Menu
▾
▴
[simuPOP-devel] SF.net SVN: simupop:[5010] trunk/test/test_18_plotter.py
|
From: <bpe...@us...> - 2016-02-10 04:04:53
|
Revision: 5010
http://sourceforge.net/p/simupop/code/5010
Author: bpeng2000
Date: 2016-02-10 04:04:51 +0000 (Wed, 10 Feb 2016)
Log Message:
-----------
Remove tests for rpy based plotter
Modified Paths:
--------------
trunk/test/test_18_plotter.py
Modified: trunk/test/test_18_plotter.py
===================================================================
--- trunk/test/test_18_plotter.py 2016-02-09 23:36:44 UTC (rev 5009)
+++ trunk/test/test_18_plotter.py 2016-02-10 04:04:51 UTC (rev 5010)
@@ -24,18 +24,9 @@
from simuPOP import *
from time import sleep
-hasRPy = True
-try:
- from simuPOP.plotter import *
-except (ImportError, RuntimeError, AttributeError):
- print("simuRPy can not be imported. Either rpy or r is not installed properly.")
- hasRPy = False
-
class TestPlotter(unittest.TestCase):
def testDerivedArgs(self):
'Testing class derivedARgs'
- if not hasRPy:
- return True
pop = Population(0)
pop.dvars().gen = 100
args = DerivedArgs(
@@ -93,8 +84,6 @@
def testVarPlotterBase(self):
'Testing byRep parameter of VarPlotter'
- if not hasRPy:
- return True
simu = Simulator(
Population(size=[50,50,100], ploidy=2, loci=[3,4], infoFields = ['migrate_to']),
rep=3)
@@ -113,8 +102,6 @@
def testVarPlotterByRep(self):
'Testing byRep parameter of VarPlotter'
- if not hasRPy:
- return True
simu = Simulator(
Population(size=[50,50,100], ploidy=2, loci=[3,4], infoFields = ['migrate_to']),
rep=3)
@@ -138,8 +125,6 @@
def testVarPlotterByDim(self):
'Testing byDim paramter of VarPlotter'
- if not hasRPy:
- return True
simu = Simulator(
Population(size=[200, 100], ploidy=2, loci=[3,4], infoFields = ['migrate_to']),
rep=3)
@@ -162,8 +147,6 @@
def testVarPlotterSelectedRep(self):
'Testing byDim paramter of VarPlotter using selected replicates'
- if not hasRPy:
- return True
simu = Simulator(
Population(size=[50, 50, 100], ploidy=2, loci=[3,4], infoFields = ['migrate_to']),
rep=5)
@@ -184,8 +167,6 @@
def testVarPlotterTogether(self):
'Testing plotting all lines together using VarPlotter'
- if not hasRPy:
- return True
simu = Simulator(
Population(size=[50, 50, 100], ploidy=2, loci=[3,4], infoFields = ['migrate_to']),
rep=3)
@@ -209,8 +190,6 @@
def testVarPlotterByRepDim(self):
'Testing byDim paramter of VarPlotter'
- if not hasRPy:
- return True
simu = Simulator(
Population(size=[200, 100], ploidy=2, loci=[3, 4], infoFields = ['migrate_to']),
rep=2)
@@ -234,8 +213,6 @@
def testVarPlotterSaveAs(self):
'Testing saveAs parameter of VarPlotter'
- if not hasRPy:
- return True
simu = Simulator(
Population(size=[50,50,100], ploidy=2, loci=[3,4], infoFields = ['migrate_to']),
rep=3)
@@ -293,8 +270,6 @@
def testVarPlotterPar(self):
'Testing parameter passing of VarPlotter'
- if not hasRPy:
- return True
simu = Simulator(
Population(size=[50,50,100], ploidy=2, loci=[3,4], infoFields=['migrate_to']),
rep=2)
@@ -317,8 +292,6 @@
def testVarPlotterHook(self):
'Testing ylim parameter of VarPlotter'
- if not hasRPy:
- return True
simu = Simulator(
Population(size=[50,50,100], ploidy=2, loci=[3,4], infoFields=['migrate_to']),
rep=3)
@@ -351,8 +324,6 @@
def testScatterPlotter(self):
'Testing ScatterPlotter'
- if not hasRPy:
- return True
import random
pop = Population([100, 200], infoFields=['x', 'y'])
initSex(pop)
@@ -373,8 +344,6 @@
def testScatterPlotterSP(self):
'Testing ScatterPlotter with multiple virtual subpopulations'
- if not hasRPy:
- return True
import random
pop = Population([100, 200], infoFields=['x', 'y'])
initSex(pop)
@@ -399,8 +368,6 @@
def testScatterPlotterSubSet(self):
'Testing ScatterPlotter with partial individuals'
- if not hasRPy:
- return True
import random
pop = Population([100, 200], infoFields=['x', 'y'])
initSex(pop)
@@ -426,274 +393,5 @@
sleep(1)
r.dev_off()
- def testInfoPlotterBase(self):
- 'Testing basic histogram using InfoPlotter'
- if not hasRPy:
- return True
- import random
- pop = Population([500, 1000], infoFields=['x'])
- initSex(pop)
- pop.setIndInfo([random.random() for i in range(100)], 'x')
- pop.evolve(
- matingScheme=RandomMating(ops=[MendelianGenoTransmitter(),
- InheritTagger(PATERNAL, infoFields='x')]),
- postOps = HistPlotter(infoFields='x', main='histogram of x in green',
- angle=60, col='green', step=2),
- #Pause(),
- gen = 5,
- )
- sleep(1)
- r.dev_off()
-
- def testInfoPlotterFields(self):
- 'Testing Stat plotter with multiple fields and subpopulations'
- if not hasRPy:
- return True
- import random
- pop = Population([500, 1000], infoFields=['x', 'y'])
- initSex(pop)
- pop.setIndInfo([random.random() for i in range(100)], 'x', 0)
- pop.setIndInfo([1 + random.random() for i in range(100)], 'x', 1)
- pop.setIndInfo([random.random() for i in range(300)], 'y')
- pop.setVirtualSplitter(SexSplitter())
- pop.evolve(
- matingScheme=RandomMating(ops=[MendelianGenoTransmitter(),
- InheritTagger(PATERNAL, infoFields='x'),
- InheritTagger(MATERNAL, infoFields='y'),
- ]),
- postOps = [
- HistPlotter(infoFields=['x', 'y'],
- subPops = [(0, 0), (0, 1)],
- col_fld=['red', 'green'],
- density_sp=[5, 20], step=2,
- main_spfld=['Field x, Male', 'Field y, Male',
- 'Field x, Female', 'Field y, Female'],
- ),
- #Pause(),
- ],
- gen = 5,
- )
- sleep(1)
- r.dev_off()
-
- def testInfoPlotterQQplot(self):
- 'Testing barplotter with multiple fields and subpopulations'
- if not hasRPy:
- return True
- import random
- pop = Population([500, 100], infoFields=['x', 'y'])
- initSex(pop)
- pop.setIndInfo([random.random() for i in range(100)], 'x', 0)
- pop.setIndInfo([1 + random.random() for i in range(100)], 'x', 1)
- pop.setIndInfo([random.random() for i in range(300)], 'y')
- pop.setVirtualSplitter(SexSplitter())
- def qqline(r, data=None, **kwargs):
- r.qqline(data)
- pop.evolve(
- matingScheme=RandomMating(ops=[MendelianGenoTransmitter(),
- InheritTagger(PATERNAL, infoFields='x'),
- InheritTagger(MATERNAL, infoFields='y'),
- ]),
- postOps = [
- QQPlotter(infoFields=['x', 'y'],
- subPops = [(0, 0), (0, 1)],
- col_fld=['red', 'green'],
- pch_sp=[1, 2],
- main_spfld=['Field x, Male', 'Field y, Male',
- 'Field x, Female', 'Field y, Female'],
- plotHook=qqline, step=2
- ),
- #Pause(),
- ],
- gen = 5,
- )
- sleep(1)
- r.dev_off()
-
- def testInfoPlotterNoFunc(self):
- 'Testing the Stat plotter when no function is specified'
- if not hasRPy:
- return True
- import random
- pop = Population([500, 100], infoFields=['x', 'y'])
- initSex(pop)
- pop.setIndInfo([random.random() for i in range(100)], 'x', 0)
- pop.setIndInfo([1 + random.random() for i in range(100)], 'x', 1)
- pop.setIndInfo([random.random() for i in range(300)], 'y')
- pop.setVirtualSplitter(SexSplitter())
- def qqplot(r, data=None, field=None, subPop=None, **kwargs):
- r.qqnorm(data, main='QQ drawn in plotHook fld: %s sp: %s' % (field, subPop))
- r.qqline(data)
- pop.evolve(
- matingScheme=RandomMating(ops=[MendelianGenoTransmitter(),
- InheritTagger(PATERNAL, infoFields='x'),
- InheritTagger(MATERNAL, infoFields='y'),
- ]),
- postOps = [
- InfoPlotter(infoFields=['x', 'y'],
- subPops = [(0, 0), (0, 1)],
- plotHook=qqplot, step=2
- ),
- #Pause(),
- ],
- gen = 5,
- )
- sleep(1)
- r.dev_off()
-
-
- def testBoxPlotterBase(self):
- 'Testing the base boxplotter'
- if not hasRPy:
- return True
- import random
- pop = Population([500, 100], infoFields=['x'])
- initSex(pop)
- pop.setIndInfo([random.random() for i in range(100)], 'x')
- pop.evolve(
- matingScheme=RandomMating(ops=[MendelianGenoTransmitter(),
- InheritTagger(PATERNAL, infoFields='x')]),
- postOps = [
- BoxPlotter(infoFields='x', xlab='x', main='boxplot for field x',
- step=2),
- #Pause(),
- ],
- gen = 5,
- )
- sleep(1)
- r.dev_off()
-
- def testBoxPlotterFields(self):
- 'Testing barplotter with multiple fields and subpopulations'
- if not hasRPy:
- return True
- import random
- pop = Population([500, 100], infoFields=['x', 'y'])
- initSex(pop)
- pop.setIndInfo([random.random() for i in range(100)], 'x', 0)
- pop.setIndInfo([1 + random.random() for i in range(100)], 'x', 1)
- pop.setIndInfo([random.random() for i in range(300)], 'y')
- pop.setVirtualSplitter(SexSplitter())
- pop.evolve(
- matingScheme=RandomMating(ops=[MendelianGenoTransmitter(),
- InheritTagger(PATERNAL, infoFields='x'),
- InheritTagger(MATERNAL, infoFields='y'),
- ]),
- postOps = BoxPlotter(infoFields=['x', 'y'], step=2),
- #Pause(),
- gen = 5,
- )
- sleep(1)
- r.dev_off()
-
- def testBoxPlotterFieldsAndSubPop(self):
- 'Testing BoxPlotter with both fields and subpopulation'
- if not hasRPy:
- return True
- import random
- pop = Population([500, 100], infoFields=['x', 'y'],
- subPopNames=['sp1', 'sp2'])
- initSex(pop)
- pop.setIndInfo([random.random() for i in range(100)], 'x', 0)
- pop.setIndInfo([1 + random.random() for i in range(100)], 'x', 1)
- pop.setIndInfo([random.random() for i in range(300)], 'y')
- pop.setVirtualSplitter(SexSplitter())
- pop.evolve(
- matingScheme=RandomMating(ops=[MendelianGenoTransmitter(),
- InheritTagger(PATERNAL, infoFields='x'),
- InheritTagger(MATERNAL, infoFields='y'),
- ]),
- postOps = [
- BoxPlotter(infoFields=['x', 'y'],
- subPops=[(0, 0), (0, 1)], style='quantile',
- step=2, main='Boxplot with 2 fields x 2 subpops',
- col='green', horizontal=True,
- ),
- #Pause(),
- ],
- gen = 5,
- )
- sleep(1)
- r.dev_off()
-
- def testBoxPlotterByField(self):
- 'Testing BoxPlotter separated by information field'
- if not hasRPy:
- return True
- import random
- pop = Population([500, 100], infoFields=['x', 'y'],
- subPopNames=['sp1', 'sp2'])
- initSex(pop)
- pop.setIndInfo([random.random() for i in range(100)], 'x', 0)
- pop.setIndInfo([1 + random.random() for i in range(100)], 'x', 1)
- pop.setIndInfo([random.random() for i in range(300)], 'y')
- pop.setVirtualSplitter(SexSplitter())
- pop.evolve(
- matingScheme=RandomMating(ops=[MendelianGenoTransmitter(),
- InheritTagger(PATERNAL, infoFields='x'),
- InheritTagger(MATERNAL, infoFields='y'),
- ]),
- postOps = BoxPlotter(infoFields=['x', 'y'], byField=True,
- subPops=[(0,0), (0,1)],
- step=2, col_fld=['yellow', 'green'],
- ),
- #Pause(),
- gen = 5,
- )
- sleep(1)
- r.dev_off()
-
- def testBoxPlotterBySubPop(self):
- 'Testing BoxPlotter separated by subpopulation'
- if not hasRPy:
- return True
- import random
- pop = Population([500, 100], infoFields=['x', 'y'], subPopNames=['', ''])
- initSex(pop)
- pop.setIndInfo([random.random() for i in range(100)], 'x', 0)
- pop.setIndInfo([1 + random.random() for i in range(100)], 'x', 1)
- pop.setIndInfo([random.random() for i in range(300)], 'y')
- pop.setVirtualSplitter(SexSplitter())
- pop.evolve(
- matingScheme=RandomMating(ops=[MendelianGenoTransmitter(),
- InheritTagger(PATERNAL, infoFields='x'),
- InheritTagger(MATERNAL, infoFields='y'),
- ]),
- postOps = BoxPlotter(infoFields=['x', 'y'], bySubPop=True,
- subPops=[(0,0), (0,1)],
- step=2, horizontal_sp=[True, False],
- ),
- #Pause(),
- gen = 5,
- )
- sleep(1)
- r.dev_off()
-
- def testBoxPlotterByFieldSubPop(self):
- 'Testing BoxPlotter separated by both field and subpopulation'
- if not hasRPy:
- return True
- import random
- pop = Population([500, 100], infoFields=['x', 'y'], subPopNames=['', ''])
- initSex(pop)
- pop.setIndInfo([random.random() for i in range(100)], 'x', 0)
- pop.setIndInfo([1 + random.random() for i in range(100)], 'x', 1)
- pop.setIndInfo([random.random() for i in range(300)], 'y')
- pop.setVirtualSplitter(SexSplitter())
- pop.evolve(
- matingScheme=RandomMating(ops=[MendelianGenoTransmitter(),
- InheritTagger(PATERNAL, infoFields='x'),
- InheritTagger(MATERNAL, infoFields='y'),
- ]),
- postOps = BoxPlotter(infoFields=['x', 'y'], bySubPop=True,
- subPops=[(0,0), (0,1)], byField=True,
- step=2, col_spfld = ['red', 'green', 'yellow', 'blue'],
- ),
- #Pause(),
- gen = 5,
- )
- sleep(1)
- r.dev_off()
-
if __name__ == '__main__':
unittest.main()
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|