dayhoff-tools 1.12.31__py3-none-any.whl → 1.12.32__py3-none-any.whl

dayhoff_tools/cli/engines_studios/engine-studio-cli.md

@@ -321,15 +321,22 @@ dh engine2 list --env sand
 
 **Output:**
 ```
-Name                           Instance ID           Type            State     
---------------------------------------------------------------------------------
-alice-work                     i-0123456789abcdef0   cpu             running   
-bob-training                   i-0fedcba987654321   a10g            running   
-batch-worker                   i-0abc123def456789   cpumax          stopped   
+Engines for AWS Account dev
+
+Name            State        User         Type         Instance ID         
+───────────────────────────────────────────────────────────────────────────
+alice-work      running      alice        cpu          i-0123456789abcdef0 
+bob-training    running      bob          a10g         i-0fedcba987654321  
+batch-worker    stopped      charlie      cpumax       i-0abc123def456789  
 
 Total: 3 engine(s)
 ```
 
+**Formatting:**
+- Engine names are displayed in blue
+- State is color-coded: green for "running", yellow for "starting/stopping", grey for "stopped"
+- Name column width adjusts dynamically to fit the longest engine name
+
 ---
 
 ### Access
@@ -744,15 +751,21 @@ dh studio2 list
 
 **Output:**
 ```
-User                 Studio ID                Size       Status         
----------------------------------------------------------------------------
-alice                vol-0123456789abcdef0    100GB      attached       
-bob                  vol-0fedcba987654321     200GB      available      
-carol                vol-0abc123def456789     150GB      available      
+User         Status       Size       Studio ID                
+──────────────────────────────────────────────────────────────
+alice        attached     100GB      vol-0123456789abcdef0    
+bob          available    200GB      vol-0fedcba987654321     
+carol        available    150GB      vol-0abc123def456789     
 
 Total: 3 studio(s)
 ```
 
+**Formatting:**
+- User names are displayed in blue
+- Status is color-coded: green for "available/attached", yellow for "attaching/detaching", red for "error"
+- User column width adjusts dynamically to fit the longest username
+- Columns are ordered: User, Status, Size, Studio ID
+
 ---
 
 ### Attachment

dayhoff_tools/cli/engines_studios/engine_commands.py

@@ -587,32 +587,56 @@ def list_engines(env: Optional[str]):
             click.echo("No engines found")
             return
 
-        # Table header - reordered per user request: Name, State, User, Type, Instance ID
+        # Calculate dynamic width for Name column (longest name + 2 for padding)
+        max_name_len = max((len(engine.get("name", "unknown")) for engine in engines), default=4)
+        name_width = max(max_name_len + 2, len("Name") + 2)
+
+        # Fixed widths for other columns
+        state_width = 12
+        user_width = 12
+        type_width = 12
+        id_width = 20
+
+        # Calculate total width for separator line
+        total_width = name_width + state_width + user_width + type_width + id_width + 4  # +4 for spaces
+
+        # Table header
         click.echo(
-            f"{'Name':<30} {'State':<12} {'User':<12} {'Type':<12} {'Instance ID':<20}"
+            f"{'Name':<{name_width}} {'State':<{state_width}} {'User':<{user_width}} {'Type':<{type_width}} {'Instance ID':<{id_width}}"
         )
-        click.echo("-" * 90)
+        click.echo("─" * total_width)
 
         # Table rows
         for engine in engines:
-            name = engine.get("name", "unknown")[:29]
-            state = engine.get("state", "unknown")[:11]
-            user = engine.get("user", "unknown")[:11]
-            engine_type = engine.get("engine_type", "unknown")[:11]
+            name = engine.get("name", "unknown")
+            state = engine.get("state", "unknown")
+            user = engine.get("user", "unknown")
+            engine_type = engine.get("engine_type", "unknown")
             instance_id = engine.get("instance_id", "unknown")
 
-            # Color the state in the list view
+            # Truncate if needed
+            if len(name) > name_width - 1:
+                name = name[:name_width - 1]
+            if len(user) > user_width - 1:
+                user = user[:user_width - 1]
+            if len(engine_type) > type_width - 1:
+                engine_type = engine_type[:type_width - 1]
+
+            # Color the name (blue)
+            name_display = f"\033[34m{name:<{name_width}}\033[0m"
+
+            # Color the state
             if state == "running":
-                state_display = f"\033[32m{state:<12}\033[0m"  # Green
+                state_display = f"\033[32m{state:<{state_width}}\033[0m"  # Green
             elif state in ["starting", "stopping", "pending"]:
-                state_display = f"\033[33m{state:<12}\033[0m"  # Yellow
+                state_display = f"\033[33m{state:<{state_width}}\033[0m"  # Yellow
             elif state == "stopped":
-                state_display = f"\033[37m{state:<12}\033[0m"  # White
+                state_display = f"\033[90m{state:<{state_width}}\033[0m"  # Grey (dim)
             else:
-                state_display = f"{state:<12}"  # No color for other states
+                state_display = f"{state:<{state_width}}"  # No color for other states
 
             click.echo(
-                f"{name:<30} {state_display} {user:<12} {engine_type:<12} {instance_id:<20}"
+                f"{name_display} {state_display} {user:<{user_width}} {engine_type:<{type_width}} {instance_id:<{id_width}}"
             )
 
         click.echo(f"\nTotal: {len(engines)} engine(s)")

dayhoff_tools/cli/engines_studios/simulators/engine_list_simulator.py

@@ -30,30 +30,54 @@ def format_list_output(engines: list[dict[str, Any]], env: str = "dev") -> None:
         print("No engines found")
         return
 
+    # Calculate dynamic width for Name column (longest name + 2 for padding)
+    max_name_len = max((len(engine.get("name", "unknown")) for engine in engines), default=4)
+    name_width = max(max_name_len + 2, len("Name") + 2)
+
+    # Fixed widths for other columns
+    state_width = 12
+    user_width = 12
+    type_width = 12
+    id_width = 20
+
+    # Calculate total width for separator line
+    total_width = name_width + state_width + user_width + type_width + id_width + 4  # +4 for spaces
+
     # Table header
-    print(f"{'Name':<12} {'State':<12} {'User':<12} {'Type':<12} {'Instance ID':<20}")
-    print("-" * 72)
+    print(f"{'Name':<{name_width}} {'State':<{state_width}} {'User':<{user_width}} {'Type':<{type_width}} {'Instance ID':<{id_width}}")
+    print("─" * total_width)
 
     # Table rows
     for engine in engines:
-        name = engine.get("name", "unknown")[:11]
-        state = engine.get("state", "unknown")[:11]
-        user = engine.get("user", "unknown")[:11]
-        engine_type = engine.get("engine_type", "unknown")[:11]
+        name = engine.get("name", "unknown")
+        state = engine.get("state", "unknown")
+        user = engine.get("user", "unknown")
+        engine_type = engine.get("engine_type", "unknown")
         instance_id = engine.get("instance_id", "unknown")
 
+        # Truncate if needed
+        if len(name) > name_width - 1:
+            name = name[:name_width - 1]
+        if len(user) > user_width - 1:
+            user = user[:user_width - 1]
+        if len(engine_type) > type_width - 1:
+            engine_type = engine_type[:type_width - 1]
+
+        # Color the name (blue)
+        name_display = colorize(f"{name:<{name_width}}", "34")
+
         # Color the state
         if state == "running":
-            state_display = colorize(f"{state:<12}", "32")  # Green
+            state_display = colorize(f"{state:<{state_width}}", "32")  # Green
         elif state in ["starting", "stopping", "pending"]:
-            state_display = colorize(f"{state:<12}", "33")  # Yellow
+            state_display = colorize(f"{state:<{state_width}}", "33")  # Yellow
         elif state == "stopped":
-            state_display = colorize(f"{state:<12}", "37")  # White
+            state_display = colorize(f"{state:<{state_width}}", "90")  # Grey (dim)
         else:
-            state_display = f"{state:<12}"  # No color for other states
+            state_display = f"{state:<{state_width}}"  # No color for other states
 
         print(
-            f"{name:<12} {state_display} {user:<12} {engine_type:<12} {instance_id:<20}"
+            f"{name_display} {state_display} {user:<{user_width}} {engine_type:<{type_width}} {instance_id:<{id_width}}"
         )
 
     print(f"\nTotal: {len(engines)} engine(s)")

dayhoff_tools/cli/engines_studios/studio_commands.py

@@ -262,18 +262,57 @@ def list_studios(env: Optional[str]):
             click.echo("No studios found")
             return
 
-        # Table header
-        click.echo(f"{'User':<20} {'Studio ID':<25} {'Size':<10} {'Status':<15}")
-        click.echo("-" * 75)
+        # Calculate dynamic width for User column (longest user + 2 for padding)
+        max_user_len = max((len(studio.get("user", "unknown")) for studio in studios), default=4)
+        user_width = max(max_user_len + 2, len("User") + 2)
+
+        # Fixed widths for other columns - reordered to [User, Status, Size, Studio ID]
+        status_width = 12
+        size_width = 10
+        id_width = 25
+
+        # Calculate total width for separator line
+        total_width = user_width + status_width + size_width + id_width + 3  # +3 for spaces
+
+        # Table header - reordered to [User, Status, Size, Studio ID]
+        click.echo(
+            f"{'User':<{user_width}} {'Status':<{status_width}} {'Size':<{size_width}} {'Studio ID':<{id_width}}"
+        )
+        click.echo("─" * total_width)
 
         # Table rows
         for studio in studios:
-            user = studio.get("user", "unknown")[:19]
-            studio_id = studio.get("studio_id", "unknown")
-            size = f"{studio.get('size_gb', 0)}GB"
+            user = studio.get("user", "unknown")
             status = studio.get("status", "unknown")
+            size = f"{studio.get('size_gb', 0)}GB"
+            studio_id = studio.get("studio_id", "unknown")
+
+            # Truncate if needed
+            if len(user) > user_width - 1:
+                user = user[:user_width - 1]
+
+            # Color the user (blue)
+            user_display = f"\033[34m{user:<{user_width}}\033[0m"
+
+            # Color the status
+            if status == "available":
+                status_display = f"\033[32m{status:<{status_width}}\033[0m"  # Green
+            elif status in ["attaching", "detaching"]:
+                status_display = f"\033[33m{status:<{status_width}}\033[0m"  # Yellow
+            elif status == "attached":
+                status_display = f"\033[32m{status:<{status_width}}\033[0m"  # Green
+            elif status in ["error", "in-use"]:
+                # "in-use" is the old status name, treat as attached (green)
+                if status == "in-use":
+                    status_display = f"\033[32m{status:<{status_width}}\033[0m"  # Green
+                else:
+                    status_display = f"\033[31m{status:<{status_width}}\033[0m"  # Red for error
+            else:
+                status_display = f"{status:<{status_width}}"  # No color for other states
 
-            click.echo(f"{user:<20} {studio_id:<25} {size:<10} {status:<15}")
+            click.echo(
+                f"{user_display} {status_display} {size:<{size_width}} {studio_id:<{id_width}}"
+            )
 
         click.echo(f"\nTotal: {len(studios)} studio(s)")
 

dayhoff_tools/deployment/deploy_aws.py

@@ -344,6 +344,47 @@ def create_or_update_job_definition(
             f"Adding mount points to job definition: {batch_job_config['mountPoints']}"
         )
 
+    # Auto-mount Primordial Drive if available
+    # This ensures all batch jobs have access to shared datasets at /primordial/
+    primordial_fs_id = get_primordial_fs_id(session)
+    if primordial_fs_id:
+        print(f"Adding Primordial Drive configuration (fs_id: {primordial_fs_id})")
+
+        # Add volume configuration
+        efs_volume = {
+            "name": "primordial",
+            "efsVolumeConfiguration": {
+                "fileSystemId": primordial_fs_id,
+                "rootDirectory": "/",
+            },
+        }
+
+        if "volumes" not in container_properties:
+            container_properties["volumes"] = []
+
+        # Check if already added to avoid duplicates
+        if not any(
+            v.get("name") == "primordial" for v in container_properties["volumes"]
+        ):
+            container_properties["volumes"].append(efs_volume)
+
+        # Add mount point
+        mount_point = {
+            "sourceVolume": "primordial",
+            "containerPath": "/primordial",
+            "readOnly": False,
+        }
+
+        if "mountPoints" not in container_properties:
+            container_properties["mountPoints"] = []
+
+        # Check if already added
+        if not any(
+            mp.get("containerPath") == "/primordial"
+            for mp in container_properties["mountPoints"]
+        ):
+            container_properties["mountPoints"].append(mount_point)
+
     # Check if job definition already exists using the session client
     try:
         existing = batch.describe_job_definitions(
@@ -385,6 +426,38 @@ def create_or_update_job_definition(
     return response["jobDefinitionName"]
 
 
+def get_primordial_fs_id(session: boto3.Session) -> Optional[str]:
+    """Fetch Primordial Drive EFS ID from SSM.
+
+    Args:
+        session: Boto3 session
+
+    Returns:
+        FileSystemId if found, None otherwise
+    """
+    ssm = session.client("ssm")
+
+    # Determine environment from profile name
+    # Default to dev if cannot determine
+    env = "dev"
+    if session.profile_name and "sand" in session.profile_name:
+        env = "sand"
+
+    param_name = f"/{env}/primordial/fs_id"
+
+    try:
+        response = ssm.get_parameter(Name=param_name)
+        return response["Parameter"]["Value"]
+    except ClientError as e:
+        # Silently fail if not found - Primordial might not be deployed in this env
+        # or we might not have permissions
+        # ParameterNotFound is a ClientError with error code "ParameterNotFound"
+        return None
+    except Exception as e:
+        print(f"Warning: Failed to check for Primordial Drive: {e}")
+        return None
+
+
 def submit_aws_batch_job(
     image_uri: str,
     config: dict[str, Any],

{dayhoff_tools-1.12.31.dist-info → dayhoff_tools-1.12.32.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dayhoff-tools
-Version: 1.12.31
+Version: 1.12.32
 Summary: Common tools for all the repos at Dayhoff Labs
 Author: Daniel Martin-Alarcon
 Author-email: dma@dayhofflabs.com

{dayhoff_tools-1.12.31.dist-info → dayhoff_tools-1.12.32.dist-info}/RECORD

@@ -13,22 +13,22 @@ dayhoff_tools/cli/engine1/studio_commands.py,sha256=VwTQujz32-uMcYusDRE73SdzRpgv
 dayhoff_tools/cli/engines_studios/__init__.py,sha256=E6aG0C6qjJnJuClemSKRFlYvLUL49MQZOvfqNQ7SDKs,159
 dayhoff_tools/cli/engines_studios/api_client.py,sha256=9I55_Ns8VHxndGjvSt_c5ZohSqMOeywQlLjyuoDEqCQ,13039
 dayhoff_tools/cli/engines_studios/auth.py,sha256=rwetV5hp4jSvK8FyvKgXCnezLOZx1aW8oiSDc6U83iE,5189
-dayhoff_tools/cli/engines_studios/engine-studio-cli.md,sha256=jwUoMrwp8OnNcOMw128NnQib9Yn2tWmupXcLLtyfass,27613
-dayhoff_tools/cli/engines_studios/engine_commands.py,sha256=x7fif4bnc0A8sDNHv3UuilUSurWv8Qhfrv9Jlp1s_QA,32750
+dayhoff_tools/cli/engines_studios/engine-studio-cli.md,sha256=uWi6MMZwlIc1PiNQ8iRtRZSVTSOmBkwWY1s2wpuRbgk,28345
+dayhoff_tools/cli/engines_studios/engine_commands.py,sha256=zhkKsXj6LzpfJ2MnNsmir-pByKOuGSXLeJU14pVJfaQ,33743
 dayhoff_tools/cli/engines_studios/progress.py,sha256=SMahdG2YmO5bEPSONrfAXVTdS6m_69Ep02t3hc2DdKQ,9264
 dayhoff_tools/cli/engines_studios/simulators/cli-simulators.md,sha256=FZJl6nehdr2Duht2cx3yijcak0yKyOaHTrTzvFTAfZs,4976
 dayhoff_tools/cli/engines_studios/simulators/demo.sh,sha256=8tYABSCxLNXqGs-4r071V9mpKNZ5DTQ34WZ-v3d5s94,5364
-dayhoff_tools/cli/engines_studios/simulators/engine_list_simulator.py,sha256=MrfcCpg8oKZ3fpr9-J8rb7pdJ7XptKuhLcVSF07xxxU,7601
+dayhoff_tools/cli/engines_studios/simulators/engine_list_simulator.py,sha256=hkuZMkCfnAD8giMVS04TeqGWMiRKhjhCmKCPRWcdPZA,8603
 dayhoff_tools/cli/engines_studios/simulators/engine_status_simulator.py,sha256=KUm3gA2MiRgGrQV7KURhb5zabM18-30z_ugRjiq5iso,13024
 dayhoff_tools/cli/engines_studios/simulators/idle_status_simulator.py,sha256=F_MfEXdPKNVDCKgJV72QyU2oMG8hLt-Bwic4yFadRXE,17570
 dayhoff_tools/cli/engines_studios/simulators/simulator_utils.py,sha256=HA08pIMJWV3OFrWj3Ca8GldvgJZfFoTOloyLK0UWMgA,6729
 dayhoff_tools/cli/engines_studios/simulators/studio_status_simulator.py,sha256=6WvpnRawJVaQf_H81zuR1_66igRRVxPxjAt8e69xjp4,5394
-dayhoff_tools/cli/engines_studios/studio_commands.py,sha256=fXj0Oo8BTWrORplg3V0dxZo1i9xX6-h2WSsdtbJQqbc,20575
+dayhoff_tools/cli/engines_studios/studio_commands.py,sha256=DX--3p15yrKC5eB86dc5m_MTb-5SB7b-kPsqW42ykaI,22417
 dayhoff_tools/cli/main.py,sha256=Nz_jtbppmvWKHZydQ0nkt_eejccJE90ces8xCGrerdY,7086
 dayhoff_tools/cli/swarm_commands.py,sha256=5EyKj8yietvT5lfoz8Zx0iQvVaNgc3SJX1z2zQR6o6M,5614
 dayhoff_tools/cli/utility_commands.py,sha256=e2P4dCCtoqMUGNyb0lFBZ6GZpl5Zslm1qqE5qIvsy38,50765
 dayhoff_tools/deployment/base.py,sha256=fM9zyhuRvIK8YqY6ooYg9j6wy_8touA_L-dkV7FA5q4,18058
-dayhoff_tools/deployment/deploy_aws.py,sha256=gfqh09hGbz0q3oPqVm0imd_CEjKF2k8moGNRIL26qqE,18614
+dayhoff_tools/deployment/deploy_aws.py,sha256=3xNuGvwDKvICfiLXVeM4Oz8MXQ363voTM-6vXHtEHZY,20987
 dayhoff_tools/deployment/deploy_gcp.py,sha256=xgaOVsUDmP6wSEMYNkm1yRNcVskfdz80qJtCulkBIAM,8860
 dayhoff_tools/deployment/deploy_utils.py,sha256=KyUFZZWn8NGT9QpR0HGqkX-huOFubvYCabko9SlC5Gg,26516
 dayhoff_tools/deployment/job_runner.py,sha256=hljvFpH2Bw96uYyUup5Ths72PZRL_X27KxlYzBMgguo,5086
@@ -47,7 +47,7 @@ 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-1.12.31.dist-info/METADATA,sha256=XXc2Zu9LH0HKmDqY-uj2MlRNYrm4sOtxIHVdzRozBgg,2981
-dayhoff_tools-1.12.31.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-dayhoff_tools-1.12.31.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
-dayhoff_tools-1.12.31.dist-info/RECORD,,
+dayhoff_tools-1.12.32.dist-info/METADATA,sha256=wg00QqtusBsm7HGPud5mkObekKEuyJoa-IYpRRquZ5k,2981
+dayhoff_tools-1.12.32.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+dayhoff_tools-1.12.32.dist-info/entry_points.txt,sha256=iAf4jteNqW3cJm6CO6czLxjW3vxYKsyGLZ8WGmxamSc,49
+dayhoff_tools-1.12.32.dist-info/RECORD,,