Update the lowest python version to 3.11 to include StrEnum

[samuell]

StrEnum is used in multiple places including tests and alembic scripts and was introduced in Python 3.11 (See https://docs.python.org/3/library/enum.html#enum.StrEnum ).

This currently breaks using the poetry environment if the user accdientally is using a python version lower than 3.11 in poetry, causing errors complaning that StrEnum is not found.

Reproducing the error:

1. Set poetry to use python 3.10:

poetry env use 3.10

2. Check out the cg repository and cd into it:

git clone [email protected]:Clinical-Genomics/cg.git
cd cg

3. Install poetry dependencies:

poetry install

4. Start the poetry shell:

poetry shell

5. Run pytest

pytest

You will now see errors like below:

$ pytest
ImportError while loading conftest '/home/shl/proj/23/01-jasen/cg/tests/conftest.py'.
tests/conftest.py:18: in <module>
    from cg.apps.crunchy import CrunchyAPI
cg/apps/crunchy/__init__.py:3: in <module>
    from .crunchy import CrunchyAPI
cg/apps/crunchy/crunchy.py:12: in <module>
    from cg.apps.crunchy import files
cg/apps/crunchy/files.py:8: in <module>
    from cg.constants.constants import FileFormat
cg/constants/__init__.py:8: in <module>
    from cg.constants.constants import (
cg/constants/constants.py:3: in <module>
    from enum import IntEnum, StrEnum
E   ImportError: cannot import name 'StrEnum' from 'enum' (/home/shl/opt/mc3/lib/python3.10/enum.py)

This is fixed though when doing:

1. Removing the old poetry env (warning, make sure you know what you are doing!):

rm -rf $(dirname $(dirname $(which python)))

2. Setting poetry to use python 3.11

poetry env use 3.11

3. Installing the poetry dependencies anew:

poetry install

4. Starting the poetry shell again

poetry shell

5. Running the pytest

pytest

(Then I get other errors, but at least different ones 🙂 ):

[...]
  File "/home/shl/.pyenv/versions/3.11.8/lib/python3.11/sqlite3/dbapi2.py", line 27, in <module>
    from _sqlite3 import *
ModuleNotFoundError: No module named '_sqlite3'

Description

Changed

• Changed the lowest allowed python version from 3.9 to 3.11 in pyproject.toml

How to prepare for test

• TBC

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This version is a

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

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