ci: fix flaky Apptainer workflow by dropping Launchpad PPA

[Copilot]

add-apt-repository ppa:apptainer/ppa intermittently times out on GitHub-hosted runners, causing CI failures unrelated to test code. Mirrors the fix from sequana/fastqc#41.

Changes

• Install: Replace PPA-based install with a direct download of the latest Apptainer .deb from GitHub releases; add apptainer --version to verify
• Cache: Drop brittle system-path caching (/usr/bin/apptainer, /usr/lib/apptainer, /etc/apptainer) and unused APT archives cache; retain only ~/.apptainer/cache; move cache step before install step
• 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
    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

[cokelaer]

@copilot check the original PR from sequana/fastqc. there was an update wrt apptainer installation

[Copilot]

@copilot check the original PR from sequana/fastqc. there was an update wrt apptainer installation

...

Updated in 61fe945. The install now fetches the latest Apptainer .deb directly from GitHub releases (matching sequana/fastqc#41 exactly), rather than using Ubuntu's default apt repos. The cache step is also moved before the install step to align with that reference PR.