opencobra/cobrapy: 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()