Added pressure parameters for models

Added multiple species convection model pressure parameters. 06/24/2024 ID v.0.5.1

build/lib/cometspy/__init__.py

@@ -0,0 +1,48 @@
+"""
+*a python package for making and running COMETS simulations.*
+
+cometspy is a straight-forward python interface to the COMETS program. 
+Use for dynamic flux-balance analysis, with multiple models, heterogenous 
+spatio-temporal environments, and evolution. 
+
+**To use this package, you must also have the actual COMETS program installed.**
+ 
+* For more information on COMETS, see https://runcomets.org
+
+* For COMETS development, see https://github.com/segrelab/comets
+
+* For development of this package, see http://github.com/segrelab/cometspy
+
+**cometspy workflow:**
+
+models -> layout, layout + params -> comets, comets.run()
+
+**cometspy hello.world**
+
+>>> import cobra.test
+>>> import cometspy as c
+>>> # make a model from a cobra model, open exchange reactions, and give a pop
+>>> tb = cobra.test.create_test_model("textbook")
+>>> m = c.model(tb)
+>>> m.initial_pop = [0, 0, 1.e-4]
+>>> m.open_exchanges()
+>>> # make a layout with the model, and give it three nutrients
+>>> l = c.layout([m])
+>>> l.set_specific_metabolite("glc__D_e", 0.01)
+>>> l.set_specific_metabolite("nh4_e", 1000, static = True)
+>>> l.set_specific_metabolite("pi_e", 1000, static = True)
+>>> # make params and change one default
+>>> p = c.params()
+>>> p.set_param("maxCycles", 100)
+>>> # make a simulation and run it!
+>>> sim = c.comets(l, p)
+>>> sim.run()
+>>> print(sim.total_biomass)
+>>> # saved data objects are pandas.DataFrames, and therefore can be plotted
+>>> # sim.total_biomass.plot(x = "cycle")
+
+"""
+from cometspy.comets import comets
+from cometspy.model import model
+from cometspy.layout import layout
+from cometspy.params import params