Example of test failure output; occurs 1/10 times or so

devel/occasional_error.txt

@@ -0,0 +1,85 @@
+============================= test session starts ==============================
+platform linux -- Python 3.5.2, pytest-3.0.5, py-1.4.32, pluggy-0.4.0
+rootdir: /home/jaime/lib/ftprime, inifile: pytest.ini
+plugins: cov-2.4.0
+collected 6 items
+
+tests/test_forwards_algorithm.py .
+tests/test_ftprime_with_simuPOP.py .
+tests/test_merge_records_with_wf.py ...F
+
+=================================== FAILURES ===================================
+_____________________________ test_simulation_runs _____________________________
+
+    def test_simulation_runs():
+
+        records = wf(N=5,ngens=5,nsamples=5,survival=0.5)
+
+        for x in records.dump_records():
+            print(x)
+
+        samples = [ (0,0) for _ in range(5) ]
+>       ts = records.tree_sequence(samples=samples)
+
+tests/test_merge_records_with_wf.py:63: 
+_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
+
+self = ARGrecorder([(5, (6, [])), (6, (6, [CoalescenceRecord(left=0.8212435323883007, right=1.0, node=6, children=(12,), time..., population=0)])), (21, (1, [CoalescenceRecord(left=0.0, right=1.0, node=21, children=(1,), time=1, population=0)]))])
+samples = [(0, 0), (0, 0), (0, 0), (0, 0), (0, 0)], mutations = None
+
+    def tree_sequence(self,samples,mutations=None):
+        '''
+            Produce a tree sequence from the ARG.
+            '''
+        ts = _msprime.TreeSequence()
+        ts.load_records(
+                coalescence_records=list(self.dump_records()),
+>               samples=samples)
+E       _msprime.LibraryError: Bad coalescence records in file: Samples must be labeled 0...n-1 and not be internal nodes.
+
+ftprime/argrecorder.py:60: LibraryError
+----------------------------- Captured stdout call -----------------------------
+t: 0
+pop: [5, 6, 7, 8, 9]
+10 9 5 1.0
+11 9 7 0.0
+12 8 6 0.8212435323883007
+t: 1
+pop: [10, 11, 7, 12, 9]
+13 10 9 0.0
+14 11 9 0.2806010848256748
+15 10 10 0.4513042068306792
+t: 2
+pop: [10, 11, 13, 14, 15]
+16 14 14 0.01065709031372597
+17 13 15 0.32783380914661153
+t: 3
+pop: [10, 11, 13, 16, 17]
+18 17 17 0.0
+19 10 16 0.6414868623681791
+t: 4
+pop: [18, 11, 13, 19, 17]
+20 19 18 0.10754762965969111
+21 11 11 0.0
+CoalescenceRecord(left=0.0, right=1.0, node=21, children=(1,), time=1, population=0)
+CoalescenceRecord(left=0.0, right=1.0, node=20, children=(3,), time=1, population=0)
+CoalescenceRecord(left=0.0, right=0.10754762965969111, node=19, children=(20,), time=2, population=0)
+CoalescenceRecord(left=0.0, right=0.10754762965969111, node=18, children=(4,), time=2, population=0)
+CoalescenceRecord(left=0.10754762965969111, right=1.0, node=18, children=(4, 20), time=2, population=0)
+CoalescenceRecord(left=0.0, right=1.0, node=17, children=(2, 18), time=3, population=0)
+CoalescenceRecord(left=0.6414868623681791, right=1.0, node=16, children=(19,), time=3, population=0)
+CoalescenceRecord(left=0.32783380914661153, right=1.0, node=15, children=(17,), time=4, population=0)
+CoalescenceRecord(left=0.0, right=0.01065709031372597, node=14, children=(16,), time=4, population=0)
+CoalescenceRecord(left=0.01065709031372597, right=1.0, node=14, children=(16,), time=4, population=0)
+CoalescenceRecord(left=0.0, right=0.32783380914661153, node=13, children=(17,), time=4, population=0)
+CoalescenceRecord(left=0.0, right=0.2806010848256748, node=11, children=(0, 14, 21), time=5, population=0)
+CoalescenceRecord(left=0.2806010848256748, right=1.0, node=11, children=(0, 21), time=5, population=0)
+CoalescenceRecord(left=0.0, right=0.4513042068306792, node=10, children=(15, 19), time=5, population=0)
+CoalescenceRecord(left=0.6414868623681791, right=1.0, node=10, children=(15,), time=5, population=0)
+CoalescenceRecord(left=0.4513042068306792, right=0.6414868623681791, node=10, children=(15, 19), time=5, population=0)
+CoalescenceRecord(left=0.0, right=0.2806010848256748, node=9, children=(10, 13), time=6, population=0)
+CoalescenceRecord(left=0.2806010848256748, right=1.0, node=9, children=(10, 13, 14), time=6, population=0)
+CoalescenceRecord(left=0.0, right=0.8212435323883007, node=8, children=(12,), time=6, population=0)
+CoalescenceRecord(left=0.0, right=1.0, node=7, children=(11,), time=6, population=0)
+CoalescenceRecord(left=0.8212435323883007, right=1.0, node=6, children=(12,), time=6, population=0)
+====================== 1 failed, 5 passed in 0.19 seconds ======================

ftprime/argrecorder.py

@@ -132,9 +132,9 @@ def merge_records(new,existing) :
                         children=children, 
                         time=time, 
                         population=population)
-                existing[k]=mod_rec
+                existing[k]=combined_rec
                 k+=1
-                existing.insert(k,combined_rec)
+                existing.insert(k,mod_rec)
                 k+=1
             else:
                 # print("dangling right")

tests/test_merge_records_with_wf.py

@@ -2,6 +2,9 @@
 import msprime
 from wf import wf
 
+def cr(l,r,n,ch,t,pop=0):
+    msprime.CoalescenceRecord(left=l, right=r, node=n, children=ch, time=t, population=pop)
+
 def test_1():
 
     new_rec=msprime.CoalescenceRecord(left=0.8, right=1.0, node=18, children=(22,), time=2, population=0)
@@ -68,3 +71,6 @@ def test_simulation_runs():
     print("Mean pairwise diversity:",ts.get_pairwise_diversity())
     print("(should be zero)")
     assert ts.get_pairwise_diversity() == 0.0
+
+    tss=ts.simplify()
+    assert tss.get_pairwise_diversity() == 0.0

tests/wf/__init__.py

@@ -51,6 +51,14 @@ def wf(N,ngens,nsamples,survival=0.0) :
                 records.add_record( left=bp, right=1.0, parent=rparent, children=(offspring,))
         # print(records)
 
+    # Hackishly, add imaginary entry so smallest internal node is equal to number of samples
+    for ind in records.keys():
+        print("ind:",ind)
+        if len(records[ind][1])>0:
+            if ind > nsamples:
+                records.add_record(left=0.0,right=1.0,parent=nsamples,children=(next(labels),))
+            break
+
     # add phony records that stand in for sampling
     samples=random.sample(pop,nsamples)
     records.add_samples(samples=samples,length=1.0)