def run_task(self, fw_spec):
# Read data from fw_spec
pipe_config_dict = fw_spec["pipe_config"]
target = fw_spec["target"]
data_file = fw_spec["data_file"]
learner_name = pipe_config_dict["learner_name"]
learner_kwargs = pipe_config_dict["learner_kwargs"]
reducer_kwargs = pipe_config_dict["reducer_kwargs"]
cleaner_kwargs = pipe_config_dict["cleaner_kwargs"]
autofeaturizer_kwargs = pipe_config_dict["autofeaturizer_kwargs"]
# Modify data_file based on computing resource
data_dir = os.environ["AMM_DATASET_DIR"]
data_file = os.path.join(data_dir, data_file)
# Modify save_dir based on computing resource
bench_dir = os.environ["AMM_SINGLE_FIT_DIR"]
base_save_dir = fw_spec["base_save_dir"]
base_save_dir = os.path.join(bench_dir, base_save_dir)
if not os.path.exists(base_save_dir):
os.makedirs(base_save_dir)
# Set up pipeline config
if learner_name == "TPOTAdaptor":
learner = TPOTAdaptor(**learner_kwargs)
elif learner_name == "rf":
warnings.warn(
"Learner kwargs passed into RF regressor/classifiers bc. rf being used."
)
learner = SinglePipelineAdaptor(
regressor=RandomForestRegressor(**learner_kwargs),
classifier=RandomForestClassifier(**learner_kwargs),
)
else:
raise ValueError("{} not supported yet!" "".format(learner_name))
pipe_config = {
"learner": learner,
"reducer": FeatureReducer(**reducer_kwargs),
"cleaner": DataCleaner(**cleaner_kwargs),
"autofeaturizer": AutoFeaturizer(**autofeaturizer_kwargs),
}
pipe = MatPipe(**pipe_config)
# Set up dataset
# Dataset should already be set up correctly as json beforehand.
# this includes targets being converted to classification, removing
# extra columns, having the names of featurization cols set to the
# same as the matpipe config, etc.
df = load_dataframe_from_json(data_file)
pipe.fit(df, target)
pipe.save(os.path.join(base_save_dir, "pipe.p"))
def test_user_features(self):
pipe = MatPipe(**debug_config)
df = self.df
df["G_VRH"] = self.extra_features
self.assertTrue("G_VRH" in df.columns)
self.assertTrue("K_VRH" in df.columns)
df_train = df.iloc[:200]
df_test = df.iloc[201:250]
pipe.fit(df_train, self.target)
# If shear modulus is included as a feature it should probably show up
# in the final pipeline
self.assertTrue("G_VRH" in pipe.learner.features)
df_test = pipe.predict(df_test, self.target)
true = df_test[self.target]
test = df_test[self.target + " predicted"]
self.assertTrue(r2_score(true, test) > 0.75)
def test_persistence_and_digest(self):
pipe = MatPipe(**debug_config)
with self.assertRaises(NotFittedError):
pipe.save()
df = self.df[-200:]
pipe.fit(df, self.target)
filename = os.path.join(test_dir, "test_pipe.p")
pipe.save(filename=filename)
pipe = MatPipe.load(filename, logger=False)
df_test = pipe.predict(self.df[-220:-201], self.target)
self.assertTrue(self.target in df_test.columns)
self.assertTrue(self.target + " predicted" in df_test.columns)
digest_file = os.path.join(test_dir, "matdigest.txt")
digest = pipe.digest(filename=digest_file)
self.assertTrue(os.path.isfile(digest_file))
self.assertTrue(isinstance(digest, str))
def test_transferability(self):
df_train = self.df.iloc[:200]
df_test = self.df.iloc[201:250]
pipe = MatPipe(**debug_config)
pipe.fit(df_train, self.target)
df_test = pipe.predict(df_test, self.target)
true = df_test[self.target]
test = df_test[self.target + " predicted"]
self.assertTrue("composition" not in df_test.columns)
self.assertTrue(r2_score(true, test) > 0.5)
# Use the same pipe object by refitting and reusing
df_train2 = self.df.iloc[250:450]
df_test2 = self.df.iloc[451:500]
pipe.fit(df_train2, self.target)
df_test2 = pipe.predict(df_test2, self.target)
true2 = df_test2[self.target]
test2 = df_test2[self.target + " predicted"]
self.assertTrue("composition" not in df_test2.columns)
self.assertTrue(r2_score(true2, test2) > 0.5)
class TestMatPipe(unittest.TestCase):
def setUp(self):
df = load_dataset("elastic_tensor_2015").rename(
columns={"formula": "composition"})
self.df = df[["composition", "K_VRH"]]
self.df_struc = df[["composition", "structure", "K_VRH"]]
self.extra_features = df["G_VRH"]
self.target = "K_VRH"
self.config = get_preset_config(config_preset, n_jobs=n_jobs)
self.config_cached = get_preset_config(config_preset,
cache_src=CACHE_SRC,
n_jobs=n_jobs)
self.pipe = MatPipe(**self.config)
self.pipe_cached = MatPipe(**self.config_cached)
@unittest.skipIf("transferability" in skip, reason)
def test_transferability(self):
df_train = self.df.iloc[:200]
df_test = self.df.iloc[201:250]
self.pipe.fit(df_train, self.target)
df_test = self.pipe.predict(df_test)
true = df_test[self.target]
test = df_test[self.target + " predicted"]
self.assertTrue("composition" not in df_test.columns)
self.assertTrue(r2_score(true, test) > 0.5)
# Use the same pipe object by refitting and reusing
df_train2 = self.df.iloc[250:450]
df_test2 = self.df.iloc[451:500]
self.pipe.fit(df_train2, self.target)
df_test2 = self.pipe.predict(df_test2)
true2 = df_test2[self.target]
test2 = df_test2[self.target + " predicted"]
self.assertTrue("composition" not in df_test2.columns)
self.assertTrue(r2_score(true2, test2) > 0.5)
@unittest.skipIf("user_features" in skip, reason)
def test_user_features(self):
df = self.df
df["G_VRH"] = self.extra_features
self.assertTrue("G_VRH" in df.columns)
self.assertTrue("K_VRH" in df.columns)
df_train = df.iloc[:200]
df_test = df.iloc[201:250]
self.pipe.fit(df_train, self.target)
# If shear modulus is included as a feature it should probably show up
# in the final pipeline
self.assertTrue("G_VRH" in self.pipe.learner.features)
df_test = self.pipe.predict(df_test)
true = df_test[self.target]
test = df_test[self.target + " predicted"]
self.assertTrue(r2_score(true, test) > 0.75)
@unittest.skipIf("predict_kwargs" in skip, reason)
def test_predict_kwargs(self):
# Test mat_pipe.predict()'s ignore and output_col kwargs.
df_train = self.df.iloc[:200]
df_test = self.df.iloc[201:250]
ef = "ExtraFeature"
df_test[ef] = [i + 100 for i in range(df_test.shape[0])]
self.pipe.fit(df_train, self.target)
self.assertTrue(ef in df_test.columns)
self.assertTrue("composition" in df_test.columns)
ignore = [ef, "composition"]
predicted_ignored = self.pipe.predict(df_test, ignore=ignore)
self.assertTrue(ef in predicted_ignored.columns)
self.assertTrue("composition" in predicted_ignored.columns)
predicted_none = self.pipe.predict(df_test, ignore=None)
self.assertFalse(ef in predicted_none.columns)
self.assertFalse("composition" in predicted_none.columns)
some = ["composition"]
predicted_some = self.pipe.predict(df_test, ignore=some)
self.assertFalse(ef in predicted_some.columns)
self.assertTrue("composition" in predicted_some.columns)
output_col_name = self.target + "_pred"
predicted_custom_col = self.pipe.predict(
df_test, output_col=output_col_name)
self.assertTrue(output_col_name in predicted_custom_col)
@unittest.skipIf("benchmarking" in skip, reason)
def test_benchmarking_no_cache(self):
pipe = self.pipe
# Make sure we can't run a cached run with no cache AF and cache pipe
with self.assertRaises(AutomatminerError):
self._run_benchmark(cache=True, pipe=pipe)
self._run_benchmark(cache=False, pipe=pipe)
@unittest.skipIf("benchmarking" in skip, reason)
def test_benchmarking_cache(self):
pipe = self.pipe_cached
# Make sure we can't run a cached run with no cache AF and cache pipe
with self.assertRaises(AutomatminerError):
self._run_benchmark(cache=False, pipe=pipe)
self._run_benchmark(cache=True, pipe=pipe)
@unittest.skipIf("persistence" in skip, reason)
def test_persistence(self):
with self.assertRaises(NotFittedError):
self.pipe.save()
df = self.df[-200:]
self.pipe.fit(df, self.target)
# Load test
self.pipe.save(filename=PIPE_PATH)
self.pipe = MatPipe.load(PIPE_PATH)
df_test = self.pipe.predict(self.df[-220:-201])
self.assertTrue(self.target in df_test.columns)
self.assertTrue(self.target + " predicted" in df_test.columns)
# Version test
self.pipe.version = "not a real version"
self.pipe.save(VERSION_PIPE_PATH)
with self.assertRaises(AutomatminerError):
MatPipe.load(VERSION_PIPE_PATH)
@unittest.skipIf("digests" in skip, reason)
def test_summarize_and_inspect(self):
df = self.df[-200:]
self.pipe.fit(df, self.target)
for ext in AMM_SUPPORTED_EXTS:
digest = self.pipe.inspect(filename=DIGEST_PATH + ext)
self.assertTrue(os.path.isfile(DIGEST_PATH + ext))
self.assertTrue(isinstance(digest, dict))
for ext in AMM_SUPPORTED_EXTS:
digest = self.pipe.summarize(filename=DIGEST_PATH + ext)
self.assertTrue(os.path.isfile(DIGEST_PATH + ext))
self.assertTrue(isinstance(digest, dict))
def _run_benchmark(self, cache, pipe):
# Test static, regular benchmark (no fittable featurizers)
df = self.df.iloc[500:600]
kfold = KFold(n_splits=2)
df_tests = pipe.benchmark(df, self.target, kfold, cache=cache)
self.assertEqual(len(df_tests), kfold.n_splits)
# Make sure we retain a good amount of test samples...
df_tests_all = pd.concat(df_tests)
self.assertGreaterEqual(len(df_tests_all), 0.95 * len(df))
# Test static subset of kfold
df2 = self.df.iloc[500:550]
df_tests2 = pipe.benchmark(df2,
self.target,
kfold,
fold_subset=[0],
cache=cache)
self.assertEqual(len(df_tests2), 1)
def tearDown(self) -> None:
digests = [DIGEST_PATH + ext for ext in AMM_SUPPORTED_EXTS]
for remnant in [CACHE_SRC, PIPE_PATH, VERSION_PIPE_PATH, *digests]:
if os.path.exists(remnant):
os.remove(remnant)
class TestMatPipe(unittest.TestCase):
def setUp(self):
df = load_dataset("elastic_tensor_2015").rename(
columns={"formula": "composition"})
self.df = df[["composition", "K_VRH"]]
self.df_struc = df[["composition", "structure", "K_VRH"]]
self.extra_features = df["G_VRH"]
self.target = "K_VRH"
self.config = get_preset_config("debug_single")
self.config_cached = get_preset_config("debug_single",
cache_src=CACHE_SRC)
self.pipe = MatPipe(**self.config)
self.pipe_cached = MatPipe(**self.config_cached)
def test_transferability(self):
df_train = self.df.iloc[:200]
df_test = self.df.iloc[201:250]
self.pipe.fit(df_train, self.target)
df_test = self.pipe.predict(df_test, self.target)
true = df_test[self.target]
test = df_test[self.target + " predicted"]
self.assertTrue("composition" not in df_test.columns)
self.assertTrue(r2_score(true, test) > 0.5)
# Use the same pipe object by refitting and reusing
df_train2 = self.df.iloc[250:450]
df_test2 = self.df.iloc[451:500]
self.pipe.fit(df_train2, self.target)
df_test2 = self.pipe.predict(df_test2, self.target)
true2 = df_test2[self.target]
test2 = df_test2[self.target + " predicted"]
self.assertTrue("composition" not in df_test2.columns)
self.assertTrue(r2_score(true2, test2) > 0.5)
def test_user_features(self):
df = self.df
df["G_VRH"] = self.extra_features
self.assertTrue("G_VRH" in df.columns)
self.assertTrue("K_VRH" in df.columns)
df_train = df.iloc[:200]
df_test = df.iloc[201:250]
self.pipe.fit(df_train, self.target)
# If shear modulus is included as a feature it should probably show up
# in the final pipeline
self.assertTrue("G_VRH" in self.pipe.learner.features)
df_test = self.pipe.predict(df_test, self.target)
true = df_test[self.target]
test = df_test[self.target + " predicted"]
self.assertTrue(r2_score(true, test) > 0.75)
@unittest.skipIf(int(os.environ.get("SKIP_INTENSIVE", 0)),
"Test too intensive for CircleCI commit builds.")
def test_benchmarking_no_cache(self):
pipe = self.pipe
# Make sure we can't run a cached run with no cache AF and cache pipe
with self.assertRaises(AutomatminerError):
self._run_benchmark(cache=True, pipe=pipe)
self._run_benchmark(cache=False, pipe=pipe)
@unittest.skipIf(int(os.environ.get("SKIP_INTENSIVE", 0)),
"Test too intensive for CircleCI commit builds.")
def test_benchmarking_cache(self):
pipe = self.pipe_cached
# Make sure we can't run a cached run with no cache AF and cache pipe
with self.assertRaises(AutomatminerError):
self._run_benchmark(cache=False, pipe=pipe)
self._run_benchmark(cache=True, pipe=pipe)
def test_persistence_and_digest(self):
with self.assertRaises(NotFittedError):
self.pipe.save()
df = self.df[-200:]
self.pipe.fit(df, self.target)
filename = os.path.join(test_dir, PIPE_PATH)
self.pipe.save(filename=filename)
self.pipe = MatPipe.load(filename, logger=False)
df_test = self.pipe.predict(self.df[-220:-201], self.target)
self.assertTrue(self.target in df_test.columns)
self.assertTrue(self.target + " predicted" in df_test.columns)
digest_file = os.path.join(test_dir, DIGEST_PATH)
digest = self.pipe.digest(filename=digest_file)
self.assertTrue(os.path.isfile(digest_file))
self.assertTrue(isinstance(digest, str))
def _run_benchmark(self, cache, pipe):
# Test static, regular benchmark (no fittable featurizers)
df = self.df.iloc[500:600]
kfold = KFold(n_splits=5)
df_tests = pipe.benchmark(df, self.target, kfold, cache=cache)
self.assertEqual(len(df_tests), kfold.n_splits)
# Make sure we retain a good amount of test samples...
df_tests_all = pd.concat(df_tests)
self.assertGreaterEqual(len(df_tests_all), 0.95 * len(df))
# Test static subset of kfold
df2 = self.df.iloc[500:550]
df_tests2 = pipe.benchmark(df2,
self.target,
kfold,
fold_subset=[0, 3],
cache=cache)
self.assertEqual(len(df_tests2), 2)
def tearDown(self):
for remnant in [CACHE_SRC, PIPE_PATH, DIGEST_PATH]:
if os.path.exists(remnant):
os.remove(remnant)