Refactor Frhodo to be a Python package

src/calculate/mech_fcns.py → frhodo/calculate/mech_fcns.py

@@ -7,10 +7,11 @@
 import cantera as ct
 from cantera import interrupts, cti2yaml#, ck2yaml, ctml2yaml
 import numpy as np
-from calculate import reactors, shock_fcns, integrate
-import ck2yaml
 from timeit import default_timer as timer
 
+from . import reactors, shock_fcns, integrate
+from .. import ck2yaml
+
 
 class Chemical_Mechanism:
     def __init__(self):

src/calculate/optimize/CheKiPEUQ_from_Frhodo.py → frhodo/calculate/optimize/CheKiPEUQ_from_Frhodo.py

@@ -6,19 +6,14 @@
 except:
     #import pathlib
     #sys.path.append(pathlib.Path(__file__).parent.absolute()) # add directory of **this** file to path
-    import calculate.optimize.CheKiPEUQ_local as CKPQ 
+    import frhodo.calculate.optimize.CheKiPEUQ_local as CKPQ
 
 try:
     import CheKiPEUQ.UserInput as UserInput
 except:
-    import calculate.optimize.CheKiPEUQ_local.UserInput as UserInput
+    from .CheKiPEUQ_local import UserInput
 
-try:
-    import CiteSoft
-except:
-    #import pathlib #The below lines are to allow CiteSoftLocal to be called regardless of user's working directory.
-    #sys.path.append(pathlib.Path(__file__).parent.absolute()) # add directory of **this** file to path
-    import CiteSoftLocal as CiteSoft
+import frhodo.CiteSoftLocal as CiteSoft
 
 #get things ready for CiteSoft entry...
 software_name = "CheKiPEUQ Bayesian Parameter Estimation"

src/calculate/optimize/CheKiPEUQ_local/InverseProblem.py → frhodo/calculate/optimize/CheKiPEUQ_local/InverseProblem.py

@@ -9,16 +9,13 @@
 from collections.abc import Iterable 
 #import mumce_py.Project as mumce_pyProject #FIXME: Eric to fix plotting/graphing issue described in issue 9 -- https://github.com/AdityaSavara/ODE-KIN-BAYES-SG-EW/issues/9
 #import mumce_py.solution mumce_pySolution
-try:
-    import CiteSoft
-except:
-    #import pathlib #The below lines are to allow CiteSoftLocal to be called regardless of user's working directory.
-    #sys.path.append(pathlib.Path(__file__).parent.absolute()) # add directory of **this** file to path
-    import CiteSoftLocal as CiteSoft
+
+import frhodo.CiteSoftLocal as CiteSoft
+
 try:
     import UnitTesterSG.nestedObjectsFunctions as nestedObjectsFunctions
-except:
-    import calculate.optimize.CheKiPEUQ_local.nestedObjectsFunctionsLocal as nestedObjectsFunctions
+except ImportError:
+    import frhodo.calculate.optimize.CheKiPEUQ_local.nestedObjectsFunctionsLocal as nestedObjectsFunctions
 
 class parameter_estimation:
     #Inside this class, a UserInput namespace is provided. This has dictionaries of UserInput choices.

src/calculate/optimize/fit_coeffs.py → frhodo/calculate/optimize/fit_coeffs.py

@@ -12,8 +12,9 @@
 from timeit import default_timer as timer
 import itertools
 
-from calculate.convert_units import OoM, Bisymlog
-from calculate.optimize.misc_fcns import penalized_loss_fcn, set_arrhenius_bnds, min_pos_system_value, max_pos_system_value
+from ..convert_units import OoM, Bisymlog
+from ..optimize.misc_fcns import penalized_loss_fcn, set_arrhenius_bnds, min_pos_system_value, max_pos_system_value
+import frhodo
 
 Ru = ct.gas_constant
 # Ru = 1.98720425864083
@@ -134,7 +135,7 @@ def ln_arrhenius_jac(T, *args):
     return popt
 
 
-path = {'main': pathlib.Path(sys.argv[0]).parents[0].resolve()}
+path = {'main': pathlib.Path(frhodo.__file__).parents[0].resolve()}  # TODO (wardlt) - Make a globally-accessible Path
 OS_type = platform.system()
 if OS_type == 'Windows':
     path['bonmin'] = path['main'] / 'bonmin/bonmin-win64/bonmin.exe'

src/calculate/optimize/fit_coeffs_pygmo.py → frhodo/calculate/optimize/fit_coeffs_pygmo.py

@@ -12,8 +12,9 @@
 from timeit import default_timer as timer
 import itertools
 
-from calculate.convert_units import OoM
-from calculate.optimize.misc_fcns import penalized_loss_fcn, set_arrhenius_bnds
+import frhodo
+from ..convert_units import OoM
+from ..optimize.misc_fcns import penalized_loss_fcn, set_arrhenius_bnds
 
 Ru = ct.gas_constant
 # Ru = 1.98720425864083
@@ -50,7 +51,7 @@ def ln_arrhenius_k(T, Ea, ln_A, n):   # LPL, HPL, Fcent
 def fit_arrhenius(rates, T, x0=[], coefNames=default_arrhenius_coefNames, bnds=[], loss='linear'):
     def fit_fcn_decorator(x0, alter_idx, jac=False):               
         def set_coeffs(*args):
-            coeffs = x0
+            coeffs = x0git
             for n, idx in enumerate(alter_idx):
                 coeffs[idx] = args[n]
             return coeffs
@@ -118,7 +119,7 @@ def ln_arrhenius_jac(T, *args):
     return popt
 
 
-path = {'main': pathlib.Path(sys.argv[0]).parents[0].resolve()}
+path = {'main': pathlib.Path(frhodo.__file__).parents[0].resolve()}  # TODO (wardlt) - Make a globally-accessible Path
 OS_type = platform.system()
 if OS_type == 'Windows':
     path['bonmin'] = path['main'] / 'bonmin/bonmin-win64/bonmin.exe'

src/calculate/optimize/fit_fcn.py → frhodo/calculate/optimize/fit_fcn.py

@@ -10,11 +10,11 @@
 from scipy import stats
 from copy import deepcopy
 
-from calculate.mech_fcns import Chemical_Mechanism
-from calculate.convert_units import OoM, Bisymlog
-from calculate.optimize.misc_fcns import weighted_quantile, outlier, penalized_loss_fcn
-from calculate.optimize.fit_coeffs import fit_coeffs
-from calculate.optimize.CheKiPEUQ_from_Frhodo import CheKiPEUQ_Frhodo_interface
+from ..mech_fcns import Chemical_Mechanism
+from ..convert_units import OoM, Bisymlog
+from ..optimize.misc_fcns import weighted_quantile, outlier, penalized_loss_fcn
+from ..optimize.fit_coeffs import fit_coeffs
+from ..optimize.CheKiPEUQ_from_Frhodo import CheKiPEUQ_Frhodo_interface
 
 mpMech = {}
 def initialize_parallel_worker(mech_dict, species_dict, coeffs, coeffs_bnds, rate_bnds):

src/calculate/optimize/mech_optimize.py → frhodo/calculate/optimize/mech_optimize.py

@@ -12,10 +12,10 @@
 
 from scipy import stats
 
-from calculate.optimize.optimize_worker import Worker
-from calculate.optimize.fit_fcn import update_mech_coef_opt
-from calculate.optimize.misc_fcns import rates, set_bnds
-from calculate.optimize.fit_coeffs import fit_generic as Troe_fit
+from ..optimize.optimize_worker import Worker
+from ..optimize.fit_fcn import update_mech_coef_opt
+from ..optimize.misc_fcns import rates, set_bnds
+from ..optimize.fit_coeffs import fit_generic as Troe_fit
 
 Ru = ct.gas_constant
 default_arrhenius_coefNames = ['activation_energy', 'pre_exponential_factor', 'temperature_exponent']

src/calculate/optimize/misc_fcns.py → frhodo/calculate/optimize/misc_fcns.py

@@ -8,6 +8,8 @@
 import cantera as ct
 import pathlib, sys
 
+import frhodo
+
 Ru = ct.gas_constant
 
 min_pos_system_value = (np.finfo(float).tiny*(1E20))**(1/2)
@@ -20,7 +22,7 @@
 
 
 # interpolation function for Z from loss function
-path = {'main': pathlib.Path(sys.argv[0]).parents[0].resolve()}
+path = {'main': pathlib.Path(frhodo.__file__).parents[0].resolve()}
 path['Z_tck_spline.dat'] = path['main'] / 'data/loss_partition_fcn_tck_spline.dat'
 
 tck = []

src/calculate/optimize/optimize_worker.py → frhodo/calculate/optimize/optimize_worker.py

@@ -12,8 +12,9 @@
 
 from timeit import default_timer as timer
 
-from calculate.optimize.fit_fcn import initialize_parallel_worker, Fit_Fun
-from calculate.optimize.misc_fcns import rates
+from ..optimize.fit_fcn import initialize_parallel_worker, Fit_Fun
+from ..optimize.misc_fcns import rates
+import frhodo
 
 
 debug = True
@@ -210,7 +211,7 @@ class WorkerSignals(QObject):
            'Optimization failed: Out of memory', 'Optimization failed: Roundoff errors limited progress',
            'Optimization failed: Forced termination']
 
-path = {'main': pathlib.Path(sys.argv[0]).parents[0].resolve()}
+path = {'main': pathlib.Path(frhodo.__file__).parents[0].resolve()}  # TODO (wardlt) - Make a globally-accessible Path
 OS_type = platform.system()
 if OS_type == 'Windows':
     path['bonmin'] = path['main'] / 'bonmin/bonmin-win64/bonmin.exe'

src/calculate/reactors.py → frhodo/calculate/reactors.py

@@ -7,8 +7,8 @@
 import cantera as ct
 from cantera import interrupts, cti2yaml#, ck2yaml, ctml2yaml
 import numpy as np
-from calculate import shock_fcns, integrate
-import ck2yaml
+from . import shock_fcns, integrate
+import frhodo.ck2yaml
 from timeit import default_timer as timer
 
 

src/main.py → frhodo/main.py

@@ -5,21 +5,20 @@
 # and licensed under BSD-3-Clause. See License.txt in the top-level 
 # directory for license and copyright information.
 
-version = '1.3.1'
 import os, sys, platform, multiprocessing, pathlib, ctypes
 # os.environ['QT_API'] = 'pyside2'        # forces pyside2
+from typing import Tuple
 
 from qtpy.QtWidgets import QMainWindow, QApplication, QMessageBox
 from qtpy import uic, QtCore, QtGui
-
 import numpy as np
-# from timeit import default_timer as timer
 
-from plot.plot_main import All_Plots as plot
-from misc_widget import MessageWindow
-from calculate import mech_fcns, reactors, convert_units
-import appdirs, options_panel_widgets, sim_explorer_widget
-import settings, config_io, save_widget, error_window, help_menu
+from .plot.plot_main import All_Plots as plot
+from .misc_widget import MessageWindow
+from .calculate import mech_fcns, reactors, convert_units
+from .version import __version__
+from . import appdirs, options_panel_widgets, sim_explorer_widget
+from . import settings, config_io, save_widget, error_window, help_menu
 
 if os.environ['QT_API'] == 'pyside2': # Silence warning: "Qt WebEngine seems to be initialized from a plugin."
     QApplication.setAttribute(QtCore.Qt.AA_ShareOpenGLContexts)
@@ -31,7 +30,7 @@
     QApplication.setAttribute(QtCore.Qt.AA_UseHighDpiPixmaps, True)
 
 # set main folder
-path = {'main': pathlib.Path(sys.argv[0]).parents[0].resolve()}
+path = {'main': pathlib.Path(__file__).parents[0].resolve()}
 
 # set appdata folder using AppDirs library (but just using the source code file)
 dirs = appdirs.AppDirs(appname='Frhodo', roaming=True, appauthor=False)
@@ -86,7 +85,7 @@ def __init__(self, app, path):
         self.initialize_settings()  # ~ 4 sec
 
         # Setup help menu
-        self.version = version
+        self.version = __version__
         help_menu.HelpMenu(self)
 
     def initialize_settings(self):  # TODO: Solving for loaded shock twice
@@ -290,17 +289,31 @@ def run_single(self, event=None, t_save=None, rxn_changed=False):
     # def raise_error(self):
         # assert False
 
-
-if __name__ == '__main__':
+
+def launch_gui() -> Tuple[QApplication, Main]:
+    """Launch the GUI
+
+    Returns:
+        - The QApplication instance
+        - Link to the main window
+    """
     if platform.system() == 'Windows':  # this is required for pyinstaller on windows
         multiprocessing.freeze_support()
 
-        if getattr(sys, 'frozen', False):   # if frozen minimize console immediately
+        if getattr(sys, 'frozen', False):  # if frozen minimize console immediately
             ctypes.windll.user32.ShowWindow(ctypes.windll.kernel32.GetConsoleWindow(), 0)
-    
+
     app = QApplication(sys.argv)
     sys.excepthook = error_window.excepthookDecorator(app, path, shut_down)
 
-    main = Main(app, path)
+    main_window = Main(app, path)
+    return app, main_window
+
+
+def main():
+    """Launch the GUI and then block until it finishes"""
+    # Launch the application
+    app, main_window = launch_gui()
+
+    # Pass the exit code forward
     sys.exit(app.exec_())
-

src/mech_widget.py → frhodo/mech_widget.py

@@ -2,17 +2,17 @@
 # and licensed under BSD-3-Clause. See License.txt in the top-level 
 # directory for license and copyright information.
 
+from copy import deepcopy
 import sys, ast, re
-import misc_widget
+
 import cantera as ct
 import numpy as np
-from copy import deepcopy
-from functools import partial
 from scipy.optimize import root_scalar
 from qtpy.QtWidgets import *
 from qtpy import QtWidgets, QtGui, QtCore
 
-from timeit import default_timer as timer
+from . import misc_widget
+
 
 def silentSetValue(obj, value):
     obj.blockSignals(True)           # stop changing text from signaling

src/misc_widget.py → frhodo/misc_widget.py

@@ -6,7 +6,7 @@
 import numpy as np
 from qtpy.QtWidgets import *
 from qtpy import QtWidgets, QtGui, QtCore
-from calculate.convert_units import OoM
+from .calculate.convert_units import OoM
 
 # Regular expression to find floats. Match groups are the whole string, the
 # whole coefficient, the decimal part of the coefficient, and the exponent

src/options_panel_widgets.py → frhodo/options_panel_widgets.py

@@ -3,17 +3,20 @@
 # directory for license and copyright information.
 
 import pathlib, os, sys
+from copy import deepcopy
+
 import numpy as np
 from scipy.optimize import minimize
 import nlopt
-import mech_widget, misc_widget, thermo_widget, series_viewer_widget, save_output
-from calculate import shock_fcns 
-from calculate.optimize.mech_optimize import Multithread_Optimize
-from calculate.convert_units import OoM
-from settings import double_sigmoid
 from qtpy.QtWidgets import *
 from qtpy import QtWidgets, QtGui, QtCore
-from copy import deepcopy
+
+from . import mech_widget, misc_widget, thermo_widget, series_viewer_widget, save_output
+from .calculate import shock_fcns
+from .calculate.optimize.mech_optimize import Multithread_Optimize
+from .calculate.convert_units import OoM
+from .settings import double_sigmoid
+
 
 
 class Initialize(QtCore.QObject):

src/plot/base_plot.py → frhodo/plot/base_plot.py

@@ -24,9 +24,9 @@
 #mpl.use("module://mplcairo.qt") # This implements mplcairo, faster/more accurate. Issues with other OSes?
 import numpy as np
 
-from calculate.convert_units import Bisymlog
-from plot.custom_mplscale import *
-from plot.custom_mpl_ticker_formatter import *
+from ..calculate.convert_units import Bisymlog
+from .custom_mplscale import *
+from .custom_mpl_ticker_formatter import *
 from timeit import default_timer as timer
 
 

src/plot/custom_mplscale.py → frhodo/plot/custom_mplscale.py

@@ -6,7 +6,7 @@
 from matplotlib import scale as mplscale
 
 import numpy as np
-from calculate.convert_units import Bisymlog
+from frhodo.calculate.convert_units import Bisymlog
 
 class AbsoluteLogScale(mplscale.LogScale):
     name = 'abslog'

src/plot/optimization_plot.py → frhodo/plot/optimization_plot.py

@@ -2,12 +2,12 @@
 # and licensed under BSD-3-Clause. See License.txt in the top-level 
 # directory for license and copyright information.
 
-import colors
+from frhodo import colors
 
 import matplotlib as mpl
 import numpy as np
 
-from plot.base_plot import Base_Plot
+from .base_plot import Base_Plot
 
 
 colormap = colors.colormap(reorder_from=1, num_shift=4)

src/plot/plot_main.py → frhodo/plot/plot_main.py

@@ -2,7 +2,7 @@
 # and licensed under BSD-3-Clause. See License.txt in the top-level 
 # directory for license and copyright information.
 
-from plot import raw_signal_plot, signal_plot, sim_explorer_plot, optimization_plot, plot_widget
+from . import raw_signal_plot, signal_plot, sim_explorer_plot, optimization_plot, plot_widget
 
 
 class All_Plots:    # container to hold all plots

src/plot/plot_widget.py → frhodo/plot/plot_widget.py

@@ -7,7 +7,7 @@
 from qtpy import QtWidgets, QtGui, QtCore
 from copy import deepcopy
 
-import misc_widget
+from .. import misc_widget
 
 class Observable_Widgets(QtCore.QObject):
     def __init__(self, parent):