Deprecate phi_grp_mapping

[ethho]

• Deprecate variable phi_grp_mapping with axes phi_grp1 and phi_grp2
• These are axes that are flattened combinations of the following axes:
  • vertex
  • age_group
  • risk_group
• Generated by InitPhiGrpMapping: https://github.com/eho-tacc/episimlab/blob/4e846e2b390cb47fcbe46a9ac073599b6ee977e3/episimlab/setup/phi.py#L12
• Consumed by FOI calculators (processes that also consume phi and phi_t): https://github.com/eho-tacc/episimlab/blob/4e846e2b390cb47fcbe46a9ac073599b6ee977e3/episimlab/foi/brute_force.py#L21
• The original idea was to allow an arbitrary number of dimensions to be encoded in these phi_grp axes
  • e.g. phi represents inter-vertex contacts or no, inter-age_group contacts or no
  • This did not solve the problem, since the encoded axes are still hard-coded when indexing in the consumer process: https://github.com/eho-tacc/episimlab/blob/4e846e2b390cb47fcbe46a9ac073599b6ee977e3/episimlab/foi/brute_force.py#L42

Objective

Deprecate phi_grp_mapping variable. FOI implementations should instead directly index a phi array like:

Coordinates:
  * vertex_i  (vertex_i) <U1 'A' 'B'
  * vertex_j  (vertex_j) <U1 'A' 'B'
  * age_i     (age_i) <U5 'young' 'old'
  * age_j     (age_j) <U5 'young' 'old'

I will apply this change to the following FOI implementations:

• [x] Brute force Python: https://github.com/eho-tacc/episimlab/blob/4e846e2b390cb47fcbe46a9ac073599b6ee977e3/episimlab/foi/brute_force.py#L42
• [x] Brute force Cython: https://github.com/eho-tacc/episimlab/blob/4e846e2b390cb47fcbe46a9ac073599b6ee977e3/episimlab/foi/bf_cython.py#L27
  • [x] ...and the Cython backend at https://github.com/eho-tacc/episimlab/blob/4e846e2b390cb47fcbe46a9ac073599b6ee977e3/episimlab/foi/bf_cython_engine.pyx#L139

[ethho]

Merged to #13