Add environment.yml to fix micromamba CI setup

[Copilot]

The CI workflow was updated to use mamba-org/setup-micromamba@v1 but the required environment.yml was never added, causing an immediate ENOENT failure before any tests could run.

Changes

• environment.yml — new minimal conda environment definition required by setup-micromamba:

  name: demultiplex
  channels:
    - conda-forge
    - defaults
  dependencies:
    - pip

• .github/workflows/main.yml:

  • Replace actions/checkout@v2 + actions/setup-python@v2 + Damona/apptainer/bcl2fastq setup with actions/checkout@v4 + mamba-org/setup-micromamba@v1
  • Drop Python 3.8, add 3.11 to matrix ([3.9, '3.10', '3.11'])
  • Pin pulp==2.7.0 --no-deps to avoid dependency conflicts
  • Add shell: bash -l {0} to steps that need the activated conda environment

• .github/workflows/pypi.yml: bump to actions/checkout@v4, actions/setup-python@v4, Python 3.11