Bump version: 0.7.0 → 0.8.0

cobra/__init__.py

@@ -13,7 +13,7 @@
     DictList, Gene, Metabolite, Model, Object, Reaction, Species)
 from cobra.util.version_info import show_versions
 
-__version__ = "0.7.0"
+__version__ = "0.8.0"
 
 # set the warning format to be prettier and fit on one line
 _cobra_path = _dirname(_abspath(__file__))

release-notes/0.8.0.md

@@ -0,0 +1,27 @@
+# Release notes for cobrapy 0.8.0
+
+## Fixes
+
+- Tests no longer generates warnings about using deprecated functions.
+- Gapfilling integrality thresholds now supported for all optlang solvers.
+
+## New features
+
+- `Model.slim_optimize()` can be used perform optimization without
+  creating a solution. Can lead to significant speedup compared to
+  `Model.optimize` when repeatedly doing optimizations and only making
+  use of the objective value as avoiding the need to fetch all values
+  from the solver object.
+- solution, model, metabolite and reaction now have html
+  representation so they give more informative prints in jupyter
+  notebooks.
+- New convenience functions `cobra.flux_analysis.find_essential_genes` and
+  `cobra.flux_analysis.find_essential_reactions`.
+- `Model.optimize` has new parameter `raise_error` to enable option to
+  get trigger exception if no feasible solution could be found.
+- `str(reaction)` now gives the more useful reaction id and the
+  reaction string.
+
+## Deprecated features
+
+- `str(reaction)` no longer gives `reaction.id`.

release-notes/next-release.md

@@ -4,21 +4,4 @@
 
 ## New features
 
-- `Model.slim_optimize()` can be used perform optimization without
-  creating a solution. Can lead to significant speedup compared to
-  `Model.optimize` when repeatedly doing optimizations and only making
-  use of the objective value as avoiding the need to fetch all values
-  from the solver object.
-- solution, model, metabolite and reaction now have html
-  representation so they give more informative prints in jupyter
-  notebooks.
-- New convenience functions `cobra.flux_analysis.find_essential_genes` and
-  `cobra.flux_analysis.find_essential_reactions`.
-- `Model.optimize` has new parameter `raise_error` to enable option to
-  get trigger exception if no feasible solution could be found.
-- `str(reaction)` now gives the more useful reaction id and the
-  reaction string.
-
 ## Deprecated features
-
-- `str(reaction)` no longer gives `reaction.id`.

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.7.0
+current_version = 0.8.0
 commit = True
 tag = True
 parse = (?P<major>\d+)

setup.py

@@ -144,7 +144,7 @@ def build_extension(self, ext):
 
 setup(
     name="cobra",
-    version="0.7.0",
+    version="0.8.0",
     packages=find_packages(),
     setup_requires=setup_requirements,
     install_requires=["future", "swiglpk", "optlang>=1.2.1",