build: major dependencies update

[uniqueg]

Description

Fixes #180
Fixes #182
Fixes #183
Fixes #184
Fixes #185
Fixes #186
Fixes #187

Conventional Commits guidelines

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

Checklist:

(most are not applicable)

• 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

Migrate project from Singularity to Apptainer, update dependencies, and streamline environment configurations

New Features:

• Standardize workflow profiles to use Apptainer instead of Singularity

Enhancements:

• Update Snakemake configuration to use container instead of Singularity
• Simplify environment configuration and dependency management

Build:

• Consolidate environment files into a single development environment configuration
• Update Conda environment to use latest Snakemake and Python versions
• Remove separate root and development environment files

CI:

• Migrate CI workflows from Ubuntu 20.04 to latest Ubuntu
• Update GitHub Actions to use Miniforge and latest Conda setup
• Replace Singularity with Apptainer in test and deployment workflows

Chores:

• Remove unused environment and configuration files
• Update project documentation and configuration references

[uniqueg]

@sourcery-ai summary

[uniqueg]

@sourcery-ai review

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request migrates the project from Singularity to Apptainer, updates major dependencies including Snakemake and Python, and streamlines environment configurations by consolidating Conda environments and updating CI workflows to use the latest Ubuntu version and Miniforge. It also updates the default samples file path and removes obsolete files.

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

File-Level Changes

Change	Details	Files
Migrated from Singularity to Apptainer by replacing Singularity directives with Apptainer and updating related configurations.	Replaced use-singularity with use-apptainer in profile configurations. Replaced singularity-args with apptainer-args in profile configurations. Replaced singularity directives with container in Snakemake rules. Updated test scripts to use Apptainer instead of Singularity. Updated CI workflows to install and use Apptainer.	.github/workflows/ci.yml profiles/local-apptainer/config.yaml profiles/slurm-apptainer/config.yaml workflow/rules/htsinfer.smk workflow/rules/sra_download.smk workflow/rules/sra_paired_end.smk workflow/rules/sra_single_end.smk tests/test_format/test_snakemake_lint.sh tests/test_integration_workflow/test.local.sh tests/test_htsinfer_with_apptainer/test.local.sh tests/test_integration_workflow/test.slurm.sh tests/test_integration_workflow/test.temp.flag.sh tests/test_integration_workflow_multiple_lanes/test.local.sh tests/test_integration_workflow_multiple_lanes/test.slurm.sh tests/test_sra_download_with_apptainer/test.local.sh tests/test_sra_download_with_apptainer/test.slurm.sh
Consolidated and updated Conda environment configurations.	Consolidated environment.yml, environment.root.yml, and environment.dev.yml into a single environment.dev.yml. Updated Conda environment to use the latest Snakemake and Python versions. Removed separate root and development environment files. Updated CI workflows to use Miniforge and the latest Conda setup.	.github/workflows/ci.yml .github/workflows/docs.yml install/environment.dev.yml install/environment.yml workflow/envs/htsinfer.yaml workflow/envs/samtools.yaml
Updated CI workflows to use the latest Ubuntu version and Miniforge.	Migrated CI workflows from Ubuntu 20.04 to the latest Ubuntu version. Updated GitHub Actions to use Miniforge for Conda environment setup. Removed redundant environment updates in CI workflows.	.github/workflows/ci.yml .github/workflows/docs.yml
Updated default samples file path.	Changed the default samples file path in config.yaml to tests/input_files/samples.tsv.	config/config.yaml
Removed obsolete files.	Removed images/rule_graph.svg. Removed install/environment.root.yml.	images/rule_graph.svg install/environment.root.yml

Assessment against linked issues

Issue	Objective	Addressed	Explanation
#180	Fix the conda environment and dependency issues that are causing the build and CI workflows to fail.	✅
#180	Update CI workflows to use the latest Ubuntu and Conda setup.	✅
#180	Migrate from Singularity to Apptainer in the workflows.	✅
#182	Upgrade Ubuntu images used in CI workflows to a supported version.	✅
#183	Replace Singularity with Apptainer in the ZARP pipeline.	✅
#183	Update ZARP to use a recent version of containerization software.	✅
#184	Upgrade ZARP to support and require Snakemake >=8.	✅
#185	Remove the pinned Python version from the CI workflows.	✅
#185	Upgrade the Snakemake dependency in install/environment.yml to use at least Python 3.11.	✅
#186	Remove Conda installation of Singularity/Apptainer.	✅
#186	Use dedicated GitHub Action to set up Apptainer.	✅
#186	Resolve the permission errors when using Singularity/Apptainer in CI.	✅
#187	Avoid upgrading or downgrading base dependencies when installing development dependencies.	✅
#187	Instead of listing only the additional development dependencies in install/environment.dev.yml, also specify the base dependencies from install/environment.dev.yml in that file.	✅

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[sourcery-ai]

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

Overall Comments:

• Consider using ubuntu-latest instead of ubuntu-20.04 for the runner image to get the latest features and security updates.
• The CI workflows now have duplicated blocks for setting up conda - consider creating a reusable workflow.

Here's what I looked at during the review

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

---

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[uniqueg]

@sourcery-ai review

[sourcery-ai]

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

Overall Comments:

• Consider using conda env export to generate environment files to ensure reproducibility.
• The CI workflows now use ubuntu-latest, ensure that this change does not introduce unexpected behavior due to differences in the environment.

Here's what I looked at during the review

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

---

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• X
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• Facebook

_{Help me be more useful! Please click 👍 or 👎 on each comment and I'll use the feedback to improve your reviews.}

[uniqueg]

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