[WIP] Adding the support of python packages to streamline the commit & PR flow

[hrushikesh-s]

Adding the support of pre-commit, flake8, mypy, coverage report, ruff linter and black -- motivation taken from jobflow package developed by Alex Ganose to improve the code quality, consistency, and reliability. The file that takes care of this is .pre-commit-config.yaml

Also, adding the support of pyproject.toml, which is the standard way for managing dependencies in projects with >= Python 3.6. This means that we can safely remove requirements.txt, requirements-dev.txt & setup.py from the repository.

[hrushikesh-s]

@idocx , most of the tests are failing mainly because of the two reasons:

• formatting issues in the code
• missing docstrings

I'm working on fixing them.

[hrushikesh-s]

Added a PR template file in .github folder.
The file resembles the PR template of jobflow python package

[hrushikesh-s]

Add the support of pyright for type checking to pyproject.toml

[hrushikesh-s]

@idocx , the CI is again failing because of the same error. Any idea of to fix it?
Just a side note, I've already pulled in all the changes that you made in #41.

[idocx]

@hrushikesh-s hmmm this is really wired.

[hrushikesh-s]

@idocx, so apparently, even after pulling in your changes, my local branch still hasn't updated itself.
But when I try to pull the master branch, github says that I'm already up to date.
Any idea what could have gone wrong?

[idocx]

@hrushikesh-s It should be this line that causes issues. Change it to

from .devices.furnace import Furnace so that it will not run add_device twice

[hrushikesh-s]

@idocx, most of the tests are failing. The following is a short summary of the failed tests:

=================================================== short test summary info ====================================================
FAILED tests/test_device_manager.py::TestDeviceManager::test_rpc - pika.exceptions.AMQPConnectionError
FAILED tests/test_device_view.py::TestDeviceView::test_occupied_device_twice - AttributeError: 'DeviceView' object has no attribute 'logger'
FAILED tests/test_device_view.py::TestDeviceView::test_occupy_device - AttributeError: 'DeviceView' object has no attribute 'logger'
FAILED tests/test_device_view.py::TestDeviceView::test_release_device - TypeError: DeviceView.release_device() got an unexpected keyword argument 'device'
FAILED tests/test_device_view.py::TestDeviceView::test_request_device_timeout - ValueError: No such device of name RobotArm
FAILED tests/test_device_view.py::TestDeviceView::test_request_device_twice - AttributeError: 'DeviceView' object has no attribute 'logger'
FAILED tests/test_device_view.py::TestDeviceView::test_request_devices_single - ValueError: No such device of name RobotArm
FAILED tests/test_experiment_manager.py::TestExperimentManager::test_handle_pending_experiments - pydantic.error_wrappers.ValidationError: 6 validation errors for InputExperiment
FAILED tests/test_experiment_manager.py::TestExperimentManager::test_mark_completed_experiments - pydantic.error_wrappers.ValidationError: 6 validation errors for InputExperiment
FAILED tests/test_experiment_view.py::TestExperimentView::test_create_experiment - pydantic.error_wrappers.ValidationError: 4 validation errors for InputExperiment
FAILED tests/test_experiment_view.py::TestExperimentView::test_get_experiment - ValueError: Cannot find an experiment with id: 650b9417c454190288723682
FAILED tests/test_experiment_view.py::TestExperimentView::test_get_experiments_with_status - pydantic.error_wrappers.ValidationError: 4 validation errors for InputExperiment
FAILED tests/test_experiment_view.py::TestExperimentView::test_update_experiment_with_status - pydantic.error_wrappers.ValidationError: 4 validation errors for InputExperiment
FAILED tests/test_experiment_view.py::TestExperimentView::test_update_sample_task_id - pydantic.error_wrappers.ValidationError: 4 validation errors for InputExperiment
FAILED tests/test_lab_view.py::TestLabView::test_request_resources - pika.exceptions.AMQPConnectionError
FAILED tests/test_lab_view.py::TestLabView::test_request_resources_empty - pika.exceptions.AMQPConnectionError
FAILED tests/test_launch.py::TestLaunch::test_submit_experiment - requests.exceptions.ConnectionError: HTTPConnectionPool(host='127.0.0.1', port=8896): Max retries exceeded with url: /api/e...
FAILED tests/test_sample_view.py::TestSampleView::test_create_sample - ValueError: Invalid sample position: furnace_table
FAILED tests/test_sample_view.py::TestSampleView::test_get_sample - ValueError: No sample found with id: 650b9425c454190288723789
FAILED tests/test_sample_view.py::TestSampleView::test_lock_sample_position - ValueError: Invalid sample position: furnace_table
FAILED tests/test_sample_view.py::TestSampleView::test_move_sample - ValueError: Invalid sample position: furnace_table
FAILED tests/test_sample_view.py::TestSampleView::test_request_device_timeout - ValueError: Position prefix `furnace_table` can only have 0 matches, but requests 1
FAILED tests/test_sample_view.py::TestSampleView::test_request_multiple_sample_positions - ValueError: Position prefix `furnace_temp` can only have 0 matches, but requests 1
FAILED tests/test_sample_view.py::TestSampleView::test_request_multiple_sample_positions_multiple_tasks - ValueError: Position prefix `furnace_temp` can only have 0 matches, but requests 2
FAILED tests/test_sample_view.py::TestSampleView::test_request_sample_position_single - ValueError: Position prefix `furnace_table` can only have 0 matches, but requests 1
FAILED tests/test_sample_view.py::TestSampleView::test_request_sample_positions_occupied - ValueError: Invalid sample position: furnace_table
FAILED tests/test_sample_view.py::TestSampleView::test_request_sample_positions_twice - ValueError: Invalid sample position: furnace_table
FAILED tests/test_task_manager.py::TestTaskManager::test_task_request_wrong_format - AttributeError: 'list' object has no attribute 'items'
FAILED tests/test_task_manager.py::TestTaskManager::test_task_request_wrong_number - AttributeError: 'list' object has no attribute 'items'
FAILED tests/test_task_manager.py::TestTaskManager::test_task_requester - AttributeError: 'list' object has no attribute 'items'
========================================== 30 failed, 9 passed, 6 warnings in 46.62s ===========================================

I'm trying to fix them now.

[idocx]

Looks pretty good! Probably we can fix the CI flow in the other PR. 👍