Refactor interface

[jan-janssen]

Summary by CodeRabbit

Release Notes

• New Features

  • Introduced a new Queues class for dynamic queue name retrieval.
  • Added read_config function to read YAML configuration files.
  • New execute_command function for executing shell commands with enhanced error handling.
  • Implemented check_queue_parameters function for validating queue parameters.

• Refactor

  • Updated import paths across multiple files to reflect a restructuring of the codebase.

[coderabbitai]

Caution

Review failed

The pull request is closed.

Walkthrough

The changes introduce a new Queues class for managing queue names, a read_config function for parsing YAML files, and modifications to the check_queue_parameters function for improved validation. Additionally, a new execute_command function is added for executing shell commands with error handling. Import statements across several files are updated to reflect a reorganization of the codebase, moving functionality from the utils module to the base module.

Changes

Files	Change Summary
pysqa/base/config.py	Added Queues class for queue management, modified check_queue_parameters for validation, and added read_config function for YAML parsing.
pysqa/base/core.py	Introduced execute_command function for executing shell commands with error handling.
pysqa/base/validate.py	Added check_queue_parameters function for validating queue parameters.
pysqa/cmd.py	Updated import of execute_command from pysqa.utils.execute to pysqa.base.core.
pysqa/ext/modular.py	Changed imports for QueueAdapterWithConfig and execute_command from pysqa.utils to pysqa.base.
pysqa/ext/remote.py	Updated imports for QueueAdapterWithConfig and execute_command from pysqa.utils to pysqa.base.
pysqa/queueadapter.py	Changed imports for QueueAdapterWithConfig, read_config, and execute_command from pysqa.utils to pysqa.base.
tests/test_basic.py	Updated imports for QueueAdapterWithConfig and value_in_range from pysqa.utils to pysqa.base.
tests/test_execute_command.py	Changed import of execute_command from pysqa.utils.execute to pysqa.base.core.
tests/test_sge.py	Updated import of value_in_range from pysqa.utils.validate to pysqa.base.validate.

Possibly related PRs

• Move validation routines to separate submodule #336: Modifications to the check_queue_parameters function, which is also updated in this PR to use a new utility function for validation.
• Implement default submission template #338: Focuses on introducing a default submission template, with changes to the BasisQueueAdapter class, potentially related to queue management.

Poem

🐰 In the meadow where queues align,
New classes and functions intertwine.
With commands that execute with grace,
YAML configs find their place.
Hops of joy in code we see,
A better world for you and me! 🌼

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