chore: update format

benchmarks/classification.py

@@ -109,7 +109,7 @@ def main():
     # Listing
     if args.long_list or args.short_list:
         already_done_models = {}
-        for (dataset_i, model_class_i, config_i) in all_classification_tasks:
+        for dataset_i, model_class_i, config_i in all_classification_tasks:
             config_n = json.dumps(config_i).replace("'", '"')
             model_name_i = model_class_i.__name__
 

benchmarks/common.py

@@ -274,7 +274,7 @@ def run_and_report_classification_metrics(
             (f1_score, "f1", "F1Score"),
         ]
 
-    for (metric, metric_id, metric_label) in metric_info:
+    for metric, metric_id, metric_label in metric_info:
         run_and_report_metric(
             y_gt,
             y_pred,
@@ -288,7 +288,7 @@ def run_and_report_regression_metrics(y_gt, y_pred, metric_id_prefix, metric_lab
     """Run several metrics and report results to progress tracker with computed name and id"""
 
     metric_info = [(r2_score, "r2_score", "R2Score"), (mean_squared_error, "MSE", "MSE")]
-    for (metric, metric_id, metric_label) in metric_info:
+    for metric, metric_id, metric_label in metric_info:
         run_and_report_metric(
             y_gt,
             y_pred,
@@ -768,6 +768,7 @@ def benchmark_name_generator(
 # - The functions support all models
 # FIXME: https://github.com/zama-ai/concrete-ml-internal/issues/1866
 
+
 # pylint: disable-next=too-many-branches, redefined-outer-name
 def benchmark_name_to_config(
     benchmark_name: str, joiner: str = "_"

benchmarks/deep_learning.py

@@ -886,7 +886,7 @@ def main():
     if args.long_list or args.short_list:
         # Print the short or long lists if asked and stop
         printed_models = set()
-        for (dataset, cnn_class, config) in all_tasks:
+        for dataset, cnn_class, config in all_tasks:
             configs = json.dumps(config).replace("'", '"')
             cnn_name = cnn_class.__name__
 

benchmarks/glm.py

@@ -113,14 +113,20 @@ def get_preprocessor() -> ColumnTransformer:
 
 def get_train_test_data(data: pandas.DataFrame) -> Tuple[pandas.DataFrame, pandas.DataFrame]:
     """Split the data into a train and test set."""
-    train_data, test_data, = train_test_split(
+    (
+        train_data,
+        test_data,
+    ) = train_test_split(
         data,
         test_size=0.2,
         random_state=0,
     )
 
     # The test set is reduced for faster FHE runs.
-    _, test_data, = train_test_split(
+    (
+        _,
+        test_data,
+    ) = train_test_split(
         test_data,
         test_size=500,
         random_state=0,

benchmarks/regression.py

@@ -109,7 +109,7 @@ def main():
     # Listing
     if args.long_list or args.short_list:
         already_done_models = {}
-        for (dataset_i, model_class_i, config_i) in all_tasks:
+        for dataset_i, model_class_i, config_i in all_tasks:
             config_n = json.dumps(config_i).replace("'", '"')
             model_name_i = model_class_i.__name__
 

conftest.py

@@ -1,4 +1,5 @@
 """PyTest configuration file."""
+
 import hashlib
 import json
 import random

deps_licenses/licenses_mac_silicon_user.txt

@@ -31,7 +31,7 @@ jsonpickle, 3.0.4, BSD License
 mpmath, 1.3.0, BSD License
 networkx, 3.1, BSD License
 numpy, 1.23.5, BSD License
-onnx, 1.16.0, Apache License v2.0
+onnx, 1.15.0, Apache License v2.0
 onnxconverter-common, 1.13.0, MIT License
 onnxmltools, 1.11.0, Apache Software License
 onnxoptimizer, 0.3.13, Apache License v2.0

deps_licenses/licenses_mac_silicon_user.txt.md5

@@ -1 +1 @@
-6a81dc377a7c438d85a5f2200ecc6a76
+180ea2b3232d89fc71be20d1707620b4

docker/release_resources/sanity_check.py

@@ -1,4 +1,5 @@
 """Sanity checks, to be sure that our package is usable"""
+
 import argparse
 import random
 import shutil

docs/advanced_examples/KNearestNeighbors.ipynb

@@ -392,9 +392,11 @@
     "def highlight_diff(row):\n",
     "    \"\"\"Custom style function to highlight mismatched predictions.\"\"\"\n",
     "    return [\n",
-    "        \"background-color: yellow\"\n",
-    "        if row[\"Majority vote (Concrete ML)\"] != row[\"Majority vote (scikit-learn)\"]\n",
-    "        else \"\"\n",
+    "        (\n",
+    "            \"background-color: yellow\"\n",
+    "            if row[\"Majority vote (Concrete ML)\"] != row[\"Majority vote (scikit-learn)\"]\n",
+    "            else \"\"\n",
+    "        )\n",
     "    ] * len(row)\n",
     "\n",
     "\n",

pyproject.toml

@@ -42,11 +42,13 @@ skorch = "0.11.0"
 torch = "1.13.1"
 typing-extensions = "4.5.0"
 brevitas = "0.8.0"
+onnx = "1.15.0"
 onnxoptimizer = "0.3.13"
+# onnxruntime versions supported by onnx versions and opsets can be found here : 
+# https://onnxruntime.ai/docs/reference/compatibility.html#onnx-opset-support
 onnxruntime = "1.17.3"
 hummingbird-ml = {version="0.4.8", extras = ["onnx"]}
 scikit-learn = "1.1.3"
-onnx = "1.16.0"
 scipy = "1.10.1"
 numpy = "1.23.5"
 protobuf = "3.20.3"

script/actions_utils/escape_quotes.py

@@ -1,4 +1,5 @@
 """Script to escape double quotes within brackets or curly braces."""
+
 import argparse
 
 parser = argparse.ArgumentParser(description="Escape double quotes in a string")

script/actions_utils/generate_scripts_benchmark.py

@@ -1,4 +1,5 @@
 """Script to generate the list of commands to run all benchmarks"""
+
 import argparse
 import datetime
 import json

script/actions_utils/json_length.py

@@ -1,4 +1,5 @@
 """Script to evaluate the length of a json file"""
+
 import argparse
 import json
 from pathlib import Path

script/actions_utils/monitor.py

@@ -1,4 +1,5 @@
 """Module to generate figure of evolution of Concrete ML-CI time on main for last 4 weeks."""
+
 import argparse
 import datetime
 import json

script/actions_utils/pytest_failed_test_report.py

@@ -1,4 +1,5 @@
 """Pytest JSON report on failed tests utils."""
+
 import argparse
 import json
 from pathlib import Path

script/actions_utils/refresh_notebooks_list.py

@@ -1,4 +1,5 @@
 """Update the list of available notebooks for the refresh_one_notebook GitHib action."""
+
 import argparse
 from pathlib import Path
 

script/actions_utils/run_commands.py

@@ -1,4 +1,5 @@
 """Script to run commands from a json file"""
+
 import argparse
 import json
 import subprocess

script/doc_utils/gen_supported_ops.py

@@ -1,4 +1,5 @@
 """Update list of supported functions in the doc."""
+
 import argparse
 from pathlib import Path
 

script/make_utils/actionlint_check_with_whitelists.py

@@ -1,4 +1,5 @@
 """ Check an actionlint log against some whitelists """
+
 import sys
 from typing import Set
 

script/make_utils/check_headers.py

@@ -1,4 +1,5 @@
 """Check that headers linked do indeed exist in target markdown files"""
+
 import os
 from pathlib import Path
 

script/make_utils/check_issues.py

@@ -1,4 +1,5 @@
 """Check linked github issues states"""
+
 import json
 import re
 import subprocess

script/nbmake_utils/notebook_finalize.py

@@ -1,4 +1,5 @@
 """Finalize Jupyter notebooks."""
+
 import argparse
 import json
 from pathlib import Path

src/concrete/__init__.py

@@ -1,4 +1,5 @@
 """Top level import."""
+
 # Do not modify, this is to have a compatible namespace package
 # https://packaging.python.org/en/latest/guides/packaging-namespace-packages/
 # #pkg-resources-style-namespace-packages

src/concrete/ml/common/__init__.py

@@ -1,2 +1,3 @@
 """Module for shared data structures and code."""
+
 from . import check_inputs, debugging, utils

src/concrete/ml/common/debugging/__init__.py

@@ -1,2 +1,3 @@
 """Module for debugging."""
+
 from .custom_assert import assert_false, assert_not_reached, assert_true

src/concrete/ml/common/debugging/custom_assert.py

@@ -1,4 +1,5 @@
 """Provide some variants of assert."""
+
 from typing import Type
 
 

src/concrete/ml/common/serialization/__init__.py

@@ -1,4 +1,5 @@
 """Serialization module."""
+
 import os
 
 from torch.nn.modules import activation

src/concrete/ml/common/serialization/decoder.py

@@ -1,4 +1,5 @@
 """Custom decoder for serialization."""
+
 import inspect
 import json
 from typing import Any, Dict, Type

src/concrete/ml/common/serialization/dumpers.py

@@ -1,4 +1,5 @@
 """Dump functions for serialization."""
+
 import json
 from typing import Any, TextIO
 

src/concrete/ml/common/serialization/encoder.py

@@ -1,4 +1,5 @@
 """Custom encoder for serialization."""
+
 import inspect
 import json
 from json.encoder import _make_iterencode  # type: ignore[attr-defined]

src/concrete/ml/common/serialization/loaders.py

@@ -1,4 +1,5 @@
 """Load functions for serialization."""
+
 import json
 from typing import IO, Any, Union
 

src/concrete/ml/deployment/__init__.py

@@ -1,2 +1,3 @@
 """Module for deployment of the FHE model."""
+
 from .fhe_client_server import FHEModelClient, FHEModelDev, FHEModelServer

src/concrete/ml/deployment/utils.py

@@ -3,6 +3,7 @@
 - Check if connection possible
 - Wait for connection to be available (with timeout)
 """
+
 import subprocess
 import time
 from pathlib import Path

src/concrete/ml/onnx/onnx_utils.py

@@ -1,4 +1,5 @@
 """Utils to interpret an ONNX model with numpy."""
+
 # Utils to interpret an ONNX model with numpy.
 
 

src/concrete/ml/pandas/__init__.py

@@ -1,4 +1,5 @@
 """Public API for encrypted data-frames."""
+
 from pathlib import Path
 from typing import Hashable, Optional, Sequence, Tuple, Union
 

src/concrete/ml/pandas/_development.py

@@ -1,4 +1,5 @@
 """Define development methods for generating client/server files."""
+
 import itertools
 from functools import partial
 from pathlib import Path

src/concrete/ml/pandas/_operators.py

@@ -1,4 +1,5 @@
 """Implement Pandas operators in FHE using encrypted data-frames."""
+
 from typing import Any, Dict, Hashable, List, Optional, Sequence, Tuple, Union
 
 import numpy

src/concrete/ml/pandas/_processing.py

@@ -1,4 +1,5 @@
 """Define pre-processing and post-processing steps for encrypted data-frames."""
+
 import copy
 from collections import defaultdict
 from typing import Dict, List, Tuple