Added uses as syntax sugar for callbacks

4 files changed, 18 insertions, 10 deletions

diff --git a/wqflask/wqflask/my_pylmm/pyLMM/kinship.py b/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
index 43e7fe36..d3792570 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
@@ -155,13 +155,12 @@ def kinship(G,computeSize=1000,numThreads=None,useBLAS=False,verbose=True):
    #    np.savetxt(outFile+".kve",Kve)
    return K      
 
-def kvakve(K, callbacks):
+def kvakve(K, uses):
    """
    Obtain eigendecomposition for K and return Kva,Kve where Kva is cleaned
    of small values < 1e-6 (notably smaller than zero)
    """
-   info = callbacks()['info']
-   mprint = callbacks()['mprint']
+   info,mprint = uses('info','mprint')
 
    info("Obtaining eigendecomposition for %dx%d matrix" % (K.shape[0],K.shape[1]) )
    Kva,Kve = linalg.eigh(K)
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 5ad644e2..2076bc84 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -57,11 +57,11 @@ import gwas
 # ---- A trick to decide on the environment:
 try:
     from wqflask.my_pylmm.pyLMM import chunks
-    from gn2 import callbacks
+    from gn2 import uses
 except ImportError:
     print("WARNING: Standalone version missing the Genenetwork2 environment\n")
     has_gn2=False
-    from standalone import callbacks
+    from standalone import uses
     pass
 
 #np.seterr('raise')
@@ -597,7 +597,7 @@ class LMM:
           # if self.verbose: sys.stderr.write("Obtaining eigendecomposition for %dx%d matrix\n" % (K.shape[0],K.shape[1]) )
           begin = time.time()
           # Kva,Kve = linalg.eigh(K)
-          Kva,Kve = kvakve(K,callbacks)
+          Kva,Kve = kvakve(K,uses)
           end = time.time()
           if self.verbose: sys.stderr.write("Total time: %0.3f\n" % (end - begin))
           print("sum(Kva),sum(Kve)=",sum(Kva),sum(Kve))
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm2.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm2.py
index 6aefb9d3..5b93ae0d 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm2.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm2.py
@@ -24,14 +24,14 @@ from scipy import optimize
 from optmatrix import matrixMult
 import kinship
 
-# A trick to decide on the environment:
+# ---- A trick to decide on the environment:
 try:
     from wqflask.my_pylmm.pyLMM import chunks
-    from gn2 import callbacks
+    from gn2 import uses
 except ImportError:
     print("WARNING: Standalone version missing the Genenetwork2 environment\n")
     has_gn2=False
-    from standalone import callbacks
+    from standalone import uses
     pass
 
 def calculateKinship(W,center=False):
@@ -194,7 +194,7 @@ class LMM2:
           # if self.verbose: sys.stderr.write("Obtaining eigendecomposition for %dx%d matrix\n" % (K.shape[0],K.shape[1]) )
           begin = time.time()
           # Kva,Kve = linalg.eigh(K)
-          Kva,Kve = kinship.kvakve(K,callbacks)
+          Kva,Kve = kinship.kvakve(K,uses)
           end = time.time()
           if self.verbose: sys.stderr.write("Total time: %0.3f\n" % (end - begin))
           print("sum(Kva),sum(Kve)=",sum(Kva),sum(Kve))
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/standalone.py b/wqflask/wqflask/my_pylmm/pyLMM/standalone.py
index bbee3cd7..705da21f 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/standalone.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/standalone.py
@@ -44,6 +44,12 @@ def callbacks():
         progress = progress,
         mprint = mprint
     )
+
+def uses(*funcs):
+    """
+    Some sugar
+    """
+    return [callbacks()[func] for func in funcs]
     
 # ----- Minor test cases:
 
@@ -69,3 +75,6 @@ if __name__ == '__main__':
             [5,0.5,0.6096595 , -0.31559815, -0.52793285, 1.16573418e-15],
             [6,0.5,0.6096595 , -0.31559815, -0.52793285, 1.16573418e-15]]
     mprint("matrix",matrix)
+    ix,dx = uses("info","debug")
+    ix("ix")
+    dx("dx")