[python-h5netcdf] 02/10: Drop the patch queue, no longer required
Ghislain Vaillant
ghisvail-guest at moszumanska.debian.org
Wed Oct 11 16:36:15 UTC 2017
This is an automated email from the git hooks/post-receive script.
ghisvail-guest pushed a commit to branch master
in repository python-h5netcdf.
commit d75bb3960aa74e7327a9427f5e66fd23d1d56958
Author: Ghislain Antony Vaillant <ghisvail at gmail.com>
Date: Wed Sep 6 08:50:27 2017 +0100
Drop the patch queue, no longer required
---
debian/patches/Add-missing-test-suite.patch | 532 ----------------------------
debian/patches/series | 1 -
2 files changed, 533 deletions(-)
diff --git a/debian/patches/Add-missing-test-suite.patch b/debian/patches/Add-missing-test-suite.patch
deleted file mode 100644
index a60ec03..0000000
--- a/debian/patches/Add-missing-test-suite.patch
+++ /dev/null
@@ -1,532 +0,0 @@
-From: Ghislain Antony Vaillant <ghisvail at gmail.com>
-Date: Thu, 9 Feb 2017 10:28:24 +0000
-Subject: Add missing test suite
-
----
- h5netcdf/tests/test_h5netcdf.py | 517 ++++++++++++++++++++++++++++++++++++++++
- 1 file changed, 517 insertions(+)
- create mode 100644 h5netcdf/tests/test_h5netcdf.py
-
-diff --git a/h5netcdf/tests/test_h5netcdf.py b/h5netcdf/tests/test_h5netcdf.py
-new file mode 100644
-index 0000000..07b5269
---- /dev/null
-+++ b/h5netcdf/tests/test_h5netcdf.py
-@@ -0,0 +1,517 @@
-+import netCDF4
-+import numpy as np
-+import sys
-+import gc
-+
-+import h5netcdf
-+from h5netcdf import legacyapi
-+from h5netcdf.compat import PY2, unicode
-+import h5py
-+import pytest
-+
-+from pytest import fixture, raises
-+
-+
-+ at pytest.fixture
-+def tmp_netcdf(tmpdir):
-+ return str(tmpdir.join('testfile.nc'))
-+
-+
-+def string_to_char(arr):
-+ """Like nc4.stringtochar, but faster and more flexible.
-+ """
-+ # ensure the array is contiguous
-+ arr = np.array(arr, copy=False, order='C')
-+ kind = arr.dtype.kind
-+ if kind not in ['U', 'S']:
-+ raise ValueError('argument must be a string')
-+ return arr.reshape(arr.shape + (1,)).view(kind + '1')
-+
-+
-+def array_equal(a, b):
-+ a, b = map(np.array, (a[...], b[...]))
-+ if a.shape != b.shape:
-+ return False
-+ try:
-+ return np.allclose(a, b)
-+ except TypeError:
-+ return (a == b).all()
-+
-+
-+_char_array = string_to_char(np.array(['a', 'b', 'c', 'foo', 'bar', 'baz'],
-+ dtype='S'))
-+
-+_string_array = np.array([['foobar0', 'foobar1', 'foobar3'],
-+ ['foofoofoo', 'foofoobar', 'foobarbar']])
-+
-+def is_h5py_char_working(tmp_netcdf, name):
-+ # https://github.com/Unidata/netcdf-c/issues/298
-+ with h5py.File(tmp_netcdf, 'r') as ds:
-+ v = ds[name]
-+ try:
-+ assert array_equal(v, _char_array)
-+ return True
-+ except Exception as e:
-+ if e.args[0] == "Can't read data (No appropriate function for conversion path)":
-+ return False
-+ else:
-+ raise
-+
-+def write_legacy_netcdf(tmp_netcdf, write_module):
-+ ds = write_module.Dataset(tmp_netcdf, 'w')
-+ ds.setncattr('global', 42)
-+ ds.other_attr = 'yes'
-+ ds.createDimension('x', 4)
-+ ds.createDimension('y', 5)
-+ ds.createDimension('z', 6)
-+ ds.createDimension('empty', 0)
-+ ds.createDimension('string3', 3)
-+
-+ v = ds.createVariable('foo', float, ('x', 'y'), chunksizes=(4, 5),
-+ zlib=True)
-+ v[...] = 1
-+ v.setncattr('units', 'meters')
-+
-+ v = ds.createVariable('y', int, ('y',), fill_value=-1)
-+ v[:4] = np.arange(4)
-+
-+ v = ds.createVariable('z', 'S1', ('z', 'string3'), fill_value=b'X')
-+ v[...] = _char_array
-+
-+ v = ds.createVariable('scalar', np.float32, ())
-+ v[...] = 2.0
-+
-+ # test creating a scalar with compression option (with should be ignored)
-+ v = ds.createVariable('intscalar', np.int64, (), zlib=6, fill_value=None)
-+ v[...] = 2
-+
-+ with raises(TypeError):
-+ ds.createVariable('boolean', np.bool_, ('x'))
-+
-+ g = ds.createGroup('subgroup')
-+ v = g.createVariable('subvar', np.int32, ('x',))
-+ v[...] = np.arange(4.0)
-+
-+ g.createDimension('y', 10)
-+ g.createVariable('y_var', float, ('y',))
-+
-+ ds.createDimension('mismatched_dim', 1)
-+ ds.createVariable('mismatched_dim', int, ())
-+
-+ v = ds.createVariable('var_len_str', str, ('x'))
-+ v[0] = u'foo'
-+
-+ ds.close()
-+
-+
-+def write_h5netcdf(tmp_netcdf):
-+ ds = h5netcdf.File(tmp_netcdf, 'w')
-+ ds.attrs['global'] = 42
-+ ds.attrs['other_attr'] = 'yes'
-+ ds.dimensions = {'x': 4, 'y': 5, 'z': 6, 'empty': 0}
-+
-+ v = ds.create_variable('foo', ('x', 'y'), float, chunks=(4, 5),
-+ compression='gzip', shuffle=True)
-+ v[...] = 1
-+ v.attrs['units'] = 'meters'
-+
-+ v = ds.create_variable('y', ('y',), int, fillvalue=-1)
-+ v[:4] = np.arange(4)
-+
-+ v = ds.create_variable('z', ('z', 'string3'), data=_char_array,
-+ fillvalue=b'X')
-+
-+ v = ds.create_variable('scalar', data=np.float32(2.0))
-+
-+ v = ds.create_variable('intscalar', data=np.int64(2))
-+
-+ with raises(TypeError):
-+ ds.create_variable('boolean', data=True)
-+
-+ g = ds.create_group('subgroup')
-+ v = g.create_variable('subvar', ('x',), np.int32)
-+ v[...] = np.arange(4.0)
-+ with raises(AttributeError):
-+ v.attrs['_Netcdf4Dimid'] = -1
-+
-+ g.dimensions['y'] = 10
-+ g.create_variable('y_var', ('y',), float)
-+ g.flush()
-+
-+ ds.dimensions['mismatched_dim'] = 1
-+ ds.create_variable('mismatched_dim', dtype=int)
-+ ds.flush()
-+
-+ dt = h5py.special_dtype(vlen=unicode)
-+ v = ds.create_variable('var_len_str', ('x',), dtype=dt)
-+ v[0] = u'foo'
-+
-+ ds.close()
-+
-+
-+def read_legacy_netcdf(tmp_netcdf, read_module, write_module):
-+ ds = read_module.Dataset(tmp_netcdf, 'r')
-+ assert ds.ncattrs() == ['global', 'other_attr']
-+ assert ds.getncattr('global') == 42
-+ if not PY2 and write_module is not netCDF4:
-+ # skip for now: https://github.com/Unidata/netcdf4-python/issues/388
-+ assert ds.other_attr == 'yes'
-+ assert set(ds.dimensions) == set(['x', 'y', 'z', 'empty', 'string3',
-+ 'mismatched_dim'])
-+ assert set(ds.variables) == set(['foo', 'y', 'z', 'intscalar', 'scalar',
-+ 'var_len_str', 'mismatched_dim'])
-+ assert set(ds.groups) == set(['subgroup'])
-+ assert ds.parent is None
-+
-+ v = ds.variables['foo']
-+ assert array_equal(v, np.ones((4, 5)))
-+ assert v.dtype == float
-+ assert v.dimensions == ('x', 'y')
-+ assert v.ndim == 2
-+ assert v.ncattrs() == ['units']
-+ if not PY2 and write_module is not netCDF4:
-+ assert v.getncattr('units') == 'meters'
-+ assert tuple(v.chunking()) == (4, 5)
-+ assert v.filters() == {'complevel': 4, 'fletcher32': False,
-+ 'shuffle': True, 'zlib': True}
-+
-+ v = ds.variables['y']
-+ assert array_equal(v, np.r_[np.arange(4), [-1]])
-+ assert v.dtype == int
-+ assert v.dimensions == ('y',)
-+ assert v.ndim == 1
-+ assert v.ncattrs() == ['_FillValue']
-+ assert v.getncattr('_FillValue') == -1
-+ assert v.chunking() == 'contiguous'
-+ assert v.filters() == {'complevel': 0, 'fletcher32': False,
-+ 'shuffle': False, 'zlib': False}
-+ ds.close()
-+
-+ #Check the behavior if h5py. Cannot expect h5netcdf to overcome these errors:
-+ if is_h5py_char_working(tmp_netcdf, 'z'):
-+ ds = read_module.Dataset(tmp_netcdf, 'r')
-+ v = ds.variables['z']
-+ assert array_equal(v, _char_array)
-+ assert v.dtype == 'S1'
-+ assert v.ndim == 2
-+ assert v.dimensions == ('z', 'string3')
-+ assert v.ncattrs() == ['_FillValue']
-+ assert v.getncattr('_FillValue') == b'X'
-+ else:
-+ ds = read_module.Dataset(tmp_netcdf, 'r')
-+
-+ v = ds.variables['scalar']
-+ assert array_equal(v, np.array(2.0))
-+ assert v.dtype == 'float32'
-+ assert v.ndim == 0
-+ assert v.dimensions == ()
-+ assert v.ncattrs() == []
-+
-+ v = ds.variables['intscalar']
-+ assert array_equal(v, np.array(2))
-+ assert v.dtype == 'int64'
-+ assert v.ndim == 0
-+ assert v.dimensions == ()
-+ assert v.ncattrs() == []
-+
-+ v = ds.variables['var_len_str']
-+ assert v.dtype == str
-+ assert v[0] == u'foo'
-+
-+ v = ds.groups['subgroup'].variables['subvar']
-+ assert ds.groups['subgroup'].parent is ds
-+ assert array_equal(v, np.arange(4.0))
-+ assert v.dtype == 'int32'
-+ assert v.ndim == 1
-+ assert v.dimensions == ('x',)
-+ assert v.ncattrs() == []
-+
-+ v = ds.groups['subgroup'].variables['y_var']
-+ assert v.shape == (10,)
-+ assert 'y' in ds.groups['subgroup'].dimensions
-+
-+ ds.close()
-+
-+
-+def read_h5netcdf(tmp_netcdf, write_module):
-+ ds = h5netcdf.File(tmp_netcdf, 'r')
-+ assert ds.name == '/'
-+ assert list(ds.attrs) == ['global', 'other_attr']
-+ assert ds.attrs['global'] == 42
-+ if not PY2 and write_module is not netCDF4:
-+ # skip for now: https://github.com/Unidata/netcdf4-python/issues/388
-+ assert ds.attrs['other_attr'] == 'yes'
-+ assert set(ds.dimensions) == set(['x', 'y', 'z', 'empty', 'string3', 'mismatched_dim'])
-+ assert set(ds.variables) == set(['foo', 'y', 'z', 'intscalar', 'scalar',
-+ 'var_len_str', 'mismatched_dim'])
-+ assert set(ds.groups) == set(['subgroup'])
-+ assert ds.parent is None
-+
-+ v = ds['foo']
-+ assert v.name == '/foo'
-+ assert array_equal(v, np.ones((4, 5)))
-+ assert v.dtype == float
-+ assert v.dimensions == ('x', 'y')
-+ assert v.ndim == 2
-+ assert list(v.attrs) == ['units']
-+ if not PY2 and write_module is not netCDF4:
-+ assert v.attrs['units'] == 'meters'
-+ assert v.chunks == (4, 5)
-+ assert v.compression == 'gzip'
-+ assert v.compression_opts == 4
-+ assert not v.fletcher32
-+ assert v.shuffle
-+
-+ v = ds['y']
-+ assert array_equal(v, np.r_[np.arange(4), [-1]])
-+ assert v.dtype == int
-+ assert v.dimensions == ('y',)
-+ assert v.ndim == 1
-+ assert list(v.attrs) == ['_FillValue']
-+ assert v.attrs['_FillValue'] == -1
-+ assert v.chunks == None
-+ assert v.compression == None
-+ assert v.compression_opts == None
-+ assert not v.fletcher32
-+ assert not v.shuffle
-+ ds.close()
-+
-+ if is_h5py_char_working(tmp_netcdf, 'z'):
-+ ds = h5netcdf.File(tmp_netcdf, 'r')
-+ v = ds['z']
-+ assert v.dtype == 'S1'
-+ assert v.ndim == 2
-+ assert v.dimensions == ('z', 'string3')
-+ assert list(v.attrs) == ['_FillValue']
-+ assert v.attrs['_FillValue'] == b'X'
-+ else:
-+ ds = h5netcdf.File(tmp_netcdf, 'r')
-+
-+ v = ds['scalar']
-+ assert array_equal(v, np.array(2.0))
-+ assert v.dtype == 'float32'
-+ assert v.ndim == 0
-+ assert v.dimensions == ()
-+ assert list(v.attrs) == []
-+
-+ v = ds.variables['intscalar']
-+ assert array_equal(v, np.array(2))
-+ assert v.dtype == 'int64'
-+ assert v.ndim == 0
-+ assert v.dimensions == ()
-+ assert list(v.attrs) == []
-+
-+ v = ds['var_len_str']
-+ assert h5py.check_dtype(vlen=v.dtype) == unicode
-+ assert v[0] == u'foo'
-+
-+ v = ds['/subgroup/subvar']
-+ assert v is ds['subgroup']['subvar']
-+ assert v is ds['subgroup/subvar']
-+ assert v is ds['subgroup']['/subgroup/subvar']
-+ assert v.name == '/subgroup/subvar'
-+ assert ds['subgroup'].name == '/subgroup'
-+ assert ds['subgroup'].parent is ds
-+ assert array_equal(v, np.arange(4.0))
-+ assert v.dtype == 'int32'
-+ assert v.ndim == 1
-+ assert v.dimensions == ('x',)
-+ assert list(v.attrs) == []
-+
-+ assert ds['/subgroup/y_var'].shape == (10,)
-+ assert ds['/subgroup'].dimensions['y'] == 10
-+
-+ ds.close()
-+
-+
-+def roundtrip_legacy_netcdf(tmp_netcdf, read_module, write_module):
-+ write_legacy_netcdf(tmp_netcdf, write_module)
-+ read_legacy_netcdf(tmp_netcdf, read_module, write_module)
-+
-+
-+def test_write_legacyapi_read_netCDF4(tmp_netcdf):
-+ roundtrip_legacy_netcdf(tmp_netcdf, netCDF4, legacyapi)
-+
-+
-+def test_roundtrip_h5netcdf_legacyapi(tmp_netcdf):
-+ roundtrip_legacy_netcdf(tmp_netcdf, legacyapi, legacyapi)
-+
-+
-+def test_write_netCDF4_read_legacyapi(tmp_netcdf):
-+ roundtrip_legacy_netcdf(tmp_netcdf, legacyapi, netCDF4)
-+
-+
-+def test_write_h5netcdf_read_legacyapi(tmp_netcdf):
-+ write_h5netcdf(tmp_netcdf)
-+ read_legacy_netcdf(tmp_netcdf, legacyapi, h5netcdf)
-+
-+
-+def test_write_h5netcdf_read_netCDF4(tmp_netcdf):
-+ write_h5netcdf(tmp_netcdf)
-+ read_legacy_netcdf(tmp_netcdf, netCDF4, h5netcdf)
-+
-+
-+def test_roundtrip_h5netcdf(tmp_netcdf):
-+ write_h5netcdf(tmp_netcdf)
-+ read_h5netcdf(tmp_netcdf, h5netcdf)
-+
-+
-+def test_write_netCDF4_read_h5netcdf(tmp_netcdf):
-+ write_legacy_netcdf(tmp_netcdf, netCDF4)
-+ read_h5netcdf(tmp_netcdf, netCDF4)
-+
-+
-+def test_write_legacyapi_read_h5netcdf(tmp_netcdf):
-+ write_legacy_netcdf(tmp_netcdf, legacyapi)
-+ read_h5netcdf(tmp_netcdf, legacyapi)
-+
-+
-+def test_repr(tmp_netcdf):
-+ write_h5netcdf(tmp_netcdf)
-+ f = h5netcdf.File(tmp_netcdf, 'r')
-+ assert 'h5netcdf.File' in repr(f)
-+ assert 'subgroup' in repr(f)
-+ assert 'foo' in repr(f)
-+ assert 'other_attr' in repr(f)
-+
-+ assert 'h5netcdf.attrs.Attributes' in repr(f.attrs)
-+ assert 'global' in repr(f.attrs)
-+
-+ d = f.dimensions
-+ assert 'h5netcdf.Dimensions' in repr(d)
-+ assert 'x=4' in repr(d)
-+
-+ g = f['subgroup']
-+ assert 'h5netcdf.Group' in repr(g)
-+ assert 'subvar' in repr(g)
-+
-+ v = f['foo']
-+ assert 'h5netcdf.Variable' in repr(v)
-+ assert 'float' in repr(v)
-+ assert 'units' in repr(v)
-+ f.close()
-+
-+ assert 'Closed' in repr(f)
-+ assert 'Closed' in repr(d)
-+ assert 'Closed' in repr(g)
-+ assert 'Closed' in repr(v)
-+
-+
-+def test_attrs_api(tmp_netcdf):
-+ with h5netcdf.File(tmp_netcdf) as ds:
-+ ds.attrs['conventions'] = 'CF'
-+ ds.dimensions['x'] = 1
-+ v = ds.create_variable('x', ('x',), 'i4')
-+ v.attrs.update({'units': 'meters', 'foo': 'bar'})
-+ assert ds._closed
-+ with h5netcdf.File(tmp_netcdf) as ds:
-+ assert len(ds.attrs) == 1
-+ assert dict(ds.attrs) == {'conventions': 'CF'}
-+ assert list(ds.attrs) == ['conventions']
-+ assert dict(ds['x'].attrs) == {'units': 'meters', 'foo': 'bar'}
-+ assert len(ds['x'].attrs) == 2
-+ assert sorted(ds['x'].attrs) == ['foo', 'units']
-+
-+
-+def test_optional_netcdf4_attrs(tmp_netcdf):
-+ with h5py.File(tmp_netcdf) as f:
-+ foo_data = np.arange(50).reshape(5, 10)
-+ f.create_dataset('foo', data=foo_data)
-+ f.create_dataset('x', data=np.arange(5))
-+ f.create_dataset('y', data=np.arange(10))
-+ f['foo'].dims.create_scale(f['x'])
-+ f['foo'].dims.create_scale(f['y'])
-+ f['foo'].dims[0].attach_scale(f['x'])
-+ f['foo'].dims[1].attach_scale(f['y'])
-+ with h5netcdf.File(tmp_netcdf, 'r') as ds:
-+ assert ds['foo'].dimensions == ('x', 'y')
-+ assert ds.dimensions == {'x': 5, 'y': 10}
-+ assert array_equal(ds['foo'], foo_data)
-+
-+
-+def test_error_handling(tmp_netcdf):
-+ with h5netcdf.File(tmp_netcdf, 'w') as ds:
-+ with raises(NotImplementedError):
-+ ds.dimensions['x'] = None
-+ ds.dimensions['x'] = 1
-+ with raises(ValueError):
-+ ds.dimensions['x'] = 2
-+ with raises(ValueError):
-+ ds.dimensions = {'x': 2}
-+ with raises(ValueError):
-+ ds.dimensions = {'y': 3}
-+ ds.create_variable('x', ('x',), dtype=float)
-+ with raises(ValueError):
-+ ds.create_variable('x', ('x',), dtype=float)
-+ ds.create_group('subgroup')
-+ with raises(ValueError):
-+ ds.create_group('subgroup')
-+
-+
-+def test_invalid_netcdf4(tmp_netcdf):
-+ with h5py.File(tmp_netcdf) as f:
-+ f.create_dataset('foo', data=np.arange(5))
-+ # labeled dimensions but no dimension scales
-+ f['foo'].dims[0].label = 'x'
-+ with h5netcdf.File(tmp_netcdf, 'r') as ds:
-+ with raises(ValueError):
-+ ds.variables['foo'].dimensions
-+
-+
-+def test_hierarchical_access_auto_create(tmp_netcdf):
-+ ds = h5netcdf.File(tmp_netcdf, 'w')
-+ ds.create_variable('/foo/bar', data=1)
-+ g = ds.create_group('foo/baz')
-+ g.create_variable('/foo/hello', data=2)
-+ assert set(ds) == set(['foo'])
-+ assert set(ds['foo']) == set(['bar', 'baz', 'hello'])
-+ ds.close()
-+
-+ ds = h5netcdf.File(tmp_netcdf, 'r')
-+ assert set(ds) == set(['foo'])
-+ assert set(ds['foo']) == set(['bar', 'baz', 'hello'])
-+ ds.close()
-+
-+def test_reading_str_array_from_netCDF4(tmp_netcdf):
-+ # This tests reading string variables created by netCDF4
-+ with netCDF4.Dataset(tmp_netcdf, 'w') as ds:
-+ ds.createDimension('foo1', _string_array.shape[0])
-+ ds.createDimension('foo2', _string_array.shape[1])
-+ ds.createVariable('bar', str, ('foo1', 'foo2'))
-+ ds.variables['bar'][:] = _string_array
-+
-+ ds = h5netcdf.File(tmp_netcdf, 'r')
-+
-+ v = ds.variables['bar']
-+ assert array_equal(v, _string_array)
-+ ds.close()
-+
-+def test_nc_properties(tmp_netcdf):
-+ with h5netcdf.File(tmp_netcdf, 'w') as ds:
-+ pass
-+ with h5py.File(tmp_netcdf, 'r') as f:
-+ assert 'h5netcdf' in f.attrs['_NCProperties']
-+
-+def test_failed_read_open_and_clean_delete(tmpdir):
-+ # A file that does not exist but is opened for
-+ # reading should only raise an IOError and
-+ # no AttributeError at garbage collection.
-+ path = str(tmpdir.join('this_file_does_not_exist.nc'))
-+ try:
-+ with h5netcdf.File(path, 'r') as ds:
-+ pass
-+ except IOError:
-+ pass
-+
-+ # Look at garbage collection:
-+ # A simple gc.collect() does not raise an exception.
-+ # Must seek the File object and imitate its del command
-+ # by forcing it to close.
-+ obj_list = gc.get_objects()
-+ for obj in obj_list:
-+ try:
-+ is_h5netcdf_File = isinstance(obj, h5netcdf.File)
-+ except AttributeError as e:
-+ is_h5netcdf_File = False
-+ if is_h5netcdf_File:
-+ obj.close()
diff --git a/debian/patches/series b/debian/patches/series
deleted file mode 100644
index fe60c2f..0000000
--- a/debian/patches/series
+++ /dev/null
@@ -1 +0,0 @@
-Add-missing-test-suite.patch
--
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