def __init__(self, model_name, repo_dir, git_repo_dir, method_defect_predictor_dir):
self.model_name = model_name
self.repo_dir = repo_dir
self.model = download_and_load_model(model_name)
assert self.model is not None
self.git_repo_dir = git_repo_dir
if git_repo_dir:
self.clone_git_repo("https://github.com/mozilla/gecko-dev", git_repo_dir)
self.method_defect_predictor_dir = method_defect_predictor_dir
if method_defect_predictor_dir:
self.clone_git_repo(
"https://github.com/lucapascarella/MethodDefectPredictor",
method_defect_predictor_dir,
"8cc47f47ffb686a29324435a0151b5fabd37f865",
)
if model_name == "regressor":
self.use_test_history = False
model_data_X_path = f"{model_name}model_data_X"
updated = download_check_etag(
URL.format(model_name=model_name, file_name=f"{model_data_X_path}.zst")
)
if updated:
zstd_decompress(model_data_X_path)
assert os.path.exists(model_data_X_path), "Decompressed X dataset exists"
model_data_y_path = f"{model_name}model_data_y"
updated = download_check_etag(
URL.format(model_name=model_name, file_name=f"{model_data_y_path}.zst")
)
if updated:
zstd_decompress(model_data_y_path)
assert os.path.exists(model_data_y_path), "Decompressed y dataset exists"
self.X = to_array(joblib.load(model_data_X_path))
self.y = to_array(joblib.load(model_data_y_path))
past_bugs_by_function_path = "data/past_bugs_by_function.pickle"
download_check_etag(
PAST_BUGS_BY_FUNCTION_URL, path=f"{past_bugs_by_function_path}.zst"
)
zstd_decompress(past_bugs_by_function_path)
assert os.path.exists(past_bugs_by_function_path)
with open(past_bugs_by_function_path, "rb") as f:
self.past_bugs_by_function = pickle.load(f)
if model_name == "testlabelselect":
self.use_test_history = True
assert db.download_support_file(
test_scheduling.TEST_LABEL_SCHEDULING_DB,
test_scheduling.PAST_FAILURES_LABEL_DB,
)
self.past_failures_data = test_scheduling.get_past_failures("label")
self.testfailure_model = download_and_load_model("testfailure")
assert self.testfailure_model is not None
def __init__(self, model_name, cache_root, git_repo_dir,
method_defect_predictor_dir):
self.model_name = model_name
self.cache_root = cache_root
assert os.path.isdir(
cache_root), f"Cache root {cache_root} is not a dir."
self.repo_dir = os.path.join(cache_root, "mozilla-central")
self.model = self.load_model(model_name)
assert self.model is not None
self.git_repo_dir = git_repo_dir
if git_repo_dir:
self.clone_git_repo("https://github.com/mozilla/gecko-dev",
git_repo_dir)
self.method_defect_predictor_dir = method_defect_predictor_dir
if method_defect_predictor_dir:
self.clone_git_repo(
"https://github.com/lucapascarella/MethodDefectPredictor",
method_defect_predictor_dir,
"fa5269b959d8ddf7e97d1e92523bb64c17f9bbcd",
)
if model_name == "regressor":
self.use_test_history = False
model_data_X_path = f"{model_name}model_data_X"
if not os.path.exists(model_data_X_path):
download_check_etag(
URL.format(model_name=model_name,
file_name=f"{model_data_X_path}.zst"))
zstd_decompress(model_data_X_path)
assert os.path.exists(
model_data_X_path), "Decompressed X dataset exists"
model_data_y_path = f"{model_name}model_data_y"
if not os.path.exists(model_data_y_path):
download_check_etag(
URL.format(model_name=model_name,
file_name=f"{model_data_y_path}.zst"))
zstd_decompress(model_data_y_path)
assert os.path.exists(
model_data_y_path), "Decompressed y dataset exists"
self.X = to_array(joblib.load(model_data_X_path))
self.y = to_array(joblib.load(model_data_y_path))
if model_name == "testselect":
self.use_test_history = True
assert db.download_support_file(test_scheduling.TEST_SCHEDULING_DB,
test_scheduling.PAST_FAILURES_DB)
self.past_failures_data = test_scheduling.get_past_failures()
self.backout_model = self.load_model("backout")
assert self.backout_model is not None
def __init__(self, cache_root, git_repo_dir, method_defect_predictor_dir):
self.cache_root = cache_root
assert os.path.isdir(
cache_root), f"Cache root {cache_root} is not a dir."
self.repo_dir = os.path.join(cache_root, "mozilla-central")
regressormodel_path = "regressormodel"
if not os.path.exists(regressormodel_path):
download_check_etag(URL.format(f"{regressormodel_path}.zst"),
f"{regressormodel_path}.zst")
zstd_decompress(regressormodel_path)
assert os.path.exists(
regressormodel_path), "Decompressed model exists"
regressormodel_data_X_path = "regressormodel_data_X"
if not os.path.exists(regressormodel_data_X_path):
download_check_etag(
URL.format(f"{regressormodel_data_X_path}.zst"),
f"{regressormodel_data_X_path}.zst",
)
zstd_decompress(regressormodel_data_X_path)
assert os.path.exists(
regressormodel_data_X_path), "Decompressed X dataset exists"
regressormodel_data_y_path = "regressormodel_data_y"
if not os.path.exists(regressormodel_data_y_path):
download_check_etag(
URL.format(f"{regressormodel_data_y_path}.zst"),
f"{regressormodel_data_y_path}.zst",
)
zstd_decompress(regressormodel_data_y_path)
assert os.path.exists(
regressormodel_data_y_path), "Decompressed y dataset exists"
self.model = RegressorModel.load(regressormodel_path)
self.X = to_array(joblib.load(regressormodel_data_X_path))
self.y = to_array(joblib.load(regressormodel_data_y_path))
self.method_defect_predictor_dir = method_defect_predictor_dir
self.clone_git_repo(
"https://github.com/lucapascarella/MethodDefectPredictor",
method_defect_predictor_dir,
"fa5269b959d8ddf7e97d1e92523bb64c17f9bbcd",
)
self.git_repo_dir = git_repo_dir
self.clone_git_repo("https://github.com/mozilla/gecko-dev",
git_repo_dir)
def print_feature_importances(self,
important_features,
class_probabilities=None):
feature_names = self.get_human_readable_feature_names()
# extract importance values from the top features for the predicted class
# when classifying
if class_probabilities is not None:
# shap_values are stored in class 1 for binary classification
if len(class_probabilities[0]) != 2:
predicted_class_index = class_probabilities.argmax(axis=-1)[0]
else:
predicted_class_index = 0
predicted_class = self.class_names[predicted_class_index]
imp_values = important_features["classes"][predicted_class][0]
shap_val = []
top_feature_names = []
for importance, index, is_positive in imp_values:
if is_positive:
shap_val.append("+" + str(importance))
else:
shap_val.append("-" + str(importance))
feature_value = np.squeeze(
to_array(important_features["values"])[:, int(index)])
top_feature_names.append(
f"{feature_names[int(index)]} = {feature_value.round(decimals=5)}"
)
shap_val = [[predicted_class] + shap_val]
# extract importance values from the top features for all the classes
# when training
else:
top_feature_names = [
feature_names[int(index)]
for importance, index, is_pos in important_features["average"]
]
shap_val = [[class_name] + imp_values[1] for class_name, imp_values
in important_features["classes"].items()]
# allow maximum of 5 columns in a row to fit the page better
print("Top {} features:".format(len(top_feature_names)))
for i in range(0, len(top_feature_names), 5):
table = []
for item in shap_val:
table.append(item[i:i + 5])
print(
tabulate(
table,
headers=(["classes"] + top_feature_names)[i:i + 5],
tablefmt="grid",
),
end="\n\n",
)
def classify(
self,
items,
probabilities=False,
importances=False,
importance_cutoff=0.15,
background_dataset=None,
):
assert items is not None
assert (self.extraction_pipeline is not None and self.clf
is not None), "The module needs to be initialized first"
if not isinstance(items, list):
items = [items]
assert isinstance(items[0], dict) or isinstance(items[0], tuple)
X = self.extraction_pipeline.transform(lambda: items)
if probabilities:
classes = self.clf.predict_proba(X)
else:
classes = self.clf.predict(X)
classes = self.overwrite_classes(items, classes, probabilities)
if importances:
pred_class_index = classes.argmax(axis=-1)[0]
pred_class = self.le.inverse_transform([pred_class_index])[0]
if background_dataset is None:
explainer = shap.TreeExplainer(self.clf)
else:
explainer = shap.TreeExplainer(
self.clf,
to_array(background_dataset(pred_class)),
feature_perturbation="interventional",
)
shap_values = explainer.shap_values(to_array(X))
# In the binary case, sometimes shap returns a single shap values matrix.
if len(classes[0]) == 2 and not isinstance(shap_values, list):
shap_values = [-shap_values, shap_values]
important_features = self.get_important_features(
importance_cutoff, shap_values)
important_features["values"] = X
top_indexes = [
int(index)
for _, index, _ in important_features["classes"][pred_class][0]
]
feature_names = self.get_human_readable_feature_names()
feature_legend = {
str(i + 1): feature_names[feature_i]
for i, feature_i in enumerate(top_indexes)
}
return (
classes,
{
"importances": important_features,
"feature_legend": feature_legend
},
)
return classes
def train(self, importance_cutoff=0.15, limit=None):
classes, self.class_names = self.get_labels()
self.class_names = sort_class_names(self.class_names)
# Get items and labels, filtering out those for which we have no labels.
X_gen, y = split_tuple_generator(lambda: self.items_gen(classes))
# Extract features from the items.
X = self.extraction_pipeline.fit_transform(X_gen)
# Calculate labels.
y = np.array(y)
if limit:
X = X[:limit]
y = y[:limit]
print(f"X: {X.shape}, y: {y.shape}")
is_multilabel = isinstance(y[0], np.ndarray)
is_binary = len(self.class_names) == 2
# Split dataset in training and test.
X_train, X_test, y_train, y_test = self.train_test_split(X, y)
if self.sampler is not None:
pipeline = make_pipeline(self.sampler, self.clf)
else:
pipeline = self.clf
tracking_metrics = {}
# Use k-fold cross validation to evaluate results.
if self.cross_validation_enabled:
scorings = ["accuracy"]
if len(self.class_names) == 2:
scorings += ["precision", "recall"]
scores = cross_validate(pipeline,
X_train,
y_train,
scoring=scorings,
cv=5)
print("Cross Validation scores:")
for scoring in scorings:
score = scores[f"test_{scoring}"]
tracking_metrics[f"test_{scoring}"] = {
"mean": score.mean(),
"std": score.std() * 2,
}
print(
f"{scoring.capitalize()}: f{score.mean()} (+/- {score.std() * 2})"
)
print(f"X_train: {X_train.shape}, y_train: {y_train.shape}")
# Training on the resampled dataset if sampler is provided.
if self.sampler is not None:
X_train, y_train = self.sampler.fit_resample(X_train, y_train)
print(
f"resampled X_train: {X_train.shape}, y_train: {y_train.shape}"
)
print(f"X_test: {X_test.shape}, y_test: {y_test.shape}")
self.clf.fit(X_train, y_train)
print("Model trained")
feature_names = self.get_human_readable_feature_names()
if self.calculate_importance and len(feature_names):
explainer = shap.TreeExplainer(self.clf)
shap_values = explainer.shap_values(X_train)
# In the binary case, sometimes shap returns a single shap values matrix.
if is_binary and not isinstance(shap_values, list):
shap_values = [-shap_values, shap_values]
summary_plot_value = shap_values[1]
summary_plot_type = "layered_violin"
else:
summary_plot_value = shap_values
summary_plot_type = None
shap.summary_plot(
summary_plot_value,
to_array(X_train),
feature_names=feature_names,
class_names=self.class_names,
plot_type=summary_plot_type,
show=False,
)
matplotlib.pyplot.savefig("feature_importance.png",
bbox_inches="tight")
matplotlib.pyplot.xlabel("Impact on model output")
matplotlib.pyplot.clf()
important_features = self.get_important_features(
importance_cutoff, shap_values)
self.print_feature_importances(important_features)
# Save the important features in the metric report too
feature_report = self.save_feature_importances(
important_features, feature_names)
tracking_metrics["feature_report"] = feature_report
print("Training Set scores:")
y_pred = self.clf.predict(X_train)
if not is_multilabel:
print(
classification_report_imbalanced(y_train,
y_pred,
labels=self.class_names))
print("Test Set scores:")
# Evaluate results on the test set.
y_pred = self.clf.predict(X_test)
if is_multilabel:
assert isinstance(
y_pred[0], np.ndarray), "The predictions should be multilabel"
print(f"No confidence threshold - {len(y_test)} classified")
if is_multilabel:
confusion_matrix = metrics.multilabel_confusion_matrix(
y_test, y_pred)
else:
confusion_matrix = metrics.confusion_matrix(
y_test, y_pred, labels=self.class_names)
print(
classification_report_imbalanced(y_test,
y_pred,
labels=self.class_names))
report = classification_report_imbalanced_values(
y_test, y_pred, labels=self.class_names)
tracking_metrics["report"] = report
print_labeled_confusion_matrix(confusion_matrix,
self.class_names,
is_multilabel=is_multilabel)
tracking_metrics["confusion_matrix"] = confusion_matrix.tolist()
confidence_thresholds = [0.6, 0.7, 0.8, 0.9]
if is_binary:
confidence_thresholds = [0.1, 0.2, 0.3, 0.4
] + confidence_thresholds
# Evaluate results on the test set for some confidence thresholds.
for confidence_threshold in confidence_thresholds:
y_pred_probas = self.clf.predict_proba(X_test)
confidence_class_names = self.class_names + ["__NOT_CLASSIFIED__"]
y_pred_filter = []
classified_indices = []
for i in range(0, len(y_test)):
if not is_binary:
argmax = np.argmax(y_pred_probas[i])
else:
argmax = 1 if y_pred_probas[i][
1] > confidence_threshold else 0
if y_pred_probas[i][argmax] < confidence_threshold:
if not is_multilabel:
y_pred_filter.append("__NOT_CLASSIFIED__")
continue
classified_indices.append(i)
if is_multilabel:
y_pred_filter.append(y_pred[i])
else:
y_pred_filter.append(argmax)
if not is_multilabel:
y_pred_filter = np.array(y_pred_filter)
y_pred_filter[classified_indices] = self.le.inverse_transform(
np.array(y_pred_filter[classified_indices], dtype=int))
classified_num = sum(1 for v in y_pred_filter
if v != "__NOT_CLASSIFIED__")
print(
f"\nConfidence threshold > {confidence_threshold} - {classified_num} classified"
)
if is_multilabel:
confusion_matrix = metrics.multilabel_confusion_matrix(
y_test[classified_indices], np.asarray(y_pred_filter))
else:
confusion_matrix = metrics.confusion_matrix(
y_test.astype(str),
y_pred_filter.astype(str),
labels=confidence_class_names,
)
print(
classification_report_imbalanced(
y_test.astype(str),
y_pred_filter.astype(str),
labels=confidence_class_names,
))
print_labeled_confusion_matrix(confusion_matrix,
confidence_class_names,
is_multilabel=is_multilabel)
self.evaluation()
if self.entire_dataset_training:
print("Retraining on the entire dataset...")
if self.sampler is not None:
X_train, y_train = self.sampler.fit_resample(X, y)
else:
X_train = X
y_train = y
print(f"X_train: {X_train.shape}, y_train: {y_train.shape}")
self.clf.fit(X_train, y_train)
with open(self.__class__.__name__.lower(), "wb") as f:
pickle.dump(self, f, protocol=pickle.HIGHEST_PROTOCOL)
if self.store_dataset:
with open(f"{self.__class__.__name__.lower()}_data_X", "wb") as f:
pickle.dump(X, f, protocol=pickle.HIGHEST_PROTOCOL)
with open(f"{self.__class__.__name__.lower()}_data_y", "wb") as f:
pickle.dump(y, f, protocol=pickle.HIGHEST_PROTOCOL)
return tracking_metrics
def __init__(
self,
model_name: str,
repo_dir: str,
git_repo_dir: str,
method_defect_predictor_dir: str,
use_single_process: bool,
skip_feature_importance: bool,
):
self.model_name = model_name
self.repo_dir = repo_dir
self.model = Model.load(download_model(model_name))
assert self.model is not None
self.git_repo_dir = git_repo_dir
if git_repo_dir:
self.clone_git_repo(
"hg::https://hg.mozilla.org/mozilla-central", git_repo_dir
)
self.method_defect_predictor_dir = method_defect_predictor_dir
if method_defect_predictor_dir:
self.clone_git_repo(
"https://github.com/lucapascarella/MethodDefectPredictor",
method_defect_predictor_dir,
"8cc47f47ffb686a29324435a0151b5fabd37f865",
)
self.use_single_process = use_single_process
self.skip_feature_importance = skip_feature_importance
if model_name == "regressor":
self.use_test_history = False
model_data_X_path = f"{model_name}model_data_X"
updated = download_check_etag(
URL.format(model_name=model_name, file_name=f"{model_data_X_path}.zst")
)
if updated:
zstd_decompress(model_data_X_path)
assert os.path.exists(model_data_X_path), "Decompressed X dataset exists"
model_data_y_path = f"{model_name}model_data_y"
updated = download_check_etag(
URL.format(model_name=model_name, file_name=f"{model_data_y_path}.zst")
)
if updated:
zstd_decompress(model_data_y_path)
assert os.path.exists(model_data_y_path), "Decompressed y dataset exists"
with open(model_data_X_path, "rb") as fb:
self.X = to_array(pickle.load(fb))
with open(model_data_y_path, "rb") as fb:
self.y = to_array(pickle.load(fb))
past_bugs_by_function_path = "data/past_fixed_bugs_by_function.json"
download_check_etag(
PAST_BUGS_BY_FUNCTION_URL, path=f"{past_bugs_by_function_path}.zst"
)
zstd_decompress(past_bugs_by_function_path)
assert os.path.exists(past_bugs_by_function_path)
with open(past_bugs_by_function_path, "r") as f:
self.past_bugs_by_function = json.load(f)
if model_name == "testlabelselect":
self.use_test_history = True
assert db.download_support_file(
test_scheduling.TEST_LABEL_SCHEDULING_DB,
test_scheduling.PAST_FAILURES_LABEL_DB,
)
self.past_failures_data = test_scheduling.get_past_failures("label", True)
self.testfailure_model = cast(
TestFailureModel, TestFailureModel.load(download_model("testfailure"))
)
assert self.testfailure_model is not None
def classify(
self,
items,
probabilities=False,
importances=False,
importance_cutoff=0.15,
background_dataset=None,
):
assert items is not None
assert (self.extraction_pipeline is not None and self.clf
is not None), "The module needs to be initialized first"
if not isinstance(items, list):
items = [items]
assert isinstance(items[0], dict) or isinstance(items[0], tuple)
X = self.extraction_pipeline.transform(lambda: items)
if probabilities:
classes = self.clf.predict_proba(X)
else:
classes = self.clf.predict(X)
classes = self.overwrite_classes(items, classes, probabilities)
if importances:
if background_dataset is None:
explainer = shap.TreeExplainer(self.clf)
else:
explainer = shap.TreeExplainer(
self.clf,
to_array(background_dataset),
feature_dependence="independent",
)
shap_values = explainer.shap_values(to_array(X))
important_features = self.get_important_features(
importance_cutoff, shap_values)
important_features["values"] = X
# Workaround: handle multi class case for force_plot to work correctly
if len(classes[0]) > 2:
pred_class_index = classes.argmax(axis=-1)[0]
explainer.expected_value = explainer.expected_value[
pred_class_index]
shap_values = shap_values[pred_class_index]
else:
pred_class_index = 0
pred_class = self.class_names[pred_class_index]
top_indexes = [
int(index) for importance, index, is_positive in
important_features["classes"][pred_class][0]
]
feature_names = self.get_human_readable_feature_names()
feature_legend = {
str(i + 1): feature_names[feature_i]
for i, feature_i in enumerate(top_indexes)
}
return (
classes,
{
"importances": important_features,
"feature_legend": feature_legend
},
)
return classes
def __init__(
self, model_name, cache_root, git_repo_dir, method_defect_predictor_dir
):
self.model_name = model_name
self.cache_root = cache_root
assert os.path.isdir(cache_root), f"Cache root {cache_root} is not a dir."
self.repo_dir = os.path.join(cache_root, "mozilla-central")
self.model = download_and_load_model(model_name)
assert self.model is not None
self.git_repo_dir = git_repo_dir
if git_repo_dir:
self.clone_git_repo("https://github.com/mozilla/gecko-dev", git_repo_dir)
self.method_defect_predictor_dir = method_defect_predictor_dir
if method_defect_predictor_dir:
self.clone_git_repo(
"https://github.com/lucapascarella/MethodDefectPredictor",
method_defect_predictor_dir,
"fa5269b959d8ddf7e97d1e92523bb64c17f9bbcd",
)
if model_name == "regressor":
self.use_test_history = False
model_data_X_path = f"{model_name}model_data_X"
updated = download_check_etag(
URL.format(model_name=model_name, file_name=f"{model_data_X_path}.zst")
)
if updated:
zstd_decompress(model_data_X_path)
assert os.path.exists(model_data_X_path), "Decompressed X dataset exists"
model_data_y_path = f"{model_name}model_data_y"
updated = download_check_etag(
URL.format(model_name=model_name, file_name=f"{model_data_y_path}.zst")
)
if updated:
zstd_decompress(model_data_y_path)
assert os.path.exists(model_data_y_path), "Decompressed y dataset exists"
self.X = to_array(joblib.load(model_data_X_path))
self.y = to_array(joblib.load(model_data_y_path))
past_bugs_by_function_path = "data/past_bugs_by_function.pickle"
download_check_etag(
PAST_BUGS_BY_FUNCTION_URL, path=f"{past_bugs_by_function_path}.zst"
)
zstd_decompress(past_bugs_by_function_path)
assert os.path.exists(past_bugs_by_function_path)
with open(past_bugs_by_function_path, "rb") as f:
self.past_bugs_by_function = pickle.load(f)
if model_name == "testselect":
self.use_test_history = True
assert db.download_support_file(
test_scheduling.TEST_SCHEDULING_DB, test_scheduling.PAST_FAILURES_DB
)
self.past_failures_data = test_scheduling.get_past_failures()
self.testfailure_model = download_and_load_model("testfailure")
assert self.testfailure_model is not None
