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0.25.0
by The COBRApy Team
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. Replacesdelete_model_genes
andundelete_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 withGPR
s that should work. MadeGPR
s that have empty parenthesis fail more comprehensibly.
Other
- Move tests to a different directory, from
src/cobra/test
totests
(#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
fromdelete.py
- Remove
_find_gene_knockout_reactions_fast
,_gene_knockout_computation
,_get_removed
fromtest_delete.py
- Remove
pymatlib
direct transfer of models to matlab process. Please usesave_matlab_model()
and then read the model in matlab.