Upgrade to Snakemake version 9

[fgypas]

Description

Upgrade Snakemake version 9

Fixes #190

Type of change

Please delete options that are not relevant.

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation updated

Conventional Commits guidelines

• I made sure the PR title follows the
  https://www.conventionalcommits.org/en/v1.0.0/

Changes to workflow inputs (sample table and/or configs)

• major (add BREAKING CHANGE: in the beginning of the PR title)
  • more fields/properties are required
  • existing ones are dropped entirely
• minor (add feat: in the beginning of the PR title)
  • optional fields/properties are added
  • required ones are made optional

Changes to workflow outputs

• major (add BREAKING CHANGE: in the beginning of the PR title)
  • changes lead to removal/change of existing outputs (format or location)
• minor (add feat: in the beginning of the PR title)
  • additional outputs are generated
  • content (but not format or location) of existing outputs changes

Everything else: patch
(add any other conventional commit in the beginning of the PR title)

Checklist:

• My code changes follow the style of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing tests pass locally with my changes
• I have updated the project's documentation

Summary by Sourcery

Upgrade Snakemake requirement to version 9.3.3 and standardize core dependencies on the conda-forge channel in both development and production environment files.

Enhancements:

• Bump Snakemake requirement to >=9.3.3 in environment.yml and environment.dev.yml
• Switch biopython, conda, graphviz, pyopenssl, python, and unzip dependencies to conda-forge channel in both environment files

[sourcery-ai]

Reviewer's Guide

The PR upgrades the Snakemake dependency to version 9.3.3 and standardizes all environment YAML dependencies to the conda-forge channel, including adding an explicit conda package in both development and production config files.

File-Level Changes

Change	Details	Files
Bump Snakemake to version >=9.3.3	Updated Snakemake constraint in environment.yml Updated Snakemake constraint in environment.dev.yml	install/environment.yml install/environment.dev.yml
Migrate dependencies to conda-forge channel	Prefixed biopython, graphviz, pyopenssl, python, and unzip with conda-forge Ensured consistent channel usage across both YAMLs	install/environment.yml install/environment.dev.yml
Add explicit conda package	Inserted conda-forge::conda entry into environment.yml Inserted conda-forge::conda entry into environment.dev.yml	install/environment.yml install/environment.dev.yml

Assessment against linked issues

Issue	Objective	Addressed	Explanation
#190	Upgrade the Snakemake version to version 9 or higher.	✅
#190	Update the yaml files to reflect the Snakemake version upgrade.	✅

Possibly linked issues

• feat: upgrade to Snakemake version 9 #190: The PR updates the Snakemake dependency in environment files to version 9.3.3, addressing the issue's request.

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[sourcery-ai]

Hey @fgypas - I've reviewed your changes and they look great!

Prompt for AI Agents

Please address the comments from this code review:
## Individual Comments

### Comment 1
<location> `install/environment.dev.yml:7` </location>
<code_context>
-  - graphviz
-  - unzip
+  - conda-forge::biopython
+  - conda-forge::conda
+  - conda-forge::graphviz
+  - conda-forge::pyopenssl>=23.2.0
</code_context>

<issue_to_address>
Including 'conda' as a dependency may be redundant within a conda environment.

Including 'conda' as a dependency can lead to conflicts since the environment is already managed by conda. Please verify if this is necessary.
</issue_to_address>

<suggested_fix>
<<<<<<< SEARCH
  - conda-forge::conda
=======
>>>>>>> REPLACE

</suggested_fix>

### Comment 2
<location> `install/environment.yml:4` </location>
<code_context>
-  - graphviz
-  - unzip
+  - conda-forge::biopython
+  - conda-forge::conda
+  - conda-forge::graphviz
+  - conda-forge::pyopenssl>=23.2.0
</code_context>

<issue_to_address>
Adding 'conda' to the environment may introduce unnecessary complexity.

Only include the conda CLI if it's strictly needed to avoid potential version or path conflicts.
</issue_to_address>

<suggested_fix>
<<<<<<< SEARCH
  - conda-forge::conda
  - conda-forge::graphviz
=======
  - conda-forge::graphviz
>>>>>>> REPLACE

</suggested_fix>

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[ninsch3000]

Thanks for the version update @fgypas. The zarp conda environment builds successfully, however, running tests with slurm fails as since version 8, Snakemake requires the use of executor plugins for cluster submission. Could you update slurm execution and corresponding docs?

[fgypas]

Hi @ninsch3000 Thank very much for looking into it. I made an update to use the general executor plugin and updated the corresponding profiles. Can you please give it a try in the cluster? Thank you in advance for your help.

[ninsch3000]

Hi @fgypas
Thanks for implementing this.
I ran all the tests for which we have a test.slurm.sh script and they all finished successfully.
As you're using the generic cluster plugin together with our old slurm*.py scripts - instead of using the snakemake slurm plugin - I assume this is because we have a highly customized setup for our HPC. Is that true? Do you assume this is portable to be used on other slurm clusters? Could you otherwise provide some comments on possible limitations in the README.
Thanks a lot again.