Merge pull request #383 from anntzer/update

nkeim · web-flow · commit df3d7d8231e9 · 2021-02-22T10:50:59.000-05:00
Drop dependency on nose for tests; fix numpy and python deprecations.
diff --git a/.travis.yml b/.travis.yml
@@ -19,7 +19,7 @@ install:
   # Append the conda-forge channel, instead of adding it. See:
   # https://github.com/conda-forge/conda-forge.github.io/issues/232)
   - conda config --append channels conda-forge
-  - conda create -n testenv --yes $DEPS nose python=$TRAVIS_PYTHON_VERSION
+  - conda create -n testenv --yes $DEPS python=$TRAVIS_PYTHON_VERSION
   - source activate testenv
   # only install pip if there are pip dependencies
   # - |
@@ -42,7 +42,7 @@ before_install:
   - export PATH=/home/travis/mc/bin:$PATH
 
 script:
-    - nosetests --nologcapture
+    - python -munittest
     # Doc Build needs: pillow matplotlib ipython sphinx sphinx_rtd_theme numpydoc
     - if [ $BUILD_DOCS == true ]; then make html --directory=./doc; fi
 
diff --git a/Dockerfile b/Dockerfile
@@ -5,7 +5,7 @@
 ##
 ##    docker build -t pims .
 ##    docker run -ti --rm pims
-##    nosetests --nologcapture
+##    python -munittest
 ##
 
 FROM continuumio/miniconda3
diff --git a/doc/source/pipelines.rst b/doc/source/pipelines.rst
@@ -135,11 +135,11 @@ unnamed lambda function in a single line:
 
 .. ipython:: python
 
-   processed_video = pims.pipeline(lambda x: x.astype(np.float))(video)
+   processed_video = pims.pipeline(lambda x: x.astype(float))(video)
    processed_frame = processed_video[0]
    print(processed_frame.shape)
 
 .. ipython:: python
    :suppress:
 
-   clean_dummy_png('.', filenames)
+   clean_dummy_png('.', filenames)
diff --git a/environment.yml b/environment.yml
@@ -20,5 +20,4 @@ dependencies:
 - moviepy
 - imageio
 - imageio-ffmpeg
-- nose
 - openjdk
diff --git a/pims/cine.py b/pims/cine.py
@@ -26,7 +26,7 @@
 import hashlib
 import sys
 import warnings
-from collections import Iterable
+from collections.abc import Iterable
 
 __all__ = ('Cine', )
 
diff --git a/pims/display.py b/pims/display.py
@@ -716,7 +716,7 @@ def plot_to_frame(fig, width=512, close_fig=False, fig_size_inches=None,
             fig.savefig(buf, format='rgba', dpi=dpi)
             buf.seek(0)
             buf_shape = (int(height_in * dpi), int(width_in * dpi), 4)
-            image = np.fromstring(buf.read(),
+            image = np.frombuffer(buf.read(),
                                   dtype='uint8').reshape(*buf_shape)
 
     if close_fig:
diff --git a/pims/ffmpeg_reader.py b/pims/ffmpeg_reader.py
@@ -216,7 +216,7 @@ def get_frame(self, j):
         self.data_buffer.seek(self._stride*j)
         s = self.data_buffer.read(self._stride)
         w, h = self._size
-        result = np.fromstring(s,
+        result = np.frombuffer(s,
             dtype='uint8').reshape((h, w, self.depth))
         return Frame(result, frame_no=j)
 
diff --git a/pims/process.py b/pims/process.py
@@ -73,7 +73,7 @@ def __init__(self, reader, crop_width, order='K'):
         # We have to know the frame shape that is returned by the reader.
         try:  # In case the reader is a FramesSequence, there is an attribute
             shape = reader.frame_shape
-            first_frame = np.empty(shape, dtype=np.bool)
+            first_frame = np.empty(shape, dtype=bool)
         except AttributeError:
             first_frame = reader[0]
             shape = first_frame.shape
diff --git a/pims/spe_stack.py b/pims/spe_stack.py
@@ -174,7 +174,7 @@ def __init__(self, filename, char_encoding=None, check_filesize=True):
             if cnt == 1:
                 #for convenience, if the array contains only one single entry,
                 #return this entry itself.
-                v = np.asscalar(v)
+                v = v.item()
             self.metadata[name] = v
 
         ### Some metadata is "special", deal with it
diff --git a/pims/tests/test_bioformats.py b/pims/tests/test_bioformats.py
@@ -8,7 +8,6 @@
 
 import os
 import unittest
-import nose
 import numpy as np
 from numpy.testing import (assert_equal, assert_almost_equal, assert_allclose)
 
@@ -20,7 +19,7 @@
 
 def _skip_if_no_bioformats():
     if not pims.bioformats.available():
-        raise nose.SkipTest('JPype is not installed. Skipping.')
+        raise unittest.SkipTest('JPype is not installed. Skipping.')
 
 
 def assert_image_equal(actual, expected):
@@ -187,7 +186,7 @@ class TestBioformatsMOV(_image_series, unittest.TestCase):
     def check_skip(self):
         _skip_if_no_bioformats()
         if not os.path.isfile(self.filename):
-            raise nose.SkipTest('File missing. Skipping.')
+            raise unittest.SkipTest('File missing. Skipping.')
 
     def setUp(self):
         self.filename = os.path.join(path, 'bioformats', 'wtembryo.mov')
@@ -212,7 +211,7 @@ class TestBioformatsIPW(_image_series, _image_stack, _image_multichannel,
     def check_skip(self):
         _skip_if_no_bioformats()
         if not os.path.isfile(self.filename):
-            raise nose.SkipTest('File missing. Skipping.')
+            raise unittest.SkipTest('File missing. Skipping.')
 
     def setUp(self):
         self.filename = os.path.join(path, 'bioformats', 'mitosis-test.ipw')
@@ -236,7 +235,7 @@ class TestBioformatsDM3(_image_single, unittest.TestCase):
     def check_skip(self):
         _skip_if_no_bioformats()
         if not os.path.isfile(self.filename):
-            raise nose.SkipTest('File missing. Skipping.')
+            raise unittest.SkipTest('File missing. Skipping.')
 
     def setUp(self):
         self.filename = os.path.join(path, 'bioformats', 'dnasample1.dm3')
@@ -259,7 +258,7 @@ class TestBioformatsLSM(_image_series, _image_stack, _image_multichannel,
     def check_skip(self):
         _skip_if_no_bioformats()
         if not os.path.isfile(self.filename):
-            raise nose.SkipTest('File missing. Skipping.')
+            raise unittest.SkipTest('File missing. Skipping.')
 
     def setUp(self):
         self.filename = os.path.join(path, 'bioformats', '2chZT.lsm')
@@ -284,7 +283,7 @@ class TestBioformatsAndorTiff(_image_series, _image_stack, _image_multichannel,
     def check_skip(self):
         _skip_if_no_bioformats()
         if not os.path.isfile(self.filename):
-            raise nose.SkipTest('File missing. Skipping.')
+            raise unittest.SkipTest('File missing. Skipping.')
 
     def setUp(self):
         self.filename = os.path.join(path, 'bioformats', 'MF-2CH-Z-T.tif')
@@ -309,7 +308,7 @@ class TestBioformatsOlympusTiff(_image_series, _image_stack, unittest.TestCase):
     def check_skip(self):
         _skip_if_no_bioformats()
         if not os.path.isfile(self.filename):
-            raise nose.SkipTest('File missing. Skipping.')
+            raise unittest.SkipTest('File missing. Skipping.')
 
     def setUp(self):
         self.filename = os.path.join(path, 'bioformats', '10-31 E1.tif')
@@ -337,7 +336,7 @@ class TestBioformatsLIFseries1(_image_single, _image_stack, _image_multichannel,
     def check_skip(self):
         _skip_if_no_bioformats()
         if not os.path.isfile(self.filename):
-            raise nose.SkipTest('File missing. Skipping.')
+            raise unittest.SkipTest('File missing. Skipping.')
 
     def setUp(self):
         self.filename = os.path.join(path, 'bioformats', 'mouse-kidney.lif')
@@ -367,7 +366,7 @@ class TestBioformatsLIFseries2(_image_single, _image_stack, _image_multichannel,
     def check_skip(self):
         _skip_if_no_bioformats()
         if not os.path.isfile(self.filename):
-            raise nose.SkipTest('File missing. Skipping.')
+            raise unittest.SkipTest('File missing. Skipping.')
 
     def setUp(self):
         self.filename = os.path.join(path, 'bioformats', 'mouse-kidney.lif')
@@ -390,7 +389,7 @@ class TestBioformatsIPL(_image_single, unittest.TestCase):
     def check_skip(self):
         _skip_if_no_bioformats()
         if not os.path.isfile(self.filename):
-            raise nose.SkipTest('File missing. Skipping.')
+            raise unittest.SkipTest('File missing. Skipping.')
 
     def setUp(self):
         self.filename = os.path.join(path, 'bioformats', 'Blend_Final.IPL')
@@ -411,7 +410,7 @@ class TestBioformatsSEQ(_image_single, _image_stack, unittest.TestCase):
     def check_skip(self):
         _skip_if_no_bioformats()
         if not os.path.isfile(self.filename):
-            raise nose.SkipTest('File missing. Skipping.')
+            raise unittest.SkipTest('File missing. Skipping.')
 
     def setUp(self):
         self.filename = os.path.join(path, 'bioformats', 'HEART.SEQ')
@@ -435,7 +434,7 @@ class TestBioformatsLEI(_image_single, _image_stack, unittest.TestCase):
     def check_skip(self):
         _skip_if_no_bioformats()
         if not os.path.isfile(self.filename):
-            raise nose.SkipTest('File missing. Skipping.')
+            raise unittest.SkipTest('File missing. Skipping.')
 
     def setUp(self):
         self.filename = os.path.join(path, 'bioformats', 'leica_stack.lei')
@@ -460,7 +459,7 @@ class TestBioformatsICS(_image_single, unittest.TestCase):
     def check_skip(self):
         _skip_if_no_bioformats()
         if not os.path.isfile(self.filename):
-            raise nose.SkipTest('File missing. Skipping.')
+            raise unittest.SkipTest('File missing. Skipping.')
 
     def setUp(self):
         self.filename = os.path.join(path, 'bioformats', 'qdna1.ics')
@@ -483,7 +482,7 @@ class TestBioformatsZPO(_image_stack, _image_multichannel, unittest.TestCase):
     def check_skip(self):
         _skip_if_no_bioformats()
         if not os.path.isfile(self.filename):
-            raise nose.SkipTest('File missing. Skipping.')
+            raise unittest.SkipTest('File missing. Skipping.')
 
     def setUp(self):
         self.filename = os.path.join(path, 'bioformats', 'KEVIN2-3.zpo')
@@ -547,5 +546,5 @@ def test_metadata_tags(self):
         assert 'PixelsPhysicalSizeX' in fields
 
 if __name__ == '__main__':
-    nose.runmodule(argv=[__file__, '-vvs'],
+    unittest.runmodule(argv=[__file__, '-vvs'],
                    exit=False)
diff --git a/pims/tests/test_cine.py b/pims/tests/test_cine.py
@@ -3,7 +3,6 @@
 import os
 from datetime import datetime
 import unittest
-import nose
 import numpy as np
 import pims
 import pims.cine
@@ -33,8 +32,8 @@ def setUp(self):
         self.sample_filename = os.path.join(tests_path, 'data',
                                             'cine_legacy.cine')
         if not os.path.exists(self.sample_filename):
-            raise nose.SkipTest('Legacy sample cine file not found. '
-                                'Skipping.')
+            raise unittest.SkipTest('Legacy sample cine file not found. '
+                                    'Skipping.')
 
         self.options = {}
         super(test_legacy_cine_sample, self).setUp()
@@ -51,8 +50,8 @@ def setUp(self):
         self.sample_filename = os.path.join(tests_path, 'data',
                                             'cine_781.cine')
         if not os.path.exists(self.sample_filename):
-            raise nose.SkipTest('Newer sample cine file not found. '
-                                'Skipping.')
+            raise unittest.SkipTest('Newer sample cine file not found. '
+                                    'Skipping.')
         self.options = {}
         super(test_new_cine_sample, self).setUp()
 
diff --git a/pims/tests/test_common.py b/pims/tests/test_common.py
@@ -9,10 +9,8 @@
 import types
 import unittest
 import pickle
-import nose
 import numpy as np
 from numpy.testing import (assert_equal, assert_allclose)
-from nose.tools import assert_true
 import pims
 
 path, _ = os.path.split(os.path.abspath(__file__))
@@ -22,50 +20,50 @@
 def _skip_if_no_PyAV():
     import pims.pyav_reader
     if not pims.pyav_reader.available():
-        raise nose.SkipTest('PyAV not found. Skipping.')
+        raise unittest.SkipTest('PyAV not found. Skipping.')
 
 
 def _skip_if_no_MoviePy():
     import pims.moviepy_reader
     if not pims.moviepy_reader.available():
-        raise nose.SkipTest('MoviePy not found. Skipping.')
+        raise unittest.SkipTest('MoviePy not found. Skipping.')
 
 
 def _skip_if_no_ImageIO_ffmpeg():
     import pims.imageio_reader
     if not pims.imageio_reader.ffmpeg_available():
-        raise nose.SkipTest('ImageIO and ffmpeg not found. Skipping.')
+        raise unittest.SkipTest('ImageIO and ffmpeg not found. Skipping.')
 
 
 def _skip_if_no_libtiff():
     import pims.tiff_stack
     if not pims.tiff_stack.libtiff_available():
-        raise nose.SkipTest('libtiff not installed. Skipping.')
+        raise unittest.SkipTest('libtiff not installed. Skipping.')
 
 
 def _skip_if_no_tifffile():
     import pims.tiff_stack
     if not pims.tiff_stack.tifffile_available():
-        raise nose.SkipTest('tifffile not installed. Skipping.')
+        raise unittest.SkipTest('tifffile not installed. Skipping.')
 
 
 def _skip_if_no_imread():
     if pims.image_sequence.imread is None:
-        raise nose.SkipTest('ImageSequence requires either matplotlib or'
-                            ' scikit-image. Skipping.')
+        raise unittest.SkipTest('ImageSequence requires either matplotlib or'
+                                ' scikit-image. Skipping.')
 
 
 def _skip_if_no_skimage():
     try:
         import skimage
     except ImportError:
-        raise nose.SkipTest('skimage not installed. Skipping.')
+        raise unittest.SkipTest('skimage not installed. Skipping.')
 
 
 def _skip_if_no_PIL():
     import pims.tiff_stack
     if not pims.tiff_stack.PIL_available():
-        raise nose.SkipTest('PIL/Pillow not installed. Skipping.')
+        raise unittest.SkipTest('PIL/Pillow not installed. Skipping.')
 
 
 def assert_image_equal(actual, expected):
@@ -254,7 +252,7 @@ def test_slice_with_generator(self):
         compare_slice_to_list(slice1, list('bcdefghij'))
         slice2 = slice1[(i for i in range(2,5))]
         assert_letters_equal(slice2, list('def'))
-        assert_true(isinstance(slice2, types.GeneratorType))
+        self.assertTrue(isinstance(slice2, types.GeneratorType))
 
 def _rescale(img):
     return (img - img.min()) / img.ptp()
@@ -604,5 +602,4 @@ def test_open_tiff(self):
         pims.open(os.path.join(path, 'stuck.tif'))
 
 if __name__ == '__main__':
-    nose.runmodule(argv=[__file__, '-vvs', '-x', '--pdb', '--pdb-failure'],
-                   exit=False)
+    unittest.main()
diff --git a/pims/tests/test_display.py b/pims/tests/test_display.py
diff --git a/pims/tests/test_factories.py b/pims/tests/test_factories.py
diff --git a/pims/tests/test_frame.py b/pims/tests/test_frame.py
diff --git a/pims/tests/test_multidimensional.py b/pims/tests/test_multidimensional.py
diff --git a/pims/tests/test_norpix.py b/pims/tests/test_norpix.py
diff --git a/pims/tests/test_process.py b/pims/tests/test_process.py

-Original file line number
+Diff line change
 - moviepy
 - imageio
 - imageio-ffmpeg
 -- nose
 - openjdk