Bump version: 0.8.2 → 0.9.0

Author: hredestig

cobra/__init__.py

@@ -13,7 +13,7 @@
     DictList, Gene, Metabolite, Model, Object, Reaction, Species)
 from cobra.util.version_info import show_versions
 
-__version__ = "0.8.2"
+__version__ = "0.9.0"
 
 # set the warning format to be prettier and fit on one line
 _cobra_path = _dirname(_abspath(__file__))

release-notes/0.9.0.md

@@ -0,0 +1,30 @@
+# Release notes for cobrapy 0.9.0
+
+## Fixes
+
+- `Model.compartment` is now a dynamic property fetching the
+  compartments from all metabolites therefore always
+  up-to-date. Assigning a dictionary to the same property updates the
+  internal dictionary of compartment descriptions. This change removes
+  the need for the check for missing compartments from
+  `validation.check_metabolite_compartment_formula`.
+- Excessively long output of html representations in jupyter notebooks are now abbreviated [#577](https://github.com/opencobra/cobrapy/pull/577).
+- Reaction forward and reverse variables are no longer cached with those object. No visible effect but simplifies the code.
+- Fix bug in summary methods when used with exchange reaction sas objective. [#595](https://github.com/opencobra/cobrapy/pull/595).
+
+## New features
+
+- `Model.objective_direction` is a new revertible property to set maximization / minimization using the context manager.
+- Change output of `production_envelope` to wide data frame format [#587](https://github.com/opencobra/cobrapy/pull/587). Also allow multiple carbon source reactions and better handling of zero-division exceptions.
+- Enable summing lists of reactions, see [#596](https://github.com/opencobra/cobrapy/pull/596)
+
+## Deprecated features
+
+- `Model.get_metabolite_compartments` is deprecated (use
+  `Model.compartments` instead).
+- `Reaction.get_compartments` is deprecated (use
+  `Reaction.compartments` instead).
+
+## Backwards incompatible changes
+
+- The format of the dataframe `production_envelope` changed listing max and min on different columns instead of the same.

release-notes/next-release.md

@@ -2,18 +2,8 @@
 
 ## Fixes
 
-- `Model.compartment` is now a dynamic property fetching the
-  compartments from all metabolites therefore always
-  up-to-date. Assigning a dictionary to the same property updates the
-  internal dictionary of compartment descriptions. This change removes
-  the need for the check for missing compartments from
-  `validation.check_metabolite_compartment_formula`.
-
 ## New features
 
 ## Deprecated features
 
-- `Model.get_metabolite_compartments` is deprecated (use
-  `Model.compartments` instead).
-- `Reaction.get_compartments` is deprecated (use
-  `Reaction.compartments` instead).
+## Backwards incompatible changes

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.8.2
+current_version = 0.9.0
 commit = True
 tag = True
 parse = (?P<major>\d+)

setup.py

@@ -144,7 +144,7 @@ def build_extension(self, ext):
 
 setup(
     name="cobra",
-    version="0.8.2",
+    version="0.9.0",
     packages=find_packages(),
     setup_requires=setup_requirements,
     install_requires=["future", "swiglpk", "optlang>=1.2.1",