WIP: flake8 compliance

Author: mattjala

.github/workflows/main.yml

@@ -44,13 +44,13 @@ jobs:
           python -m pip install flake8 pytest
           if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
 
-      # - name: Lint with flake8
-      #  shell: bash
-      #  run: |
-      #    # stop the build if there are Python syntax errors or undefined names
-      #    flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-      #    # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-      #    flake8 . --count --max-complexity=10 --max-line-length=127 --statistics
+      - name: Lint with flake8
+       shell: bash
+       run: |
+         # stop the build if there are Python syntax errors or undefined names
+         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+         flake8 . --count --max-complexity=10 --max-line-length=127 --statistics
 
       - name: Install package
         shell: bash

h5pyd/__init__.py

@@ -34,12 +34,12 @@
 
 
 __doc__ = \
-"""
+    """
     This is the h5pyd package, a Python interface to the HDF REST Server.
 
     Version %s
 
-""" % (version.version)
+    """ % (version.version)
 
 
 def enable_ipython_completer():

setup.cfg

@@ -2,4 +2,5 @@
 max-line-length = 120
 # E402: module level import not at top of file
 # C901: too complex
-ignore = E402, C901
+# F401: unused exports are necessary in __init__.py
+ignore = E402, C901, F401

test/hl/test_dataset_getitem.py

@@ -60,14 +60,15 @@
 Update using new NULL dataset constructor once h5py 2.7 is out.
 """
 
+
 class TestEmpty(TestCase):
 
     def setUp(self):
         TestCase.setUp(self)
         filename = self.getFileName("dataset_testempty")
         print("filename:", filename)
         self.f = h5py.File(filename, 'w')
-        self.dset = self.f.create_dataset('x',dtype='S10')
+        self.dset = self.f.create_dataset('x', dtype='S10')
         self.empty_obj = h5py.Empty(np.dtype("S10"))
 
     def test_ndim(self):
@@ -100,7 +101,7 @@ def test_slice(self):
     def test_multi_block_slice(self):
         """ MultiBlockSlice -> ValueError """
         """ TBD """
-        #with self.assertRaises(ValueError):
+        # with self.assertRaises(ValueError):
         #    self.dset[h5py.MultiBlockSlice()]
 
     def test_index(self):
@@ -111,7 +112,7 @@ def test_index(self):
     def test_indexlist(self):
         """ index list -> ValueError """
         with self.assertRaises(ValueError):
-            self.dset[[1,2,5]]
+            self.dset[[1, 2, 5]]
 
     def test_mask(self):
         """ mask -> ValueError """
@@ -123,7 +124,7 @@ def test_fieldnames(self):
         """ field name -> ValueError """
         with self.assertRaises(ValueError):
             self.dset['field']
-      
+
 
 class TestScalarFloat(TestCase):
 
@@ -175,7 +176,7 @@ def test_index(self):
     def test_indexlist(self):
         """ index list -> ValueError """
         with self.assertRaises(ValueError):
-            self.dset[[1,2,5]]
+            self.dset[[1, 2, 5]]
 
     # FIXME: NumPy permits this
     def test_mask(self):
@@ -198,9 +199,9 @@ def setUp(self):
         print("filename:", filename)
         self.f = h5py.File(filename, 'w')
         self.data = np.array((42.5, -118, "Hello"), dtype=[('a', 'f'), ('b', 'i'), ('c', '|S10')])
-        #self.dset = self.f.create_dataset('x', data=self.data)
+        # self.dset = self.f.create_dataset('x', data=self.data)
         self.dset = self.f.create_dataset('x', (), dtype=[('a', 'f'), ('b', 'i'), ('c', '|S10')])
-        self.dset[...] =  (42.5, -118, "Hello")
+        self.dset[...] = (42.5, -118, "Hello")
 
     def test_ndim(self):
         """ Verify number of dimensions """
@@ -246,7 +247,7 @@ def test_index(self):
     def test_indexlist(self):
         """ index list -> ValueError """
         with self.assertRaises(ValueError):
-            self.dset[[1,2,5]]
+            self.dset[[1, 2, 5]]
 
     # FIXME: NumPy permits this
     def test_mask(self):
@@ -259,13 +260,12 @@ def test_mask(self):
     @ut.skip
     def test_fieldnames(self):
         """ field name -> bare value """
-        #TBD: fix when field access is supported in hsds
+        # TBD: fix when field access is supported in hsds
         out = self.dset['a']
         self.assertIsInstance(out, np.float32)
         self.assertEqual(out, self.dset['a'])
 
 
-
 class TestScalarArray(TestCase):
 
     def setUp(self):
@@ -279,7 +279,7 @@ def setUp(self):
         try:
             self.dset[...] = self.data
         except (IOError, OSError) as oe:
-            #TBD this is failing on HSDS
+            # TBD this is failing on HSDS
             if not self.is_hsds():
                 raise oe
 
@@ -454,7 +454,7 @@ def test_index_outofrange(self):
             self.dset[100]
 
     def test_indexlist_simple(self):
-        self.assertNumpyBehavior(self.dset, self.data, np.s_[[1,2,5]])
+        self.assertNumpyBehavior(self.dset, self.data, np.s_[[1, 2, 5]])
 
     def test_indexlist_single_index_ellipsis(self):
         self.assertNumpyBehavior(self.dset, self.data, np.s_[[0], ...])
@@ -475,12 +475,12 @@ def test_indexlist_outofrange(self):
     def test_indexlist_nonmonotonic(self):
         """ we require index list values to be strictly increasing """
         with self.assertRaises(TypeError):
-            self.dset[[1,3,2]]
+            self.dset[[1, 3, 2]]
 
     def test_indexlist_repeated(self):
         """ we forbid repeated index values """
         with self.assertRaises(TypeError):
-            self.dset[[1,1,2]]
+            self.dset[[1, 1, 2]]
 
     def test_mask_true(self):
         self.assertNumpyBehavior(self.dset, self.data, np.s_[self.data > -100])
@@ -509,7 +509,7 @@ def setUp(self):
         filename = self.getFileName("dataset_test2dzerofloat")
         print("filename:", filename)
         self.f = h5py.File(filename, 'w')
-        self.data = np.ones((0,3), dtype='f')
+        self.data = np.ones((0, 3), dtype='f')
         self.dset = self.f.create_dataset('x', data=self.data)
 
     def test_ndim(self):
@@ -521,7 +521,8 @@ def test_shape(self):
         self.assertEqual(self.dset.shape, (0, 3))
 
     def test_indexlist(self):
-        self.assertNumpyBehavior(self.dset, self.data, np.s_[:,[0,1,2]])
+        self.assertNumpyBehavior(self.dset, self.data, np.s_[:, [0, 1, 2]])
+
 
 class Test2DFloat(TestCase):
 
@@ -530,9 +531,9 @@ def setUp(self):
         filename = self.getFileName("dataset_test2dfloat")
         print("filename:", filename)
         self.f = h5py.File(filename, 'w')
-        self.data = np.ones((5,3), dtype='f')
+        self.data = np.ones((5, 3), dtype='f')
         self.dset = self.f.create_dataset('x', data=self.data)
-         
+
     def test_ndim(self):
         """ Verify number of dimensions """
         self.assertEqual(self.dset.ndim, 2)
@@ -543,14 +544,14 @@ def test_size(self):
 
     def test_nbytes(self):
         """ Verify nbytes """
-        self.assertEqual(self.dset.nbytes, 15*self.data.dtype.itemsize) 
+        self.assertEqual(self.dset.nbytes, 15 * self.data.dtype.itemsize)
 
     def test_shape(self):
         """ Verify shape """
         self.assertEqual(self.dset.shape, (5, 3))
 
     def test_indexlist(self):
-        self.assertNumpyBehavior(self.dset, self.data, np.s_[:,[0,1,2]])
+        self.assertNumpyBehavior(self.dset, self.data, np.s_[:, [0, 1, 2]])
 
     @ut.expectedFailure
     def test_index_emptylist(self):
@@ -559,18 +560,20 @@ def test_index_emptylist(self):
         # with h5py 3.2.1 at least
         self.assertNumpyBehavior(self.dset, self.data, np.s_[[]])
 
+
 class Test3DFloat(TestCase):
 
     def setUp(self):
         TestCase.setUp(self)
         filename = self.getFileName("dataset_test3dfloat")
         print("filename:", filename)
         self.f = h5py.File(filename, 'w')
-        self.data = np.ones((4,6,8), dtype='f')
+        self.data = np.ones((4, 6, 8), dtype='f')
         self.dset = self.f.create_dataset('x', data=self.data, dtype='f')
 
     def test_index_simple(self):
-        self.assertNumpyBehavior(self.dset, self.data, np.s_[1,2:4,3:6])
+        self.assertNumpyBehavior(self.dset, self.data, np.s_[1, 2:4, 3:6])
+
 
 class TestVeryLargeArray(TestCase):
 
@@ -585,6 +588,7 @@ def setUp(self):
     def test_size(self):
         self.assertEqual(self.dset.size, 2**31)
 
+
 if __name__ == '__main__':
     loglevel = logging.ERROR
     logging.basicConfig(format='%(asctime)s %(message)s', level=loglevel)

test/hl/test_dataset_initializer.py

@@ -10,7 +10,6 @@
 # request a copy from [email protected].                                     #
 ##############################################################################
 import logging
-import numpy as np
 
 import config
 
@@ -21,8 +20,8 @@
 
 from common import ut, TestCase
 
-class TestDatasetInitializer(TestCase):
 
+class TestDatasetInitializer(TestCase):
 
     def test_create_arange_dset(self):
         filename = self.getFileName("create_arange_dset")
@@ -36,9 +35,9 @@ def test_create_arange_dset(self):
         start = 10
         step = 2
         dims = (extent,)
-        initializer="arange"
+        initializer = "arange"
         initializer_opts = [f"--start={start}", f"--step={step}"]
-        kwargs = {"dtype": "i8", "initializer":initializer, "initializer_opts": initializer_opts}
+        kwargs = {"dtype": "i8", "initializer": initializer, "initializer_opts": initializer_opts}
         dset = f.create_dataset('arange_dset', dims, **kwargs)
 
         self.assertEqual(dset.name, "/arange_dset")
@@ -56,6 +55,7 @@ def test_create_arange_dset(self):
 
         f.close()
 
+
 if __name__ == '__main__':
     loglevel = logging.ERROR
     logging.basicConfig(format='%(asctime)s %(message)s', level=loglevel)

test/hl/test_dataset_objref.py

@@ -21,7 +21,6 @@
 
 class TestObjRef(TestCase):
 
-
     def test_create(self):
         filename = self.getFileName("objref_test")
         print(filename)
@@ -133,7 +132,6 @@ def test_create(self):
             self.assertEqual(obj.id.id, d1.id.id)  # ref to d1
         self.assertEqual(obj.name, "/g2/d1")
 
-
     def test_delete(self):
         filename = self.getFileName("objref_delete_test")
         print(filename)
@@ -142,15 +140,15 @@ def test_delete(self):
         self.assertTrue('/' in f)
 
         # create a dataset
-        dset = f.create_dataset('dset', data=[1,2,3])
+        dset = f.create_dataset('dset', data=[1, 2, 3])
         dset_ref = dset.ref
 
         f.attrs["dset_ref"] = dset_ref
         del f['dset']
         try:
             f[dset_ref]
         except ValueError:
-            pass # expected
+            pass  # expected
 
         f.close()