Version 0.2.2

charlesrocabert · Jun 15, 2019 · beaba77 · beaba77
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diff --git a/python_metevolsim.egg-info/PKG-INFO → MetEvolSim.egg-info/PKG-INFO b/python_metevolsim.egg-info/PKG-INFO → MetEvolSim.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
-Name: python-metevolsim
-Version: 0.2.1
+Name: MetEvolSim
+Version: 0.2.2
 Summary: MetEvolSim (Metabolome Evolution Simulator) Python Package
 Home-page: https://github.com/charlesrocabert/MetEvolSim
 Author: Charles Rocabert, Gábor Boross, Balázs Papp
@@ -55,7 +55,7 @@ Description: <h1 align="center">MetEvolSim</h1>
 
         &bullet; To install the current release of MetEvolSim:
         ```shell
-        pip install python-metevolsim
+        pip install MetEvolSim
         ```
 
         Alternatively, download the <a href="https://github.com/charlesrocabert/MetEvolSim/releases/latest">latest release</a> in the folder of your choice and unzip it. Then follow the instructions below:
@@ -72,13 +72,13 @@ Description: <h1 align="center">MetEvolSim</h1>
 
         ```python
         # Import metevolsim package
-        import python-metevolsim as metevolsim
+        import MetEvolSim
 
         # Create an objective function
         target_fluxes = [['ATPase', 1.0], ['PDC', 1.0]]
 
         # Load the SBML metabolic model
-        model = metevolsim.Model(sbml_filename='glycolysis.xml', objective_function=target_fluxes, copasi_path='/Applications/COPASI/CopasiSE')
+        model = MetEvolSim.Model(sbml_filename='glycolysis.xml', objective_function=target_fluxes, copasi_path='/Applications/COPASI/CopasiSE')
 
         # Print some informations on the metabolic model
         print(model.get_number_of_species())
@@ -110,7 +110,7 @@ Description: <h1 align="center">MetEvolSim</h1>
 
         ```python
         # Load a Markov Chain Monte Carlo (MCMC) instance
-        mcmc = metevolsim.MCMC(sbml_filename='glycolysis.xml', objective_function=target_fluxes, total_iterations=10000, sigma=0.01, selection_scheme="MUTATION_ACCUMULATION", selection_threshold=1e-4, copasi_path='/Applications/COPASI/CopasiSE')
+        mcmc = MetEvolSim.MCMC(sbml_filename='glycolysis.xml', objective_function=target_fluxes, total_iterations=10000, sigma=0.01, selection_scheme="MUTATION_ACCUMULATION", selection_threshold=1e-4, copasi_path='/Applications/COPASI/CopasiSE')
 
         # Initialize the MCMC instance 
         mcmc.initialize()
@@ -126,7 +126,7 @@ Description: <h1 align="center">MetEvolSim</h1>
         ### Sensitivity analysis:
         ```python
         # Load a sensitivity analysis instance
-        sa = metevolsim.SensitivityAnalysis(sbml_filename='glycolysis.xml', factor_range=1.0, factor_step=0.01, copasi_path='/Applications/COPASI/CopasiSE')
+        sa = MetEvolSim.SensitivityAnalysis(sbml_filename='glycolysis.xml', factor_range=1.0, factor_step=0.01, copasi_path='/Applications/COPASI/CopasiSE')
 
         # Initialize the sensitivity analysis instance 
         sa.initialize()
@@ -140,11 +140,11 @@ Description: <h1 align="center">MetEvolSim</h1>
         ## Help <a name="help"></a>
         To get some help on a MetEvolSim class or method, use the Python help function:
         ```python
-        help(metevolsim.Model.set_species_initial_value)
+        help(MetEvolSim.Model.set_species_initial_value)
         ```
         to obtain a quick description and the list of parameters and outputs:
         ```
-        Help on function set_species_initial_value in module metevolsim:
+        Help on function set_species_initial_value in module MetEvolSim:
 
         set_species_initial_value(self, species_id, value)
             Set the initial concentration of the species 'species_id' in the

diff --git a/python_metevolsim.egg-info/SOURCES.txt → MetEvolSim.egg-info/SOURCES.txt b/python_metevolsim.egg-info/SOURCES.txt → MetEvolSim.egg-info/SOURCES.txt
@@ -3,17 +3,17 @@ MANIFEST.in
 README.md
 setup.cfg
 setup.py
+MetEvolSim.egg-info/PKG-INFO
+MetEvolSim.egg-info/SOURCES.txt
+MetEvolSim.egg-info/dependency_links.txt
+MetEvolSim.egg-info/requires.txt
+MetEvolSim.egg-info/top_level.txt
 example/.DS_Store
 example/models/.DS_Store
 example/models/holzhutter2004.xml
 example/models/holzhutter2004_objective_function.txt
 metevolsim/__init__.py
 metevolsim/metevolsim.py
-python_metevolsim.egg-info/PKG-INFO
-python_metevolsim.egg-info/SOURCES.txt
-python_metevolsim.egg-info/dependency_links.txt
-python_metevolsim.egg-info/requires.txt
-python_metevolsim.egg-info/top_level.txt
 scripts/.DS_Store
 scripts/plot_evolution_rate.R
 scripts/plot_sensitivity_analysis.R

diff --git a/..._metevolsim.egg-info/dependency_links.txt → MetEvolSim.egg-info/dependency_links.txt b/..._metevolsim.egg-info/dependency_links.txt → MetEvolSim.egg-info/dependency_links.txt
diff --git a/python_metevolsim.egg-info/requires.txt → MetEvolSim.egg-info/requires.txt b/python_metevolsim.egg-info/requires.txt → MetEvolSim.egg-info/requires.txt
diff --git a/python_metevolsim.egg-info/top_level.txt → MetEvolSim.egg-info/top_level.txt b/python_metevolsim.egg-info/top_level.txt → MetEvolSim.egg-info/top_level.txt
diff --git a/README.md b/README.md
@@ -46,7 +46,7 @@ pip install numpy python-libsbml
 
 &bullet; To install the current release of MetEvolSim:
 ```shell
-pip install python-metevolsim
+pip install MetEvolSim
 ```
 
 Alternatively, download the <a href="https://github.com/charlesrocabert/MetEvolSim/releases/latest">latest release</a> in the folder of your choice and unzip it. Then follow the instructions below:
@@ -63,13 +63,13 @@ MetEvolSim takes as an input any <a href="http://sbml.org/Main_Page">SBML</a> me
 
 ```python
 # Import metevolsim package
-import python-metevolsim as metevolsim
+import MetEvolSim
 
 # Create an objective function
 target_fluxes = [['ATPase', 1.0], ['PDC', 1.0]]
 
 # Load the SBML metabolic model
-model = metevolsim.Model(sbml_filename='glycolysis.xml', objective_function=target_fluxes, copasi_path='/Applications/COPASI/CopasiSE')
+model = MetEvolSim.Model(sbml_filename='glycolysis.xml', objective_function=target_fluxes, copasi_path='/Applications/COPASI/CopasiSE')
 
 # Print some informations on the metabolic model
 print(model.get_number_of_species())
@@ -101,7 +101,7 @@ Three types of evolution experiments are available:
 
 ```python
 # Load a Markov Chain Monte Carlo (MCMC) instance
-mcmc = metevolsim.MCMC(sbml_filename='glycolysis.xml', objective_function=target_fluxes, total_iterations=10000, sigma=0.01, selection_scheme="MUTATION_ACCUMULATION", selection_threshold=1e-4, copasi_path='/Applications/COPASI/CopasiSE')
+mcmc = MetEvolSim.MCMC(sbml_filename='glycolysis.xml', objective_function=target_fluxes, total_iterations=10000, sigma=0.01, selection_scheme="MUTATION_ACCUMULATION", selection_threshold=1e-4, copasi_path='/Applications/COPASI/CopasiSE')
 
 # Initialize the MCMC instance 
 mcmc.initialize()
@@ -117,7 +117,7 @@ while not stop_MCMC:
 ### Sensitivity analysis:
 ```python
 # Load a sensitivity analysis instance
-sa = metevolsim.SensitivityAnalysis(sbml_filename='glycolysis.xml', factor_range=1.0, factor_step=0.01, copasi_path='/Applications/COPASI/CopasiSE')
+sa = MetEvolSim.SensitivityAnalysis(sbml_filename='glycolysis.xml', factor_range=1.0, factor_step=0.01, copasi_path='/Applications/COPASI/CopasiSE')
 
 # Initialize the sensitivity analysis instance 
 sa.initialize()
@@ -131,11 +131,11 @@ while not stop_SA:
 ## Help <a name="help"></a>
 To get some help on a MetEvolSim class or method, use the Python help function:
 ```python
-help(metevolsim.Model.set_species_initial_value)
+help(MetEvolSim.Model.set_species_initial_value)
 ```
 to obtain a quick description and the list of parameters and outputs:
 ```
-Help on function set_species_initial_value in module metevolsim:
+Help on function set_species_initial_value in module MetEvolSim:
 
 set_species_initial_value(self, species_id, value)
     Set the initial concentration of the species 'species_id' in the

diff --git a/.../python_metevolsim-0.2.1-py3-none-any.whl → dist/MetEvolSim-0.2.1-py3-none-any.whl b/.../python_metevolsim-0.2.1-py3-none-any.whl → dist/MetEvolSim-0.2.1-py3-none-any.whl
diff --git a/dist/MetEvolSim-0.2.1.tar.gz b/dist/MetEvolSim-0.2.1.tar.gz
diff --git a/.../python_metevolsim-0.2.0-py3-none-any.whl → dist/MetEvolSim-0.2.2-py3-none-any.whl b/.../python_metevolsim-0.2.0-py3-none-any.whl → dist/MetEvolSim-0.2.2-py3-none-any.whl
diff --git a/dist/MetEvolSim-0.2.2.tar.gz b/dist/MetEvolSim-0.2.2.tar.gz
diff --git a/dist/python-metevolsim-0.2.0.tar.gz b/dist/python-metevolsim-0.2.0.tar.gz
diff --git a/dist/python-metevolsim-0.2.1.tar.gz b/dist/python-metevolsim-0.2.1.tar.gz
diff --git a/scripts/run_mcmc.py b/scripts/run_mcmc.py
@@ -28,7 +28,7 @@
 import sys
 import time
 import numpy as np
-import metevolsim
+import MetEvolSim
 
 ### Read command line arguments ###
 def readArgs( argv ):
@@ -334,7 +334,7 @@ def load_objective_function( filename ):
 	#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
 	# 5) Run the MCMC algorithm          #
 	#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
-	mcmc       = metevolsim.MCMC(arguments["sbml-filename"], objective_function, arguments["nb-iterations"], arguments["selection-sigma"], arguments["selection-scheme"], arguments["selection-threshold"], arguments["copasi-path"])
+	mcmc       = MetEvolSim.MCMC(arguments["sbml-filename"], objective_function, arguments["nb-iterations"], arguments["selection-sigma"], arguments["selection-scheme"], arguments["selection-threshold"], arguments["copasi-path"])
 	stop_mcmc  = False
 	start_time = time.time()
 	mcmc.initialize()

diff --git a/setup.py b/setup.py
@@ -41,8 +41,8 @@
 	long_description = f.read()
 
 setup(
-	name                          = "python-metevolsim",
-	version                       = "0.2.1",
+	name                          = "MetEvolSim",
+	version                       = "0.2.2",
 	license                       = "GNU General Public License v3 (GPLv3)",
 	description                   = "MetEvolSim (Metabolome Evolution Simulator) Python Package",
 	long_description              = long_description,