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Fix failing nc_tools tests #113

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merged 3 commits into from
Dec 21, 2024
Merged

Fix failing nc_tools tests #113

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9c45437
Improve test assertions for nc_tools output verification
douglatornell Dec 21, 2024
27f26e3
Revert test URL change from GitHub to Bitbucket
douglatornell Dec 21, 2024
5c2a7d5
Fix typo in docstring
douglatornell Dec 21, 2024
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2 changes: 1 addition & 1 deletion SalishSeaTools/salishsea_tools/namelist.py
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Original file line number Diff line number Diff line change
Expand Up @@ -275,7 +275,7 @@ def namelist2dict(file_or_file_object):

def _namelist2dict(file_object):
"""
Converts a file_object containng a namelist to a dictionary.
Converts a file_object containing a namelist to a dictionary.
"""
namelist_dict = {}
for group_name, group_values in group_generator(tokenizer(file_object)):
Expand Down
109 changes: 77 additions & 32 deletions SalishSeaTools/tests/test_nc_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -76,31 +76,40 @@ def test_show_dimensions(capsys, nc_dataset):
"""show_dimensions prints dimension string representation
"""
nc_dataset.createDimension('foo', 42)

nc_tools.show_dimensions(nc_dataset)

expected = ['"<class \'netCDF4.Dimension\'>": name = \'foo\', size = 42']
out, err = capsys.readouterr()
assert out.splitlines()[0] == (
"<class 'netCDF4._netCDF4.Dimension'>: name = 'foo', size = 42")
assert out.splitlines() == expected


def test_show_dimensions_order(capsys, nc_dataset):
"""show_dimensions prints dimension in order they were defined
"""
nc_dataset.createDimension('foo', 42)
nc_dataset.createDimension('bar', 24)

nc_tools.show_dimensions(nc_dataset)

expected = [
'"<class \'netCDF4.Dimension\'>": name = \'foo\', size = 42',
'"<class \'netCDF4.Dimension\'>": name = \'bar\', size = 24',
]
out, err = capsys.readouterr()
assert out.splitlines()[2] == (
"<class 'netCDF4._netCDF4.Dimension'>: name = 'bar', size = 24")
assert out.splitlines() == expected


def test_show_variables(capsys, nc_dataset):
"""show_variables prints list of variable names
"""
nc_dataset.createDimension('x', 42)
nc_dataset.createVariable('foo', float, ('x',))

nc_tools.show_variables(nc_dataset)

out, err = capsys.readouterr()
assert out.splitlines()[0] == "odict_keys(['foo'])"
assert out.splitlines() == ["dict_keys(['foo'])"]


def test_show_variables_order(capsys, nc_dataset):
Expand All @@ -109,9 +118,11 @@ def test_show_variables_order(capsys, nc_dataset):
nc_dataset.createDimension('x', 42)
nc_dataset.createVariable('foo', float, ('x',))
nc_dataset.createVariable('bar', float, ('x',))

nc_tools.show_variables(nc_dataset)

out, err = capsys.readouterr()
assert out.splitlines()[0] == "odict_keys(['foo', 'bar'])"
assert out.splitlines() == ["dict_keys(['foo', 'bar'])"]


def test_show_variable_attrs(capsys, nc_dataset):
Expand All @@ -120,16 +131,19 @@ def test_show_variable_attrs(capsys, nc_dataset):
nc_dataset.createDimension('x', 42)
foo = nc_dataset.createVariable('foo', float, ('x',))
foo.units = 'm'

nc_tools.show_variable_attrs(nc_dataset)

expected = [
"<class 'netCDF4.Variable'>",
"float64 foo(x)",
" units: m",
"unlimited dimensions: ",
"current shape = (42,)",
"filling on, default _FillValue of 9.969209968386869e+36 used",
]
out, err = capsys.readouterr()
assert out == (
"<class 'netCDF4._netCDF4.Variable'>\n"
"float64 foo(x)\n"
" units: m\n"
"unlimited dimensions: \n"
"current shape = (42,)\n"
"filling on, default _FillValue of 9.969209968386869e+36 used\n\n"
)
assert out.splitlines() == expected


def test_show_variable_attrs_order(capsys, nc_dataset):
Expand All @@ -138,39 +152,70 @@ def test_show_variable_attrs_order(capsys, nc_dataset):
nc_dataset.createDimension('x', 42)
nc_dataset.createVariable('foo', float, ('x',))
nc_dataset.createVariable('bar', float, ('x',))

nc_tools.show_variable_attrs(nc_dataset)

expected = [
"<class 'netCDF4.Variable'>",
"float64 foo(x)",
"unlimited dimensions: ",
"current shape = (42,)",
"filling on, default _FillValue of 9.969209968386869e+36 used",
"<class 'netCDF4.Variable'>",
"float64 bar(x)",
"unlimited dimensions: ",
"current shape = (42,)",
"filling on, default _FillValue of 9.969209968386869e+36 used",
]
out, err = capsys.readouterr()
assert out.splitlines()[7] == 'float64 bar(x)'
assert out.splitlines() == expected


def test_show_variable_attrs_spec_var(capsys, nc_dataset):
def test_show_variable_attrs_specified_var(capsys, nc_dataset):
"""show_variable_attrs prints string repr of specified variable
"""
nc_dataset.createDimension('x', 42)
foo = nc_dataset.createVariable('foo', float, ('x',))
foo.units = 'm'
nc_dataset.createVariable('bar', float, ('x',))

nc_tools.show_variable_attrs(nc_dataset, 'foo')

expected = [
"<class 'netCDF4.Variable'>",
"float64 foo(x)",
" units: m",
"unlimited dimensions: ",
"current shape = (42,)",
"filling on, default _FillValue of 9.969209968386869e+36 used",
]
out, err = capsys.readouterr()
assert out == (
"<class 'netCDF4._netCDF4.Variable'>\n"
"float64 foo(x)\n"
" units: m\n"
"unlimited dimensions: \n"
"current shape = (42,)\n"
"filling on, default _FillValue of 9.969209968386869e+36 used\n\n"
)
assert out.splitlines() == expected


def test_show_variable_attrs_spec_var_order(capsys, nc_dataset):
def test_show_variable_attrs_specified_var_order(capsys, nc_dataset):
"""show_variable_attrs prints specified vars in order they were defined
"""
nc_dataset.createDimension('x', 42)
nc_dataset.createVariable('foo', float, ('x',))
nc_dataset.createVariable('bar', float, ('x',))

nc_tools.show_variable_attrs(nc_dataset, 'foo', 'bar')

expected = [
"<class 'netCDF4.Variable'>",
"float64 foo(x)",
"unlimited dimensions: ",
"current shape = (42,)",
"filling on, default _FillValue of 9.969209968386869e+36 used",
"<class 'netCDF4.Variable'>",
"float64 bar(x)",
"unlimited dimensions: ",
"current shape = (42,)",
"filling on, default _FillValue of 9.969209968386869e+36 used",
]
out, err = capsys.readouterr()
assert out.splitlines()[7] == 'float64 bar(x)'
assert out.splitlines() == expected


def test_time_origin_value(nc_dataset):
Expand Down Expand Up @@ -372,12 +417,12 @@ def test_init_dataset_attrs_no_oversrite_quiet(

@patch(
'salishsea_tools.nc_tools.hg.default_url',
return_value='ssh://hg@github.com/SalishSeaCast/foo')
return_value='ssh://hg@bitbucket.org/SalishSeaCast/foo')
def test_notebook_hg_url(mock_dflt_url):
"""_notebook_hg_url returns expected URL
"""
url = nc_tools._notebook_hg_url('bar.ipynb')
assert url == 'https://github.com/SalishSeaCast/foo/src/tip/bar.ipynb'
assert url == 'https://bitbucket.org/SalishSeaCast/foo/src/tip/bar.ipynb'


def test_notebook_hg_url_no_notebook_name():
Expand All @@ -397,22 +442,22 @@ def test_notebook_hg_url_REQUIRED(mock_dflt_url):

@patch(
'salishsea_tools.nc_tools.hg.default_url',
return_value='ssh://hg@github.com/SalishSeaCast/foo')
return_value='ssh://hg@bitbucket.org/SalishSeaCast/foo')
def test_notebook_hg_url_adds_ipynb(mock_dflt_url):
"""_notebook_hg_url adds .ipynb extension if notebook name lacks it
"""
url = nc_tools._notebook_hg_url('bar')
assert url == 'https://github.com/SalishSeaCast/foo/src/tip/bar.ipynb'
assert url == 'https://bitbucket.org/SalishSeaCast/foo/src/tip/bar.ipynb'


@patch(
'salishsea_tools.nc_tools.hg.default_url',
return_value='ssh://hg@github.com/SalishSeaCast/foo')
return_value='ssh://hg@bitbucket.org/SalishSeaCast/foo')
def test_nc_file_hg_url(mock_dflt_url):
"""_nc_file_hg_url returns expected URL
"""
url = nc_tools._nc_file_hg_url('../bar/baz.nc')
assert url == 'https://github.com/SalishSeaCast/foo/src/tip/baz.nc'
assert url == 'https://bitbucket.org/SalishSeaCast/foo/src/tip/baz.nc'


def test_nc_file_hg_url_no_nc_filepath():
Expand Down
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