dependency updates

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}
@@ -15,15 +15,15 @@ tag_name = {new_version}
 name = sbmlsim
 url = https://github.com/matthiaskoenig/sbmlsim
 download_url = https://pypi.org/project/sbmlsim
-project_urls = 
+project_urls =
 	Source Code = https://github.com/matthiaskoenig/sbmlsim
 	Documentation = https://sbmlsim.readthedocs.io
 	Bug Tracker = https://github.com/matthiaskoenig/sbmlsim/issues
 author = Matthias Koenig
 author_email = konigmatt@googlemail.com
 maintainer = Matthias Koenig
 maintainer_email = konigmatt@googlemail.com
-classifiers = 
+classifiers =
 	Development Status :: 4 - Beta
 	Intended Audience :: Science/Research
 	License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
@@ -37,78 +37,82 @@ license = LGPL-3.0
 description = sbmlsim are utilities for simulation of SBML.
 long_description = file: README.rst
 long_description_content_type = text/x-rst
-keywords = 
+keywords =
 	modeling
 	standardization
 	SBML
 
 [options]
 zip_safe = True
 python_requires = >=3.7
-install_requires = 
-	sbmlutils>=0.4.12
-	numpy>=1.19.3
+install_requires =
+	sbmlutils>=0.5.1
+	numpy>=1.21
 	depinfo>=0.1.7
-	scipy>=1.6.0
-	sympy>=1.7.1
-	pandas>=1.2.1
+	scipy>=1.7
+	sympy>=1.7
+	pandas>=1.3
+    pint>=0.17
+    Jinja2>=3.0
+    ray>=1.6.0
+    xarray>=0.19
+
 	tables>=3.6.1
-	xarray>=0.18.2
 	bottleneck>=1.3.2
-	pint>=0.16.1
-	Jinja2>=2.11.2
-
+
 	python-libsbml-experimental>=5.19.0
+    libroadrunner-experimental>=2.0.10
 	python-libsedml>=2.0.23
 	python-libcombine>=0.2.13
 	python-libnuml>=1.1.3
-
-	libroadrunner-experimental>=2.0.10
-
+
 	psutil>=5.6.3
 	setproctitle>=1.1.10
-	
-	matplotlib>=3.3.3
+
+	matplotlib>=3.4
 	plotly>=4.12.0
 	altair>=4.1.0
 	altair_viewer
-	seaborn>=0.10.1
-	
-	coloredlogs
+	seaborn>=0.11.1
+
+	coloredlogs>=14.0
 	pyDOE>=0.3.8
-
-	Sphinx
-	sphinx_rtd_theme
-	recommonmark
-
-	ray>=1.2.0
-tests_require = 
+
+tests_require =
 	tox
 packages = find:
-package_dir = 
+package_dir =
 	= src
 include_package_data = True
 
 [options.packages.find]
 where = src
 
 [options.extras_require]
-development = 
+development =
 	black
 	bump2version
 	isort
 	tox
 	mypy
 	pytest>=6.1
 	pytest-cov>=2.8.1
+docs =
+	sphinx>=3.4.3
+    recommonmark
+	ipykernel>=5.4.3
+	nbsphinx>=0.8.1
+	sphinx_rtd_theme>=0.5.1
+	pypandoc>=1.5
+	sphinx-autoapi>=1.7.0
 
 [bdist_wheel]
 universal = 1
 
 [bumpversion:part:release]
 optional_value = placeholder
 first_value = placeholder
-values = 
+values =
 	placeholder
 	a