dayhoff-tools 1.2.1__py3-none-any.whl → 1.2.3__py3-none-any.whl

dayhoff_tools/cli/cloud_commands.py

@@ -999,7 +999,7 @@ def aws_status(
     else:
         print(f"Credential status: {RED}not authenticated{NC}")
         print(f"\nTo authenticate, run:")
-        print(f"  {YELLOW}dh aws login --profile {target_profile}{NC}")
+        print(f"  {YELLOW}dh aws login{NC}")
 
 
 @aws_app.command("login")

dayhoff_tools/cli/utility_commands.py

@@ -126,12 +126,32 @@ def import_from_warehouse_typer() -> None:
     import questionary
     from dayhoff_tools.warehouse import import_from_warehouse
 
-    # Ensure execution from root
-    cwd = Path(os.getcwd())
-    if cwd.parent.name != "workspaces" or str(cwd.parent.parent) != cwd.root:
-        raise Exception(
-            f"This command must be executed from the repo's root directory (/workspaces/reponame). Current directory: {cwd}"
-        )
+    # Check if we're in Lightning Studio
+    if _is_lightning_studio():
+        # Lightning Studio behavior
+        _check_dvc_initialized()
+        _configure_studio_cache()
+
+        # Ensure we're running from repo root using REPO_ROOT env var
+        repo_root = os.environ.get("REPO_ROOT")
+        if not repo_root:
+            raise Exception(
+                "REPO_ROOT environment variable not set. Make sure you're in a repo with an active UV virtual environment."
+            )
+
+        current_dir = os.getcwd()
+        if current_dir != repo_root:
+            raise Exception(
+                f"This command must be run from the repo root. "
+                f"Current directory: {current_dir}, Expected: {repo_root}"
+            )
+    else:
+        # Original devcontainer behavior - ensure execution from root
+        cwd = Path(os.getcwd())
+        if cwd.parent.name != "workspaces" or str(cwd.parent.parent) != cwd.root:
+            raise Exception(
+                f"This command must be executed from the repo's root directory (/workspaces/reponame). Current directory: {cwd}"
+            )
 
     # Use questionary for prompts instead of typer
     warehouse_path = questionary.text("Warehouse path:").ask()
@@ -172,12 +192,32 @@ def add_to_warehouse_typer() -> None:
     import questionary
     from dayhoff_tools.warehouse import add_to_warehouse
 
-    # Ensure execution from root
-    cwd = Path(os.getcwd())
-    if cwd.parent.name != "workspaces" or str(cwd.parent.parent) != cwd.root:
-        raise Exception(
-            f"This command must be executed from the repo's root directory (/workspaces/reponame). Current directory: {cwd}"
-        )
+    # Check if we're in Lightning Studio
+    if _is_lightning_studio():
+        # Lightning Studio behavior
+        _check_dvc_initialized()
+        _configure_studio_cache()
+
+        # Ensure we're running from repo root using REPO_ROOT env var
+        repo_root = os.environ.get("REPO_ROOT")
+        if not repo_root:
+            raise Exception(
+                "REPO_ROOT environment variable not set. Make sure you're in a repo with an active UV virtual environment."
+            )
+
+        current_dir = os.getcwd()
+        if current_dir != repo_root:
+            raise Exception(
+                f"This command must be run from the repo root. "
+                f"Current directory: {current_dir}, Expected: {repo_root}"
+            )
+    else:
+        # Original devcontainer behavior - ensure execution from root
+        cwd = Path(os.getcwd())
+        if cwd.parent.name != "workspaces" or str(cwd.parent.parent) != cwd.root:
+            raise Exception(
+                f"This command must be executed from the repo's root directory (/workspaces/reponame). Current directory: {cwd}"
+            )
 
     # Prompt for the data file path
     warehouse_path = questionary.text("Data file to be registered:").ask()
@@ -647,5 +687,46 @@ def update_dependencies(
 
 
 # ----------------------
-# Cloud credential guard
+# Lightning Studio Commands
 # ----------------------
+
+
+def _is_lightning_studio() -> bool:
+    """Check if we're running in Lightning Studio environment."""
+    return os.path.exists("/teamspace/studios/this_studio")
+
+
+def _check_dvc_initialized() -> None:
+    """Check if DVC is initialized in the current directory."""
+    if not os.path.exists(".dvc"):
+        raise Exception(
+            "DVC is not initialized in this repository. Run 'dvc init' first."
+        )
+
+
+def _configure_studio_cache() -> None:
+    """Configure DVC to use studio-level cache if not already configured."""
+    studio_cache_dir = "/teamspace/studios/this_studio/.dvc_cache"
+
+    # Create cache directory if it doesn't exist
+    os.makedirs(studio_cache_dir, exist_ok=True)
+
+    # Check current cache configuration
+    try:
+        result = subprocess.run(
+            ["dvc", "cache", "dir"], capture_output=True, text=True, check=True
+        )
+        current_cache = result.stdout.strip()
+
+        if current_cache != studio_cache_dir:
+            print(
+                f"Configuring DVC cache to use studio-level directory: {studio_cache_dir}"
+            )
+            # Use --local flag to save in .dvc/config.local (git-ignored)
+            subprocess.run(
+                ["dvc", "cache", "dir", studio_cache_dir, "--local"], check=True
+            )
+            print("✅ DVC cache configured for Lightning Studio (in .dvc/config.local)")
+    except subprocess.CalledProcessError:
+        # If cache dir command fails, try to set it anyway
+        subprocess.run(["dvc", "cache", "dir", studio_cache_dir, "--local"], check=True)

{dayhoff_tools-1.2.1.dist-info → dayhoff_tools-1.2.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: dayhoff-tools
-Version: 1.2.1
+Version: 1.2.3
 Summary: Common tools for all the repos at Dayhoff Labs
 Author: Daniel Martin-Alarcon
 Author-email: dma@dayhofflabs.com

{dayhoff_tools-1.2.1.dist-info → dayhoff_tools-1.2.3.dist-info}/RECORD

@@ -2,10 +2,10 @@ dayhoff_tools/__init__.py,sha256=M5zThPyEBRYa5CfwlzKhcqTevWn3OKu62cjV6Zqie2A,469
 dayhoff_tools/chemistry/standardizer.py,sha256=uMn7VwHnx02nc404eO6fRuS4rsl4dvSPf2ElfZDXEpY,11188
 dayhoff_tools/chemistry/utils.py,sha256=jt-7JgF-GeeVC421acX-bobKbLU_X94KNOW24p_P-_M,2257
 dayhoff_tools/cli/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-dayhoff_tools/cli/cloud_commands.py,sha256=D_qreTPdshhzeUnwSWpr9HJ8sdTC0iiKqD2BK1LCJe4,40931
+dayhoff_tools/cli/cloud_commands.py,sha256=33qcWLmq-FwEXMdL3F0OHm-5Stlh2r65CldyEZgQ1no,40904
 dayhoff_tools/cli/main.py,sha256=47EGb28ALaYFc7oAUGlY1D66AIDmc4RZiXxN-gPVrpQ,4519
 dayhoff_tools/cli/swarm_commands.py,sha256=5EyKj8yietvT5lfoz8Zx0iQvVaNgc3SJX1z2zQR6o6M,5614
-dayhoff_tools/cli/utility_commands.py,sha256=ER4VrJt4hu904MwrcltUXjwBWT4uFrP-aPXjdXyT3F8,24685
+dayhoff_tools/cli/utility_commands.py,sha256=qs8vH9TBFHsOPC3X8cU3qZigM3dDn-2Ytq4o_F2WubU,27874
 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
@@ -26,7 +26,7 @@ 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=TqV8nex1AluNaL4JuXH5zuu9P7qmE89lSo6f_oViy6U,14965
-dayhoff_tools-1.2.1.dist-info/METADATA,sha256=1BHhN2LYqP4IynY7VhaBU62zbN219QAwChrJIqJG7qo,2842
-dayhoff_tools-1.2.1.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-dayhoff_tools-1.2.1.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
-dayhoff_tools-1.2.1.dist-info/RECORD,,
+dayhoff_tools-1.2.3.dist-info/METADATA,sha256=xJbC0wrh9ZuguuDzKouBca3FwaPKFrfjA54n4LAFSiw,2842
+dayhoff_tools-1.2.3.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+dayhoff_tools-1.2.3.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
+dayhoff_tools-1.2.3.dist-info/RECORD,,