dayhoff-tools 1.5.5__py3-none-any.whl → 1.5.7__py3-none-any.whl

dayhoff_tools/cli/engine_commands.py

@@ -415,7 +415,7 @@ def update_ssh_config_entry(engine_name: str, instance_id: str, ssh_user: str, i
 Host {engine_name} {SSH_MANAGED_COMMENT}
     HostName {instance_id}
     User {ssh_user}
-    ProxyCommand sh -c \"AWS_SSM_IDLE_TIMEOUT={idle_timeout} aws ssm start-session --target %h --document-name AWS-StartSSHSession --parameters 'portNumber=%p,idleTimeout={idle_timeout}'\"\n"""
+    ProxyCommand sh -c \"AWS_SSM_IDLE_TIMEOUT={idle_timeout} aws ssm start-session --target %h --document-name AWS-StartSSHSession --parameters 'portNumber=%p'\"\n"""
 
     # Check if entry already exists
     host_line = f"Host {engine_name} {SSH_MANAGED_COMMENT}"
@@ -1029,7 +1029,7 @@ def config_ssh(
                     f"Host {engine['name']} {SSH_MANAGED_COMMENT}",
                     f"    HostName {engine['instance_id']}",
                     f"    User {ssh_user}",
-                    f"    ProxyCommand sh -c \"AWS_SSM_IDLE_TIMEOUT=600 aws ssm start-session --target %h --document-name AWS-StartSSHSession --parameters 'portNumber=%p,idleTimeout=600'\"",
+                    f"    ProxyCommand sh -c \"AWS_SSM_IDLE_TIMEOUT=600 aws ssm start-session --target %h --document-name AWS-StartSSHSession --parameters 'portNumber=%p'\"",
                 ]
             )
 

dayhoff_tools/warehouse.py

@@ -9,6 +9,25 @@ from zoneinfo import ZoneInfo
 # Import cloud helper lazily inside functions to avoid heavy deps at module load
 
 
+def _find_project_root() -> Path | None:
+    """
+    Find the project root by searching upwards from the current directory for
+    a `.git` directory or a `pyproject.toml` file.
+
+    Returns:
+        The path to the project root, or None if not found.
+    """
+    current_dir = Path.cwd().resolve()
+    while current_dir != current_dir.parent:
+        if (current_dir / ".git").is_dir() or (current_dir / "pyproject.toml").is_file():
+            return current_dir
+        current_dir = current_dir.parent
+    # Check the final directory in the hierarchy (e.g., '/')
+    if (current_dir / ".git").is_dir() or (current_dir / "pyproject.toml").is_file():
+        return current_dir
+    return None
+
+
 def _warn_if_gcp_default_sa(force_prompt: bool = False) -> None:
     """Warn the user when the active gcloud principal is the default VM service
     account.  See detailed docstring later in file (duplicate for early
@@ -528,11 +547,17 @@ def import_from_warehouse_typer() -> None:
     import questionary
 
     # Ensure execution from root directory
-    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}"
+    project_root = _find_project_root()
+    cwd = Path.cwd()
+    if not project_root or project_root != cwd:
+        error_msg = (
+            "This command must be run from the project's root directory, which is"
+            " expected to contain a `.git` folder or a `pyproject.toml` file.\n"
+            f"Current directory: {cwd}"
         )
+        if project_root:
+            error_msg += f"\nDetected project root: {project_root}"
+        raise Exception(error_msg)
 
     # Use questionary for prompts instead of typer
     warehouse_path = questionary.text("Warehouse path:").ask()
@@ -574,11 +599,17 @@ def get_from_warehouse_typer() -> None:
     import questionary
 
     # Ensure execution from root directory
-    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}"
+    project_root = _find_project_root()
+    cwd = Path.cwd()
+    if not project_root or project_root != cwd:
+        error_msg = (
+            "This command must be run from the project's root directory, which is"
+            " expected to contain a `.git` folder or a `pyproject.toml` file.\n"
+            f"Current directory: {cwd}"
         )
+        if project_root:
+            error_msg += f"\nDetected project root: {project_root}"
+        raise Exception(error_msg)
 
     # Use questionary for prompts instead of typer
     warehouse_path = questionary.text("Warehouse path:").ask()
@@ -619,11 +650,17 @@ def add_to_warehouse_typer() -> None:
     import questionary
 
     # Ensure execution from root directory
-    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}"
+    project_root = _find_project_root()
+    cwd = Path.cwd()
+    if not project_root or project_root != cwd:
+        error_msg = (
+            "This command must be run from the project's root directory, which is"
+            " expected to contain a `.git` folder or a `pyproject.toml` file.\n"
+            f"Current directory: {cwd}"
         )
+        if project_root:
+            error_msg += f"\nDetected project root: {project_root}"
+        raise Exception(error_msg)
 
     # Prompt for the data file path
     warehouse_path = questionary.text("Data file to be registered:").ask()

{dayhoff_tools-1.5.5.dist-info → dayhoff_tools-1.5.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: dayhoff-tools
-Version: 1.5.5
+Version: 1.5.7
 Summary: Common tools for all the repos at Dayhoff Labs
 Author: Daniel Martin-Alarcon
 Author-email: dma@dayhofflabs.com

{dayhoff_tools-1.5.5.dist-info → dayhoff_tools-1.5.7.dist-info}/RECORD

@@ -3,7 +3,7 @@ dayhoff_tools/chemistry/standardizer.py,sha256=uMn7VwHnx02nc404eO6fRuS4rsl4dvSPf
 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=33qcWLmq-FwEXMdL3F0OHm-5Stlh2r65CldyEZgQ1no,40904
-dayhoff_tools/cli/engine_commands.py,sha256=H2ZSBrANlSPj90qnPoFm_UpmzhPIgeCy3xHocOjjySs,89518
+dayhoff_tools/cli/engine_commands.py,sha256=_WzJpxwGVmN0vem6oVi5FosQkKaEGCLUgoUHoKSWejg,89475
 dayhoff_tools/cli/main.py,sha256=tRN7WCBHg6uyNp6rA54pKTCoVmBntta2i0Yas3bUpZ4,4853
 dayhoff_tools/cli/swarm_commands.py,sha256=5EyKj8yietvT5lfoz8Zx0iQvVaNgc3SJX1z2zQR6o6M,5614
 dayhoff_tools/cli/utility_commands.py,sha256=FRZTPrjsG_qmIIqoNxd1Q1vVkS_5w8aY33IrVYVNCLg,18131
@@ -26,8 +26,8 @@ dayhoff_tools/intake/structure.py,sha256=ufN3gAodQxhnt7psK1VTQeu9rKERmo_PhoxIbB4
 dayhoff_tools/intake/uniprot.py,sha256=BZYJQF63OtPcBBnQ7_P9gulxzJtqyorgyuDiPeOJqE4,16456
 dayhoff_tools/logs.py,sha256=DKdeP0k0kliRcilwvX0mUB2eipO5BdWUeHwh-VnsICs,838
 dayhoff_tools/sqlite.py,sha256=jV55ikF8VpTfeQqqlHSbY8OgfyfHj8zgHNpZjBLos_E,18672
-dayhoff_tools/warehouse.py,sha256=fV3goH2cH1Y0oLpGERnu4p70P2JfByJHjBh_oMRv9C0,23134
-dayhoff_tools-1.5.5.dist-info/METADATA,sha256=zr2RT0qJFuM_UPL46hNBBErmMBZFfTrI5h0NVEyUiWQ,2914
-dayhoff_tools-1.5.5.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-dayhoff_tools-1.5.5.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
-dayhoff_tools-1.5.5.dist-info/RECORD,,
+dayhoff_tools/warehouse.py,sha256=heaYc64qplgN3_1WVPFmqj53goStioWwY5NqlWc4c0s,24453
+dayhoff_tools-1.5.7.dist-info/METADATA,sha256=APBk7rddBNxAjWSsibYM8Fx5B_BRJXRHi61rqjBRGZg,2914
+dayhoff_tools-1.5.7.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+dayhoff_tools-1.5.7.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
+dayhoff_tools-1.5.7.dist-info/RECORD,,