chore: prepare release notes for 0.25.0

Author: Midnighter

release-notes/0.25.0.md

@@ -0,0 +1,41 @@
+# 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 `GPR`s that should work. Made `GPR`s 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.
+

release-notes/next-release.md

@@ -2,44 +2,10 @@
 
 ## New features
 
-Added knock_out_model_genes to simulate knock-outs, setting
-reaction bounds of effected 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 metaboilte
-and reaction annotations.
-
 ## Fixes
 
-`model.copy()` will now correctly copy GPRs.
-
-Fixed 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
 
-Moved tests to a different directory, from `src/cobra/test` 
-to `tests`
-
-Added two tests for GPR fixes
-test_gpr_wrong_input()
-test_gpr_that_needs_two_replacements()
-
 ## Deprecated features
 
-Deprecated delete_model_genes, undelete_model_genes.
-
 ## Backwards incompatible changes
-
-removed find_gene_knockout_reactions from delete.py
-
-removed _find_gene_knockout_reactions_fast, 
-_gene_knockout_computation, _get_removed 
-from test_delete.py
-Removed pymatlib direct transfer of models to matlab process. 
-Please use save_matlab_model() and then read the model in matlab.
-