Maintenance update (#32)

* added long_description read from README

* black format

* flake8 fixes

* version bump

* removed extra white spaces

* bumped dependency version

* removed PDFs from repo

examples/kitchen_sink.py

@@ -1,75 +1,63 @@
-from pyxdsm.XDSM import (XDSM, OPT, SUBOPT, SOLVER, DOE, 
-                         IFUNC, FUNC, GROUP, IGROUP, METAMODEL)
-
-# styling names for the boxes
-opt = 'Optimization'
-subopt = 'SubOptimization'
-solver = 'MDA'
-doe = 'DOE'
-ifunc = 'ImplicitFunction'
-func = 'Function'
-group = 'Group'
-igroup = 'ImplicitGroup'
-metamodel = 'Metamodel'
+from pyxdsm.XDSM import XDSM, OPT, SUBOPT, SOLVER, DOE, IFUNC, FUNC, GROUP, IGROUP, METAMODEL
 
 x = XDSM()
 
-x.add_system('opt', opt, r'\text{Optimizer}')
-x.add_system('DOE', doe, r'\text{DOE}')
-x.add_system('MDA', solver, r'\text{Newton}')
-x.add_system('D1', func, 'D_1')
+x.add_system("opt", OPT, r"\text{Optimizer}")
+x.add_system("DOE", DOE, r"\text{DOE}")
+x.add_system("MDA", SOLVER, r"\text{Newton}")
+x.add_system("D1", FUNC, "D_1")
 
 # can fade out blocks to allow for emphasis on sub-sections of XDSM
-x.add_system('D2', ifunc, 'D_2', faded=True)
+x.add_system("D2", IFUNC, "D_2", faded=True)
 
-x.add_system('D3', ifunc, 'D_3')
-x.add_system('subopt', subopt, 'SubOpt')
-x.add_system('G1', group, 'G_1')
-x.add_system('G2', igroup, 'G_2')
-x.add_system('MM', metamodel, 'MM')
+x.add_system("D3", IFUNC, "D_3")
+x.add_system("subopt", SUBOPT, "SubOpt")
+x.add_system("G1", GROUP, "G_1")
+x.add_system("G2", IGROUP, "G_2")
+x.add_system("MM", METAMODEL, "MM")
 
 # if you give the label as a list or tuple, it splits it onto multiple lines
-x.add_system('F', func, ('F', r'\text{Functional}'))
+x.add_system("F", FUNC, ("F", r"\text{Functional}"))
 
 # stacked can be used to represent multiple instances that can be run in parallel
-x.add_system('H', func, 'H', stack=True)
+x.add_system("H", FUNC, "H", stack=True)
 
-x.add_process(['opt', 'DOE', 'MDA', 'D1', 'D2', 'subopt', 'G1', 'G2', 'MM', 'F', 'H', 'opt'], arrow=True)
+x.add_process(["opt", "DOE", "MDA", "D1", "D2", "subopt", "G1", "G2", "MM", "F", "H", "opt"], arrow=True)
 
-x.connect('opt', 'D1', ['x', 'z', 'y_2'], label_width=2)
-x.connect('opt', 'D2', ['z', 'y_1'])
-x.connect('opt', 'D3', 'z, y_1')
-x.connect('opt', 'subopt', 'z, y_1')
-x.connect('subopt', 'G1', 'z_2')
-x.connect('subopt', 'G2', 'z_2')
-x.connect('subopt', 'MM', 'z_2')
-x.connect('opt', 'G2', 'z')
-x.connect('opt', 'F', 'x, z')
-x.connect('opt', 'F', 'y_1, y_2')
+x.connect("opt", "D1", ["x", "z", "y_2"], label_width=2)
+x.connect("opt", "D2", ["z", "y_1"])
+x.connect("opt", "D3", "z, y_1")
+x.connect("opt", "subopt", "z, y_1")
+x.connect("subopt", "G1", "z_2")
+x.connect("subopt", "G2", "z_2")
+x.connect("subopt", "MM", "z_2")
+x.connect("opt", "G2", "z")
+x.connect("opt", "F", "x, z")
+x.connect("opt", "F", "y_1, y_2")
 
 # you can also stack variables
-x.connect('opt', 'H', 'y_1, y_2', stack=True)
+x.connect("opt", "H", "y_1, y_2", stack=True)
 
-x.connect('D1', 'opt', r'\mathcal{R}(y_1)')
-x.connect('D2', 'opt', r'\mathcal{R}(y_2)')
+x.connect("D1", "opt", r"\mathcal{R}(y_1)")
+x.connect("D2", "opt", r"\mathcal{R}(y_2)")
 
-x.connect('F', 'opt', 'f')
-x.connect('H', 'opt', 'h', stack=True)
+x.connect("F", "opt", "f")
+x.connect("H", "opt", "h", stack=True)
 
 # can specify inputs to represent external information coming into the XDSM
-x.add_input('D1', 'P_1')
-x.add_input('D2', 'P_2')
-x.add_input('opt', r'x_0', stack=True)
+x.add_input("D1", "P_1")
+x.add_input("D2", "P_2")
+x.add_input("opt", r"x_0", stack=True)
 
 # can put outputs on the left or right sides
-x.add_output('opt', r'x^*, z^*', side='right')
-x.add_output('D1', r'y_1^*', side='left')
-x.add_output('D2', r'y_2^*', side='left')
-x.add_output('F', r'f^*', side='right')
-x.add_output('H', r'h^*', side='right')
-x.add_output('opt', r'y^*', side='left')
+x.add_output("opt", r"x^*, z^*", side="right")
+x.add_output("D1", r"y_1^*", side="left")
+x.add_output("D2", r"y_2^*", side="left")
+x.add_output("F", r"f^*", side="right")
+x.add_output("H", r"h^*", side="right")
+x.add_output("opt", r"y^*", side="left")
 
-x.add_process(['output_opt', 'opt', 'left_output_opt'])
+x.add_process(["output_opt", "opt", "left_output_opt"])
 
-x.write('kitchen_sink', cleanup=False)
-x.write_sys_specs('sink_specs')
+x.write("kitchen_sink", cleanup=False)
+x.write_sys_specs("sink_specs")

examples/mat_eqn.py

@@ -10,19 +10,19 @@
 lin_system.add_variable(2, size=1, text="b")
 
 lin_system.add_variable(3, size=1, text="c")
-lin_system.add_variable(4, size=2, )
-lin_system.add_variable(5, size=2, )
+lin_system.add_variable(4, size=2)
+lin_system.add_variable(5, size=2)
 
 lin_system.add_variable(6, size=1, text="d")
-lin_system.add_variable(7, size=2, )
-lin_system.add_variable(8, size=2, )
+lin_system.add_variable(7, size=2)
+lin_system.add_variable(8, size=2)
 
 lin_system.add_variable(9, size=1, text="e")
-lin_system.add_variable(10, size=2, )
-lin_system.add_variable(11, size=2, )
+lin_system.add_variable(10, size=2)
+lin_system.add_variable(11, size=2)
 
 # variable identifiers can be any hashable object
-lin_system.add_variable('f', size=1, text="f")
+lin_system.add_variable("f", size=1, text="f")
 
 lin_system.connect(1, [4, 5, 7, 8, 10, 11])
 lin_system.connect(2, [4, 5, 7, 8, 10, 11])
@@ -39,26 +39,25 @@
 lin_system.connect(10, 11)
 lin_system.connect(11, 10)
 
-lin_system.connect(11, 'f')
+lin_system.connect(11, "f")
 
 ################################
 # setup the equation
 ################################
 lin_system.jacobian()
 lin_system.spacer()
-lin_system.vector(base_color='red', highlight=[0, 0, 2, 2, 2, 0, 0, 0, 0, 0, 0, 0])
+lin_system.vector(base_color="red", highlight=[0, 0, 2, 2, 2, 0, 0, 0, 0, 0, 0, 0])
 lin_system.spacer()
-lin_system.vector(base_color='red', highlight=[0, 0, 0, 0, 0, 2, 2, 2, 0, 0, 0, 0])
+lin_system.vector(base_color="red", highlight=[0, 0, 0, 0, 0, 2, 2, 2, 0, 0, 0, 0])
 lin_system.spacer()
-lin_system.vector(base_color='red', highlight=[0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 2, 2])
+lin_system.vector(base_color="red", highlight=[0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 2, 2])
 lin_system.spacer()
-lin_system.operator('=')
-lin_system.vector(base_color='green', highlight=[1,1,2,1,1,1,1,1,1,1,1,1])
+lin_system.operator("=")
+lin_system.vector(base_color="green", highlight=[1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1])
 lin_system.spacer()
-lin_system.vector(base_color='green', highlight=[1,1,1,1,1,2,1,1,1,1,1,1])
+lin_system.vector(base_color="green", highlight=[1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1])
 lin_system.spacer()
-lin_system.vector(base_color='green', highlight=[1,1,1,1,1,1,1,1,2,1,1,1])
+lin_system.vector(base_color="green", highlight=[1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1])
 lin_system.spacer()
 
-lin_system.write('mat_eqn_example')
-
+lin_system.write("mat_eqn_example")

examples/mdf.py

@@ -3,29 +3,29 @@
 # Change `use_sfmath` to False to use computer modern
 x = XDSM(use_sfmath=True)
 
-x.add_system('opt', OPT, r'\text{Optimizer}')
-x.add_system('solver', SOLVER, r'\text{Newton}')
-x.add_system('D1', FUNC, 'D_1')
-x.add_system('D2', FUNC, 'D_2')
-x.add_system('F', FUNC, 'F')
-x.add_system('G', FUNC, 'G')
+x.add_system("opt", OPT, r"\text{Optimizer}")
+x.add_system("solver", SOLVER, r"\text{Newton}")
+x.add_system("D1", FUNC, "D_1")
+x.add_system("D2", FUNC, "D_2")
+x.add_system("F", FUNC, "F")
+x.add_system("G", FUNC, "G")
 
-x.connect('opt', 'D1', 'x, z')
-x.connect('opt', 'D2', 'z')
-x.connect('opt', 'F', 'x, z')
-x.connect('solver', 'D1', 'y_2')
-x.connect('solver', 'D2', 'y_1')
-x.connect('D1', 'solver', r'\mathcal{R}(y_1)')
-x.connect('solver', 'F', 'y_1, y_2')
-x.connect('D2', 'solver', r'\mathcal{R}(y_2)')
-x.connect('solver', 'G', 'y_1, y_2')
+x.connect("opt", "D1", "x, z")
+x.connect("opt", "D2", "z")
+x.connect("opt", "F", "x, z")
+x.connect("solver", "D1", "y_2")
+x.connect("solver", "D2", "y_1")
+x.connect("D1", "solver", r"\mathcal{R}(y_1)")
+x.connect("solver", "F", "y_1, y_2")
+x.connect("D2", "solver", r"\mathcal{R}(y_2)")
+x.connect("solver", "G", "y_1, y_2")
 
-x.connect('F', 'opt', 'f')
-x.connect('G', 'opt', 'g')
+x.connect("F", "opt", "f")
+x.connect("G", "opt", "g")
 
-x.add_output('opt', 'x^*, z^*', side='left')
-x.add_output('D1', 'y_1^*', side='left')
-x.add_output('D2', 'y_2^*', side='left')
-x.add_output('F', 'f^*', side='left')
-x.add_output('G', 'g^*', side='left')
-x.write('mdf')
+x.add_output("opt", "x^*, z^*", side="left")
+x.add_output("D1", "y_1^*", side="left")
+x.add_output("D2", "y_2^*", side="left")
+x.add_output("F", "f^*", side="left")
+x.add_output("G", "g^*", side="left")
+x.write("mdf")