Merge pull request #46 from lldelisle/fix_new_numpy

Release 17

Author: bgruening

.gitignore

@@ -14,7 +14,6 @@ dist/
 downloads/
 eggs/
 .eggs/
-lib/
 lib64/
 parts/
 sdist/

azure-pipelines.yml

@@ -9,12 +9,14 @@ jobs:
     vmImage: 'ubuntu-latest'
   strategy:
     matrix:
-      Python36:
-        python.version: '3.6'
       Python37:
         python.version: '3.7'
       Python38:
         python.version: '3.8'
+      Python39:
+        python.version: '3.9'
+      Python310:
+        python.version: '3.10'
 
   steps:
   - bash: |
@@ -44,16 +46,17 @@ jobs:
 - job: 'OSX'
   timeoutInMinutes: 0
   pool:
-    vmImage: 'macOS-10.14'
+    vmImage: 'macOS-11'
   strategy:
     matrix:
-      Python36:
-        python.version: '3.6'
       Python37:
         python.version: '3.7'
       Python38:
         python.version: '3.8'
-
+      Python39:
+        python.version: '3.9'
+      Python310:
+        python.version: '3.10'
   steps:
   - bash: |
       echo "##vso[task.prependpath]$CONDA/bin"

hicmatrix/HiCMatrix.py

@@ -628,7 +628,7 @@ def keepOnlyTheseChr(self, chromosome_list):
         size = self.matrix.shape
         # initialize a 1D array containing the columns (and rows) to
         # select. By default none are selected
-        sel = np.empty(size[0], dtype=np.bool)
+        sel = np.empty(size[0], dtype=bool)
         sel[:] = False
 
         for chrName in list(self.interval_trees):

hicmatrix/_version.py

@@ -1,2 +1,2 @@
-__version__ = '16'
+__version__ = '17'
 # Version number differs from HiCExplorer!

hicmatrix/lib/cool.py

@@ -94,13 +94,13 @@ def load(self):
                 del _features
 
             if self.matrixFormat is None or self.matrixFormat == 'csr':
-                matrix = csr_matrix((data, (instances, features)), shape=(np.int(cooler_file.info['nbins']), np.int(cooler_file.info['nbins'])), dtype=count_dtype)
+                matrix = csr_matrix((data, (instances, features)), shape=(int(cooler_file.info['nbins']), int(cooler_file.info['nbins'])), dtype=count_dtype)
             elif self.matrixFormat == 'lil':
-                matrix = lil_matrix((data, (instances, features)), shape=(np.int(cooler_file.info['nbins']), np.int(cooler_file.info['nbins'])), dtype=count_dtype)
+                matrix = lil_matrix((data, (instances, features)), shape=(int(cooler_file.info['nbins']), int(cooler_file.info['nbins'])), dtype=count_dtype)
             elif self.matrixFormat == 'dok':
-                matrix = dok_matrix((data, (instances, features)), shape=(np.int(cooler_file.info['nbins']), np.int(cooler_file.info['nbins'])), dtype=count_dtype)
+                matrix = dok_matrix((data, (instances, features)), shape=(int(cooler_file.info['nbins']), int(cooler_file.info['nbins'])), dtype=count_dtype)
             # elif  self.matrixFormat == 'raw':
-            #     matrix = [instances, features, data, np.int(cooler_file.info['nbins'])]
+            #     matrix = [instances, features, data, int(cooler_file.info['nbins'])]
             del data
             del instances
             del features
@@ -116,7 +116,7 @@ def load(self):
             data = matrixDataFrameChunk['count'].values.astype(count_dtype)
             instances = matrixDataFrameChunk['bin1_id'].values.astype(used_dtype)
             features = matrixDataFrameChunk['bin2_id'].values.astype(used_dtype)
-            # matrix = [_instances, _features, _data, np.int(cooler_file.info['nbins'])]
+            # matrix = [_instances, _features, _data, int(cooler_file.info['nbins'])]
             # return matrix, None, None, None, None
         else:
             if len(self.chrnameList) == 1:
@@ -219,7 +219,7 @@ def load(self):
                             log.debug('div')
                             data /= instances_factors
                         log.debug('non')
-                        return [instances, features, data, np.int(cooler_file.info['nbins'])], None, None, None, None
+                        return [instances, features, data, int(cooler_file.info['nbins'])], None, None, None, None
                     else:
                         if self.correctionOperator == '*':
                             matrix.data *= instances_factors
@@ -229,7 +229,7 @@ def load(self):
                             log.debug('hu')
 
         elif self.matrixOnly:
-            return [instances, features, data, np.int(cooler_file.info['nbins'])], None, None, None, None
+            return [instances, features, data, int(cooler_file.info['nbins'])], None, None, None, None
 
         cut_intervals = []
         if not self.noCutIntervals:

hicmatrix/test/test_HiCMatrix.py

@@ -561,7 +561,7 @@ def test_reorderChromosomes_fail():
     false_chr_order = ['a', 'b', 'c']
     with pytest.raises(Exception) as context:
         hic.reorderChromosomes(false_chr_order)
-    assert("Chromosome name 'c' not found." in str(context.value))
+    assert "Chromosome name 'c' not found." in str(context.value)
 
 
 def test_reorderBins():

requirements.txt

@@ -1,4 +1,4 @@
-numpy >= 1.16.*
+numpy >= 1.20
 scipy >= 1.2.*
 pandas >= 0.25.*
 pytables >= 3.5.*

setup.py

@@ -93,7 +93,7 @@ def checkProgramIsInstalled(self, program, args, where_to_download,
             sys.stderr.write("Error: {}".format(e))
 
 
-install_requires_py = ["numpy >= 1.16.*",
+install_requires_py = ["numpy >= 1.20",
                        "scipy >= 1.2.*",
                        "tables >= 3.5.*",
                        "pandas >= 0.25.*",