def test_harvest_cases_new(self, fn3_fba_runner, fn3_fba_ds, dict_cases):
if dict_cases:
cases = [{
'a': 1,
'b': 3
}, {
'a': 1,
'b': 4
}, {
'a': 2,
'b': 3
}, {
'a': 2,
'b': 4
}]
else:
cases = [(1, 3), (1, 4), (2, 3), (2, 4)]
with tempfile.TemporaryDirectory() as tmpdir:
fl_pth = os.path.join(tmpdir, 'test.h5')
h = Harvester(fn3_fba_runner, fl_pth)
h.harvest_cases(cases)
hds = load_ds(fl_pth)
assert h.last_ds.identical(fn3_fba_ds)
assert h.full_ds.identical(fn3_fba_ds)
assert hds.identical(fn3_fba_ds)
def test_io_only_real(self, ds_real, engine_save, engine_load):
with tempfile.TemporaryDirectory() as tmpdir:
save_ds(ds_real,
os.path.join(tmpdir, "test.h5"),
engine=engine_save)
ds2 = load_ds(os.path.join(tmpdir, "test.h5"), engine=engine_load)
assert ds_real.equals(ds2)
def test_h5netcdf_dask(self, ds1):
ds = ds1.chunk()
with tempfile.TemporaryDirectory() as tmpdir:
save_ds(ds, os.path.join(tmpdir, "test.h5"), engine='h5netcdf')
ds2 = load_ds(os.path.join(tmpdir, "test.h5"))
assert ds1.identical(ds2)
ds2.close()
def test_h5netcdf_dask(self, ds1):
ds = ds1.chunk()
with tempfile.TemporaryDirectory() as tmpdir:
save_ds(ds, os.path.join(tmpdir, "test.h5"), engine='h5netcdf')
ds2 = load_ds(os.path.join(tmpdir, "test.h5"))
assert ds1.identical(ds2)
ds2.close()
def test_dask_load(self, ds_real, engine_load):
with tempfile.TemporaryDirectory() as tmpdir:
save_ds(ds_real, os.path.join(tmpdir, "test.nc"))
ds2 = load_ds(os.path.join(tmpdir, "test.nc"),
engine=engine_load,
chunks=1)
assert ds2.chunks['b'] == (1, 1)
assert ds_real.identical(ds2)
ds2.close()
def test_harvest_combos_new(self, fn3_fba_runner, fn3_fba_ds):
with tempfile.TemporaryDirectory() as tmpdir:
fl_pth = os.path.join(tmpdir, 'test.h5')
h = Harvester(fn3_fba_runner, fl_pth)
h.harvest_combos((('a', (1, 2)), ('b', (3, 4))))
hds = load_ds(fl_pth)
assert h.last_ds.identical(fn3_fba_ds)
assert h.full_ds.identical(fn3_fba_ds)
assert hds.identical(fn3_fba_ds)
def test_harvest_combos_new(self, fn3_fba_runner, fn3_fba_ds):
with tempfile.TemporaryDirectory() as tmpdir:
fl_pth = os.path.join(tmpdir, 'test.h5')
h = Harvester(fn3_fba_runner, fl_pth)
h.harvest_combos((('a', (1, 2)), ('b', (3, 4))))
hds = load_ds(fl_pth)
assert h.last_ds.identical(fn3_fba_ds)
assert h.full_ds.identical(fn3_fba_ds)
assert hds.identical(fn3_fba_ds)
def test_dask_load(self, ds_real, engine_load):
with tempfile.TemporaryDirectory() as tmpdir:
save_ds(ds_real, os.path.join(tmpdir, "test.nc"))
ds2 = load_ds(os.path.join(tmpdir, "test.nc"),
engine=engine_load,
chunks=1)
assert ds2.chunks['b'] == (1, 1)
assert ds_real.identical(ds2)
ds2.close()
def test_harvest_cases_merge(self, fn3_fba_runner, fn3_fba_ds):
with tempfile.TemporaryDirectory() as tmpdir:
fl_pth = os.path.join(tmpdir, 'test.h5')
h = Harvester(fn3_fba_runner, fl_pth)
h.harvest_cases([(1, 3), (2, 4)])
h.harvest_cases([(1, 4), (2, 3)])
hds = load_ds(fl_pth)
assert not h.last_ds.identical(fn3_fba_ds)
assert h.full_ds.identical(fn3_fba_ds)
assert hds.identical(fn3_fba_ds)
def test_harvest_cases_merge(self, fn3_fba_runner, fn3_fba_ds):
with tempfile.TemporaryDirectory() as tmpdir:
fl_pth = os.path.join(tmpdir, 'test.h5')
h = Harvester(fn3_fba_runner, fl_pth)
h.harvest_cases([(1, 3), (2, 4)])
h.harvest_cases([(1, 4), (2, 3)])
hds = load_ds(fl_pth)
assert not h.last_ds.identical(fn3_fba_ds)
assert h.full_ds.identical(fn3_fba_ds)
assert hds.identical(fn3_fba_ds)
def test_save_merge_ds(self, ds1, ds2, ds3):
with tempfile.TemporaryDirectory() as tmpdir:
fname = os.path.join(tmpdir, "test.h5")
save_merge_ds(ds1, fname)
save_merge_ds(ds2, fname)
with raises(xr.MergeError):
save_merge_ds(ds3, fname)
save_merge_ds(ds3, fname, overwrite=True)
exp = ds3.combine_first(xr.merge([ds1, ds2]))
assert load_ds(fname).identical(exp)
def test_harvest_cases_new(self, fn3_fba_runner, fn3_fba_ds, dict_cases):
if dict_cases:
cases = [{'a': 1, 'b': 3}, {'a': 1, 'b': 4},
{'a': 2, 'b': 3}, {'a': 2, 'b': 4}]
else:
cases = [(1, 3), (1, 4), (2, 3), (2, 4)]
with tempfile.TemporaryDirectory() as tmpdir:
fl_pth = os.path.join(tmpdir, 'test.h5')
h = Harvester(fn3_fba_runner, fl_pth)
h.harvest_cases(cases)
hds = load_ds(fl_pth)
assert h.last_ds.identical(fn3_fba_ds)
assert h.full_ds.identical(fn3_fba_ds)
assert hds.identical(fn3_fba_ds)
def test_harvest_combos_new_sow_reap_separate(self, fn3_fba_runner,
fn3_fba_ds):
with tempfile.TemporaryDirectory() as tmpdir:
fl_pth = os.path.join(tmpdir, 'test.h5')
h = Harvester(fn3_fba_runner, fl_pth)
crop = h.Crop(parent_dir=tmpdir, num_batches=2)
crop.sow_combos((('a', (1, 2)), ('b', (3, 4))))
for i in [1, 2]:
grow(i, crop)
crop.reap()
hds = load_ds(fl_pth)
assert h.last_ds.identical(fn3_fba_ds)
assert h.full_ds.identical(fn3_fba_ds)
assert hds.identical(fn3_fba_ds)
def test_harvest_combos_new_sow_reap_separate(self, fn3_fba_runner,
fn3_fba_ds):
with tempfile.TemporaryDirectory() as tmpdir:
fl_pth = os.path.join(tmpdir, 'test.h5')
h = Harvester(fn3_fba_runner, fl_pth)
crop = h.Crop(parent_dir=tmpdir, num_batches=2)
crop.sow_combos((('a', (1, 2)), ('b', (3, 4))))
for i in [1, 2]:
grow(i, crop)
crop.reap()
hds = load_ds(fl_pth)
assert h.last_ds.identical(fn3_fba_ds)
assert h.full_ds.identical(fn3_fba_ds)
assert hds.identical(fn3_fba_ds)
def test_harvest_combos_new_sow_and_reap(self, fn3_fba_runner, fn3_fba_ds):
with tempfile.TemporaryDirectory() as tmpdir:
fl_pth = os.path.join(tmpdir, 'test.h5')
h = Harvester(fn3_fba_runner, fl_pth)
crop = h.Crop(parent_dir=tmpdir, num_batches=2)
def concurrent_grow():
# wait for cases to be sown
time.sleep(0.5)
for i in [1, 2]:
grow(i, crop)
with ThreadPoolExecutor(1) as pool:
pool.submit(concurrent_grow)
crop.sow_combos((('a', (1, 2)), ('b', (3, 4))))
crop.reap(wait=True)
hds = load_ds(fl_pth)
assert h.last_ds.identical(fn3_fba_ds)
assert h.full_ds.identical(fn3_fba_ds)
assert hds.identical(fn3_fba_ds)
def test_harvest_combos_new_sow_and_reap(self, fn3_fba_runner, fn3_fba_ds):
with tempfile.TemporaryDirectory() as tmpdir:
fl_pth = os.path.join(tmpdir, 'test.h5')
h = Harvester(fn3_fba_runner, fl_pth)
crop = h.Crop(parent_dir=tmpdir, num_batches=2)
def concurrent_grow():
# wait for cases to be sown
time.sleep(0.5)
for i in [1, 2]:
grow(i, crop)
with ThreadPoolExecutor(1) as pool:
pool.submit(concurrent_grow)
crop.sow_combos((('a', (1, 2)), ('b', (3, 4))))
crop.reap(wait=True)
hds = load_ds(fl_pth)
assert h.last_ds.identical(fn3_fba_ds)
assert h.full_ds.identical(fn3_fba_ds)
assert hds.identical(fn3_fba_ds)
def test_io_complex_data(self, ds1, engine_save, engine_load):
with tempfile.TemporaryDirectory() as tmpdir:
save_ds(ds1, os.path.join(tmpdir, "test.h5"), engine=engine_save)
ds2 = load_ds(os.path.join(tmpdir, "test.h5"), engine=engine_load)
assert ds1.identical(ds2)
def test_io_only_real(self, ds_real, engine_save, engine_load):
with tempfile.TemporaryDirectory() as tmpdir:
save_ds(ds_real, os.path.join(tmpdir, "test.h5"),
engine=engine_save)
ds2 = load_ds(os.path.join(tmpdir, "test.h5"), engine=engine_load)
assert ds_real.equals(ds2)
def test_io_complex_data(self, ds1, engine_save, engine_load):
with tempfile.TemporaryDirectory() as tmpdir:
save_ds(ds1, os.path.join(tmpdir, "test.h5"), engine=engine_save)
ds2 = load_ds(os.path.join(tmpdir, "test.h5"), engine=engine_load)
assert ds1.identical(ds2)