0.25.0

Release notes for cobrapy 0.25.0

New features

• Add knock_out_model_genes to simulate knock-outs, setting
  reaction bounds of affected reactions to zero and returning a list
  of reactions that were knocked-out. Replaces delete_model_genes
  and undelete_model_genes since it is context sensitive.
• Improve reading of matlab models which will include metabolite
  and reaction annotations.

Fixes

• model.copy() will now correctly copy GPRs.
• Fix an error where matlab models can not be read if their bounds exceed the
  configuration default in some cases.
• Fixed some bugs in GPR().from_string() where it was using the unmodified string,
  leading to errors with GPRs that should work. Made GPRs that have empty
  parenthesis fail more comprehensibly.

Other

• Move tests to a different directory, from src/cobra/test to tests (#1191).
• Add two tests for GPR fixes:
  • test_gpr_wrong_input()
  • test_gpr_that_needs_two_replacements()
• Clean up Python syntax (#1152, #1153, #1171, #1173, #1182)

Deprecated features

• Deprecate delete_model_genes, undelete_model_genes

Backwards incompatible changes

• Remove find_gene_knockout_reactions from delete.py
• Remove _find_gene_knockout_reactions_fast,
  _gene_knockout_computation, _get_removed
  from test_delete.py
• Remove pymatlib direct transfer of models to matlab process.
  Please use save_matlab_model() and then read the model in matlab.