cloudos-cli 2.88.2__tar.gz → 2.89.1__tar.gz

{cloudos_cli-2.88.2 → cloudos_cli-2.89.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cloudos_cli
-Version: 2.88.2
+Version: 2.89.1
 Summary: Python package for interacting with CloudOS
 Home-page: https://github.com/lifebit-ai/cloudos-cli
 Author: David Piñeyro
@@ -753,9 +753,8 @@ cloudos job run --profile my_profile --workflow-name rnatoy --job-config cloudos
 Please note that HPC execution does not support the following parameters and all of them will be ignored:
 
 - `--job-queue`
-- `--resumable | --do-not-save-logs`
+- `--resumable` | `--do-not-save-logs`
 - `--instance-type` | `--instance-disk` | `--cost-limit`
-- `--storage-mode` | `--lustre-size`
 - `--wdl-mainfile` | `--wdl-importsfile` | `--cromwell-token`
 
 #### Check Job Status
@@ -800,19 +799,21 @@ The output shows a rich table with job information and pagination details:
 ```console
 Executing list...
 
-                                                    Job List                                                    
-┏━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┓
-┃ Status ┃ Name         ┃ Project     ┃ Owner    ┃ Pipeline     ┃ ID                      ┃ Submit time  ┃
-┡━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━┩
-│ ✓      │ analysis_run │ test-proj   │ John     │ rnatoy       │ 692ee71c40e98ed6ed529e43│ 2025-12-02   │
-│        │              │             │ Doe      │              │                         │ 15:30:45     │
-│ ◐      │ test_job     │ research    │ Jane     │ VEP          │ 692ee81d50f98ed7fe639f54│ 2025-12-02   │
-│        │              │             │ Smith    │              │                         │ 14:20:30     │
-└────────┴──────────────┴─────────────┴──────────┴──────────────┴─────────────────────────┴──────────────┘
+┏━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━┓
+┃ Status ┃ ID                       ┃ Pipeline     ┃ Name           ┃ Project      ┃ Owner    ┃ Runtime ┃
+┡━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━┩
+│ ✓      │ 692ee71c40e98ed6ed529e43 │ rnatoy       │ analysis_run   │ test-proj    │ John Doe │ 15m 30s │
+│ ◐      │ 692ee81d50f98ed7fe639f54 │ VEP          │ test_job       │ research     │ Jane Sm… │ 2m 15s  │
+└────────┴──────────────────────────┴──────────────┴────────────────┴──────────────┴──────────┴─────────┘
+
+Legend: ✓ = Completed  |  ◐ = Running  |  ✗ = Failed  |  ■ = Aborted  |  ○ = Initialising  |  ? = Unknown
 
 Showing 10 of 45 total jobs | Page 1 of 5
 ```
 
+> [!NOTE]
+> **Responsive Table Display**: The table automatically adapts to your terminal width, intelligently selecting which columns to display. Narrow terminals show essential columns (Status, ID, Pipeline, Name), while wider terminals progressively add more information (Project, Owner, Runtime, Cost, timestamps, etc.). The table ensures only complete columns are shown and always renders with proper borders.
+
 **Status Indicators**
 
 Jobs are displayed with colored visual status indicators:

{cloudos_cli-2.88.2 → cloudos_cli-2.89.1}/README.md

@@ -718,9 +718,8 @@ cloudos job run --profile my_profile --workflow-name rnatoy --job-config cloudos
 Please note that HPC execution does not support the following parameters and all of them will be ignored:
 
 - `--job-queue`
-- `--resumable | --do-not-save-logs`
+- `--resumable` | `--do-not-save-logs`
 - `--instance-type` | `--instance-disk` | `--cost-limit`
-- `--storage-mode` | `--lustre-size`
 - `--wdl-mainfile` | `--wdl-importsfile` | `--cromwell-token`
 
 #### Check Job Status
@@ -765,19 +764,21 @@ The output shows a rich table with job information and pagination details:
 ```console
 Executing list...
 
-                                                    Job List                                                    
-┏━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┓
-┃ Status ┃ Name         ┃ Project     ┃ Owner    ┃ Pipeline     ┃ ID                      ┃ Submit time  ┃
-┡━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━┩
-│ ✓      │ analysis_run │ test-proj   │ John     │ rnatoy       │ 692ee71c40e98ed6ed529e43│ 2025-12-02   │
-│        │              │             │ Doe      │              │                         │ 15:30:45     │
-│ ◐      │ test_job     │ research    │ Jane     │ VEP          │ 692ee81d50f98ed7fe639f54│ 2025-12-02   │
-│        │              │             │ Smith    │              │                         │ 14:20:30     │
-└────────┴──────────────┴─────────────┴──────────┴──────────────┴─────────────────────────┴──────────────┘
+┏━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━┳━━━━━━━━━┓
+┃ Status ┃ ID                       ┃ Pipeline     ┃ Name           ┃ Project      ┃ Owner    ┃ Runtime ┃
+┡━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━┩
+│ ✓      │ 692ee71c40e98ed6ed529e43 │ rnatoy       │ analysis_run   │ test-proj    │ John Doe │ 15m 30s │
+│ ◐      │ 692ee81d50f98ed7fe639f54 │ VEP          │ test_job       │ research     │ Jane Sm… │ 2m 15s  │
+└────────┴──────────────────────────┴──────────────┴────────────────┴──────────────┴──────────┴─────────┘
+
+Legend: ✓ = Completed  |  ◐ = Running  |  ✗ = Failed  |  ■ = Aborted  |  ○ = Initialising  |  ? = Unknown
 
 Showing 10 of 45 total jobs | Page 1 of 5
 ```
 
+> [!NOTE]
+> **Responsive Table Display**: The table automatically adapts to your terminal width, intelligently selecting which columns to display. Narrow terminals show essential columns (Status, ID, Pipeline, Name), while wider terminals progressively add more information (Project, Owner, Runtime, Cost, timestamps, etc.). The table ensures only complete columns are shown and always renders with proper borders.
+
 **Status Indicators**
 
 Jobs are displayed with colored visual status indicators:

cloudos_cli-2.89.1/cloudos_cli/_version.py

@@ -0,0 +1 @@
+__version__ = '2.89.1'

{cloudos_cli-2.88.2 → cloudos_cli-2.89.1}/cloudos_cli/bash/cli.py

@@ -75,15 +75,7 @@ def bash():
               help='The amount of memory, in GB, to use for the task\'s master node. Default=4.',
               type=int,
               default=4)
-@click.option('--storage-mode',
-              help=('Either \'lustre\' or \'regular\'. Indicates if the user wants to select ' +
-                    'regular or lustre storage. Default=regular.'),
-              default='regular')
-@click.option('--lustre-size',
-              help=('The lustre storage to be used when --storage-mode=lustre, in GB. It should ' +
-                    'be 1200 or a multiple of it. Default=1200.'),
-              type=int,
-              default=1200)
+
 @click.option('--wait-completion',
               help=('Whether to wait to job completion and report final ' +
                     'job status.'),
@@ -136,8 +128,6 @@ def run_bash_job(ctx,
                  instance_disk,
                  cpus,
                  memory,
-                 storage_mode,
-                 lustre_size,
                  wait_completion,
                  wait_time,
                  repository_platform,
@@ -194,8 +184,6 @@ def run_bash_job(ctx,
                       nextflow_version=None,
                       instance_type=instance_type,
                       instance_disk=instance_disk,
-                      storage_mode=storage_mode,
-                      lustre_size=lustre_size,
                       execution_platform=execution_platform,
                       hpc_id=None,
                       cost_limit=cost_limit,
@@ -296,15 +284,6 @@ def run_bash_job(ctx,
               help='The amount of memory, in GB, to use for the task\'s master node. Default=4.',
               type=int,
               default=4)
-@click.option('--storage-mode',
-              help=('Either \'lustre\' or \'regular\'. Indicates if the user wants to select ' +
-                    'regular or lustre storage. Default=regular.'),
-              default='regular')
-@click.option('--lustre-size',
-              help=('The lustre storage to be used when --storage-mode=lustre, in GB. It should ' +
-                    'be 1200 or a multiple of it. Default=1200.'),
-              type=int,
-              default=1200)
 @click.option('--wait-completion',
               help=('Whether to wait to job completion and report final ' +
                     'job status.'),
@@ -391,8 +370,6 @@ def run_bash_array_job(ctx,
                        instance_disk,
                        cpus,
                        memory,
-                       storage_mode,
-                       lustre_size,
                        wait_completion,
                        wait_time,
                        repository_platform,
@@ -525,8 +502,6 @@ def run_bash_array_job(ctx,
                       nextflow_version=None,
                       instance_type=instance_type,
                       instance_disk=instance_disk,
-                      storage_mode=storage_mode,
-                      lustre_size=lustre_size,
                       execution_platform=execution_platform,
                       hpc_id=None,
                       cost_limit=cost_limit,

cloudos_cli-2.89.1/cloudos_cli/constants.py

@@ -0,0 +1,75 @@
+"""Global constants for CloudOS CLI."""
+
+# Job status constants
+JOB_COMPLETED = 'completed'
+JOB_FAILED = 'failed'
+JOB_ABORTED = 'aborted'
+
+# Nextflow version constants
+AWS_NEXTFLOW_VERSIONS = ['22.10.8', '24.04.4', '25.04.8', '25.10.4']
+AZURE_NEXTFLOW_VERSIONS = ['22.11.1-edge']
+HPC_NEXTFLOW_VERSIONS = ['22.10.8']
+AWS_NEXTFLOW_LATEST = '25.10.4'
+AZURE_NEXTFLOW_LATEST = '22.11.1-edge'
+HPC_NEXTFLOW_LATEST = '22.10.8'
+
+# Nextflow version defaults by workflow type
+PLATFORM_WORKFLOW_NEXTFLOW_VERSION = '22.10.8'  # For Lifebit Platform workflows (modules)
+USER_WORKFLOW_NEXTFLOW_VERSION = '24.04.4'  # For user-imported workflows
+
+# Job abort states
+ABORT_JOB_STATES = ['running', 'initializing']
+
+# Request interval for Cromwell
+REQUEST_INTERVAL_CROMWELL = 30
+
+# Global constants for CloudOS CLI
+CLOUDOS_URL = 'https://cloudos.lifebit.ai'
+INIT_PROFILE = 'initialisingProfile'
+
+# Job status symbol mapping
+JOB_STATUS_SYMBOLS = {
+    "completed": "[bold green]✓[/bold green]",
+    "running": "[bold bright_black]◐[/bold bright_black]",
+    "failed": "[bold red]✗[/bold red]",
+    "aborted": "[bold orange3]■[/bold orange3]",
+    "aborting": "[bold orange3]⊡[/bold orange3]",
+    "initialising": "[bold bright_black]○[/bold bright_black]",
+    "scheduled": "[bold cyan]◷[/bold cyan]",
+    "n/a": "[bold bright_black]?[/bold bright_black]"
+}
+
+# Column priority groups for responsive table display
+COLUMN_PRIORITY_GROUPS = {
+    'minimal': ['status', 'id', 'name'],
+    'essential': ['status', 'id', 'name', 'pipeline'],
+    'important': ['project', 'owner', 'run_time', 'cost'],
+    'useful': ['submit_time', 'end_time', 'commit'],
+    'extended': ['resources', 'storage_type']
+}
+
+# Essential columns priority order for auto-selection
+ESSENTIAL_COLUMN_PRIORITY = ['status', 'id', 'name', 'pipeline']
+
+# Additional columns priority order for auto-selection
+ADDITIONAL_COLUMN_PRIORITY = [
+    'project', 'owner', 'run_time', 'cost',
+    'submit_time', 'end_time', 'commit', 'resources', 'storage_type'
+]
+
+# Column configurations for job list table
+COLUMN_CONFIGS = {
+    'status': {"header": "Status", "style": "cyan", "no_wrap": True, "min_width": 6, "max_width": 6},
+    'name': {"header": "Name", "style": "green", "overflow": "fold", "no_wrap": False, "min_width": 6, "max_width": 14},
+    'project': {"header": "Project", "style": "magenta", "overflow": "fold", "no_wrap": False, "min_width": 6, "max_width": 18},
+    'owner': {"header": "Owner", "style": "blue", "overflow": "fold", "no_wrap": False, "min_width": 4, "max_width": 14},
+    'pipeline': {"header": "Pipeline", "style": "yellow", "overflow": "fold", "no_wrap": False, "min_width": 8, "max_width": 14},
+    'id': {"header": "ID", "style": "white", "overflow": "ellipsis", "no_wrap": True, "min_width": 24, "max_width": 24},
+    'submit_time': {"header": "Submit", "style": "cyan", "no_wrap": True, "min_width": 12, "max_width": 16},
+    'end_time': {"header": "End", "style": "cyan", "no_wrap": True, "min_width": 12, "max_width": 16},
+    'run_time': {"header": "Runtime", "style": "green", "no_wrap": True, "min_width": 8, "max_width": 12},
+    'commit': {"header": "Commit", "style": "magenta", "no_wrap": True, "min_width": 9, "max_width": 10},
+    'cost': {"header": "Cost", "style": "yellow", "no_wrap": True, "min_width": 8, "max_width": 12},
+    'resources': {"header": "Resources", "style": "blue", "overflow": "ellipsis", "no_wrap": True, "min_width": 8, "max_width": 16},
+    'storage_type': {"header": "Storage", "style": "white", "no_wrap": True, "min_width": 8, "max_width": 10}
+}

{cloudos_cli-2.88.2 → cloudos_cli-2.89.1}/cloudos_cli/jobs/cli.py

@@ -119,15 +119,6 @@ def job():
               help='The disk space of the master node instance, in GB. Default=500.',
               type=int,
               default=500)
-@click.option('--storage-mode',
-              help=('Either \'lustre\' or \'regular\'. Indicates if the user wants to select ' +
-                    'regular or lustre storage. Default=regular.'),
-              default='regular')
-@click.option('--lustre-size',
-              help=('The lustre storage to be used when --storage-mode=lustre, in GB. It should ' +
-                    'be 1200 or a multiple of it. Default=1200.'),
-              type=int,
-              default=1200)
 @click.option('--wait-completion',
               help=('Whether to wait to job completion and report final ' +
                     'job status.'),
@@ -219,8 +210,6 @@ def run(ctx,
         nextflow_version,
         instance_type,
         instance_disk,
-        storage_mode,
-        lustre_size,
         wait_completion,
         wait_time,
         wdl_mainfile,
@@ -267,11 +256,9 @@ def run(ctx,
               '\t--job-queue\n' +
               '\t--resumable | --do-not-save-logs\n' +
               '\t--instance-type | --instance-disk | --cost-limit\n' +
-              '\t--storage-mode | --lustre-size\n' +
               '\t--wdl-mainfile | --wdl-importsfile | --cromwell-token\n')
         wdl_mainfile = None
         wdl_importsfile = None
-        storage_mode = 'regular'
         save_logs = False
     if accelerate_file_staging:
         if execution_platform != 'aws':
@@ -377,7 +364,7 @@ def run(ctx,
                                 'Docker account to CloudOS before using ' +
                                 '--use-private-docker-repository option.')
             print('Use private Docker repository has been selected. A custom job ' +
-                  'queue to support private Docker containers and/or Lustre FSx will be created for ' +
+                  'queue to support private Docker containers will be created for ' +
                   'your job. The selected job queue will serve as a template.')
             docker_login = True
     else:
@@ -402,8 +389,6 @@ def run(ctx,
                       nextflow_version=nextflow_version,
                       instance_type=instance_type,
                       instance_disk=instance_disk,
-                      storage_mode=storage_mode,
-                      lustre_size=lustre_size,
                       execution_platform=execution_platform,
                       hpc_id=hpc_id,
                       workflow_type=workflow_type,

{cloudos_cli-2.88.2 → cloudos_cli-2.89.1}/cloudos_cli/jobs/job.py

@@ -309,8 +309,6 @@ class Job(Cloudos):
                                  nextflow_version,
                                  instance_type,
                                  instance_disk,
-                                 storage_mode,
-                                 lustre_size,
                                  execution_platform,
                                  hpc_id,
                                  workflow_type,
@@ -381,12 +379,6 @@ class Job(Cloudos):
             Name of the instance type to be used for the job master node, for example for AWS EC2 c5.xlarge
         instance_disk : int
             The disk space of the master node instance, in GB.
-        storage_mode : string
-            Either 'lustre' or 'regular'. Indicates if the user wants to select regular
-            or lustre storage.
-        lustre_size : int
-            The lustre storage to be used when --storage-mode=lustre, in GB. It should be 1200 or
-            a multiple of it.
         execution_platform : string ['aws'|'azure'|'hpc']
             The execution platform implemented in your CloudOS.
         hpc_id : string
@@ -511,15 +503,6 @@ class Job(Cloudos):
         if len(example_parameters) > 0:
             for example_param in example_parameters:
                 workflow_params.append(example_param)
-        if storage_mode == "lustre":
-            click.secho('\nLustre storage has been selected. Please, be sure that this kind of ' +
-                  'storage is available in your CloudOS workspace.\n', fg='yellow', bold=True)
-            if lustre_size % 1200:
-                raise ValueError('Please, specify a lustre storage size of 1200 or a multiple of it. ' +
-                                 f'{lustre_size} is not a valid number.')
-        if storage_mode not in ['lustre', 'regular']:
-            raise ValueError('Please, use either \'lustre\' or \'regular\' for --storage-mode ' +
-                             f'{storage_mode} is not allowed')
         params = {
             "parameters": workflow_params,
             "project": project_id,
@@ -534,8 +517,6 @@ class Job(Cloudos):
                 "computeCostLimit": cost_limit,
                 "optim": "test"
             },
-            "lusterFsxStorageSizeInGb": lustre_size,
-            "storageMode": storage_mode,
             "instanceType": instance_type,
             "usesFusionFileSystem": use_mountpoints,
             "accelerateSavingResults": accelerate_saving_results
@@ -610,8 +591,6 @@ class Job(Cloudos):
                  nextflow_version='22.10.8',
                  instance_type='c5.xlarge',
                  instance_disk=500,
-                 storage_mode='regular',
-                 lustre_size=1200,
                  execution_platform='aws',
                  hpc_id=None,
                  workflow_type='nextflow',
@@ -676,12 +655,6 @@ class Job(Cloudos):
             Name of the instance type to be used for the job master node, for example for AWS EC2 c5.xlarge
         instance_disk : int
             The disk space of the master node instance, in GB.
-        storage_mode : string
-            Either 'lustre' or 'regular'. Indicates if the user wants to select regular
-            or lustre storage.
-        lustre_size : int
-            The lustre storage to be used when --storage-mode=lustre, in GB. It should be 1200 or
-            a multiple of it.
         execution_platform : string ['aws'|'azure'|'hpc']
             The execution platform implemented in your CloudOS.
         hpc_id : string
@@ -751,8 +724,6 @@ class Job(Cloudos):
                                                nextflow_version,
                                                instance_type,
                                                instance_disk,
-                                               storage_mode,
-                                               lustre_size,
                                                execution_platform,
                                                hpc_id,
                                                workflow_type,