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

effigies · effigies · commit e53db3dcf08c · 2020-11-29T07:34:26.000-05:00
diff --git a/.travis.yml b/.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
diff --git a/.zenodo.json b/.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",
diff --git a/Changelog b/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.
 
diff --git a/doc/source/old/ioimplementation.rst b/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
-    
-    
-    
diff --git a/nibabel/benchmarks/bench_arrayproxy_slicing.py b/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]
diff --git a/nibabel/cifti2/parse_cifti2.py b/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':
diff --git a/nibabel/externals/netcdf.py b/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:
diff --git a/nibabel/freesurfer/io.py b/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
diff --git a/nibabel/freesurfer/tests/test_io.py b/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:
diff --git a/nibabel/minc1.py b/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 """
diff --git a/nibabel/minc2.py b/nibabel/minc2.py
@@ -101,7 +101,7 @@ 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 HDF5 scalar """
diff --git a/nibabel/nicom/ascconv.py b/nibabel/nicom/ascconv.py
@@ -89,7 +89,10 @@ def assign2atoms(assign_ast, default_class=int):
             target = target.value
             prev_target_type = OrderedDict
         elif isinstance(target, ast.Subscript):
-            index = target.slice.value.n
+            if isinstance(target.slice, ast.Constant):  # PY39
+                index = target.slice.n
+            else:  # PY38
+                index = target.slice.value.n
             atoms.append(Atom(target, prev_target_type, index))
             target = target.value
             prev_target_type = list
diff --git a/nibabel/quaternions.py b/nibabel/quaternions.py
@@ -28,8 +28,8 @@
 import math
 import numpy as np
 
-MAX_FLOAT = np.maximum_sctype(np.float)
-FLOAT_EPS = np.finfo(np.float).eps
+MAX_FLOAT = np.maximum_sctype(float)
+FLOAT_EPS = np.finfo(float).eps
 
 
 def fillpositive(xyz, w2_thresh=None):
@@ -43,7 +43,7 @@ def fillpositive(xyz, w2_thresh=None):
        threshold to determine if w squared is really negative.
        If None (default) then w2_thresh set equal to
        ``-np.finfo(xyz.dtype).eps``, if possible, otherwise
-       ``-np.finfo(np.float).eps``
+       ``-np.finfo(np.float64).eps``
 
     Returns
     -------
diff --git a/nibabel/tests/test_arraywriters.py b/nibabel/tests/test_arraywriters.py
@@ -468,7 +468,7 @@ def test_io_scaling():
 
 def test_input_ranges():
     # Test we get good precision for a range of input data
-    arr = np.arange(-500, 501, 10, dtype=np.float)
+    arr = np.arange(-500, 501, 10, dtype=np.float64)
     bio = BytesIO()
     working_type = np.float32
     work_eps = np.finfo(working_type).eps
@@ -542,7 +542,7 @@ def test_nan2zero():
 def test_byte_orders():
     arr = np.arange(10, dtype=np.int32)
     # Test endian read/write of types not requiring scaling
-    for tp in (np.uint64, np.float, np.complex):
+    for tp in (np.uint64, np.float64, np.complex128):
         dt = np.dtype(tp)
         for code in '<>':
             ndt = dt.newbyteorder(code)
@@ -554,7 +554,7 @@ def test_byte_orders():
 
 
 def test_writers_roundtrip():
-    ndt = np.dtype(np.float)
+    ndt = np.dtype(np.float64)
     arr = np.arange(3, dtype=ndt)
     # intercept
     aw = SlopeInterArrayWriter(arr, ndt, calc_scale=False)
@@ -831,7 +831,7 @@ def test_finite_range_nan():
         ([np.inf, 1], (1, 1)),  # only look at finite values
         ([-np.inf, 1], (1, 1)),
         ([[], []], (np.inf, -np.inf)),  # empty array
-        (np.array([[-3, 0, 1], [2, -1, 4]], dtype=np.int), (-3, 4)),
+        (np.array([[-3, 0, 1], [2, -1, 4]], dtype=int), (-3, 4)),
         (np.array([[1, 0, 1], [2, 3, 4]], dtype=np.uint), (0, 4)),
         ([0., 1, 2, 3], (0, 3)),
         # Complex comparison works as if they are floats
@@ -859,7 +859,7 @@ def test_finite_range_nan():
                 # Check float types work as complex
                 in_arr = np.array(in_arr)
                 if in_arr.dtype.kind == 'f':
-                    c_arr = in_arr.astype(np.complex)
+                    c_arr = in_arr.astype(np.complex128)
                     try:
                         aw = awt(c_arr, out_type, **kwargs)
                     except WriterError:
diff --git a/nibabel/tests/test_euler.py b/nibabel/tests/test_euler.py
@@ -18,7 +18,7 @@
 import pytest
 from numpy.testing import assert_array_equal, assert_array_almost_equal
 
-FLOAT_EPS = np.finfo(np.float).eps
+FLOAT_EPS = np.finfo(np.float64).eps
 
 # Example rotations """
 eg_rots = []
diff --git a/nibabel/tests/test_proxy_api.py b/nibabel/tests/test_proxy_api.py
@@ -66,7 +66,7 @@
 
 def _some_slicers(shape):
     ndim = len(shape)
-    slicers = np.eye(ndim).astype(np.int).astype(object)
+    slicers = np.eye(ndim).astype(int).astype(object)
     slicers[slicers == 0] = slice(None)
     for i in range(ndim):
         if i % 2:
diff --git a/nibabel/tests/test_scaling.py b/nibabel/tests/test_scaling.py
@@ -43,7 +43,7 @@
     ([np.inf, 1], (1, 1)),  # only look at finite values
     ([-np.inf, 1], (1, 1)),
     ([[], []], (np.inf, -np.inf)),  # empty array
-    (np.array([[-3, 0, 1], [2, -1, 4]], dtype=np.int), (-3, 4)),
+    (np.array([[-3, 0, 1], [2, -1, 4]], dtype=int), (-3, 4)),
     (np.array([[1, 0, 1], [2, 3, 4]], dtype=np.uint), (0, 4)),
     ([0., 1, 2, 3], (0, 3)),
     # Complex comparison works as if they are floats
@@ -64,7 +64,7 @@ def test_finite_range(in_arr, res):
     assert finite_range(flat_arr, True) == res + (has_nan,)
     # Check float types work as complex
     if in_arr.dtype.kind == 'f':
-        c_arr = in_arr.astype(np.complex)
+        c_arr = in_arr.astype(np.complex128)
         assert finite_range(c_arr) == res
         assert finite_range(c_arr, True) == res + (has_nan,)
 
@@ -181,7 +181,7 @@ def test_scaling_in_abstract(category0, category1, overflow):
 
 def check_int_a2f(in_type, out_type):
     # Check that array to / from file returns roughly the same as input
-    big_floater = np.maximum_sctype(np.float)
+    big_floater = np.maximum_sctype(np.float64)
     info = type_info(in_type)
     this_min, this_max = info['min'], info['max']
     if not in_type in np.sctypes['complex']:
diff --git a/nibabel/tests/test_testing.py b/nibabel/tests/test_testing.py
@@ -23,7 +23,7 @@ def test_assert_allclose_safely():
     # Broadcastable matrices
     a = np.ones((2, 3))
     b = np.ones((3, 2, 3))
-    eps = np.finfo(np.float).eps
+    eps = np.finfo(np.float64).eps
     a[0, 0] = 1 + eps
     assert_allclose_safely(a, b)
     a[0, 0] = 1 + 1.1e-5
diff --git a/nibabel/tests/test_volumeutils.py b/nibabel/tests/test_volumeutils.py
diff --git a/nibabel/volumeutils.py b/nibabel/volumeutils.py
diff --git a/setup.cfg b/setup.cfg

Original file line number	Diff line number	Diff line change
`@@ -171,7 +171,9 @@`
`171`	`171`	`"orcid": "0000-0003-4662-0558"`
`172`	`172`	`},`
`173`	`173`	`{`
`174`		`- "name": "Klug, Julian"`
	`174`	`+ "affiliation": "University of Geneva, Switzerland",`
	`175`	`+ "name": "Klug, Julian",`
	`176`	`+ "orcid": "0000-0002-4849-9811"`
`175`	`177`	`},`
`176`	`178`	`{`
`177`	`179`	`"affiliation": "SRI International",`
Original file line number	Diff line number	Diff line change
`@@ -46,7 +46,7 @@`
`46`	`46`	`('?', '?', '?', ':'),`
`47`	`47`	`]`
`48`	`48`
`49`		`-KEEP_OPENS = [False, True, 'auto']`
	`49`	`+KEEP_OPENS = [False, True]`
`50`	`50`
`51`	`51`	`if HAVE_INDEXED_GZIP:`
`52`	`52`	`HAVE_IGZIP = [False, True]`