Added functionality for pressure model for the species. 06/26/2024

This completes the built of multiple species convection model functionality.

build/lib/cometspy/comets.py

@@ -21,9 +21,9 @@
 __copyright__ = "Copyright 2024, The COMETS Consortium"
 __credits__ = ["Djordje Bajic", "Jean Vila", "Jeremy Chacon", "Ilija Dukovski"]
 __license__ = "MIT"
-__version__ = "0.5.0"
-__comets_compatibility__ = "2.12.0" # version of comets this was tested with (except signaling)
-__comets_compatibility_signaling__ = "2.12.0" # version signaling was tested with
+__version__ = "0.5.1"
+__comets_compatibility__ = "2.12.2" # version of comets this was tested with (except signaling)
+__comets_compatibility_signaling__ = "2.12.2" # version signaling was tested with
 
 __maintainer__ = "Djordje Bajic"
 __email__ = "[email protected]"

build/lib/cometspy/model.py

@@ -117,6 +117,10 @@ def __init__(self, model : cobra.Model = None, randomtag : bool = False):
         self.optimizer = 'GUROBI'
         self.obj_style = 'MAXIMIZE_OBJECTIVE_FLUX'
 
+        self.multispecies_convmodel_flag = False
+
+
+
         if model is not None:
             if isinstance(model, cobra.Model):
                 self.load_cobra_model(model, randomtag)
@@ -339,6 +343,21 @@ def add_convection_parameters(self, packedDensity : float =1.,
                                       'elasticModulus': elasticModulus,
                                       'frictionConstant': frictionConstant,
                                       'convDiffConstant': convDiffConstant}
+
+    def add_multspecies_convmodel_parameters(self, pressureKappa : float, pressureExponent : float, packBiomass : float, maxPressure : float):
+        if not isinstance(pressureKappa, float):
+            raise ValueError('pressureKappa must be a float')
+        if not isinstance(pressureExponent, float):
+            raise ValueError('pressureExponent must be a float')
+        if not isinstance(packBiomass, float):
+            raise ValueError('packBiomass must be a float')
+        if not isinstance(maxPressure, float):
+            raise ValueError('maxPressure must be a float')
+        self.multispecies_convmodel_flag = True
+        self.multimodel_parameters = {'pressureKappa': pressureKappa,
+                                      'pressureExponent': pressureExponent,
+                                      'packBiomass': packBiomass,
+                                      'maxPressure': maxPressure}
 
     def add_noise_variance_parameter(self, noiseVariance : float):
         """ sets the noise variance parameter 
@@ -1074,6 +1093,11 @@ def write_comets_model(self, working_dir : str = None):
                 for key, value in self.convection_parameters.items():
                     f.write(key + ' ' + str(value) + '\n')
                     f.write(r'//' + '\n')
+
+            if self.multispecies_convmodel_flag:
+                for key, value in self.multimodel_parameters.items():
+                    f.write(key + ' ' + str(value) + '\n')
+                    f.write(r'//' + '\n')
 
             if self.nonlinear_diffusion_flag:
                 for key, value in self.nonlinear_diffusion_parameters.items():

cometspy.egg-info/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.1
 Name: cometspy
-Version: 0.5.0
+Version: 0.5.1
 Summary: The Python interface to COMETS
 Home-page: https://github.com/segrelab/cometspy
-Download-URL: https://github.com/segrelab/cometspy/archive/v0.5.0.tar.gz
+Download-URL: https://github.com/segrelab/cometspy/archive/v0.5.1.tar.gz
 Author: The COMETSPy Core Team
 Author-email: [email protected]
 License: GPL

setup.py

@@ -4,13 +4,13 @@
 setup(
     name='cometspy',
     packages=['cometspy'],
-    version='0.5.0',
+    version='0.5.1',
     license='GPL',
     description='The Python interface to COMETS',
     author='The COMETSPy Core Team',
     author_email='[email protected]',
     url='https://github.com/segrelab/cometspy',
-    download_url='https://github.com/segrelab/cometspy/archive/v0.5.0.tar.gz',  # New releases here!! 
+    download_url='https://github.com/segrelab/cometspy/archive/v0.5.1.tar.gz',  # New releases here!! 
     keywords=['metabolism', 'dynamic', 'flux', 'balance', 'analysis', 'spatial', 'evolution'],
     install_requires=[
         # I get to this in a second