Fix compatibility with Python 3.11

.github/workflows/python-app.yml

@@ -28,10 +28,10 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
-      - name: Install boost
-        run: |
-          sudo apt-get install libboost-all-dev
-          ln -s /usr/include/boost/ ./boost_1_70_0
+      # - name: Install boost
+      #   run: |
+      #     sudo apt-get install libboost1.74-all-dev
+      #     ln -s /usr/include/boost/ ./boost_1_74_0
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

requirements.txt

@@ -1,2 +1,3 @@
 numpy
 matplotlib
+setuptools

setup.py

@@ -98,8 +98,8 @@ def is_maverick():
 # versions are not available, and will most likely work just fine.
 boost_versions = ['1_35_0', '1_36_0', '1_37_0', '1_38_0', '1_39_0', '1_40_0',
     '1_42_0', '1_43_0', '1_44_0', '1_45_0', '1_46_0', '1_46_1', '1_47_0',
-    '1_48_0', '1_70_0']
-invalid_boost_versions = ['1_41_0']
+    '1_48_0', '1_62_0', '1_72_0', '1_74_0']
+invalid_boost_versions = ['1_41_0', '1_71_0']
 
 included_version = [x for x in boost_versions if os.path.isdir('boost_' + x)]
 invalid_version = [x for x in invalid_boost_versions if os.path.isdir('boost_' + x)]
@@ -127,23 +127,25 @@ def downloadProgress(count, blockSize, totalSize):
     import tarfile
     downloadProgress.counter = 0
     try:
-        BOOST_URL = 'http://downloads.sourceforge.net/project/boost/boost/1.70.0/boost_1_70_0.tar.gz?r=&ts=1440446866&use_mirror=iweb'
-        sys.stdout.write('Downloading boost C++ library 1.70.0 ')
+        boost_version = boost_versions[-1]
+        dot_boost_version = boost_version.replace('_', '.')
+        BOOST_URL = f'http://downloads.sourceforge.net/project/boost/boost/{dot_boost_version}/boost_{boost_version}.tar.gz?r=&ts=1440446866&use_mirror=iweb'
+        sys.stdout.write(f'Downloading boost C++ library {dot_boost_version}')
         sys.stdout.flush()
-        if not os.path.isfile('boost_1_70_0.tar.gz'):
-            urlretrieve(BOOST_URL, 'boost_1_70_0.tar.gz', downloadProgress)
+        if not os.path.isfile(f'boost_{boost_version}.tar.gz'):
+            urlretrieve(BOOST_URL, f'boost_{boost_version}.tar.gz', downloadProgress)
         sys.stdout.write('\n')
         # extract needed files
-        with tarfile.open('boost_1_70_0.tar.gz', 'r:gz') as tar:
-            files = [h for h in tar.getmembers() if h.name.startswith('boost_1_70_0/boost') \
-                or h.name.startswith('boost_1_70_0/libs/iostreams') \
-                or h.name.startswith('boost_1_70_0/libs/serialization') \
-                or h.name.startswith('boost_1_70_0/libs/regex') \
-                or h.name.startswith('boost_1_70_0/libs/detail') ]
+        with tarfile.open(f'boost_{boost_version}.tar.gz', 'r:gz') as tar:
+            files = [h for h in tar.getmembers() if h.name.startswith(f'boost_{boost_version}/boost') \
+                or h.name.startswith(f'boost_{boost_version}/libs/iostreams') \
+                or h.name.startswith(f'boost_{boost_version}/libs/serialization') \
+                or h.name.startswith(f'boost_{boost_version}/libs/regex') \
+                or h.name.startswith(f'boost_{boost_version}/libs/detail') ]
             sys.stdout.write('Extracting %d files\n' % len(files))
             tar.extractall(members=files)
         EMBEDED_BOOST = True
-        boost_dir = 'boost_1_70_0'
+        boost_dir = f'boost_{boost_version}'
     except Exception as e:
         print(e)
         print('The boost C++ library version 1.49.0 is not found under the current directory. Will try to use the system libraries.')
@@ -766,6 +768,3 @@ def ModuInfo(modu, SIMUPOP_VER, SIMUPOP_REV):
         cmdclass = {'build_py': build_py},
         **setup_params
     )
-
-
-

src/sampling.py

@@ -92,8 +92,6 @@
     MALE, AFFECTED, tagID, getRNG
 
 import random
-def random_shuffle(x):
-    random.shuffle(x, getRNG().randUniform)
 
 def isSequence(obj):
     return hasattr(obj, '__iter__')
@@ -173,7 +171,7 @@ def drawSamples(self, pop, numOfSamples):
         '''
         if numOfSamples < 0:
             raise ValueError("Negative number of samples are unacceptable")
-        # 
+        #
         return [self.drawSample(pop) for x in range(numOfSamples)]
 
 
@@ -200,7 +198,7 @@ def drawSample(self, input_pop):
                 size = self.pop.popSize()
             # randomly choose size individuals
             values = list(range(self.pop.popSize()))
-            random_shuffle(values)
+            random.shuffle(values)
             indexes = values[:size]
         else:
             indexes = []
@@ -210,7 +208,7 @@ def drawSample(self, input_pop):
                     print('Warning: sample size (%d) at subpopulation %d is greater than subpopulation size %d ' \
                         % (size, sp, self.pop.subPopSize(sp)))
                 values = list(range(self.pop.subPopBegin(sp), self.pop.subPopEnd(sp)))
-                random_shuffle(values)
+                random.shuffle(values)
                 indexes.extend(values[:size])
         return self.pop.extractIndividuals(indexes = indexes)
 
@@ -308,14 +306,14 @@ def drawSample(self, input_pop):
             self.prepareSample(input_pop)
         #
         if not isSequence(self.cases):
-            random_shuffle(self.affected)
-            random_shuffle(self.unaffected)
+            random.shuffle(self.affected)
+            random.shuffle(self.unaffected)
             indexes = self.affected[:self.cases] + self.unaffected[:self.controls]
         else:
             indexes = []
             for sp in range(self.pop.numSubPop()):
-                random_shuffle(self.affected[sp])
-                random_shuffle(self.unaffected[sp])
+                random.shuffle(self.affected[sp])
+                random.shuffle(self.unaffected[sp])
                 indexes.extend(self.affected[sp][:self.cases[sp]])
                 indexes.extend(self.unaffected[sp][:self.controls[sp]])
         return self.pop.extractIndividuals(indexes = indexes)
@@ -332,7 +330,7 @@ def drawCaseControlSample(pop, cases, controls, subPops=ALL_AVAIL):
     specified (virtual) subpopulations. This function returns a population with
     all extracted individuals.
     '''
-    return CaseControlSampler(cases, controls, subPops).drawSample(pop) 
+    return CaseControlSampler(cases, controls, subPops).drawSample(pop)
 
 
 def drawCaseControlSamples(pop, cases, controls, numOfSamples=1, subPops=ALL_AVAIL):
@@ -341,7 +339,7 @@ def drawCaseControlSamples(pop, cases, controls, numOfSamples=1, subPops=ALL_AVA
     populations. Please refer to function ``drawCaseControlSample`` for a
     detailed descriptions of parameters.
     '''
-    return CaseControlSampler(cases, controls, subPops).drawSamples(pop, numOfSamples) 
+    return CaseControlSampler(cases, controls, subPops).drawSamples(pop, numOfSamples)
 
 
 class PedigreeSampler(BaseSampler):
@@ -399,7 +397,7 @@ def drawSample(self, input_pop):
                     % (self.families, len(self.selectedIDs)))
             # a tuple might be returned
             self.selectedIDs = list(self.selectedIDs)
-            random_shuffle(self.selectedIDs)
+            random.shuffle(self.selectedIDs)
             # we select families one by one to exclude overlapping families.
             IDs = set()
             cnt = 0
@@ -422,7 +420,7 @@ def drawSample(self, input_pop):
                 #
                 # a tuple might be returned
                 self.selectedIDs[sp] = list(self.selectedIDs[sp])
-                random_shuffle(self.selectedIDs[sp])
+                random.shuffle(self.selectedIDs[sp])
                 # we select families one by one to exclude overlapping families.
                 cnt = 0
                 for id in self.selectedIDs[sp]:
@@ -475,7 +473,7 @@ def prepareSample(self, input_pop):
                     subPops=sp))
 
 
-def drawAffectedSibpairSample(pop, families, subPops=ALL_AVAIL, 
+def drawAffectedSibpairSample(pop, families, subPops=ALL_AVAIL,
     idField='ind_id', fatherField='father_id', motherField='mother_id'):
     '''Draw affected sibpair samples from a population. If a single
     ``families`` is given, affected sibpairs and their parents are drawn
@@ -488,9 +486,9 @@ def drawAffectedSibpairSample(pop, families, subPops=ALL_AVAIL,
     '''
     return AffectedSibpairSampler(families, subPops, idField, fatherField,
         motherField).drawSample(pop)
-
 
-def drawAffectedSibpairSamples(pop, families, numOfSamples=1, subPops=ALL_AVAIL, 
+
+def drawAffectedSibpairSamples(pop, families, numOfSamples=1, subPops=ALL_AVAIL,
     idField='ind_id', fatherField='father_id', motherField='mother_id'):
     '''Draw ``numOfSamples`` affected sibpair samplesa from population ``pop`` and
     return a list of populations. Please refer to function
@@ -625,7 +623,7 @@ def drawNuclearFamilySample(pop, families, numOffspring, affectedParents=0,
     '''
     return NuclearFamilySampler(families, numOffspring, affectedParents,
         affectedOffspring, subPops, idField, fatherField, motherField).drawSample(pop)
- 
+
 
 def drawNuclearFamilySamples(pop, families, numOffspring, affectedParents=0,
     affectedOffspring=0, numOfSamples=1, subPops=ALL_AVAIL, idField='ind_id',
@@ -777,7 +775,7 @@ def drawThreeGenFamilySample(pop, families, numOffspring, pedSize, numOfAffected
     '''
     return ThreeGenFamilySampler(families, numOffspring, pedSize, numOfAffected,
         subPops, idField, fatherField, motherField).drawSample(pop)
- 
+
 
 def drawThreeGenFamilySamples(pop, families, numOffspring, pedSize, numOfAffected=0,
     numOfSamples=1, subPops=ALL_AVAIL, idField='ind_id', fatherField='father_id',
@@ -836,4 +834,3 @@ def drawCombinedSamples(pop, samplers, numOfSamples=1, idField='ind_id'):
     parameters ``samplers`` and ``idField``.
     '''
     return CombinedSampler(samplers, idField=idField).drawSamples(pop, numOfSamples)
-