Updating package structure

ryansmcgee · Mar 5, 2020 · 812e74d · 812e74d
1 parent 3a168db
commit 812e74d
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Showing 6 changed files with 14 additions and 16 deletions.
diff --git a/dist/pycrobe-0.2.2.tar.gz b/dist/pycrobe-0.2.2.tar.gz
diff --git a/examples/__init__.py b/examples/__init__.py
diff --git a/examples/bla_test.py b/examples/bla_test.py
@@ -1,9 +1,9 @@
 import numpy
 import pandas
 
-from pycrobe.standard import *
-from pycrobe.betalactamase import *
-
+# from pycrobe.standard import *
+# from pycrobe.betalactamase import *
+import pycrobe
 
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -15,13 +15,13 @@
 
 strains 	= {}
 for i, strainName in enumerate(strainNames):
-	strains[strainName] = BlaStrain(name = strainName, 					
+	strains[strainName] = pycrobe.BlaStrain(name = strainName, 					
 									max_growth_rate 					= 2, 
 									max_lysis_rate 						= 1, 				
 									halfmax_lysis_drug_conc 			= 0.125,			# ug/mL <- scMIC for Bla-free strain
 									lysis_hill_coefficient 				= 5,				# ?
 									betalactamase = 
-										BetaLactamase(
+										pycrobe.BetaLactamase(
 											name = "Bla-"+strainName, 
 											decay_rate_intracellular 	= 0, 
 											decay_rate_extracellular 	= 0, 
@@ -51,16 +51,16 @@
 
 
 volume 	= 5.0 # mL 
-culture = Culture(	media=Media(volume=volume, 
-								drugs=[BetaLactam(name="CTX", concentration=0.25)], 
-								nutrient=Nutrient(name="LB", concentration=2e9)),
+culture = pycrobe.Culture(	media=pycrobe.Media(volume=volume, 
+								drugs=[pycrobe.BetaLactam(name="CTX", concentration=0.25)], 
+								nutrient=pycrobe.Nutrient(name="LB", concentration=2e9)),
 				  	inoculums=[
-				  				BlaInoculum(strain=strains[strainName], cell_count=(1e5/len(strains))*volume) for strainName in strains.keys()
+				  				pycrobe.BlaInoculum(strain=strains[strainName], cell_count=(1e5/len(strains))*volume) for strainName in strains.keys()
 				  			  ],
-					dynamics=BetaLactamaseDynamics() )
+					dynamics=pycrobe.BetaLactamaseDynamics() )
 culture.info()
 
-incubator = Incubator(set_temp=37.0, temp_std_batch=0.5, temp_std_location=0.25, temp_std_transient=0.00)
+incubator = pycrobe.Incubator(set_temp=37.0, temp_std_batch=0.5, temp_std_location=0.25, temp_std_transient=0.00)
 
 incubator.incubate(cultures=[culture], time=24, dt=0.01)
 

diff --git a/pycrobe.egg-info/PKG-INFO b/pycrobe.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
 Metadata-Version: 1.1
 Name: pycrobe
-Version: 0.2.1
+Version: 0.2.2
 Summary: A simple package for simulations of microbial growth experiments with realistic sources of error.
 Home-page: https://github.com/ryansmcgee/pycrobe
 Author: Ryan Seamus McGee

diff --git a/pycrobe.egg-info/requires.txt b/pycrobe.egg-info/requires.txt
@@ -1,2 +1,3 @@
 numpy
+scipy
 pandas
diff --git a/setup.py b/setup.py
@@ -10,6 +10,4 @@
 		url='https://github.com/ryansmcgee/pycrobe',
 		download_url='https://github.com/ryansmcgee/pycrobe/archive/v0.2.tar.gz',
 		install_requires=['numpy', 'scipy', 'pandas'],
-
-
-      zip_safe=False)
+		zip_safe=False)
-Original file line number
+Diff line change
@@ -1,2 +1,3 @@
     numpy
+    scipy
     pandas