Auto-merged develop -> beta (No conflicts, CI passed)

.travis.yml

@@ -24,15 +24,16 @@ before_install:
   - sudo apt-get -qq update
   - sudo apt-get -qq install gfortran libblas-dev liblapack-dev
   - sudo apt-get -qq install openmpi-bin openmpi-common openssh-client openssh-server libopenmpi1.3 libopenmpi-dbg libopenmpi-dev >/dev/null
-  - sudo bash CI/install.sh # Only install texlive and extensions if we need them
+  - travis_wait 30 "sudo bash CI/install.sh >/dev/null"
   - "export DISPLAY=:99.0"
   - "sh -e /etc/init.d/xvfb start" #some tests require a display
   - sleep 3 # give xvfb some time to start
 
+# I'm attempting to remove this..?
+#- pip install --global-option=build_ext --global-option="-I/usr/include/suitesparse" cvxpy cvxopt
 install:
   - travis_retry travis_wait pip install -r requirements.txt
-  - pip install --global-option=build_ext --global-option="-I/usr/include/suitesparse" cvxpy cvxopt >/dev/null
-  - pip install ipython mpi4py zmq coverage msgpack-python cython psutil >/dev/null
+  - pip install ipython mpi4py zmq coverage msgpack-python cython dill psutil >/dev/null
   - pip install -e . >/dev/null
 
 cache:

CI/install.sh

@@ -1,5 +1,6 @@
 #!/bin/bash
 # This script needs to be run as admin
+sudo apt-get update
 
 ##An example of how to search for a file in apt packages
 ## (useful for debugging TravisCI build errors)
@@ -19,46 +20,36 @@
 apt-get install libsuitesparse-dev
 cp /usr/lib/liblapack.so /usr/lib/libsuitesparseconfig.so
 
+sudo add-apt-repository ppa:ubuntu-toolchain-r/test
+sudo apt-get update
 
-#Latex is no longer needed!
-#echo "Checking if pdflatex install is needed"
-#
-#if [ "$ReportA" == "True" ]; then
-#    apt-get -qq install texlive-full
-#fi
-#
-#if [ "$Drivers" == "True" ]; then
-#    apt-get -qq install texlive-latex-base
-#fi
-#
-#if [ "$ReportA" == "True" ] || [ "$Drivers" == "True" ]; then
-#    echo "Installing pdflatex requirements"
-#    pushd /usr/share/texmf-texlive/
-#    wget http://mirrors.ctan.org/install/macros/latex/contrib/etoolbox.tds.zip
-#    wget http://mirrors.ctan.org/install/macros/latex/contrib/adjustbox.tds.zip
-#    wget http://mirrors.ctan.org/install/macros/latex/contrib/collectbox.tds.zip
-#    wget http://mirrors.ctan.org/install/macros/latex/contrib/pdfcomment.tds.zip
-#    wget http://mirrors.ctan.org/install/macros/latex/contrib/datetime2.tds.zip
-#    wget http://mirrors.ctan.org/install/macros/generic/tracklang.tds.zip
-#    wget http://mirrors.ctan.org/install/macros/latex/contrib/bezos.tds.zip
-#    wget http://mirrors.ctan.org/install/macros/latex/contrib/hyperref.tds.zip
-#    wget http://mirrors.ctan.org/install/macros/latex/contrib/oberdiek.tds.zip
-#    wget http://mirrors.ctan.org/install/macros/generic/ifxetex.tds.zip
-#    wget http://mirrors.ctan.org/install/macros/latex/contrib/standalone.tds.zip
-#    unzip -o etoolbox.tds.zip 
-#    unzip -o adjustbox.tds.zip 
-#    unzip -o collectbox.tds.zip 
-#    unzip -o pdfcomment.tds.zip 
-#    unzip -o datetime2.tds.zip 
-#    unzip -o tracklang.tds.zip 
-#    unzip -o bezos.tds.zip 
-#    unzip -o hyperref.tds.zip 
-#    unzip -o oberdiek.tds.zip 
-#    unzip -o ifxetex.tds.zip 
-#    unzip -o standalone.tds.zip 
-#    texhash  
-#    popd
-#else
-#    echo "pdflatex is not required for these tests (ReportA is not set to \"True\")"
-#fi
+sudo update-alternatives --remove-all gcc
+sudo update-alternatives --remove-all g++
+sudo apt-get install gcc-4.8
+sudo apt-get install g++-4.8
+sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 20
+sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 20
+sudo update-alternatives --config gcc
+sudo update-alternatives --config g++
+sudo apt-get update
+sudo apt-get upgrade -y
+sudo apt-get dist-upgrade
 
+export CXX=g++
+
+sudo apt remove cmake
+
+# Install the following version of CMAKE
+version=3.11
+build=1
+mkdir ~/temp
+cd ~/temp
+wget https://cmake.org/files/v$version/cmake-$version.$build.tar.gz
+tar -xzvf cmake-$version.$build.tar.gz
+cd cmake-$version.$build/
+./bootstrap
+make -j4
+sudo make install
+cd ..
+rm -r temp
+cmake --version

optional-requirements.txt

@@ -1,5 +1,4 @@
 ### Optional Requirements ###
-cvxpy
 mpi4py
 deap
 psutil

packages/pygsti/construction/datasetconstruction.py

@@ -67,7 +67,7 @@ def generate_fake_data(gatesetOrDataset, gatestring_list, nSamples,
         manually incrementing seeds between those calls.
 
     aliasDict : dict, optional
-        A dictionary mapping single gate labels into tuples of one or more 
+        A dictionary mapping single gate labels into tuples of one or more
         other gate labels which translate the given gate strings before values
         are computed using `gatesetOrDataset`.  The resulting Dataset, however,
         contains the *un-translated* gate strings as keys.
@@ -78,7 +78,7 @@ def generate_fake_data(gatesetOrDataset, gatestring_list, nSamples,
 
     comm : mpi4py.MPI.Comm, optional
         When not ``None``, an MPI communicator for distributing the computation
-        across multiple processors and ensuring that the *same* dataset is 
+        across multiple processors and ensuring that the *same* dataset is
         generated on each processor.
 
 
@@ -89,7 +89,7 @@ def generate_fake_data(gatesetOrDataset, gatestring_list, nSamples,
 
     """
     TOL = 1e-10
-    
+
     if isinstance(gatesetOrDataset, _ds.DataSet):
         dsGen = gatesetOrDataset
         gsGen = None
@@ -111,42 +111,64 @@ def generate_fake_data(gatesetOrDataset, gatestring_list, nSamples,
                                       for s in gatestring_list ]
             all_probs = gsGen.bulk_probs(trans_gatestring_list)
             #all_dprobs = gsGen.bulk_dprobs(gatestring_list) #DEBUG - not needed here!!!
-                
+
         for k,s in enumerate(gatestring_list):
 
             #print("DB GEN %d of %d (len %d)" % (k,len(gatestring_list),len(s)))
             trans_s = _gstrc.translate_gatestring(s, aliasDict)
             if gsGen:
                 ps = all_probs[trans_s]
-    
+
                 if sampleError in ("binomial","multinomial"):
                     #Adjust to probabilities if needed (and warn if not close to in-bounds)
-                    for ol in ps: 
+                    for ol in ps:
                         if ps[ol] < 0:
                             if ps[ol] < -TOL: _warnings.warn("Clipping probs < 0 to 0")
                             ps[ol] = 0.0
-                        elif ps[ol] > 1: 
+                        elif ps[ol] > 1:
                             if ps[ol] > (1+TOL): _warnings.warn("Clipping probs > 1 to 1")
                             ps[ol] = 1.0
             else:
                 ps = _collections.OrderedDict([ (ol,frac) for ol,frac
                                                 in dsGen[trans_s].fractions.items()])
-                            
+
             if gsGen and sampleError in ("binomial","multinomial"):
                 #Check that sum ~= 1 (and nudge if needed) since binomial and
                 #  multinomial random calls assume this.
                 psum = sum(ps.values())
-                if psum > 1:
-                    if psum > 1+TOL: _warnings.warn("Adjusting sum(probs) > 1 to 1")
-                    extra_p = (psum-1.0) * (1.000000001) # to sum < 1+eps (numerical prec insurance)
-                    for lbl in ps:
-                        if extra_p > 0:
-                            x = min(ps[lbl],extra_p)
-                            ps[lbl] -= x; extra_p -= x
-                        else: break
-                #TODO: add adjustment if psum < 1?
-                assert(1.-TOL <= sum(ps.values()) <= 1.+TOL)
-
+                adjusted = False
+                if psum > 1+TOL:
+                    adjusted = True
+                    _warnings.warn("Adjusting sum(probs) > 1 to 1")
+                if psum < 1-TOL:
+                    adjusted = True
+                    _warnings.warn("Adjusting sum(probs) < 1 to 1")
+                # The following while loop is needed if the data generating gateset
+                # is bad enough that one loop over the probabilities is not enough
+                OVERTOL  = 1.0 + TOL
+                UNDERTOL = 1.0 - TOL
+                normalized = lambda : UNDERTOL <= sum(ps.values()) <= OVERTOL
+                while not normalized():
+                    if psum > 1:
+                        extra_p = (psum-1.0) * OVERTOL
+                        for lbl in ps:
+                            if extra_p > 0:
+                                x = min(ps[lbl],extra_p)
+                                ps[lbl] -= x; extra_p -= x
+                            else: break
+                    elif psum < 1:
+                        needed_p = abs((psum-1.0) * UNDERTOL)
+                        for lbl in ps:
+                            if needed_p > 0:
+                                x = min(ps[lbl], needed_p)
+                                ps[lbl] += x # ADD here rather than subtract
+                                needed_p -= x
+                            else: break
+                    psum = sum(ps.values())
+                assert normalized(), 'psum={}'.format(psum)
+                if adjusted:
+                    _warnings.warn('Adjustment finished')
+
             if nSamples is None and dsGen is not None:
                 N = dsGen[trans_s].total #use the number of samples from the generating dataset
                  #Note: total() accounts for other intermediate-measurment branches automatically
@@ -155,27 +177,27 @@ def generate_fake_data(gatesetOrDataset, gatestring_list, nSamples,
                     N = nSamples[k] #try to treat nSamples as a list
                 except:
                     N = nSamples #if not indexable, nSamples should be a single number
-        
+
             #Weight the number of samples according to a WeightedGateString
             if isinstance(s, _gs.WeightedGateString):
                 nWeightedSamples = int(round(s.weight * N))
             else:
                 nWeightedSamples = N
-    
+
             counts = {} #don't use an ordered dict here - add_count_dict will sort keys
             labels = sorted(list(ps.keys())) # "outcome labels" - sort for consistent generation
             if sampleError == "binomial":
                 assert(len(labels) == 2)
                 ol0,ol1 = labels[0], labels[1]
                 counts[ol0] = rndm.binomial(nWeightedSamples, ps[ol0])
                 counts[ol1] = nWeightedSamples - counts[ol0]
-                
+
             elif sampleError == "multinomial":
                 countsArray = rndm.multinomial(nWeightedSamples,
-                        [ps[ol] for ol in labels], size=1) # well-ordered list of probs
+                        sorted([ps[ol] for ol in labels]), size=1) # well-ordered list of probs
                 for i,ol in enumerate(labels):
                     counts[ol] = countsArray[0,i]
-                    
+
             else:
                 for outcomeLabel,p in ps.items():
                     pc = _np.clip(p,0,1)
@@ -184,13 +206,13 @@ def generate_fake_data(gatesetOrDataset, gatestring_list, nSamples,
                     elif sampleError == "round":
                         counts[outcomeLabel] = int(round(nWeightedSamples*pc))
                     else: raise ValueError("Invalid sample error parameter: '%s'  Valid options are 'none', 'round', 'binomial', or 'multinomial'" % sampleError)
-                    
+
             dataset.add_count_dict(s, counts)
         dataset.done_adding_data()
 
     if comm is not None: # broadcast to non-root procs
         dataset = comm.bcast(dataset if (comm.Get_rank() == 0) else None,root=0)
-                    
+
     return dataset
 
 
@@ -199,20 +221,20 @@ def merge_outcomes(dataset,label_merge_dict):
     Creates a DataSet which merges certain outcomes in input DataSet;
     used, for example, to aggregate a 2-qubit 4-outcome DataSet into a 1-qubit 2-outcome
     DataSet.
-    
+
     Parameters
     ----------
     dataset : DataSet object
-        The input DataSet whose results will be compiled according to the rules 
+        The input DataSet whose results will be compiled according to the rules
         set forth in label_merge_dict
 
     label_merge_dict : dictionary
-        The dictionary whose keys define the new DataSet outcomes, and whose items 
+        The dictionary whose keys define the new DataSet outcomes, and whose items
         are lists of input DataSet outcomes that are to be summed together.  For example,
         if a two-qubit DataSet has outcome labels "00", "01", "10", and "11", and
         we want to ''trace out'' the second qubit, we could use label_merge_dict =
         {'0':['00','01'],'1':['10','11']}.
-    
+
     Returns
     -------
     merged_dataset : DataSet object

packages/pygsti/tools/profile.py

@@ -0,0 +1,21 @@
+import cProfile
+from mpi4py import MPI
+
+def profile(filename=None, comm=MPI.COMM_WORLD):
+  def prof_decorator(f):
+    def wrap_f(*args, **kwargs):
+      pr = cProfile.Profile()
+      pr.enable()
+      result = f(*args, **kwargs)
+      pr.disable()
+
+      if filename is None:
+        pr.print_stats()
+      else:
+        filename_r = filename #+ ".{}".format(comm.rank)
+        pr.dump_stats(filename_r)
+
+      return result
+    return wrap_f
+  return prof_decorator
+

requirements.txt

@@ -5,3 +5,6 @@ plotly
 ply
 nose
 msgpack # For IO specifically.. make optional?
+# Since this is needed to complete unit tests, I'm making it fully required - LSaldyt
+cvxopt
+cvxpy~=0.2.28

test/checkDocs.py

@@ -2,31 +2,47 @@
 import os.path, importlib, pkgutil, sys
 import pygsti
 
+from pprint import pprint
+
 from inspect import *
+import inspect
+
+missing = []
+
+def check_args_in_docstring(item):
+    args, _, kwargs, _ = getargspec(item)
+    if kwargs is None:
+        kwargs = []
+    for arg in args + [k for k, v in kwargs]:
+        if item.__doc__ is None or arg not in item.__doc__:
+            missing.append(item)
 
 def check_function(f):
-    pass
+    print('Checking function')
+    check_args_in_docstring(f)
 
 def check_class(c):
-    pass
+    check(c)
 
 def check_method(m):
-    pass
+    check_args_in_docstring(m)
 
-def check_module(module):
+def check(module):
     for member in getmembers(module):
-        if isfunction(member):
-            pass
-        if ismethod(member):
-            pass
-        if isclass(member):
-            pass
-        if ismodule(member):
-            check_module(member)
-        print(member)
+        if 'pygsti' in str(member[1]):
+            name, member = member
+            if isfunction(member):
+                check_function(member)
+            if ismethod(member):
+                check_method(member)
+            if isclass(member):
+                check_class(member)
+            if ismodule(member):
+                check(member)
 
 def main(args):
-    check_module(pygsti)
+    check(pygsti)
+    pprint(missing)
     return 0
 
 if __name__ == '__main__':