Merge pull request #1079 from effigies/mnt/nep29

NEP29: Require Python 3.7+, numpy 1.17+, declare 3.10 support

Author: effigies

.github/workflows/pre-release.yml

@@ -26,7 +26,7 @@ jobs:
     strategy:
       matrix:
         os: ['ubuntu-latest', 'windows-latest', 'macos-latest']
-        python-version: ["3.8", "3.9", "3.10.0-rc.1"]
+        python-version: ["3.9", "3.10"]
         architecture: ['x64', 'x86']
         install: ['setup']
         check: ['test']
@@ -36,7 +36,7 @@ jobs:
         include:
           # Pydicom master
           - os: ubuntu-latest
-            python-version: 3.8
+            python-version: "3.10"
             install: setup
             check: test
             pip-flags: ''
@@ -47,10 +47,6 @@ jobs:
             architecture: x86
           - os: macos-latest
             architecture: x86
-          - os: windows-latest
-            python-version: "3.10.0-rc.1"
-          - os: macos-latest
-            python-version: "3.10.0-rc.1"
 
     env:
       DEPENDS: ${{ matrix.depends }}

.github/workflows/stable.yml

@@ -29,7 +29,7 @@ jobs:
     strategy:
       matrix:
         os: ['ubuntu-latest', 'windows-latest', 'macos-latest']
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: [3.7, 3.8, 3.9, "3.10"]
         architecture: ['x64', 'x86']
         install: ['pip']
         check: ['test']
@@ -39,52 +39,52 @@ jobs:
         include:
           # Basic dependencies only
           - os: ubuntu-latest
-            python-version: 3.6
+            python-version: 3.7
             install: setup
             check: test
             pip-flags: ''
             depends: REQUIREMENTS
             optional-depends: ''
           # Absolute minimum dependencies
           - os: ubuntu-latest
-            python-version: 3.6
+            python-version: 3.7
             install: setup
             check: test
             pip-flags: ''
             depends: MIN_REQUIREMENTS
             optional-depends: ''
           # Absolute minimum dependencies plus old MPL, Pydicom, Pillow
           - os: ubuntu-latest
-            python-version: 3.6
+            python-version: 3.7
             install: setup
             check: test
             pip-flags: ''
             depends: MIN_REQUIREMENTS
             optional-depends: MIN_OPT_DEPENDS
           # Clean install imports only with package-declared dependencies
           - os: ubuntu-latest
-            python-version: 3.6
+            python-version: 3.7
             install: pip
             check: skiptests
             pip-flags: ''
             depends: ''
           # Check all installation methods
           - os: ubuntu-latest
-            python-version: 3.8
+            python-version: "3.10"
             install: wheel
             check: test
             pip-flags: ''
             depends: REQUIREMENTS
             optional-depends: DEFAULT_OPT_DEPENDS
           - os: ubuntu-latest
-            python-version: 3.8
+            python-version: "3.10"
             install: sdist
             check: test
             pip-flags: ''
             depends: REQUIREMENTS
             optional-depends: DEFAULT_OPT_DEPENDS
           - os: ubuntu-latest
-            python-version: 3.8
+            python-version: "3.10"
             install: archive
             check: test
             pip-flags: ''

.travis.yml

@@ -6,7 +6,7 @@
 
 os: linux
 arch: arm64
-dist: xenial
+dist: focal
 language: python
 cache: pip
 
@@ -21,10 +21,10 @@ env:
         - CHECK_TYPE="test"
 
 python:
-    - 3.6
     - 3.7
     - 3.8
     - 3.9
+    - "3.10"
 
 # Set up virtual environment, build package, build from depends
 before_install:

min-requirements.txt

@@ -1,4 +1,4 @@
 # Auto-generated by tools/update_requirements.py
-numpy ==1.15
+numpy ==1.17
 packaging ==17.0
 setuptools

nibabel/_h5py_compat.py

@@ -158,7 +158,7 @@ class Minc2Image(Minc1Image):
     def from_file_map(klass, file_map, *, mmap=True, keep_file_open=None):
         # Import of h5py might take awhile for MPI-enabled builds
         # So we are importing it here "on demand"
-        from ._h5py_compat import h5py
+        import h5py
         holder = file_map['image']
         if holder.filename is None:
             raise MincError('MINC2 needs filename for load')

nibabel/minc2.py

@@ -24,13 +24,7 @@
 
 from itertools import zip_longest
 
-try:
-    from contextlib import nullcontext
-except ImportError:  # PY36
-    from contextlib import contextmanager
-    @contextmanager
-    def nullcontext():
-        yield
+from contextlib import nullcontext
 
 
 def test_data(subdir=None, fname=None):

nibabel/testing/__init__.py

@@ -32,7 +32,7 @@
 
 from ..optpkg import optional_package
 _, have_scipy, _ = optional_package('scipy')
-from .._h5py_compat import have_h5py
+_, have_h5py, _ = optional_package('h5py')
 
 from .. import (AnalyzeImage, Spm99AnalyzeImage, Spm2AnalyzeImage,
                 Nifti1Pair, Nifti1Image, Nifti2Pair, Nifti2Image,

nibabel/tests/test_h5py_compat.py

@@ -10,15 +10,16 @@
 from nibabel.analyze import AnalyzeImage
 from nibabel.nifti1 import Nifti1Image
 from nibabel.nifti2 import Nifti2Image
-from .._h5py_compat import have_h5py
 
 from nibabel import imageclasses
 from nibabel.imageclasses import spatial_axes_first, class_map, ext_map
 
-
+from nibabel.optpkg import optional_package
 from nibabel.testing import clear_and_catch_warnings
 
 
+have_h5py = optional_package('h5py')[1]
+
 DATA_DIR = pjoin(dirname(__file__), 'data')
 
 MINC_3DS = ('minc1_1_scale.mnc',)

nibabel/tests/test_image_api.py

@@ -36,8 +36,7 @@ def test_read_img_data():
     ]
     fnames_test += [pathlib.Path(p) for p in fnames_test]
     for fname in fnames_test:
-        # os.path.join doesn't work between str / os.PathLike in py3.5
-        fpath = pjoin(data_path, str(fname))
+        fpath = pjoin(data_path, fname)
         if isinstance(fname, pathlib.Path):
             fpath = pathlib.Path(fpath)
         img = load(fpath)
@@ -56,8 +55,7 @@ def test_read_img_data():
             up_fpath = pjoin(tmpdir, str(fname).upper())
             if isinstance(fname, pathlib.Path):
                 up_fpath = pathlib.Path(up_fpath)
-            # shutil doesn't work with os.PathLike in py3.5
-            shutil.copyfile(str(fpath), str(up_fpath))
+            shutil.copyfile(fpath, up_fpath)
             img = load(up_fpath)
             assert_array_equal(img.dataobj, data)
             del img

nibabel/tests/test_imageclasses.py

@@ -13,12 +13,14 @@
 
 from .. import minc2
 from ..minc2 import Minc2File, Minc2Image
-from .._h5py_compat import h5py, have_h5py, setup_module
 
+from ..optpkg import optional_package
 from ..testing import data_path
 
 from . import test_minc1 as tm2
 
+h5py, have_h5py, setup_module = optional_package('h5py')
+
 # Example images in format expected for ``test_image_api``, adding ``zooms``
 # item.
 EXAMPLE_IMAGES = [

nibabel/tests/test_loadsave.py

@@ -14,13 +14,14 @@
 
 import numpy as np
 
-from .._h5py_compat import h5py, have_h5py, setup_module
-
 from .nibabel_data import get_nibabel_data, needs_nibabel_data
 from .. import load as top_load, Nifti1Image
+from ..optpkg import optional_package
 
 from numpy.testing import (assert_array_equal, assert_almost_equal)
 
+h5py, have_h5py, setup_module = optional_package('h5py')
+
 MINC2_PATH = pjoin(get_nibabel_data(), 'nitest-minc2')
 
 

nibabel/tests/test_minc2.py

@@ -44,7 +44,6 @@
 from .. import minc1
 from ..externals.netcdf import netcdf_file
 from .. import minc2
-from .._h5py_compat import h5py, have_h5py
 from .. import ecat
 from .. import parrec
 from ..casting import have_binary128
@@ -57,12 +56,15 @@
 
 from ..testing import data_path as DATA_PATH, assert_dt_equal, clear_and_catch_warnings
 from ..deprecator import ExpiredDeprecationError
+from ..optpkg import optional_package
 
 from ..tmpdirs import InTemporaryDirectory
 
 from .test_api_validators import ValidateAPI
 from .test_parrec import EG_REC, VARY_REC
 
+h5py, have_h5py, _ = optional_package('h5py')
+
 
 def _some_slicers(shape):
     ndim = len(shape)

nibabel/tests/test_minc2_data.py

@@ -1,4 +1,4 @@
 # Auto-generated by tools/update_requirements.py
-numpy >=1.15
+numpy >=1.17
 packaging >=17.0
 setuptools

nibabel/tests/test_proxy_api.py

@@ -13,10 +13,10 @@ classifiers =
     License :: OSI Approved :: MIT License
     Operating System :: OS Independent
     Programming Language :: Python
-    Programming Language :: Python :: 3.6
     Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
     Topic :: Scientific/Engineering
 license = MIT License
 description = Access a multitude of neuroimaging data formats
@@ -28,9 +28,9 @@ provides =
     nisext
 
 [options]
-python_requires = >=3.6
+python_requires = >=3.7
 install_requires =
-    numpy >=1.15
+    numpy >=1.17
     packaging >=17.0
     setuptools
 zip_safe = False
@@ -59,7 +59,6 @@ style =
 test =
     coverage
     pytest !=5.3.4
-    pytest <7 ; python_version == "3.6"
     pytest-cov
     pytest-doctestplus
 zstd =