def filled_collection(self, tmpdir):
# returns (a bundle of [t1, t2, t3], then individal references to each)
with tmpdir.as_cwd():
t1 = dtr.Treant('larry')
t2 = dtr.Treant('curly')
t3 = dtr.Treant('moe')
b = dtr.Bundle((t1, t2, t3))
return b, (t1, t2, t3)
def test_tags_filter(self, collection, testtreant,
testtreant2, tmpdir):
with tmpdir.as_cwd():
maple = dtr.Treant('maple')
pine = dtr.Treant('pine')
maple.tags.add({'tree', 'new jersey', 'deciduous'})
pine.tags.add({'tree', 'new york', 'evergreen'})
col = collection(maple, pine)
tags = col.tags
maple_bund = dtr.Bundle(maple)
pine_bund = dtr.Bundle(pine)
assert len(tags.any) == 5
# filter using single tags
assert tags.filter('tree') == col
assert tags.filter({'tree'}) == dtr.Bundle()
assert tags.filter('deciduous') == maple_bund
assert tags.filter('evergreen') == pine_bund
assert tags.filter('new jersey') == maple_bund
assert tags.filter('new york') == pine_bund
# filter Treants that DON'T have a given tag
assert tags.filter({'new york'}) == maple_bund
assert tags.filter({'deciduous'}) == pine_bund
# filter Treants containing all of the tags
assert tags.filter(['deciduous', 'tree']) == maple_bund
assert tags.filter(['evergreen', 'tree']) == pine_bund
assert tags.filter(['deciduous', 'new york']) == dtr.Bundle()
# filter Treants containing any of the tags tags
assert tags.filter(('evergreen', 'tree')) == col
assert tags.filter(('deciduous', 'new york')) == col
assert tags.filter(('evergreen', 'new york')) == pine_bund
# filter Treants that exclude any of the provided tags
assert tags.filter({'deciduous', 'new york'}) == col
assert tags.filter({'deciduous', 'new jersey'}) == pine_bund
assert tags.filter({'evergreen', 'tree'}) == maple_bund
# complex logic tests
# give those that are evergreen or in NY AND also not deciduous
selection = [('evergreen', 'new york'), {'deciduous'}]
assert tags.filter(selection) == pine_bund
# give those that are evergreen or in NY AND also not a tree
selection = [('evergreen', 'new york'), {'tree'}]
assert tags.filter(selection) == dtr.Bundle()
# give a tree that's in NJ OR anything that's not evergreen
selection = (['tree', 'new jersey'], {'evergreen'})
assert tags.filter(selection) == maple_bund
# cannot be a tree in NJ, AND must also be deciduous
# I.e., give all deciduous things that aren't trees in NJ
selection = [{'tree', 'new jersey'}, 'deciduous']
assert tags.filter(selection) == dtr.Bundle()
def filled_bundle(self, tmpdir):
with tmpdir.as_cwd():
t1 = dtr.Treant('one')
t2 = dtr.Treant('two')
t3 = dtr.Treant('three')
t4 = dtr.Treant('four')
t1.tags.add('odd', 'one')
t2.tags.add('even', 'two')
t3.tags.add('odd', 'three')
t4.tags.add('even', 'four')
t1.categories.add(is_even=False, value=1)
t2.categories.add(is_even=True, value=2)
t3.categories.add(is_even=False, value=3)
t4.categories.add(is_even=True, value=4)
return [t1, t2, t3, t4], dtr.Bundle([t1, t2, t3, t4])
def test_submit_test_prompt_yes(cli_runner, tmpdir, data, monkeypatch):
"""Test whether promt answer no works."""
with tmpdir.as_cwd():
# Test that we can force restart already run benchmarks.
# Monkeypatch a few functions
monkeypatch.setattr("subprocess.call", lambda x: True)
monkeypatch.setattr(
"mdbenchmark.cli.submit.get_batch_command", lambda: "sbatch"
)
monkeypatch.setattr(
"mdbenchmark.cli.submit.detect_md_engine", lambda x: gromacs
)
monkeypatch.setattr(
"mdbenchmark.cli.submit.cleanup_before_restart", lambda engine, sim: True
)
result = cli_runner.invoke(
cli,
[
"submit",
"--directory={}".format(data["analyze-files-gromacs-one-unstarted"]),
],
input="y\n",
)
df = pd.read_csv(data["gromacs/test_prompt.csv"], index_col=0)
s = print_dataframe(df, False)
output = (
"Benchmark Summary:\n"
+ s
+ "\nThe above benchmarks will be submitted. Continue? [y/N]: y\n"
+ "Submitting a total of 1 benchmarks.\n"
+ "Submitted all benchmarks. Run mdbenchmark analyze once they are finished to get the results.\n"
)
assert result.exit_code == 0
assert result.output == output
# Lazy way of resetting the value of `started` to `false`.
# TODO: We need to clean up all of our unit tests...
treant = dtr.Bundle(data["analyze-files-gromacs-one-unstarted"] + "/1")
treant.categories["started"] = False
def test_tags_set_behavior(self, collection, tmpdir):
with tmpdir.as_cwd():
t1 = dtr.Treant('maple')
t2 = dtr.Treant('pine')
t3 = dtr.Treant('juniper')
t1.tags.add({'tree', 'new jersey', 'deciduous'})
t2.tags.add({'tree', 'new york', 'evergreen'})
t3.tags.add({'shrub', 'new york', 'evergreen'})
col = collection(t1, t2, t3)
trees = dtr.Bundle('maple', 'pine')
evergreens = dtr.Bundle('pine', 'juniper')
tags = col.tags
assert len(tags.any) == 6
# test equality: __eq__ (==)
assert t1.tags == {'tree', 'new jersey', 'deciduous'}
assert t2.tags == {'tree', 'new york', 'evergreen'}
assert t3.tags == {'shrub', 'new york', 'evergreen'}
# test subset: __lt__ (<)
assert not t1.tags < {'tree', 'new jersey', 'deciduous'}
assert tags < {'tree', 'new jersey', 'deciduous'}
assert t1.tags < tags.any
assert t2.tags < tags.any
assert t3.tags < tags.any
# test difference: __sub__ (-)
assert t1.tags - {'tree'} == {'new jersey', 'deciduous'}
assert trees.tags - {'tree'} == set()
# test right difference: __rsub__ (-)
evergreen_ny_shrub = {'evergreen', 'new york', 'shrub'}
dec_nj_sh = {'deciduous', 'new jersey', 'shrub'}
assert tags.any - t1.tags == evergreen_ny_shrub
assert tags.any - evergreens.tags - trees.tags == dec_nj_sh
assert {'tree'} - trees.tags == set()
# test union: __or__ (|)
evergreen_ny_shrub = {'evergreen', 'new york', 'shrub'}
assert evergreens.tags | t3.tags == evergreen_ny_shrub
assert t1.tags | t2.tags | t3.tags == tags.any
# test right union: __ror__ (|)
assert {'shrub'} | evergreens.tags == evergreen_ny_shrub
assert t3.tags | {'tree'} == {'tree'} | t3.tags
# test intersection: __and__ (&)
evergreen_ny = {'evergreen', 'new york'}
assert evergreens.tags & t3.tags == evergreen_ny
assert t1.tags & t2.tags & t3.tags == tags.all
# test right intersection: __rand__ (&)
assert evergreen_ny_shrub & evergreens.tags == evergreen_ny
assert t3.tags & {'shrub'} == {'shrub'} & t3.tags
# test symmetric difference: __xor__ (^)
evergreen_ny_tree = {'evergreen', 'new york', 'tree'}
assert trees.tags ^ evergreens.tags == evergreen_ny_tree
assert evergreens.tags ^ t3.tags == {'shrub'}
assert t1.tags ^ t2.tags ^ t3.tags == dec_nj_sh
# test right symmetric difference: __rxor__ (^)
assert {'new york'} ^ evergreens.tags == {'evergreen'}
assert {'shrub'} ^ trees.tags == t2.tags ^ t3.tags
# type_error_msg = "Operands must be AggTags, Tags, or a set."
with pytest.raises(TypeError) as e:
['tree'] == trees.tags
# assert e.value.message == type_error_msg
with pytest.raises(TypeError) as e:
trees.tags < ['tree']
# assert e.value.message == type_error_msg
with pytest.raises(TypeError) as e:
['tree'] - trees.tags
# assert e.value.message == type_error_msg
with pytest.raises(TypeError) as e:
trees.tags - ['tree']
# assert e.value.message == type_error_msg
with pytest.raises(TypeError) as e:
['tree'] | trees.tags
# assert e.value.message == type_error_msg
with pytest.raises(TypeError) as e:
trees.tags | ['tree']
# assert e.value.message == type_error_msg
with pytest.raises(TypeError) as e:
['tree'] & trees.tags
# assert e.value.message == type_error_msg
with pytest.raises(TypeError) as e:
trees.tags & ['tree']
# assert e.value.message == type_error_msg
with pytest.raises(TypeError) as e:
['tree'] ^ trees.tags
# assert e.value.message == type_error_msg
with pytest.raises(TypeError) as e:
trees.tags ^ ['tree']