Merge remote-tracking branch 'upstream/maint/3.2.x'

Author: effigies

.travis.yml

@@ -16,10 +16,8 @@ env:
         - DEPENDS="numpy scipy matplotlib h5py pillow pydicom indexed_gzip"
         - INSTALL_TYPE="setup"
         - CHECK_TYPE="test"
-        - EXTRA_WHEELS="https://3f23b170c54c2533c070-1c8a9b3114517dc5fe17b7c3f8c63a43.ssl.cf2.rackcdn.com"
         - NIGHTLY_WHEELS="https://pypi.anaconda.org/scipy-wheels-nightly/simple"
-        - EXTRA_PIP_FLAGS="--find-links=$EXTRA_WHEELS"
-        - PRE_PIP_FLAGS="--pre $EXTRA_PIP_FLAGS --extra-index-url $NIGHTLY_WHEELS"
+        - PRE_PIP_FLAGS="--pre --extra-index-url $NIGHTLY_WHEELS"
 
 python:
     - 3.7
@@ -30,7 +28,7 @@ jobs:
     - arch: arm64
       python: 3.6
       env:
-        - DEPENDS="numpy"
+        - DEPENDS="numpy scipy pillow pydicom"
         - EXTRA_PIP_FLAGS="$PRE_PIP_FLAGS"
     # Basic dependencies only
     - python: 3.6
@@ -62,6 +60,11 @@ jobs:
     - python: 3.8
       env:
         - EXTRA_PIP_FLAGS="$PRE_PIP_FLAGS"
+    # test 3.9 against pre-release builds of dependencies that support it
+    - python: 3.9
+      env:
+        - DEPENDS="numpy scipy h5py pillow pydicom"
+        - EXTRA_PIP_FLAGS="$PRE_PIP_FLAGS"
     # OSX Python support is basically accidental. Take whatever version we can
     # get and test with full dependencies...
     - os: osx

.zenodo.json

@@ -171,7 +171,9 @@
       "orcid": "0000-0003-4662-0558"
     },
     {
-      "name": "Klug, Julian"
+      "affiliation": "University of Geneva, Switzerland",
+      "name": "Klug, Julian",
+      "orcid": "0000-0002-4849-9811"
     },
     {
       "affiliation": "SRI International",

Changelog

@@ -25,8 +25,20 @@ Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).
 
 References like "pr/298" refer to github pull request numbers.
 
+3.2.1 (Saturday 28 November 2020)
+=================================
+
+Bug fix release in the 3.2.x series.
+
+Maintenance
+-----------
+* Drop references to builtin types in Numpy namespace like ``np.float``
+  (pr/964) (EL, reviewed by CM)
+* Ensure compatibility with Python 3.9 (pr/963) (CM)
+
+
 3.2.0 (Tuesday 20 October 2020)
-==============================
+===============================
 
 New feature release in the 3.2.x series.
 

doc/source/old/ioimplementation.rst

@@ -101,10 +101,10 @@ By use case.
     >>> mod_data[0,0] = 99
     >>> np.all(img4.data = mod_data)
     True
-    
+
     Prepare image for later writing
 
-    >>> img5 = Image(np.zeros(2,3,4)) 
+    >>> img5 = Image(np.zeros(2,3,4))
     >>> fp, fname2 = tempfile.mkstemp('.nii')
     >>> img5.set_filespec(fname2)
     >>> # then do some things to the image
@@ -115,7 +115,7 @@ By use case.
     >>> from nibabel.ioimps import guessed_imp
     >>> fp, fname3 = tempfile.mkstemp('.nii')
     >>> ioimp = guessed_imp(fname3)
-    >>> ioimp.set_data_dtype(np.float)
+    >>> ioimp.set_data_dtype(np.float64)
     >>> ioimp.set_data_shape((2,3,4)) # set_data_shape method
     >>> slice_def = (slice(None), slice(None), 0)
     >>> ioimp.write_slice(data[slice_def], slice_def) # write_slice method
@@ -124,6 +124,3 @@ By use case.
     Traceback (most recent call last):
        ...
     ImageIOError: data write is not contiguous
-    
-    
-    

nibabel/benchmarks/bench_arrayproxy_slicing.py

@@ -46,7 +46,7 @@
     ('?', '?', '?', ':'),
 ]
 
-KEEP_OPENS = [False, True, 'auto']
+KEEP_OPENS = [False, True]
 
 if HAVE_INDEXED_GZIP:
     HAVE_IGZIP = [False, True]

nibabel/cifti2/parse_cifti2.py

@@ -517,28 +517,28 @@ def flush_chardata(self):
             # conversion to numpy array
             c = BytesIO(data.strip().encode('utf-8'))
             vertices = self.struct_state[-1]
-            vertices.extend(np.loadtxt(c, dtype=np.int, ndmin=1))
+            vertices.extend(np.loadtxt(c, dtype=int, ndmin=1))
             c.close()
 
         elif self.write_to == 'VoxelIndices':
             # conversion to numpy array
             c = BytesIO(data.strip().encode('utf-8'))
             parent = self.struct_state[-1]
-            parent.voxel_indices_ijk.extend(np.loadtxt(c, dtype=np.int).reshape(-1, 3))
+            parent.voxel_indices_ijk.extend(np.loadtxt(c, dtype=int).reshape(-1, 3))
             c.close()
 
         elif self.write_to == 'VertexIndices':
             # conversion to numpy array
             c = BytesIO(data.strip().encode('utf-8'))
             index = self.struct_state[-1]
-            index.extend(np.loadtxt(c, dtype=np.int, ndmin=1))
+            index.extend(np.loadtxt(c, dtype=int, ndmin=1))
             c.close()
 
         elif self.write_to == 'TransformMatrix':
             # conversion to numpy array
             c = BytesIO(data.strip().encode('utf-8'))
             transform = self.struct_state[-1]
-            transform.matrix = np.loadtxt(c, dtype=np.float)
+            transform.matrix = np.loadtxt(c, dtype=np.float64)
             c.close()
 
         elif self.write_to == 'Label':

nibabel/externals/netcdf.py

@@ -219,7 +219,7 @@ class netcdf_file(object):
 
         >>> data = time[:]
         >>> data.base.base  # doctest: +ELLIPSIS
-        <mmap.mmap object at 0x...>
+        <mmap.mmap ...>
 
     If the data is to be processed after the file is closed, it needs
     to be copied to main memory:

nibabel/freesurfer/io.py

@@ -49,7 +49,7 @@ def _fread3_many(fobj, n):
         An array of 3 byte int
     """
     b1, b2, b3 = np.fromfile(fobj, ">u1", 3 * n).reshape(-1,
-                                                         3).astype(np.int).T
+                                                         3).astype(int).T
     return (b1 << 16) + (b2 << 8) + b3
 
 
@@ -148,14 +148,14 @@ def read_geometry(filepath, read_metadata=False, read_stamp=False):
             nvert = _fread3(fobj)
             nquad = _fread3(fobj)
             (fmt, div) = (">i2", 100.) if magic == QUAD_MAGIC else (">f4", 1.)
-            coords = np.fromfile(fobj, fmt, nvert * 3).astype(np.float) / div
+            coords = np.fromfile(fobj, fmt, nvert * 3).astype(np.float64) / div
             coords = coords.reshape(-1, 3)
             quads = _fread3_many(fobj, nquad * 4)
             quads = quads.reshape(nquad, 4)
             #
             #   Face splitting follows
             #
-            faces = np.zeros((2 * nquad, 3), dtype=np.int)
+            faces = np.zeros((2 * nquad, 3), dtype=int)
             nface = 0
             for quad in quads:
                 if (quad[0] % 2) == 0:
@@ -182,7 +182,7 @@ def read_geometry(filepath, read_metadata=False, read_stamp=False):
         else:
             raise ValueError("File does not appear to be a Freesurfer surface")
 
-    coords = coords.astype(np.float)  # XXX: due to mayavi bug on mac 32bits
+    coords = coords.astype(np.float64)  # XXX: due to mayavi bug on mac 32bits
 
     ret = (coords, faces)
     if read_metadata:
@@ -589,7 +589,7 @@ def read_label(filepath, read_scalars=False):
         Only returned if `read_scalars` is True.  Array of scalar data for each
         vertex.
     """
-    label_array = np.loadtxt(filepath, dtype=np.int, skiprows=2, usecols=[0])
+    label_array = np.loadtxt(filepath, dtype=int, skiprows=2, usecols=[0])
     if read_scalars:
         scalar_array = np.loadtxt(filepath, skiprows=2, usecols=[-1])
         return label_array, scalar_array

nibabel/freesurfer/tests/test_io.py

@@ -157,7 +157,7 @@ def test_write_morph_data():
         with pytest.raises(ValueError):
             write_morph_data('test.curv', np.zeros(shape), big_num)
         # Windows 32-bit overflows Python int
-        if np.dtype(np.int) != np.dtype(np.int32):
+        if np.dtype(int) != np.dtype(np.int32):
             with pytest.raises(ValueError):
                 write_morph_data('test.curv',  strided_scalar((big_num,)))
         for shape in bad_shapes:

nibabel/minc1.py

@@ -137,7 +137,7 @@ def _get_valid_range(self):
         if valid_range[0] < info.min or valid_range[1] > info.max:
             raise ValueError('Valid range outside input '
                              'data type range')
-        return np.asarray(valid_range, dtype=np.float)
+        return np.asarray(valid_range, dtype=np.float64)
 
     def _get_scalar(self, var):
         """ Get scalar value from NetCDF scalar """