Update snakemake to match conda

[AroneyS]

• test_short_read_recovery_fast
• test_short_read_recovery_queue_submission
• test_batch_recovery

[Copilot]

Pull Request Overview

This PR updates the Snakemake integration to align with the conda environment specifications. The key changes are:

• Updating Snakemake import paths to use "snakemake.common.configfile" from previous locations.
• Modifying the command-line argument for Snakemake commands by appending "rules" to the "--snakemake-cmds" parameter.
• Adjusting dependency and Python version requirements in the configuration and CI workflow files.

Reviewed Changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
test/test_recover.py	Updated Snakemake import and modified command-line arguments in recovery tests.
test/test_assemble.py	Modified command-line argument in assembly tests to include "rules".
aviary/modules/processor.py	Updated import path for load_configfile to reflect new Snakemake structure.
aviary.yml	Revised dependency definitions to enforce Python 3.11 and updated Snakemake version along with executor plugins.
.github/workflows/test-aviary.yml	Updated Python version from 3.10 to 3.11 for CI testing.
.github/workflows/python-publish.yml	Updated Python version for publish workflow from 3.10 to 3.11.

Comments suppressed due to low confidence (3)

test/test_recover.py:32

• Verify that appending 'rules' to the '--snakemake-cmds' argument is intentional; if so, consider adding a comment or updating documentation to clarify its effect in dryrun mode.

f"--snakemake-cmds \" --quiet rules\" "

test/test_assemble.py:29

• Ensure that the addition of 'rules' in the '--snakemake-cmds' parameter is consistent with the intended test behavior and update any supporting materials as necessary.

f"--snakemake-cmds \" --quiet rules\" "

aviary/modules/processor.py:43

• Confirm that updating the import for load_configfile to 'snakemake.common.configfile' does not inadvertently affect other parts of the module that may rely on previous import paths.

from snakemake.common.configfile import load_configfile

[AroneyS]

Getting this error: Ecogenomics/CheckM#411
Maybe something updated and broke in the CheckM env

[AroneyS]

From linked issue, its likely due to OOM.