0.26.0

Release notes for cobrapy 0.26.0

New features

• View number of genes in model notebook representation.
• added support for Python 3.11

Fixes

• serializes GPRs to strings to avoid massive storage usage
• Reformatted example files (e_coli_core.xml, mini_cobra.xml, mini.json, mini.yml, textbook.xml.gz) to be more compliant with identifiers.org.
• ncbigi is not a valid identifiers.org, so it was replaced with ncbiprotein.
• make sbml.py subsystem reading add partonomy, which matches the definition
  of SBO:0000633 (see https://sourceforge.net/p/sbo/term-request/113/)
• Correct reading and writing of subsystem in mat.
• General cleanup of code in mat.py
• fix the pandas deprecation warning in find_external_compartment
• fix an issue where creating a Formula object would give a recursion error

Other

• Resolve flake8 issues and add missing type annotations and docstrings in src/cobra/io and tests/test_io (#1212).
• Updated model.py and test_model.py to Python 3.6+, including type annotations and docstrings.
• Resolve remaining flake8 issues and enable the check in GitHub Actions Lint workflow (#1272).

Deprecated features

• dropped support for Python 3.6

Backwards incompatible changes

• Removed model.add_reaction() and replaced remaining usages of it with model.add_reactions()
• Removed the following tests: test_add_remove_reaction_benchmark, test_add_reaction,
  test_add_reaction_context, test_add_reaction_from_other_model, test_add_cobra_reaction
• Removed model.__add__ and model.__iadd__ - use model.merge to replace them.
• Remove Model().description().
• Remove Model().get_metabolite_compartments().