patch: clean main (#291)

* refactor: move functionality from main file

* test: update imports

* docs: updage changes and version

* refactor: jobs

* refactor: update missing code

* refactor: link

* ci: add run and abort

* ci: adds job resume

* ci: adds configure tests

* ci: adds configure tests + workdir --delete

* ci: remove typo duplicate

* ci: update resume option

* ci: refactor to not have hardcoded jobs

* ci: update job_workdir, job_resume to run before delete_workdir

* ci: add job id dependency

* refactor: remove unsed files

* ci: change dependency for workdir --delete

* ci: update workdir --delete

* ci: update resume

* ci: update resume

* update wait completion

* update resume job id

* ci: update resume output

* review: add debug to all commands

* review: resolve Leila's conversations

* review: add python versions 3.9, 3.11, 3.15 for all the tests

* review: change latest supported python versions 3.13 for all the tests

* review: use exit 1

* review: moved imports at the top

* Update CHANGELOG.md

Co-authored-by: dapineyro <45285897+dapineyro@users.noreply.github.com>

* Update cloudos_cli/_version.py

Co-authored-by: dapineyro <45285897+dapineyro@users.noreply.github.com>

* revert: use python 3.9 only for now in platform tests

* refactor: add missing variable

* ci: update versions

* refactor: add constants in own file

* ci: filter by default queue

* ci: fix intermittent failure

* refactor: remove unused interpolations

* style: remove whitespaces

* style: remove whitespaces

* ci: temporarily disable filter-queue

---------

Co-authored-by: dapineyro <45285897+dapineyro@users.noreply.github.com>

Author: danielboloc

.github/workflows/ci.yml

@@ -1,5 +1,12 @@
 ## lifebit-ai/cloudos-cli: changelog
 
+## v2.79.0 (2026-01-28)
+
+### Patch
+
+- Refactor `__main__.py` to move commands into separate files for better organization
+- Improve CI/CD pipeline to test additional functionalities and use dynamically generated job IDs from tests instead of predefined values
+
 ## v2.78.0 (2026-01-13)
 
 ### Feat

CHANGELOG.md

@@ -1 +1 @@
-__version__ = '2.78.0'
+__version__ = '2.79.0'

cloudos_cli/__main__.py

@@ -0,0 +1 @@
+"""Bash job-related CLI commands."""

cloudos_cli/_version.py

@@ -0,0 +1,49 @@
+"""CLI commands for CloudOS configuration management."""
+
+import rich_click as click
+from cloudos_cli.configure.configure import ConfigurationProfile
+from cloudos_cli.logging.logger import update_command_context_from_click
+from cloudos_cli.utils.cli_helpers import pass_debug_to_subcommands
+
+
+# Create the configure group
+@click.group(cls=pass_debug_to_subcommands(), invoke_without_command=True)
+@click.option('--profile', help='Profile to use from the config file', default='default')
+@click.option('--make-default',
+              is_flag=True,
+              help='Make the profile the default one.')
+@click.pass_context
+def configure(ctx, profile, make_default):
+    """CloudOS configuration."""
+    print(configure.__doc__ + '\n')
+    update_command_context_from_click(ctx)
+    profile = profile or ctx.obj['profile']
+    config_manager = ConfigurationProfile()
+
+    if ctx.invoked_subcommand is None and profile == "default" and not make_default:
+        config_manager.create_profile_from_input(profile_name="default")
+
+    if profile != "default" and not make_default:
+        config_manager.create_profile_from_input(profile_name=profile)
+    if make_default:
+        config_manager.make_default_profile(profile_name=profile)
+
+
+@configure.command('list-profiles')
+def list_profiles():
+    """List all available configuration profiles."""
+    config_manager = ConfigurationProfile()
+    config_manager.list_profiles()
+
+
+@configure.command('remove-profile')
+@click.option('--profile',
+              help='Name of the profile. Not using this option will lead to profile named "deafults" being generated',
+              required=True)
+@click.pass_context
+def remove_profile(ctx, profile):
+    """Remove a configuration profile."""
+    update_command_context_from_click(ctx)
+    profile = profile or ctx.obj['profile']
+    config_manager = ConfigurationProfile()
+    config_manager.remove_profile(profile)

cloudos_cli/bash/__init__.py

@@ -3,6 +3,7 @@
 import configparser
 import click
 from cloudos_cli.logging.logger import update_command_context_from_click
+from cloudos_cli.constants import CLOUDOS_URL, INIT_PROFILE
 
 
 class ConfigurationProfile:
@@ -257,7 +258,7 @@ def create_profile_from_input(self, profile_name):
             config[profile_name]['default'] = str(default_profile)
         if session_id is not None:
             config[profile_name]['session_id'] = session_id
-        
+
 
         with open(self.config_file, 'w') as conf_file:
             config.write(conf_file)
@@ -361,10 +362,10 @@ def make_default_profile(self, profile_name):
 
     def load_profile(self, profile_name):
         """Load a profile from the config and credentials files dynamically.
-        
+
         This method now returns ALL parameters from the profile, not just predefined ones.
         This makes it extensible - you can add new parameters to profiles without modifying this method.
-        
+
         Parameters:
         ----------
         profile_name : str
@@ -374,12 +375,12 @@ def load_profile(self, profile_name):
         dict
             A dictionary containing all profile parameters. Returns all keys from both
             credentials and config files for the specified profile.
-            
+
         Examples
         --------
         # If you add accelerate_saving_results to your profile config:
         config[profile_name]['accelerate_saving_results'] = 'true'
-        
+
         # It will automatically be included in the returned dictionary:
         profile_data = load_profile('myprofile')
         # profile_data will contain 'accelerate_saving_results': 'true'
@@ -399,19 +400,19 @@ def load_profile(self, profile_name):
 
         # Dynamically load all parameters from the profile
         profile_data = {}
-        
+
         # Load all items from credentials file
         if credentials.has_section(profile_name):
             for key, value in credentials[profile_name].items():
                 profile_data[key] = value
-        
+
         # Load all items from config file
         if config.has_section(profile_name):
             for key, value in config[profile_name].items():
                 # Skip the 'default' flag as it's not a user parameter
                 if key != 'default':
                     profile_data[key] = value
-        
+
         return profile_data
 
     def check_if_profile_exists(self, profile_name):
@@ -480,7 +481,7 @@ def get_param_value(ctx, param_value, param_name, default_value, required=False,
     def load_profile_and_validate_data(self, ctx, init_profile, cloudos_url_default, profile, required_dict, **cli_params):
         """
         Load profile data and validate required parameters dynamically.
-        
+
         This method now accepts any parameters via **cli_params, making it extensible.
         You can add new parameters to profiles (like accelerate_saving_results) without
         modifying this method.
@@ -500,7 +501,7 @@ def load_profile_and_validate_data(self, ctx, init_profile, cloudos_url_default,
         **cli_params : dict
             All CLI parameters passed as keyword arguments. Any parameter can be passed here
             and will be resolved from the profile if available.
-            
+
             Examples: apikey, cloudos_url, workspace_id, project_name, workflow_name, 
                      execution_platform, repository_platform, session_id, procurement_id,
                      accelerate_saving_results, etc.
@@ -509,7 +510,7 @@ def load_profile_and_validate_data(self, ctx, init_profile, cloudos_url_default,
         -------
         dict
             A dictionary containing all loaded and validated parameters.
-            
+
         Examples
         --------
         # Add a new parameter to profile without changing this method:
@@ -524,7 +525,7 @@ def load_profile_and_validate_data(self, ctx, init_profile, cloudos_url_default,
         if profile != init_profile:
             # Load profile data
             profile_data = self.load_profile(profile_name=profile)
-            
+
             # Dynamically process all parameters passed in cli_params
             for param_name, cli_value in cli_params.items():
                 profile_value = profile_data.get(param_name, "")
@@ -539,7 +540,7 @@ def load_profile_and_validate_data(self, ctx, init_profile, cloudos_url_default,
                     required=is_required, 
                     missing_required_params=missing
                 )
-                
+
                 # Convert empty strings to None for optional parameters
                 # This prevents issues with functions that expect None for unset values
                 if resolved_value == "" and not is_required:
@@ -592,11 +593,6 @@ def load_profile_and_validate_data(self, ctx, init_profile, cloudos_url_default,
         return resolved_params
 
 
-# Not part of the class, but related to configuration
-# Global constants for CloudOS CLI
-CLOUDOS_URL = 'https://cloudos.lifebit.ai'
-INIT_PROFILE = 'initialisingProfile'
-
 # Define all standard configuration keys with their default empty values
 # This is the single source of truth for configuration fields
 STANDARD_CONFIG_KEYS = {

cloudos_cli/bash/cli.py

@@ -0,0 +1,24 @@
+"""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']
+AZURE_NEXTFLOW_VERSIONS = ['22.11.1-edge']
+HPC_NEXTFLOW_VERSIONS = ['22.10.8']
+AWS_NEXTFLOW_LATEST = '24.04.4'
+AZURE_NEXTFLOW_LATEST = '22.11.1-edge'
+HPC_NEXTFLOW_LATEST = '22.10.8'
+
+# 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'