dayhoff-tools 1.7.1__py3-none-any.whl → 1.7.3__py3-none-any.whl

dayhoff_tools/cli/main.py

@@ -1,6 +1,7 @@
 """Entry file for the CLI, which aggregates and aliases all commands."""
 
 import sys
+from importlib.metadata import PackageNotFoundError, version
 
 import typer
 
@@ -21,7 +22,20 @@ from dayhoff_tools.warehouse import (
     import_from_warehouse_typer,
 )
 
-app = typer.Typer()
+def _get_dht_version() -> str:
+    try:
+        return version("dayhoff-tools")
+    except PackageNotFoundError:
+        # Fallback to package __version__ if running from source
+        try:
+            from dayhoff_tools import __version__  # type: ignore
+
+            return __version__
+        except Exception:
+            return "unknown"
+
+
+app = typer.Typer(help=f"Dayhoff Tools (dh) v{_get_dht_version()}\n\nUse 'dh --version' to print version and exit.")
 
 # Utility commands
 app.command("clean")(delete_local_branch)
@@ -50,6 +64,27 @@ app.add_typer(engine_app, name="engine", help="Manage compute engines for develo
 app.add_typer(studio_app, name="studio", help="Manage persistent development studios.")
 
 
+@app.callback(invoke_without_command=True)
+def _version_option(
+    ctx: typer.Context,
+    version_flag: bool = typer.Option(
+        False,
+        "--version",
+        "-v",
+        help="Print version and exit.",
+        is_eager=True,
+    )
+):
+    """Global options for the dh CLI (e.g., version)."""
+    if version_flag:
+        typer.echo(_get_dht_version())
+        raise typer.Exit()
+    # If no subcommand provided, show help instead of 'Missing command'
+    if ctx.invoked_subcommand is None:
+        typer.echo(ctx.get_help())
+        raise typer.Exit()
+
+
 @app.command("wheel")
 def build_and_upload_wheel_command(
     bump: str = typer.Option(

dayhoff_tools/cli/utility_commands.py

@@ -112,6 +112,7 @@ def build_and_upload_wheel(bump_part: str = "patch"):
     print("Using UV_PUBLISH_TOKEN for authentication.")
 
     pyproject_path = "pyproject.toml"
+    mac_manifest_path = "pyproject.mac.toml"
     current_version = None  # Initialize in case the first try block fails
 
     try:
@@ -173,6 +174,25 @@ def build_and_upload_wheel(bump_part: str = "patch"):
         with open(pyproject_path, "w") as f:
             f.write(new_content)
         print(f"Updated {pyproject_path} with version {new_version}")
+
+        # Mirror version in pyproject.mac.toml if present (best-effort)
+        mac_updated = False
+        try:
+            mac_path = Path(mac_manifest_path)
+            if mac_path.exists():
+                mac_content = mac_path.read_text()
+                mac_pattern = re.compile(
+                    f'^version\s*=\s*"{re.escape(current_version)}"', re.MULTILINE
+                )
+                mac_new_content, mac_replacements = mac_pattern.subn(
+                    f'version = "{new_version}"', mac_content
+                )
+                if mac_replacements > 0:
+                    mac_path.write_text(mac_new_content)
+                    mac_updated = True
+                    print(f"Updated {mac_manifest_path} with version {new_version}")
+        except Exception as e:
+            print(f"Warning: Could not update {mac_manifest_path}: {e}")
         # --- End Version Bumping Logic ---
 
         # Build wheel and sdist
@@ -191,6 +211,27 @@ def build_and_upload_wheel(bump_part: str = "patch"):
 
         print(f"Successfully built and uploaded version {new_version} to PyPI")
 
+        # Re-install DHT in current venv when building from DHT itself
+        try:
+            proj_name = None
+            try:
+                proj_toml = toml.load(pyproject_path)
+                proj_name = (
+                    proj_toml.get("project", {}).get("name")
+                    if isinstance(proj_toml, dict)
+                    else None
+                )
+            except Exception:
+                pass
+            if proj_name == "dayhoff-tools":
+                print("Re-installing dayhoff-tools into the active environment…")
+                reinstall_cmd = ["uv", "pip", "install", "-e", "."]
+                print(f"Running command: {BLUE}{' '.join(reinstall_cmd)}{RESET}")
+                subprocess.run(reinstall_cmd, check=True)
+                print("dayhoff-tools reinstalled in the current environment.")
+        except subprocess.CalledProcessError as e:
+            print(f"Warning: Failed to reinstall dayhoff-tools locally: {e}")
+
     except FileNotFoundError:
         print(f"Error: {pyproject_path} not found.")
         # No version change happened, so no rollback needed
@@ -219,6 +260,24 @@ def build_and_upload_wheel(bump_part: str = "patch"):
                     print(
                         f"Warning: Could not find version {new_version} to revert in {pyproject_path}."
                     )
+
+                # Also revert mac manifest if we updated it
+                try:
+                    mac_path = Path(mac_manifest_path)
+                    if mac_path.exists():
+                        mac_content_revert = mac_path.read_text()
+                        mac_reverted, mac_num = pattern_revert.subn(
+                            f'version = "{current_version}"', mac_content_revert
+                        )
+                        if mac_num > 0:
+                            mac_path.write_text(mac_reverted)
+                            print(
+                                f"Successfully reverted version in {mac_manifest_path}."
+                            )
+                except Exception as e2:
+                    print(
+                        f"Warning: Failed to revert version change in {mac_manifest_path}: {e2}"
+                    )
             except Exception as revert_e:
                 print(
                     f"Warning: Failed to revert version change in {pyproject_path}: {revert_e}"
@@ -248,6 +307,23 @@ def build_and_upload_wheel(bump_part: str = "patch"):
                     print(
                         f"Warning: Could not find version {new_version} to revert in {pyproject_path}."
                     )
+                # Also revert mac manifest if necessary
+                try:
+                    mac_path = Path(mac_manifest_path)
+                    if mac_path.exists():
+                        mac_content_revert = mac_path.read_text()
+                        mac_reverted, mac_num = pattern_revert.subn(
+                            f'version = "{current_version}"', mac_content_revert
+                        )
+                        if mac_num > 0:
+                            mac_path.write_text(mac_reverted)
+                            print(
+                                f"Successfully reverted version in {mac_manifest_path}."
+                            )
+                except Exception as e2:
+                    print(
+                        f"Warning: Failed to revert version change in {mac_manifest_path}: {e2}"
+                    )
             except Exception as revert_e:
                 print(
                     f"Warning: Failed to revert version change in {pyproject_path}: {revert_e}"
@@ -265,42 +341,72 @@ def install_dependencies(
         help="Install the local project package itself (with 'full' extras) into the environment.",
     ),
 ):
-    """Install dependencies based on pyproject.toml.
-
-    Ensures uv.lock matches pyproject.toml and syncs the environment.
-    When -p is used, installs the local project with its [full] optional dependencies.
+    """Install dependencies respecting Mac devcontainer flow and the active venv.
+
+    Behavior:
+    - If running on Mac devcontainer (STUDIO_PLATFORM=mac) and `pyproject.mac.toml` exists:
+      * Ensure `.mac_uv_project/pyproject.toml` is a copy of `pyproject.mac.toml`
+      * Run `uv lock` and `uv sync` in `.mac_uv_project` and always target the active venv with `--active`
+      * If `install_project` is true, install the project from repo root into the active env (editable, [full])
+    - Otherwise (default path):
+      * Operate in repo root, ensure lock, and `uv sync --active` so we don't create `.venv` accidentally
+      * If `install_project` is true, sync without `--no-install-project` (installs project)
     """
     # ANSI color codes
     BLUE = "\033[94m"
     RESET = "\033[0m"
 
     try:
-        # Step 1: Ensure lock file matches pyproject.toml
-        print("Ensuring lock file matches pyproject.toml...")
-        lock_cmd = ["uv", "lock"]
-        print(f"Running command: {BLUE}{' '.join(lock_cmd)}{RESET}")
-        subprocess.run(lock_cmd, check=True, capture_output=True)
-
-        if install_project:
-            # Step 2a: Install the project with 'full' extras
-            print("Installing the local project with 'full' extras...")
-            # The .[full] syntax tells pip to install the current project ('.')
-            # with its 'full' optional dependencies.
-            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.")
+        is_mac = os.environ.get("STUDIO_PLATFORM") == "mac"
+        mac_manifest = Path("pyproject.mac.toml")
+        if is_mac and mac_manifest.exists():
+            # Mac devcontainer flow
+            mac_uv_dir = Path(".mac_uv_project")
+            mac_uv_dir.mkdir(parents=True, exist_ok=True)
+            mac_pyproject = mac_uv_dir / "pyproject.toml"
+            mac_pyproject.write_text(mac_manifest.read_text())
+
+            # Ensure lock matches manifest (in mac temp dir)
+            print("Ensuring lock file matches pyproject.mac.toml (Mac devcon)…")
+            lock_cmd = ["uv", "lock"]
+            print(f"Running command: {BLUE}{' '.join(lock_cmd)}{RESET}")
+            subprocess.run(lock_cmd, check=True, capture_output=True, cwd=str(mac_uv_dir))
+
+            # Sync into the active environment
+            if install_project:
+                print("Syncing dependencies into ACTIVE env and installing project [full]…")
+                sync_cmd = ["uv", "sync", "--all-groups", "--active"]
+                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
+                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.")
+            else:
+                print("Syncing dependencies into ACTIVE env (project not installed)…")
+                sync_cmd = ["uv", "sync", "--all-groups", "--no-install-project", "--active"]
+                print(f"Running command: {BLUE}{' '.join(sync_cmd)}{RESET}")
+                subprocess.run(sync_cmd, check=True, cwd=str(mac_uv_dir))
+                print("Dependencies synced successfully (project not installed).")
         else:
-            # Original behavior: Sync environment without installing the project
-            print(
-                "Syncing environment with lock file (project itself will not be installed)..."
-            )
-            # --all-groups ensures all non-project dependencies (like dev) are installed
-            sync_cmd = ["uv", "sync", "--all-groups", "--no-install-project"]
-            print(f"Running command: {BLUE}{' '.join(sync_cmd)}{RESET}")
-            subprocess.run(sync_cmd, check=True)
-            print("Dependencies synced successfully (project not installed).")
+            # Default behavior in repo root, but ensure we target the active env
+            print("Ensuring lock file matches pyproject.toml…")
+            lock_cmd = ["uv", "lock"]
+            print(f"Running command: {BLUE}{' '.join(lock_cmd)}{RESET}")
+            subprocess.run(lock_cmd, check=True, capture_output=True)
+
+            if install_project:
+                print("Syncing dependencies into ACTIVE env (installing project)…")
+                sync_cmd = ["uv", "sync", "--all-groups", "--active"]
+                print(f"Running command: {BLUE}{' '.join(sync_cmd)}{RESET}")
+                subprocess.run(sync_cmd, check=True)
+            else:
+                print("Syncing dependencies into ACTIVE env (project not installed)…")
+                sync_cmd = ["uv", "sync", "--all-groups", "--no-install-project", "--active"]
+                print(f"Running command: {BLUE}{' '.join(sync_cmd)}{RESET}")
+                subprocess.run(sync_cmd, check=True)
+                print("Dependencies synced successfully (project not installed).")
 
     except subprocess.CalledProcessError as e:
         stderr_output = e.stderr.decode() if e.stderr else "No stderr output."
@@ -327,19 +433,27 @@ def update_dependencies(
         help="Update all dependencies instead of just dayhoff-tools.",
     ),
 ):
-    """Update dependencies to newer versions.
-
-    Default Action (no flags): Updates only 'dayhoff-tools' package to latest,
-                               updates pyproject.toml, and syncs.
-
-    Flags:
-    --all/-a: Updates all dependencies to latest compatible versions (`uv lock --upgrade`)
-              and syncs the environment. Overrides the default.
+    """Update dependencies to newer versions (Mac-aware, active venv friendly).
+
+    - Default Action (no flags): Updates only 'dayhoff-tools' package to latest,
+      updates the manifest's version constraint, and syncs.
+    - Flags:
+      --all/-a: Updates all dependencies (uv lock --upgrade) and syncs.
+
+    Mac devcontainer behavior:
+    - If STUDIO_PLATFORM=mac and `pyproject.mac.toml` exists, operate in `.mac_uv_project/`:
+      copy `pyproject.mac.toml` to `.mac_uv_project/pyproject.toml`, run uv there, and always
+      use `--active` for sync so installs target the active venv.
+    - Update the constraint inside `pyproject.mac.toml`. If not found, try `pyproject.toml`.
+    Otherwise (non-Mac), operate in repo root and also target the active venv during sync.
     """
     # ANSI color codes
     BLUE = "\033[94m"
     RESET = "\033[0m"
 
+    is_mac = os.environ.get("STUDIO_PLATFORM") == "mac"
+    mac_manifest = Path("pyproject.mac.toml")
+    mac_uv_dir = Path(".mac_uv_project")
     lock_file_path = Path("uv.lock")
     pyproject_path = Path("pyproject.toml")
 
@@ -363,10 +477,19 @@ def update_dependencies(
         )
 
     try:
+        # Choose working directory for uv operations
+        uv_cwd = None
+        manifest_path_for_constraint = pyproject_path
+        if is_mac and mac_manifest.exists():
+            mac_uv_dir.mkdir(parents=True, exist_ok=True)
+            (mac_uv_dir / "pyproject.toml").write_text(mac_manifest.read_text())
+            uv_cwd = str(mac_uv_dir)
+            lock_file_path = mac_uv_dir / "uv.lock"
+            manifest_path_for_constraint = mac_manifest
         # Step 1: Run the update lock command
         print(action_description)
         print(f"Running command: {BLUE}{' '.join(lock_cmd)}{RESET}")
-        subprocess.run(lock_cmd, check=True, capture_output=True)
+        subprocess.run(lock_cmd, check=True, capture_output=True, cwd=uv_cwd)
 
         # Step 2: Update pyproject.toml only if doing the dayhoff update (default)
         if run_pyproject_update:
@@ -395,9 +518,9 @@ def update_dependencies(
                 return
 
             print(f"Found dayhoff-tools version {locked_version} in lock file.")
-            print(f"Updating {pyproject_path} version constraint...")
+            print(f"Updating {manifest_path_for_constraint} version constraint...")
             try:
-                content = pyproject_path.read_text()
+                content = manifest_path_for_constraint.read_text()
 
                 package_name = "dayhoff-tools"
                 package_name_esc = re.escape(package_name)
@@ -420,27 +543,41 @@ def update_dependencies(
 
                 new_content, num_replacements = pattern.subn(_repl, content)
                 if num_replacements > 0:
-                    pyproject_path.write_text(new_content)
+                    manifest_path_for_constraint.write_text(new_content)
                     print(
-                        f"Updated dayhoff-tools constraint in {pyproject_path} to '{new_constraint_text}'"
+                        f"Updated dayhoff-tools constraint in {manifest_path_for_constraint} to '{new_constraint_text}'"
                     )
                 else:
-                    print(
-                        f"Warning: Could not find dayhoff-tools dependency line in {pyproject_path} to update constraint."
-                    )
+                    # Fallback: try the root pyproject if we were targeting mac manifest
+                    if manifest_path_for_constraint != pyproject_path and pyproject_path.exists():
+                        content2 = pyproject_path.read_text()
+                        new_content2, n2 = pattern.subn(_repl, content2)
+                        if n2 > 0:
+                            pyproject_path.write_text(new_content2)
+                            print(
+                                f"Updated dayhoff-tools constraint in {pyproject_path} to '{new_constraint_text}'"
+                            )
+                        else:
+                            print(
+                                f"Warning: Could not find dayhoff-tools dependency line in {manifest_path_for_constraint} or {pyproject_path} to update constraint."
+                            )
+                    else:
+                        print(
+                            f"Warning: Could not find dayhoff-tools dependency line in {manifest_path_for_constraint} to update constraint."
+                        )
             except FileNotFoundError:
-                print(f"Error: {pyproject_path} not found.")
+                print(f"Error: {manifest_path_for_constraint} not found.")
                 return
             except Exception as e:
-                print(f"Error updating {pyproject_path}: {e}")
+                print(f"Error updating {manifest_path_for_constraint}: {e}")
                 print("Proceeding with sync despite pyproject.toml update error.")
 
         # Step 3: Sync environment
         print("Syncing environment with updated lock file...")
         # Always use --no-install-project for updates
-        sync_cmd = ["uv", "sync", "--all-groups", "--no-install-project"]
+        sync_cmd = ["uv", "sync", "--all-groups", "--no-install-project", "--active"]
         print(f"Running command: {BLUE}{' '.join(sync_cmd)}{RESET}")
-        subprocess.run(sync_cmd, check=True)
+        subprocess.run(sync_cmd, check=True, cwd=uv_cwd)
 
         # Final status message
         if update_all:

{dayhoff_tools-1.7.1.dist-info → dayhoff_tools-1.7.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: dayhoff-tools
-Version: 1.7.1
+Version: 1.7.3
 Summary: Common tools for all the repos at Dayhoff Labs
 Author: Daniel Martin-Alarcon
 Author-email: dma@dayhofflabs.com

{dayhoff_tools-1.7.1.dist-info → dayhoff_tools-1.7.3.dist-info}/RECORD

@@ -4,9 +4,9 @@ dayhoff_tools/chemistry/utils.py,sha256=jt-7JgF-GeeVC421acX-bobKbLU_X94KNOW24p_P
 dayhoff_tools/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 dayhoff_tools/cli/cloud_commands.py,sha256=33qcWLmq-FwEXMdL3F0OHm-5Stlh2r65CldyEZgQ1no,40904
 dayhoff_tools/cli/engine_commands.py,sha256=_NQI9x4VKtAC9vTDdA4NGrILf2kb005t3Kw0aZ5oroE,96485
-dayhoff_tools/cli/main.py,sha256=tRN7WCBHg6uyNp6rA54pKTCoVmBntta2i0Yas3bUpZ4,4853
+dayhoff_tools/cli/main.py,sha256=LLMybU9KbtV_F4rwvoYAQZKTTF1nswlSZIfDMKdkh00,5925
 dayhoff_tools/cli/swarm_commands.py,sha256=5EyKj8yietvT5lfoz8Zx0iQvVaNgc3SJX1z2zQR6o6M,5614
-dayhoff_tools/cli/utility_commands.py,sha256=FRZTPrjsG_qmIIqoNxd1Q1vVkS_5w8aY33IrVYVNCLg,18131
+dayhoff_tools/cli/utility_commands.py,sha256=1GeflsuINXvTS1Ib7_UqGLHSixqn0tQXYx-NEarwveo,25859
 dayhoff_tools/deployment/base.py,sha256=mYp560l6hSDFtyY2H42VoM8k9VUzfwuiyh9Knqpgc28,17441
 dayhoff_tools/deployment/deploy_aws.py,sha256=GvZpE2YIFA5Dl9rkAljFjtUypmPDNbWgw8NicHYTP24,18265
 dayhoff_tools/deployment/deploy_gcp.py,sha256=xgaOVsUDmP6wSEMYNkm1yRNcVskfdz80qJtCulkBIAM,8860
@@ -27,7 +27,7 @@ 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=heaYc64qplgN3_1WVPFmqj53goStioWwY5NqlWc4c0s,24453
-dayhoff_tools-1.7.1.dist-info/METADATA,sha256=SfgSoCKU9G3NVk4aeQprKBvjn8-bHUXPy5jT2EIS1sA,2914
-dayhoff_tools-1.7.1.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-dayhoff_tools-1.7.1.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
-dayhoff_tools-1.7.1.dist-info/RECORD,,
+dayhoff_tools-1.7.3.dist-info/METADATA,sha256=WAnl4yvnUfIK6m7enSKQ154Pcy0IplNFNrXnVhsmy1c,2914
+dayhoff_tools-1.7.3.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+dayhoff_tools-1.7.3.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
+dayhoff_tools-1.7.3.dist-info/RECORD,,