Update supported Python versions (#1293)

* remove python 3.6 and add 3.11

* pin benchmark

* fix version pin

Author: cdiener

.github/workflows/main.yml

@@ -20,7 +20,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
     timeout-minutes: 360
 
     steps:

.github/workflows/safety.yml

@@ -16,7 +16,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
     timeout-minutes: 120
 
     steps:

release-notes/next-release.md

@@ -3,6 +3,7 @@
 ## New features
 
 * View number of genes in model notebook representation.
+* added support for Python 3.11
 
 ## Fixes
 
@@ -23,6 +24,8 @@
 
 ## 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,

setup.cfg

@@ -6,7 +6,7 @@ parse = (?P<major>\d+)
 	\.(?P<minor>\d+)
 	\.(?P<patch>\d+)
 	(?P<release>[a]*)(?P<num>\d*)
-serialize = 
+serialize =
 	{major}.{minor}.{patch}{release}{num}
 	{major}.{minor}.{patch}
 tag_name = {new_version}
@@ -15,33 +15,33 @@ tag_name = {new_version}
 name = cobra
 url = https://opencobra.github.io/cobrapy
 download_url = https://pypi.org/project/cobra
-project_urls = 
+project_urls =
 	Source Code = https://github.com/opencobra/cobrapy
 	Documentation = https://cobrapy.readthedocs.io
 	Bug Tracker = https://github.com/opencobra/cobrapy/issues
 author = The cobrapy core development team.
 author_email = [email protected]
 maintainer = Moritz E. Beber
 maintainer_email = [email protected]
-classifiers = 
+classifiers =
 	Development Status :: 5 - Production/Stable
 	Intended Audience :: Science/Research
 	License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)
 	License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+)
 	Natural Language :: English
 	Operating System :: OS Independent
-	Programming Language :: Python :: 3.6
 	Programming Language :: Python :: 3.7
 	Programming Language :: Python :: 3.8
 	Programming Language :: Python :: 3.9
 	Programming Language :: Python :: 3.10
+	Programming Language :: Python :: 3.11
 	Programming Language :: Python :: Implementation :: CPython
 	Topic :: Scientific/Engineering :: Bio-Informatics
 license = LGPL-2.0-or-later OR GPL-2.0-or-later
 description = COBRApy is a package for constraint-based modeling of metabolic networks.
 long_description = file: README.rst, INSTALL.rst
 long_description_content_type = text/x-rst
-keywords = 
+keywords =
 	metabolism
 	biology
 	constraint-based
@@ -53,7 +53,7 @@ keywords =
 
 [options]
 zip_safe = True
-install_requires = 
+install_requires =
 	appdirs ~=1.4
 	depinfo ~=1.7
 	diskcache ~=5.0
@@ -68,24 +68,24 @@ install_requires =
 	rich >=8.0
 	ruamel.yaml ~=0.16
 	swiglpk
-tests_require = 
+tests_require =
 	tox
 packages = find:
-package_dir = 
+package_dir =
 	= src
 
 [options.packages.find]
 where = src
 
 [options.package_data]
-cobra = 
+cobra =
 	data/*
 	io/*.json
 
 [options.extras_require]
-array = 
+array =
 	scipy
-development = 
+development =
 	black
 	bumpversion
 	isort
@@ -97,7 +97,7 @@ universal = 1
 [bumpversion:part:release]
 optional_value = placeholder
 first_value = placeholder
-values = 
+values =
 	placeholder
 	a
 

tox.ini

@@ -1,13 +1,14 @@
 [tox]
-envlist = isort, black, flake8, safety, py3{6,7,8,9,10}, coverage
+envlist = isort, black, flake8, safety, py3{7,8,9,10,11}, coverage
 
 [gh-actions]
 python =
     3.6: install, py36
     3.7: install, py37
     3.8: install, py38
-    3.9: install, py39, coverage
-    3.10: install, py310
+    3.9: install, py39
+    3.10: install, py310, coverage
+    3.11: install, py311
 
 [testenv]
 extras =
@@ -16,7 +17,7 @@ deps=
     jsonschema
     osqp~=0.6 ; python_version < "3.10"
     pytest
-    pytest-benchmark
+    pytest-benchmark~=4.0
     pytest-mock
     pytest-raises
 commands =
@@ -30,7 +31,7 @@ deps=
     jsonschema
     osqp~=0.6 ; python_version < "3.10"
     pytest
-    pytest-benchmark
+    pytest-benchmark~=4.0
     pytest-cov
     pytest-mock
     pytest-raises