Path("pyproject.toml").exists():
+                        Path("pyproject.toml").unlink()
+                    if backup_created and Path("pyproject.toml.sync.bak").exists():
+                        Path("pyproject.toml.sync.bak").rename("pyproject.toml")
             else:
                 print("Syncing dependencies into ACTIVE env (project not installed)…")
                 sync_cmd = [
@@ -624,12 +645,35 @@ def sync_with_toml(
                     ]
                     print(f"Running command: {BLUE}{' '.join(sync_cmd)}{RESET}")
                     subprocess.run(sync_cmd, check=True, cwd=str(aws_uv_dir))
+
                     # Install project from repo root (where source code actually is)
+                    # Temporarily create pyproject.toml at repo root for UV
                     print("Installing project with 'full' extras from repo root…")
-                    pip_install_cmd = ["uv", "pip", "install", "-e", ".[full]"]
-                    print(f"Running command: {BLUE}{' '.join(pip_install_cmd)}{RESET}")
-                    subprocess.run(pip_install_cmd, check=True)
-                    print("Project installed with 'full' extras successfully.")
+                    temp_pyproject = False
+                    backup_created = False
+                    try:
+                        if not Path("pyproject.toml").exists():
+                            # Create temp pyproject.toml from platform manifest
+                            Path("pyproject.toml").write_text(aws_manifest.read_text())
+                            temp_pyproject = True
+                        elif Path("pyproject.toml").is_symlink():
+                            # Backup existing symlink
+                            Path("pyproject.toml").rename("pyproject.toml.sync.bak")
+                            Path("pyproject.toml").write_text(aws_manifest.read_text())
+                            backup_created = True
+
+                        pip_install_cmd = ["uv", "pip", "install", "-e", ".[full]"]
+                        print(
+                            f"Running command: {BLUE}{' '.join(pip_install_cmd)}{RESET}"
+                        )
+                        subprocess.run(pip_install_cmd, check=True)
+                        print("Project installed with 'full' extras successfully.")
+                    finally:
+                        # Clean up temp pyproject.toml
+                        if temp_pyproject and Path("pyproject.toml").exists():
+                            Path("pyproject.toml").unlink()
+                        if backup_created and Path("pyproject.toml.sync.bak").exists():
+                            Path("pyproject.toml.sync.bak").rename("pyproject.toml")
                 else:
                     print(
                         "Syncing dependencies into ACTIVE env (project not installed)…"
@@ -680,6 +724,64 @@ def _get_all_platform_manifests():
     return manifest_files
 
 
+def _resolve_package_version(package_name: str) -> str | None:
+    """Resolve a package version by running uv lock and parsing the lock file.
+
+    Args:
+        package_name: Name of the package to resolve
+
+    Returns:
+        Resolved version string, or None if resolution failed
+    """
+    import os
+
+    try:
+        # Determine which manifest to use (prefer Mac, then AWS)
+        platform = os.environ.get("STUDIO_PLATFORM", "aws")
+        manifest_path = None
+        uv_dir = None
+
+        if platform == "mac" and Path("pyproject.mac.toml").exists():
+            manifest_path = Path("pyproject.mac.toml")
+            uv_dir = Path(".mac_uv_project")
+        elif Path("pyproject.aws.toml").exists():
+            manifest_path = Path("pyproject.aws.toml")
+            uv_dir = Path(".aws_uv_project")
+        elif Path("pyproject.mac.toml").exists():
+            # Fallback to Mac if AWS doesn't exist
+            manifest_path = Path("pyproject.mac.toml")
+            uv_dir = Path(".mac_uv_project")
+        else:
+            return None
+
+        # Create temp directory and copy manifest
+        uv_dir.mkdir(parents=True, exist_ok=True)
+        (uv_dir / "pyproject.toml").write_text(manifest_path.read_text())
+
+        # Copy README if it exists
+        if Path("README.md").exists():
+            (uv_dir / "README.md").write_text(Path("README.md").read_text())
+
+        # Run uv lock (suppress output)
+        subprocess.run(["uv", "lock"], cwd=str(uv_dir), check=True, capture_output=True)
+
+        # Parse lock file
+        lock_file = uv_dir / "uv.lock"
+        if not lock_file.exists():
+            return None
+
+        lock_data = toml.load(lock_file)
+        for package in lock_data.get("package", []):
+            if package.get("name") == package_name:
+                return package.get("version")
+
+        return None
+
+    except Exception as e:
+        print(f"Warning: Failed to resolve version: {e}")
+        return None
+
+
 def _update_all_manifests_for_dayhoff_tools(new_version: str):
     """Update dayhoff-tools constraint in all platform manifests."""
     import re
@@ -756,8 +858,9 @@ def add_dependency(
     section_name = "dev dependencies" if dev else "main dependencies"
     print(f"Adding '{package}' to {section_name} in all platform manifests...")
 
-    # Parse package name to check for duplicates
+    # Parse package name to check for duplicates and version specs
     package_name = re.split(r"[<>=~!\[]", package)[0].strip()
+    has_version_spec = any(c in package for c in ["<", ">", "=", "~", "!"])
 
     for manifest_file in manifest_files:
         try:
@@ -841,6 +944,50 @@ def add_dependency(
             print(f"Error updating {manifest_file}: {e}")
 
     print(f"\n✅ Added '{package}' to all platform manifests")
+
+    # If no version specified, resolve and add version constraint
+    if not has_version_spec:
+        print(f"\n🔍 Resolving version for '{package_name}'...")
+        resolved_version = _resolve_package_version(package_name)
+
+        if resolved_version:
+            print(f"📌 Resolved to version {resolved_version}")
+            print(
+                f"Updating manifests with version constraint '>={resolved_version}'..."
+            )
+
+            # Update all manifests to add version constraint
+            for manifest_file in manifest_files:
+                try:
+                    content = manifest_file.read_text()
+                    # Replace unversioned package with versioned one
+                    pattern = re.compile(
+                        rf'^(\s*["\']){re.escape(package_name)}(["\'],?)(.*)$',
+                        re.MULTILINE,
+                    )
+
+                    def replace_with_version(match):
+                        prefix = match.group(1)
+                        suffix = match.group(2)
+                        rest = match.group(3)
+                        return (
+                            f"{prefix}{package_name}>={resolved_version}{suffix}{rest}"
+                        )
+
+                    new_content = pattern.sub(replace_with_version, content)
+                    manifest_file.write_text(new_content)
+                    print(f"✅ Updated {manifest_file} with version constraint")
+                except Exception as e:
+                    print(f"Warning: Could not update version in {manifest_file}: {e}")
+
+            print(
+                f"\n✅ Added '{package_name}>={resolved_version}' to all platform manifests"
+            )
+        else:
+            print(
+                f"⚠️  Could not resolve version for '{package_name}', left unversioned"
+            )
+
     print(
         f"\nRun {BLUE}dh tomlsync{RESET} to install the new dependency in your environment."
     )

{dayhoff_tools-1.11.6.dist-info → dayhoff_tools-1.11.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dayhoff-tools
-Version: 1.11.6
+Version: 1.11.8
 Summary: Common tools for all the repos at Dayhoff Labs
 Author: Daniel Martin-Alarcon
 Author-email: dma@dayhofflabs.com
@@ -29,7 +29,6 @@ Requires-Dist: pyyaml (>=6.0)
 Requires-Dist: questionary (>=2.0.1)
 Requires-Dist: rdkit-pypi (>=2022.9.5) ; extra == "full"
 Requires-Dist: requests (>=2.31.0)
-Requires-Dist: seaborn
 Requires-Dist: sentencepiece (>=0.2.0) ; extra == "embedders"
 Requires-Dist: sentencepiece (>=0.2.0) ; extra == "full"
 Requires-Dist: sqlalchemy (>=2.0.40,<3.0.0) ; extra == "full"

{dayhoff_tools-1.11.6.dist-info → dayhoff_tools-1.11.8.dist-info}/RECORD

@@ -12,7 +12,7 @@ dayhoff_tools/cli/engine/shared.py,sha256=Ecx6I1jtzmxQDn3BezKpgpQ4SJeZf4SZjUCLg-
 dayhoff_tools/cli/engine/studio_commands.py,sha256=VwTQujz32-uMcYusDRE73SdzRpgvIkv7ZAF4zRv6AzA,30266
 dayhoff_tools/cli/main.py,sha256=Ii5boey--93yGthB_eS2LC7ZR3WHGsJXDHY7uElEtso,6169
 dayhoff_tools/cli/swarm_commands.py,sha256=5EyKj8yietvT5lfoz8Zx0iQvVaNgc3SJX1z2zQR6o6M,5614
-dayhoff_tools/cli/utility_commands.py,sha256=tU6fv8wnchxj8xuBR6lXI1_3tpyxcDxzqO7zyBXAfoY,44012
+dayhoff_tools/cli/utility_commands.py,sha256=iMj2Oj6Q9LcUTwwZismFqc2QTW_oSeIDR1o_eC7kj-Q,50331
 dayhoff_tools/deployment/base.py,sha256=48KE76QlWMeIZJefcBOZVbyChS2V_mgs7IQ31odPV2o,17806
 dayhoff_tools/deployment/deploy_aws.py,sha256=gfqh09hGbz0q3oPqVm0imd_CEjKF2k8moGNRIL26qqE,18614
 dayhoff_tools/deployment/deploy_gcp.py,sha256=xgaOVsUDmP6wSEMYNkm1yRNcVskfdz80qJtCulkBIAM,8860
@@ -33,7 +33,7 @@ dayhoff_tools/intake/uniprot.py,sha256=BZYJQF63OtPcBBnQ7_P9gulxzJtqyorgyuDiPeOJq
 dayhoff_tools/logs.py,sha256=DKdeP0k0kliRcilwvX0mUB2eipO5BdWUeHwh-VnsICs,838
 dayhoff_tools/sqlite.py,sha256=jV55ikF8VpTfeQqqlHSbY8OgfyfHj8zgHNpZjBLos_E,18672
 dayhoff_tools/warehouse.py,sha256=UETBtZD3r7WgvURqfGbyHlT7cxoiVq8isjzMuerKw8I,24475
-dayhoff_tools-1.11.6.dist-info/METADATA,sha256=4z45zpr5kaL-2WFPAxStOG5hpgm_23EgsyDWW_rUt58,3003
-dayhoff_tools-1.11.6.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-dayhoff_tools-1.11.6.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
-dayhoff_tools-1.11.6.dist-info/RECORD,,
+dayhoff_tools-1.11.8.dist-info/METADATA,sha256=BVSPi89Q4l1JH1DPOXHcwbxq9U1jJ66KJCaqsz5Sqrg,2980
+dayhoff_tools-1.11.8.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+dayhoff_tools-1.11.8.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
+dayhoff_tools-1.11.8.dist-info/RECORD,,