1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36
|
# 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()`.
|