ci: fix flaky Apptainer workflow by replacing Launchpad PPA install

[Copilot]

add-apt-repository ppa:apptainer/ppa intermittently times out on GitHub-hosted runners, causing CI failures unrelated to the actual test code.

Changes

• Install method: Replace PPA-based install with a direct .deb download from Apptainer's GitHub releases (auto-detects latest version), eliminating the Launchpad network dependency
• Cache cleanup: Drop brittle caches of system paths (/usr/bin/apptainer, /usr/lib/apptainer, /etc/apptainer) and unused APT archives cache; retain only ~/.apptainer/cache
• Action version: Bump actions/cache@v3 → actions/cache@v4

# Before
- name: Install Apptainer
  if: steps.cache-apptainer.outputs.cache-hit != 'true'
  run: |
    sudo apt-get install -y software-properties-common
    sudo add-apt-repository -y ppa:apptainer/ppa   # ← flaky network call
    sudo apt-get update && sudo apt-get install -y apptainer

# After
- name: Install Apptainer
  run: |
    APPTAINER_VERSION=$(curl -s https://api.github.com/repos/apptainer/apptainer/releases/latest \
      | grep '"tag_name"' | cut -d'"' -f4 | sed 's/v//')
    wget -q "https://github.com/apptainer/apptainer/releases/download/v${APPTAINER_VERSION}/apptainer_${APPTAINER_VERSION}_amd64.deb"
    sudo apt-get install -y "./apptainer_${APPTAINER_VERSION}_amd64.deb"
    apptainer --version

Mirrors the fix applied in sequana/fastqc#41.

[codacy-production]

Up to standards ✅

🟢 Issues 0 issues

Results:
0 new issues

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[coveralls]

Coverage Report for CI Build 25228012699

Coverage remained the same at 91.667%

Details

• Coverage remained the same as the base build.
• Patch coverage: No coverable lines changed in this PR.
• No coverage regressions found.

Uncovered Changes

No uncovered changes found.

Coverage Regressions

No coverage regressions found.

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Coverage Stats

Relevant Lines:	60
Covered Lines:	55
Line Coverage:	91.67%
Coverage Strength:	1.83 hits per line

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💛 - Coveralls