build: major dependencies update

[uniqueg]

Fixes #94
Further fixes additional issues addressed in zavolanlab/zarp#181

Type of change

• Breaking change (fix or feature that would cause existing functionality
  to not work as expected)
• Build update

Checklist

• I have performed a self-review of my own code
• My code follows the existing coding style, lints and generates no new
  warnings
• I have added type annotations to all function/method signatures, and I
  have added type annotations for any local variables that are non-trivial,
  potentially ambiguous or might otherwise benefit from explicit typing.
• I have commented my code in hard-to-understand areas
• I have added Google-style
  docstrings
  to all new modules, classes,
  methods/functions or updated previously existing ones
• I have added tests that prove my fix is effective or that my feature
  works
• New and existing unit tests pass locally with my changes and I have not
  reduced the code coverage relative to the previous state
• I have updated any sections of the app's documentation that are affected
  by the proposed changes

Breaking changes

• Enumerator for dependency embedding strategy requires APPTAINER instead of SINGULARITY

Summary by Sourcery

Update project dependencies, CI workflows, and replace Singularity with Apptainer for container management

New Features:

• Replace Singularity with Apptainer as the container management system

Enhancements:

• Update dependency versions
• Modify Snakemake executor to support Apptainer
• Remove Singularity-specific references in documentation

Build:

• Update Python version support to 3.11
• Update Conda and environment configuration
• Remove root-specific environment files
• Update project classifiers to reflect Python version support

CI:

• Upgrade GitHub Actions workflows to latest versions
• Update Conda setup to use Miniforge
• Add Apptainer installation step in CI workflows
• Modify test and documentation workflow configurations

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request updates the project's dependencies and build configurations. It migrates from Singularity to Apptainer, updates Conda environment configurations, and adjusts CI workflows to use Miniforge. The changes also include updating dependency embedding strategies and supported Python versions.

No diagrams generated as the changes look simple and do not need a visual representation.

File-Level Changes

Change	Details	Files
Updated CI workflow configurations to use Miniforge, Conda, and Apptainer for setting up the environment and running tests.	Replaced conda-incubator/setup-miniconda@v2 with conda-incubator/setup-miniconda@v3 to set up Miniforge. Configured Conda with environment.dev.yml, miniforge-version, conda-remove-defaults, channel-priority, auto-update-conda, and activate-environment. Added a step to install Apptainer using eWaterCycle/setup-apptainer@v2 with a specified version. Removed Python version and Mamba version specifications from the setup. Removed matrix strategy for unit and integration tests. Updated actions/checkout to v4.	.github/workflows/tests.yml .github/workflows/docs.yml
Updated dependency specifications in environment.yml and environment.dev.yml to include specific versions and remove unnecessary channels.	Added bioconda::genomepy >=0.15.0 and bioconda::snakemake >=8 as dependencies. Removed the channels section. Updated python version to >=3.11. Removed types-PyYAML >=6.0.11 and added types-pyyaml >=6.0.11. Removed upper bound for pandas version.	install/environment.dev.yml install/environment.yml
Renamed SINGULARITY to APPTAINER in code and documentation to reflect the change in container technology.	Replaced --use-singularity with --use-apptainer in the Snakemake command compilation. Replaced --singularity-args with --apptainer-args in the Snakemake command compilation. Changed SINGULARITY to APPTAINER in the DependencyEmbeddingStrategies enum. Updated documentation to refer to Apptainer instead of Singularity.	zarp/snakemake/run.py tests/snakemake/test_run.py zarp/config/enums.py docs/includes/references.md docs/guides/initialization.md docs/guides/installation.md tests/config/test_args.py
Removed root environment files.	Deleted environment.dev.root.yml. Deleted environment.root.yml.	install/environment.dev.root.yml install/environment.root.yml
Updated setup.py to reflect changes in supported Python versions.	Removed specific Python versions 3.9 and 3.10 and replaced them with a general Python 3 specification.	setup.py

Assessment against linked issues

Issue	Objective	Addressed	Explanation
#94	Fix the bug where ZARP-cli fails when conda's channel priority is set to strict due to conflicts with biopython versions.	✅

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[sourcery-ai]

Hey @uniqueg - I've reviewed your changes - here's some feedback:

Overall Comments:

• Consider using a dependabot configuration file to automate dependency updates.
• The switch from Singularity to Apptainer is a breaking change that should be communicated clearly to users.

Here's what I looked at during the review

• 🟡 General issues: 2 issues found
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

---

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 100.00%. Comparing base (e9a3887) to head (874bb0d).

Additional details and impacted files

@@            Coverage Diff            @@
##               dev       #97   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           24        24           
  Lines         1263      1263           
=========================================
  Hits          1263      1263           

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