Add pre-commit hooks (#60)

* Add pre-commit

* Run pre-commit

* Address codeQL

Author: the-david-oy

.github/workflows/codeql.yml

@@ -0,0 +1,84 @@
+# Copyright 2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions
+# are met:
+#  * Redistributions of source code must retain the above copyright
+#    notice, this list of conditions and the following disclaimer.
+#  * Redistributions in binary form must reproduce the above copyright
+#    notice, this list of conditions and the following disclaimer in the
+#    documentation and/or other materials provided with the distribution.
+#  * Neither the name of NVIDIA CORPORATION nor the names of its
+#    contributors may be used to endorse or promote products derived
+#    from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS ``AS IS'' AND ANY
+# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+# PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY
+# OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+name: "CodeQL"
+
+on:
+  pull_request:
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # Details on CodeQL's query packs refer to:
+        # https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        queries: +security-and-quality
+
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, Go, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v2
+
+    # Command-line programs to run using the OS shell.
+    # See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+    #   If the Autobuild fails above, remove it and uncomment the following three lines.
+    #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+    # - run: |
+    #   echo "Run, Build Application using script"
+    #   ./location_of_script_within_repo/buildscript.sh
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2
+      with:
+        category: "/language:${{matrix.language}}"

.github/workflows/pre-commit.yaml

@@ -0,0 +1,39 @@
+# Copyright 2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions
+# are met:
+#  * Redistributions of source code must retain the above copyright
+#    notice, this list of conditions and the following disclaimer.
+#  * Redistributions in binary form must reproduce the above copyright
+#    notice, this list of conditions and the following disclaimer in the
+#    documentation and/or other materials provided with the distribution.
+#  * Neither the name of NVIDIA CORPORATION nor the names of its
+#    contributors may be used to endorse or promote products derived
+#    from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS ``AS IS'' AND ANY
+# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+# PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY
+# OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+name: pre-commit
+
+on:
+  pull_request:
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-22.04
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v3
+    - uses: pre-commit/[email protected]
+

.pre-commit-config.yaml

@@ -0,0 +1,74 @@
+# Copyright 2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions
+# are met:
+#  * Redistributions of source code must retain the above copyright
+#    notice, this list of conditions and the following disclaimer.
+#  * Redistributions in binary form must reproduce the above copyright
+#    notice, this list of conditions and the following disclaimer in the
+#    documentation and/or other materials provided with the distribution.
+#  * Neither the name of NVIDIA CORPORATION nor the names of its
+#    contributors may be used to endorse or promote products derived
+#    from this software without specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS ``AS IS'' AND ANY
+# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+# PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY
+# OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+repos:
+- repo: https://github.com/timothycrosley/isort
+  rev: 5.12.0
+  hooks:
+  - id: isort
+    additional_dependencies: [toml]
+- repo: https://github.com/psf/black
+  rev: 23.1.0
+  hooks:
+  - id: black
+    types_or: [python, cython]
+- repo: https://github.com/PyCQA/flake8
+  rev: 5.0.4
+  hooks:
+  - id: flake8
+    args: [--max-line-length=88, --select=C,E,F,W,B,B950, --extend-ignore = E203,E501]
+    types_or: [python, cython]
+- repo: https://github.com/pre-commit/mirrors-clang-format
+  rev: v16.0.5
+  hooks:
+  - id: clang-format
+    types_or: [c, c++, cuda, proto, textproto, java]
+    args: ["-fallback-style=none", "-style=file", "-i"]
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.2.4
+  hooks:
+  - id: codespell
+    additional_dependencies: [tomli]
+    args: ["--toml", "pyproject.toml"]
+    exclude: (?x)^(.*stemmer.*|.*stop_words.*|^CHANGELOG.md$)
+# More details about these pre-commit hooks here:
+# https://pre-commit.com/hooks.html
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+  - id: check-case-conflict
+  - id: check-executables-have-shebangs
+  - id: check-merge-conflict
+  - id: check-json
+  - id: check-toml
+  - id: check-yaml
+    exclude: ^deploy(\/[^\/]+)*\/templates\/.*$
+  - id: check-shebang-scripts-are-executable
+  - id: end-of-file-fixer
+    types_or: [c, c++, cuda, proto, textproto, java, python]
+  - id: mixed-line-ending
+  - id: requirements-txt-fixer
+  - id: trailing-whitespace

Conceptual_Guide/Part_1-model_deployment/README.md

@@ -112,7 +112,7 @@ torch.onnx.export(model, trace_input, "str.onnx", verbose=True)
 
 ### Setting up the model repository
 
-A [model repository](https://docs.nvidia.com/deeplearning/triton-inference-server/user-guide/docs/user_guide/model_repository.html) is Triton's way of reading your models and any associated metadata with each model (configurations, version files, etc.). These model repositories can live in a local or network attatched filesystem, or in a cloud object store like AWS S3, Azure Blob Storage or Google Cloud Storage. For more details on model repository location, refer to [the documentation](https://docs.nvidia.com/deeplearning/triton-inference-server/user-guide/docs/user_guide/model_repository.html#model-repository-locations). Servers can use also multiple different model repositories. For simplicity, this explanation only uses a single repository stored in the [local filesystem](https://docs.nvidia.com/deeplearning/triton-inference-server/user-guide/docs/user_guide/model_repository.html#local-file-system), in the following format:
+A [model repository](https://docs.nvidia.com/deeplearning/triton-inference-server/user-guide/docs/user_guide/model_repository.html) is Triton's way of reading your models and any associated metadata with each model (configurations, version files, etc.). These model repositories can live in a local or network attached filesystem, or in a cloud object store like AWS S3, Azure Blob Storage or Google Cloud Storage. For more details on model repository location, refer to [the documentation](https://docs.nvidia.com/deeplearning/triton-inference-server/user-guide/docs/user_guide/model_repository.html#model-repository-locations). Servers can use also multiple different model repositories. For simplicity, this explanation only uses a single repository stored in the [local filesystem](https://docs.nvidia.com/deeplearning/triton-inference-server/user-guide/docs/user_guide/model_repository.html#local-file-system), in the following format:
 
 ```bash
 # Example repository structure

Conceptual_Guide/Part_1-model_deployment/client.py

@@ -25,15 +25,15 @@
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 import math
-import numpy as np
+
 import cv2
+import numpy as np
 import tritonclient.http as httpclient
 
 SAVE_INTERMEDIATE_IMAGES = False
 
 
 def detection_preprocessing(image: cv2.Mat) -> np.ndarray:
-
     inpWidth = 640
     inpHeight = 480
 
@@ -154,7 +154,7 @@ def recognition_postprocessing(scores: np.ndarray) -> str:
     text = ""
     alphabet = "0123456789abcdefghijklmnopqrstuvwxyz"
 
-    scores = np.transpose(scores, (1,0,2))
+    scores = np.transpose(scores, (1, 0, 2))
 
     for i in range(scores.shape[0]):
         c = np.argmax(scores[i][0])
@@ -172,7 +172,6 @@ def recognition_postprocessing(scores: np.ndarray) -> str:
 
 
 if __name__ == "__main__":
-
     # Setting up client
     client = httpclient.InferenceServerClient(url="localhost:8000")
 

Conceptual_Guide/Part_1-model_deployment/utils/model.py

@@ -234,7 +234,6 @@ def __init__(self, input_channels, output_channels, num_classes):
         self.Prediction = nn.Linear(self.SequenceModeling_output, num_classes)
 
     def forward(self, input):
-
         """Feature extraction stage"""
         visual_feature = self.FeatureExtraction(input)
         visual_feature = self.AdaptiveAvgPool(

Conceptual_Guide/Part_2-improving_resource_utilization/README.md

@@ -1,4 +1,4 @@
-<!-- 
+<!--
 # Copyright 2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
 #
 # Redistribution and use in source and binary forms, with or without
@@ -29,14 +29,14 @@
 
 # Dynamic Batching & Concurrent Model Execution
 
-| Navigate to | [Part 1: Model Deployment](../Part_1-model_deployment/) | [Part 3: Optimizing Triton Configuration](../Part_3-optimizing_triton_configuration/) | 
+| Navigate to | [Part 1: Model Deployment](../Part_1-model_deployment/) | [Part 3: Optimizing Triton Configuration](../Part_3-optimizing_triton_configuration/) |
 | ------------ | --------------- | --------------- |
 
-Part-1 of this series introduced the mechanisms to set up a Triton Inference Server. This iteration discusses the concept of dynamic batching and concurrent model execution. These are important features that can be used to reduce latency as well as increase throughput via higher resource utilization. 
+Part-1 of this series introduced the mechanisms to set up a Triton Inference Server. This iteration discusses the concept of dynamic batching and concurrent model execution. These are important features that can be used to reduce latency as well as increase throughput via higher resource utilization.
 
 ## What is Dynamic Batching?
 
-Dynamic batching, in reference to the Triton Inference Server, refers to the functionality which allows the combining of one or more inference requests into a single batch (which has to be created dynamically) to maximize throughput. 
+Dynamic batching, in reference to the Triton Inference Server, refers to the functionality which allows the combining of one or more inference requests into a single batch (which has to be created dynamically) to maximize throughput.
 
 Dynamic batching can be enabled and configured on per model basis by specifying selections in the model's `config.pbtxt`. Dynamic Batching can be enabled with its default settings by adding the following to the `config.pbtxt` file:
 ```
@@ -55,7 +55,7 @@ Let's discuss a sample scenario(refer the diagram below). Say there are 5 infere
 
 In the case where no dynamic batching is used, all requests are processed sequentially, which means that it takes `5X ms` to process all the requests. This process is quite wasteful as each batch processing could have processed more batches than it did in sequential execution.
 
-Using Dynamic batching in this case leads to more efficient packing of requests into the GPU memory resulting in a considerably faster `3X ms`. It also reduces the latency of responses as more queries can be processed in fewer cycles. If the use of `delay` is considered, `A`, `B`, `C` and `D`, `E` can be batched together to get even better utilization of resources. 
+Using Dynamic batching in this case leads to more efficient packing of requests into the GPU memory resulting in a considerably faster `3X ms`. It also reduces the latency of responses as more queries can be processed in fewer cycles. If the use of `delay` is considered, `A`, `B`, `C` and `D`, `E` can be batched together to get even better utilization of resources.
 
 **Note:** The above is an extreme version of an ideal case scenario. In practice, not all elements of execution can be perfectly parallelized, resulting in longer execution time for larger batches.
 
@@ -72,14 +72,14 @@ instance_group [
     kind: KIND_GPU
     gpus: [ 0, 1 ]
   }
-] 
+]
 ```
 
 Let's take the previous example and discuss the effect of adding multiple models for parallel execution. In this example, instead of having a single model process five queries, two models are spawned. ![Multiple Model Instances](./img/multi_instance.PNG)
 
 For a "no dynamic batching" case, as there are model models to execute, the queries are distributed equally. Users can also add [priorities](https://github.com/triton-inference-server/server/blob/main/docs/model_configuration.md#priority) to prioritize or de-prioritize any specific instance group.
 
-When considering the case of multiple instances with dynamic batches enabled, the following happens. Owing to the availability of another instance, query `B` which arrives with some delay can be executed using the second instance. With some delay allocated, instance 1 gets filled and launched by time `T = X/2` and since queries `D` and `E` stack up to fill up to the maximum batch size, the second model can start inference without any delay. 
+When considering the case of multiple instances with dynamic batches enabled, the following happens. Owing to the availability of another instance, query `B` which arrives with some delay can be executed using the second instance. With some delay allocated, instance 1 gets filled and launched by time `T = X/2` and since queries `D` and `E` stack up to fill up to the maximum batch size, the second model can start inference without any delay.
 
 The key takeaway from the above examples is that the Triton Inference Server provides flexibility with respect to policies related to creating more efficient batching, thus enabling better resource utilization, resulting in reduced latency and increased throughput.
 
@@ -118,7 +118,7 @@ torch.onnx.export(model, trace_input, "str.onnx", verbose=True, dynamic_axes={'i
 As discussed in `Part 1`, a model repository is a filesystem based repository of models and configuration schema used by the Triton Inference Server (refer to `Part 1` for a more detailed explanation for model repositories). For this example, the model repository structure would need to be set up in the following manner:
 ```
 model_repository
-|   
+|
 |-- text_recognition
     |
     |-- config.pbtxt