Extend and reconfigure tests

Add skimed file testing
Split o3skim tests into multiple files

tests/conftest.py

+"""Pytest configuration file."""
+
+import os
+
+import o3skim
+import pytest
+import tests.mockup as mockup_data
+import xarray
+
+# configurations ----------------------------------------------------
+year_line = range(2000, 2022)
+
+sources = ["SourceSplit", "SourceMerged"]
+sources_example = "tests/sources_example.yaml"
+sources_err = "tests/sources_err.yaml"
+
+models = ["ModelTCO3", "ModelVMRO3", "ModelALL"]
+models_tco3 = ['ModelTCO3', 'ModelALL']
+models_vmro3 = ['ModelVMRO3', 'ModelALL']
+
+
+# session fixtures ---------------------------------------------------
+@pytest.fixture(scope='session')
+def data_dir(tmpdir_factory):
+    data_dir = tmpdir_factory.mktemp("data")
+    for source in sources:
+        source_dir = data_dir.join(source)
+        os.mkdir(source_dir)
+        with o3skim.utils.cd(source_dir):
+            if source == 'SourceMerged':
+                mockup_data.combined(year_line)
+                mockup_data.noise(name='merged_noise.nc')
+            if source == 'SourceSplit':
+                mockup_data.tco3(year_line)
+                mockup_data.noise(name='tco3_noise.nc')
+                mockup_data.vmro3(year_line)
+                mockup_data.noise(name='vmro3_noise.nc')
+    return data_dir
+
+
+@pytest.fixture(scope='session')
+def config_file(request):
+    return request.param
+
+
+@pytest.fixture(scope='session')
+def config_dict(config_file):
+    return o3skim.utils.load(config_file)
+
+
+# package fixtures --------------------------------------------------
+
+
+# module fixtures ---------------------------------------------------
+@pytest.fixture(scope='module')
+def output_dir(tmpdir_factory):
+    return tmpdir_factory.mktemp("output")
+
+
+@pytest.fixture(scope='module')
+def groupby(request):
+    return request.param
+
+
+@pytest.fixture(scope='module')
+def source_name(request):
+    return request.param
+
+
+@pytest.fixture(scope='module')
+def source(config_dict, source_name, data_dir):
+    with o3skim.utils.cd(data_dir):
+        source = o3skim.Source(source_name, config_dict[source_name])
+    return source
+
+
+@pytest.fixture(scope='module')
+def skimmed(groupby, source, output_dir):
+    with o3skim.utils.cd(output_dir):
+        source.skim(groupby=groupby)
+        yield groupby, source.name
+
+
+# class fixtures --------------------------------------------------
+
+
+# function fixtures -------------------------------------------------
+@pytest.fixture()
+def model_name(request):
+    return request.param
+
+
+@pytest.fixture()
+def model(source, model_name):
+    return source[model_name]
+
+
+@pytest.fixture()
+def year(request):
+    return request.param
+
+
+@pytest.fixture()
+def variable(request):
+    return request.param
+
+
+@pytest.fixture()
+def skimed_file(skimmed, model_name, variable, year):
+    groupby, source_name = skimmed
+    with o3skim.utils.cd("{}_{}".format(source_name, model_name)):
+        if not groupby:
+            yield "{}.nc".format(variable)
+        if groupby == 'year':
+            yield "{}_{}-{}.nc".format(variable, year, year + 1)
+        if groupby == 'decade':
+            yield "{}_{}-{}.nc".format(variable, year, year + 10)
+
+
+@pytest.fixture()
+def skimmed_model(skimed_file):
+    with xarray.open_dataset(skimed_file) as model:
+        yield model

tests/test_errors.py

-"""Unittest module template."""
-
-import os
-import pytest
-
-import o3skim
-import xarray
-import tests.mockup as mockup_data
-
-
-# Test configurations ----------------------------------------------
-configuration_file = "tests/sources_err.yaml"
-year_line = range(2000, 2022)
-
-sources = ["SourceSplit"]
-# models = ["ModelBadName", "ModelBadPath", "ModelMissingCoords",
-#           "ModelBadCoords", "ModelExtraCoords"]
-
-config = o3skim.utils.load(configuration_file)
-
-
-# Module fixtures ---------------------------------------------------
-@ pytest.fixture(scope='module')
-def data_dir(tmpdir_factory):
-    data_dir = tmpdir_factory.mktemp("data")
-    for source in sources:
-        source_dir = data_dir.join(source)
-        os.mkdir(source_dir)
-        with o3skim.utils.cd(source_dir):
-            if source == 'SourceMerged':
-                mockup_data.combined(year_line)
-                mockup_data.noise(name='merged_noise.nc')
-            if source == 'SourceSplit':
-                mockup_data.tco3(year_line)
-                mockup_data.noise(name='tco3_noise.nc')
-                mockup_data.vmro3(year_line)
-                mockup_data.noise(name='vmro3_noise.nc')
-    with o3skim.utils.cd(data_dir):
-        yield data_dir
-
-
-# Source Tests ------------------------------------------------------
-@ pytest.fixture(scope='module')
-def source_config(request, data_dir):
-    source_name = request.param
-    yield source_name, config[source_name]
-
-
-@ pytest.fixture(scope='class')
-def source(source_config):
-    source_name, collections = source_config
-    yield o3skim.Source(source_name, collections)
-
-
-@ pytest.mark.parametrize('source_config', sources, indirect=True)
-class Test_Exceptions:
-
-    def test_constructor(self, source_config):
-        source_name, collections = source_config
-        source = o3skim.Source(source_name, collections)
-        assert source.name == source_name
-        assert source.models == []
-        assert True
-
-    def test_skimming(self, source):
-        assert None == source.skim(groupby=None)
-        assert None == source.skim(groupby='year')
-        assert None == source.skim(groupby='decade')
-        assert True
-

tests/test_o3skim.py

-"""Unittest module template."""
-
-import os
-import pytest
-
-import o3skim
-import xarray
-import tests.mockup as mockup_data
-
-# Test configurations ----------------------------------------------
-configuration_file = "tests/sources_example.yaml"
-year_line = range(2000, 2022)
-
-sources = ["SourceSplit", "SourceMerged"]
-models = ["ModelTCO3", "ModelVMRO3", "ModelALL"]
-
-models_tco3 = ['ModelTCO3', 'ModelALL']
-models_vmro = ['ModelVMRO3', 'ModelALL']
-
-config = o3skim.utils.load(configuration_file)
-
-
-# Module fixtures ---------------------------------------------------
-@pytest.fixture(scope='module')
-def data_dir(tmpdir_factory):
-    data_dir = tmpdir_factory.mktemp("data")
-    for source in sources:
-        source_dir = data_dir.join(source)
-        os.mkdir(source_dir)
-        with o3skim.utils.cd(source_dir):
-            if source == 'SourceMerged':
-                mockup_data.combined(year_line)
-                mockup_data.noise(name='merged_noise.nc')
-            if source == 'SourceSplit':
-                mockup_data.tco3(year_line)
-                mockup_data.noise(name='tco3_noise.nc')
-                mockup_data.vmro3(year_line)
-                mockup_data.noise(name='vmro3_noise.nc')
-    with o3skim.utils.cd(data_dir):
-        yield data_dir
-
-
-# Source Tests ------------------------------------------------------
-@pytest.fixture(scope='module')
-def source_name(request):
-    source_name = request.param
-    yield source_name
-
-
-@pytest.fixture(scope='class')
-def source(source_name, data_dir):
-    yield o3skim.Source(source_name, config[source_name])
-
-
-@pytest.mark.parametrize('source_name', sources, indirect=True)
-class TestSource:
-
-    def test_constructor(self, source_name, data_dir):
-        source = o3skim.Source(source_name, config[source_name])
-        assert type(source.name) is str
-        assert type(source.models) is list
-
-    def test_skimming(self, source):
-        assert None == source.skim(groupby=None)
-        assert None == source.skim(groupby='year')
-        assert None == source.skim(groupby='decade')
-
-
-# Model Tests ------------------------------------------------------
-@pytest.fixture(scope='class')
-def model_name(request):
-    model_name = request.param
-    yield model_name
-
-
-@pytest.fixture(scope='class')
-def model(source, model_name):
-    yield source[model_name]
-
-
-@pytest.mark.parametrize('source_name', sources, indirect=True)
-class TestModel:
-
-    @pytest.mark.parametrize('model_name', models, indirect=True)
-    def test_model_properties(self, model):
-        assert isinstance(model, xarray.Dataset)
-        assert model.time.size != 0
-
-    @pytest.mark.parametrize('model_name', ['ModelTCO3'], indirect=True)
-    def test_tco3_coordinates(self, model):
-        assert 'time' in model.coords
-        assert not 'plev' in model.coords
-        assert 'lat' in model.coords
-        assert 'lon' in model.coords
-
-    @pytest.mark.parametrize('model_name', ['ModelVMRO3'], indirect=True)
-    def test_vmro3_coordinates(self, model):
-        assert 'time' in model.coords
-        assert 'plev' in model.coords
-        assert 'lat' in model.coords
-        assert 'lon' in model.coords
-
-    @pytest.mark.parametrize('model_name', ['ModelALL'], indirect=True)
-    def test_all_coordinates(self, model):
-        assert 'time' in model.coords
-        assert 'plev' in model.coords
-        assert 'lat' in model.coords
-        assert 'lon' in model.coords
-
-
-# Skimming Tests ----------------------------------------------------
-
-@pytest.fixture(scope='class')
-def groupby(request):
-    return request.param
-
-
-@pytest.fixture(scope='class')
-def skimmed(groupby, source):
-    output_dir = "{}_groupby_{}".format(source.name, groupby)
-    os.mkdir(output_dir)
-    with o3skim.utils.cd(output_dir):
-        source.skim(groupby=groupby)
-        yield source.name
-
-
-@pytest.fixture(scope='class')
-def skimmed_model(model_name, skimmed):
-    source_name = skimmed
-    with o3skim.utils.cd(source_name + "_" + model_name):
-        yield source_name, model_name
-
-
-@pytest.mark.parametrize('source_name', sources, indirect=True)
-@pytest.mark.parametrize('groupby', [None], indirect=True)
-class TestSkimming_NoGroup:
-
-    @pytest.mark.parametrize('model_name', models_tco3, indirect=True)
-    def test_skimmed_tco3(self, skimmed_model):
-        assert os.path.isfile("tco3_zm.nc")
-
-    @pytest.mark.parametrize('model_name', models_vmro, indirect=True)
-    def test_skimmed_vmro3(self, skimmed_model):
-        assert os.path.isfile("vmro3_zm.nc")
-
-
-@pytest.mark.parametrize('source_name', sources, indirect=True)
-@pytest.mark.parametrize('groupby', ['year'], indirect=True)
-class TestSkimming_ByYear:
-
-    @pytest.mark.parametrize('model_name', models_tco3, indirect=True)
-    def test_skimmed_tco3(self, skimmed_model):
-        for y in year_line:
-            assert os.path.isfile("tco3_zm_{}-{}.nc".format(y, y + 1))
-
-    @pytest.mark.parametrize('model_name', models_vmro, indirect=True)
-    def test_skimmed_vmro3(self, skimmed_model):
-        for y in year_line:
-            assert os.path.isfile("vmro3_zm_{}-{}.nc".format(y, y + 1))
-
-
-@pytest.mark.parametrize('source_name', sources, indirect=True)
-@pytest.mark.parametrize('groupby', ['decade'], indirect=True)
-class TestSkimming_ByDecade:
-
-    @pytest.mark.parametrize('model_name', models_tco3, indirect=True)
-    def test_skimmed_tco3(self, skimmed_model):
-        for y in year_line:
-            if y % 10 == 0:
-                assert os.path.isfile("tco3_zm_{}-{}.nc".format(y, y + 10))
-            else:
-                assert not os.path.isfile("tco3_zm_{}-{}.nc".format(y, y + 10))
-
-    @pytest.mark.parametrize('model_name', models_vmro, indirect=True)
-    def test_skimmed_vmro3(self, skimmed_model):
-        for y in year_line:
-            if y % 10 == 0:
-                assert os.path.isfile("vmro3_zm_{}-{}.nc".format(y, y + 10))
-            else:
-                assert not os.path.isfile("vmro3_zm_{}-{}.nc".format(y, y + 10))

tests/test_sources.py

+"""Pytest module to test sources as blackbox."""
+
+import os
+
+import o3skim
+import pytest
+import tests.conftest as conftest
+import xarray
+
+
+@pytest.mark.parametrize('config_file', [conftest.sources_example], indirect=True)
+@pytest.mark.parametrize('source_name', conftest.sources, indirect=True)
+class TestSource:
+
+    def test_constructor(self, config_dict, source_name, data_dir):
+        with o3skim.utils.cd(data_dir):
+            source = o3skim.Source(source_name, config_dict[source_name])
+            assert type(source.name) is str
+            assert type(source.models) is list
+            assert source.models != []
+
+    def test_skimming(self, source, output_dir):
+        with o3skim.utils.cd(output_dir):
+            assert None == source.skim(groupby=None)
+            assert None == source.skim(groupby='year')
+            assert None == source.skim(groupby='decade')
+
+    @pytest.mark.parametrize('model_name', conftest.models, indirect=True)
+    def test_model_properties(self, model):
+        assert isinstance(model, xarray.Dataset)
+        assert model.time.size != 0
+
+
+@pytest.mark.parametrize('config_file', [conftest.sources_err], indirect=True)
+@pytest.mark.parametrize('source_name', ["SourceSplit"], indirect=True)
+class TestExceptions:
+
+    def test_constructor(self, config_dict, source_name, data_dir):
+        with o3skim.utils.cd(data_dir):
+            source = o3skim.Source(source_name, config_dict[source_name])
+            assert source.name == source_name
+            assert source.models == []
+            assert True
+
+    def test_skimming(self, source):
+        assert None == source.skim(groupby=None)
+        assert None == source.skim(groupby='year')
+        assert None == source.skim(groupby='decade')
+        assert True

tests/test_tco3.py

+"""Pytest module to test tco3 data as blackbox."""
+
+import os
+
+import o3skim
+import pytest
+import tests.conftest as conftest
+import xarray
+
+
+def pytest_generate_tests(metafunc):
+    config_file = conftest.sources_example
+    metafunc.parametrize("config_file", [config_file], indirect=True)
+    metafunc.parametrize("source_name", conftest.sources, indirect=True)
+    metafunc.parametrize("variable", ["tco3_zm"], indirect=True)
+
+
+class TestModel:
+
+    @pytest.mark.parametrize('model_name', conftest.models_tco3, indirect=True)
+    def test_tco3_coordinates(self, model, variable):
+        assert 'time' in model.coords
+        assert 'lat' in model.coords
+        assert 'lon' in model.coords
+
+    @pytest.mark.parametrize('model_name', ["ModelTCO3"], indirect=True)
+    def test_tco3_no_extra_coordinates(self, model, variable):
+        assert len(model.coords) == 3
+
+
+@pytest.mark.parametrize('groupby', [None], indirect=True)
+class TestSkimming_NoGroup:
+
+    @pytest.mark.parametrize('model_name', conftest.models_tco3, indirect=True)
+    @pytest.mark.parametrize('year', [None], indirect=True)
+    def test_isTCO3file(self, skimed_file):
+        assert os.path.isfile(skimed_file)
+
+    @pytest.mark.parametrize('model_name', conftest.models_tco3, indirect=True)
+    @pytest.mark.parametrize('year', [None], indirect=True)
+    def test_skimmed_tco3(self, skimmed_model):
+        assert 'tco3_zm' in skimmed_model.var()
+        assert 'time' in skimmed_model.coords
+        assert not 'plev' in skimmed_model.coords
+        assert 'lat' in skimmed_model.coords
+        assert not 'lon' in skimmed_model.coords
+
+
+@pytest.mark.parametrize('groupby', ['year'], indirect=True)
+class TestSkimming_ByYear:
+
+    @pytest.mark.parametrize('model_name', conftest.models_tco3, indirect=True)
+    @pytest.mark.parametrize('year', list(conftest.year_line), indirect=True)
+    def test_isTCO3file(self, skimed_file):
+        assert os.path.isfile(skimed_file)
+
+    @pytest.mark.parametrize('model_name', conftest.models_tco3, indirect=True)
+    @pytest.mark.parametrize('year', list(conftest.year_line), indirect=True)
+    def test_skimmed_tco3(self, skimmed_model):
+        assert 'tco3_zm' in skimmed_model.var()
+        assert 'time' in skimmed_model.coords
+        assert not 'plev' in skimmed_model.coords
+        assert 'lat' in skimmed_model.coords
+        assert not 'lon' in skimmed_model.coords
+
+
+@pytest.mark.parametrize('groupby', ['decade'], indirect=True)
+class TestSkimming_ByDecade:
+
+    @pytest.mark.parametrize('model_name', conftest.models_tco3, indirect=True)
+    @pytest.mark.parametrize('year', [y for y in conftest.year_line if y % 10 == 0], indirect=True)
+    def test_isTCO3file(self, skimed_file):
+        assert os.path.isfile(skimed_file)
+
+    @pytest.mark.parametrize('model_name', conftest.models_tco3, indirect=True)
+    @pytest.mark.parametrize('year', [y for y in conftest.year_line if y % 10 != 0], indirect=True)
+    def test_isNotTCO3file(self, skimed_file, year):
+        assert not os.path.isfile(skimed_file)
+
+    @pytest.mark.parametrize('model_name', conftest.models_tco3, indirect=True)
+    @pytest.mark.parametrize('year', [y for y in conftest.year_line if y % 10 == 0], indirect=True)
+    def test_skimmed_tco3(self, skimmed_model):
+        assert 'tco3_zm' in skimmed_model.var()
+        assert 'time' in skimmed_model.coords
+        assert not 'plev' in skimmed_model.coords
+        assert 'lat' in skimmed_model.coords
+        assert not 'lon' in skimmed_model.coords

tests/test_vmro3.py

+"""Pytest module to test vmro3 data as blackbox."""
+
+import os
+
+import o3skim
+import pytest
+import tests.conftest as conftest
+import xarray
+
+
+def pytest_generate_tests(metafunc):
+    config_file = conftest.sources_example
+    metafunc.parametrize("config_file", [config_file], indirect=True)
+    metafunc.parametrize("source_name", conftest.sources, indirect=True)
+    metafunc.parametrize("variable", ["vmro3_zm"], indirect=True)
+
+
+class TestModel:
+
+    @pytest.mark.parametrize('model_name', conftest.models_vmro3, indirect=True)
+    def test_vmro3_coordinates(self, model, variable):
+        assert 'time' in model.coords
+        assert 'plev' in model.coords
+        assert 'lat' in model.coords
+        assert 'lon' in model.coords
+
+    @pytest.mark.parametrize('model_name', ["ModelVMRO3"], indirect=True)
+    def test_vmro3_no_extra_coordinates(self, model, variable):
+        assert len(model.coords) == 4
+
+
+@pytest.mark.parametrize('groupby', [None], indirect=True)
+class TestSkimming_NoGroup:
+
+    @pytest.mark.parametrize('model_name', conftest.models_vmro3, indirect=True)
+    @pytest.mark.parametrize('year', [None], indirect=True)
+    def test_isVMRO3file(self, skimed_file):
+        assert os.path.isfile(skimed_file)
+
+    @pytest.mark.parametrize('model_name', conftest.models_vmro3, indirect=True)
+    @pytest.mark.parametrize('year', [None], indirect=True)
+    def test_skimmed_vmro3(self, skimmed_model):
+        assert 'vmro3_zm' in skimmed_model.var()
+        assert 'time' in skimmed_model.coords
+        assert 'plev' in skimmed_model.coords
+        assert 'lat' in skimmed_model.coords
+        assert not 'lon' in skimmed_model.coords
+
+
+@pytest.mark.parametrize('groupby', ['year'], indirect=True)
+class TestSkimming_ByYear:
+
+    @pytest.mark.parametrize('model_name', conftest.models_vmro3, indirect=True)
+    @pytest.mark.parametrize('year', list(conftest.year_line), indirect=True)
+    def test_isVMRO3file(self, skimed_file):
+        assert os.path.isfile(skimed_file)
+
+    @pytest.mark.parametrize('model_name', conftest.models_vmro3, indirect=True)
+    @pytest.mark.parametrize('year', list(conftest.year_line), indirect=True)
+    def test_skimmed_vmro3(self, skimmed_model):
+        assert 'vmro3_zm' in skimmed_model.var()
+        assert 'time' in skimmed_model.coords
+        assert 'plev' in skimmed_model.coords
+        assert 'lat' in skimmed_model.coords
+        assert not 'lon' in skimmed_model.coords
+
+
+@pytest.mark.parametrize('groupby', ['decade'], indirect=True)
+class TestSkimming_ByDecade:
+
+    @pytest.mark.parametrize('model_name', conftest.models_vmro3, indirect=True)
+    @pytest.mark.parametrize('year', [y for y in conftest.year_line if y % 10 == 0], indirect=True)
+    def test_isVMRO3file(self, skimed_file):
+        assert os.path.isfile(skimed_file)
+
+    @pytest.mark.parametrize('model_name', conftest.models_vmro3, indirect=True)
+    @pytest.mark.parametrize('year', [y for y in conftest.year_line if y % 10 != 0], indirect=True)
+    def test_isNotVMRO3file(self, skimed_file, year):
+        assert not os.path.isfile(skimed_file)
+
+    @pytest.mark.parametrize('model_name', conftest.models_vmro3, indirect=True)
+    @pytest.mark.parametrize('year', [y for y in conftest.year_line if y % 10 == 0], indirect=True)
+    def test_skimmed_vmro3(self, skimmed_model):
+        assert 'vmro3_zm' in skimmed_model.var()
+        assert 'time' in skimmed_model.coords
+        assert 'plev' in skimmed_model.coords
+        assert 'lat' in skimmed_model.coords