feat: updated simulators

Author: jonrkarr

Dockerfile-assets/Pipfile

@@ -5,45 +5,46 @@ name = "pypi"
 
 [packages]
 ipython = "*"
-biosimulators-utils = {version = ">=0.1.145", extras = ["bngl", "cellml", "escher", "lems", "logging", "neuroml", "sbml", "smoldyn"]}
-numpy = "<1.22" # to avoid pre-release
+biosimulators-utils = {version = ">=0.1.166", extras = ["bngl", "cellml", "escher", "lems", "logging", "neuroml", "sbml", "smoldyn"]}
+numpy = "<1.22.0" # because Assiumulo requires numpy < 1.22
 # AMICI
 amici = "<=0.11.21" # avoid latest version because this requires SymPy >= 1.9 and CBMPy can't handle this because it (a) no version > 1.9 is available and (b) CBMpy can't handle versions of SymPy that don't have microversion numbers
-biosimulators-amici = ">=0.1.21"
+biosimulators-amici = ">=0.1.22"
 # BioNetGen
-biosimulators-bionetgen = ">=0.1.19"
+biosimulators-bionetgen = ">=0.1.20"
 # BoolNet
 biosimulators-boolnet = ">=0.1.18"
 # CBMPy
 sympy = "!=1.8,!=1.9" # avoid versions without microversion numbers because CBMPy can't handle versions with only major and minor numbers
 biosimulators-cbmpy = ">=0.1.14"
 # COBRApy
-biosimulators-cobrapy = ">=0.1.21"
+biosimulators-cobrapy = ">=0.1.23"
 # COPASI
 biosimulators-copasi = ">=0.1.34"
 # GillesPy2
-biosimulators-gillespy2 = ">=0.1.35"
+biosimulators-gillespy2 = ">=0.1.37"
 # GINsim
 biosimulators-ginsim = ">=0.0.9"
 # LibSBMLSim
 biosimulators-libsbmlsim = ">=0.0.6"
 # MASSpy
-biosimulators-masspy = ">=0.0.6"
+biosimulators-masspy = ">=0.0.9"
 # PySCeS
 cython = "<3" # to avoid prelease
-# assimulo = {version = ">=3.2.8", ref = "Assimulo-3.2.8", git = "https://github.com/modelon-community/Assimulo.git"} # commented out because pipenv can't install assimulo; see https://github.com/pypa/pipenv/issues/4768
+# assimulo = {version = ">=3.2.9", ref = "Assimulo-3.2.9", git = "https://github.com/modelon-community/Assimulo.git"} # commented out because pipenv can't install assimulo; see https://github.com/pypa/pipenv/issues/4768
 biosimulators-pysces = ">=0.1.25"
 # pyNeuroML
-biosimulators-pyneuroml = {version = ">=0.0.14", extras = ["brian2", "netpyne", "neuron"]}
+biosimulators-pyneuroml = {version = ">=0.0.16", extras = ["brian2", "netpyne", "neuron"]}
 # RBApy
 rbapy = {version = ">=1.0.2", git = "https://github.com/biosimulators/RBApy.git"}
 biosimulators-rbapy = ">=0.0.4"
 # Smoldyn
 smoldyn = ">=2.67"
 # tellurium
+libroadrunner = "<2.2.0" # 2.2.0 requires numpy >= 1.22, which conflicts with Assimulo
 biosimulators-tellurium = ">=0.1.25"
 # XPP
-biosimulators-xpp = ">=0.0.9"
+biosimulators-xpp = ">=0.0.12"
 
 [dev-packages]
 pyyaml = "*"