Initial commit

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: 'bug'
+assignees: ''
+
+---
+## Description
+(A clear and concise description of what the bug is.)
+
+## How to Reproduce?
+(If you developed your own code, please provide a short script that reproduces the error. For existing examples, please provide link.)
+
+### Steps to reproduce
+(Please provide minimal example of code snippet that reproduces the error. For existing examples, please provide link.)
+
+```python
+put code here
+```
+
+(Paste the commands you ran that produced the error.)
+
+1.
+2.
+
+## What have you tried to solve it?
+
+1.
+2.
+
+## Error message or code output
+(Paste the complete error message, including stack trace, or the undesired output that the above snippet produces.)
+
+```
+put error or undesired output here
+```
+
+## Environment
+- Operating system:
+- Python version:
+- PECOS version:
+
+(Add as much information about your environment as possible, e.g. dependencies versions.)

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an enhancement, feature request, or idea for this project
+title: ''
+labels: 'enhancement'
+assignees: ''
+
+---
+
+## Description
+(A clear and concise description of what the feature is.)
+- If the proposal is about a new model, provide description of what the model is.
+- If the proposal is about an API, provide mock examples if possible.
+
+## References
+- list reference and related literature
+- list known implementations

.github/PULL_REQUEST_TEMPLATE.md

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+*Issue #, if available:*
+
+*Description of changes:*
+
+
+By submitting this pull request, I confirm that my contribution is made under the terms of the Apache 2.0 license.

.github/build_pypi_wheel.sh

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+#!/bin/bash
+set -e
+
+# Get pip
+echo "Build wheel using Python version $PIP_VER..."
+PIP=$(ls /opt/python/cp${PIP_VER//./}-cp*/bin/pip)
+if [ -z $PIP ]; then
+   echo "No pip found for version $PIP_VER, exit"
+   exit 1
+fi
+echo "pip: $($PIP --version)"
+
+
+# Install dependencies
+echo "Install dependencies..."
+$PIP install setuptools wheel twine auditwheel
+yum install -y openblas-devel
+
+
+# Build wheel
+PECOS_SOURCE=$DOCKER_MNT/
+WHEEL_OUTPUT_FOLDER=$DOCKER_MNT/$WHEEL_DIR
+
+$PIP wheel $PECOS_SOURCE --no-deps -w $WHEEL_OUTPUT_FOLDER
+WHEEL_NAME=$(ls $WHEEL_OUTPUT_FOLDER)
+
+echo "Temporary wheel: $(ls $WHEEL_OUTPUT_FOLDER)"
+auditwheel show $WHEEL_OUTPUT_FOLDER/$WHEEL_NAME
+
+echo "Auditing wheel to platform $PLAT..."
+auditwheel repair $WHEEL_OUTPUT_FOLDER/$WHEEL_NAME -w $WHEEL_OUTPUT_FOLDER
+rm $WHEEL_OUTPUT_FOLDER/$WHEEL_NAME
+
+echo "Audited wheel: $(ls $WHEEL_OUTPUT_FOLDER)"
+auditwheel show $WHEEL_OUTPUT_FOLDER/$(ls $WHEEL_OUTPUT_FOLDER)

.github/workflows/build_pypi.yml

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+name: Pypi Build and Release
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    name: Build PyPI Wheel
+    strategy:
+      max-parallel: 4
+      fail-fast: false
+      matrix:
+        python-version: [3.6, 3.7, 3.8, 3.9]
+        build_platform: ["manylinux2014_x86_64"]
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v1
+
+    - name: Build Wheel
+      env:
+        DOCKER_IMG: quay.io/pypa/${{ matrix.build_platform }}
+        DOCKER_MNT: pypi_build
+        WHEEL_DIR: wheel # wheel location
+      run: |
+        echo "Build wheel for PECOS using Python version ${{ matrix.python-version }}..."
+        docker run --rm -v $(pwd):/$DOCKER_MNT \
+        --env PLAT=${{ matrix.build_platform }} --env PIP_VER=${{ matrix.python-version }} \
+        --env DOCKER_MNT=$DOCKER_MNT --env WHEEL_DIR=$WHEEL_DIR \
+        $DOCKER_IMG /bin/bash /$DOCKER_MNT/.github/build_pypi_wheel.sh
+
+    - name: Check Version Tag
+      id: check-ver-tag
+      run: |
+        if [[ "${{ github.event_name }}" == "push" ]] && \
+           [[ "${{ github.event.ref }}" =~ ^refs/tags/v[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
+            echo ::set-output name=match::true
+        fi
+
+    - name: Upload to PyPI
+      if: steps.check-ver-tag.outputs.match == 'true' # Only upload for tags v*.*.*
+      env:
+        TWINE_USERNAME: ${{ secrets. PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets. PYPI_PASSWORD }}
+        WHEEL_DIR: wheel # same as Build-Wheel/WHEEL_DIR
+      run: |
+        WHEEL=$(ls $(pwd)/$WHEEL_DIR)
+        if [ -z $WHEEL ]; then
+          echo "Wheel build not successful, exit"
+          exit 1
+        fi
+        echo "Will upload $WHEEL to PyPI..."
+        pip install twine --upgrade
+        python3 -m twine upload $(pwd)/$WHEEL_DIR/$WHEEL --verbose

.github/workflows/codeql.yml

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+name: "Code scanning - action"
+
+on:
+  push:
+  pull_request:
+  schedule:
+    - cron: '0 19 * * 0'
+
+jobs:
+  CodeQL-Build:
+    name: CodeQL
+    # CodeQL runs on ubuntu-latest
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python','cpp' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python' ]
+        # Learn more:
+        # https://docs.github.com/en/free-pro-team@latest/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#changing-the-languages-that-are-analyzed
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      with:
+        languages: ${{ matrix.language }}
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, 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@v1
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v1

.github/workflows/pytest.yml

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+name: Python Unit Tests
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    name: Python Unit Tests
+    strategy:
+      max-parallel: 4
+      fail-fast: false
+      matrix:
+        python-version: [3.6, 3.7, 3.8, 3.9]
+        platform: [ubuntu-16.04, ubuntu-18.04, ubuntu-20.04]
+
+    runs-on: ${{ matrix.platform }}
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install pip
+        python -m pip install --upgrade pip
+        pip install pytest pytest-coverage
+        pip install -v --editable .
+    - name: Test with pytest
+      run: |
+        pytest

.github/workflows/style_type_check.yml

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+name: Style and type checks
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    name: Style and Type Checks
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.7
+    - name: Install dependencies
+      run: |
+        python -m pip install pip
+        python -m pip install --upgrade pip
+    - name: Style checks
+      run: |
+        pip install black
+        python -m black -v --check --config .style_type.cfg --line-length=100 --diff ./pecos
+        python -m black -v --check --config .style_type.cfg --line-length=100 --diff ./test
+    - name: Type checks
+      run: |
+        pip install mypy
+        python -m mypy -v --config-file .style_type.cfg -p pecos
+        python -m mypy -v --config-file .style_type.cfg `find ./test/ -type f -name "*.py"`
+      if: ${{ success() || failure() }}
+    # - name: Check license headers
+    #   run: python .devtools/license check src test

.style_type.cfg

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+[isort]
+line_length = 100
+multi_line_output = 3
+include_trailing_comma = true
+
+[mypy]
+ignore_missing_imports = true

CODE_OF_CONDUCT.md

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+## Code of Conduct
+This project has adopted the [Amazon Open Source Code of Conduct](https://aws.github.io/code-of-conduct).
+For more information see the [Code of Conduct FAQ](https://aws.github.io/code-of-conduct-faq) or contact
+opensource-codeofconduct@amazon.com with any additional questions or comments.

CONTRIBUTING.md

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+# Contributing Guidelines
+
+Thank you for your interest in contributing to our project. Whether it's a bug report, new feature, correction, or additional
+documentation, we greatly value feedback and contributions from our community.
+
+Please read through this document before submitting any issues or pull requests to ensure we have all the necessary
+information to effectively respond to your bug report or contribution.
+
+
+## Reporting Bugs/Feature Requests
+
+We welcome you to use the GitHub issue tracker to report bugs or suggest features.
+
+When filing an issue, please check existing open, or recently closed, issues to make sure somebody else hasn't already
+reported the issue. Please try to include as much information as you can. Details like these are incredibly useful:
+
+* A reproducible test case or series of steps
+* The version of our code being used
+* Any modifications you've made relevant to the bug
+* Anything unusual about your environment or deployment
+
+
+## Contributing via Pull Requests
+Contributions via pull requests are much appreciated. Before sending us a pull request, please ensure that:
+
+1. You are working against the latest source on the `mainline` branch.
+2. You check existing open, and recently merged, pull requests to make sure someone else hasn't addressed the problem already.
+3. You open an issue to discuss any significant work - we would hate for your time to be wasted. If there is an existing issue your are interested in working on, you should comment on it so others don't start working on the same issue.
+
+To send us a pull request, please:
+
+1. Create a personal fork of the project on Github webpage. Clone the fork on your local machine.
+2. Add the original repository as a remote called `upstream`. Your remote repo on Github is called `origin`.
+    ```
+    git remote add upstream https://github.com/amzn/pecos.git
+    git remote -v # Display all remotes to double-check
+    ```
+3. If you created your fork a while ago, be sure to pull upstream changes into your local repository.
+    ```
+    git checkout mainline
+    git pull -r upstream
+    ```
+4. Create a new branch from `mainline` to work on.
+5. Implement your code on the new branch:
+    * Follow the code style of the project.
+    * Write or adapt tests as needed.
+    * Add or change the documentation as needed.
+6. **Ensure local style/type checks and tests pass.**
+7. Commit using clear messages. **Squash your commits into a single commit.**
+8. Push your branch to **your fork** `origin` on Github.
+    ```
+    git push --set-upstream origin <BRANCH NAME>
+    ```
+9. On GitHub webpage's pull request panel, open a pull request into **original repository** `upstream` from **your fork**. *(NOTE: this is the default option if one does not make changes when creating PR)*
+    * Carefully fill out PR template
+    * Click on "Draft PR" on drop-down menu to double-check by oneself
+    * When ready, click on “Ready for review”
+10. Pay attention to any automated CI failures reported in the pull request, and stay involved in the conversation.
+12. If you need to make changes to the pull request, simply modify on your branch by **amend** the commit, and then *force-push* to your `origin` branch. The pull request will automatically update its timeline:
+    ```
+    # Do modification
+    git commit -a --amend
+    git push -f
+    ```
+11. Once the pull request is approved and merged, pull the changes from upstream to your local repo and delete your extra branch(es).
+
+GitHub provides additional document on [forking a repository](https://help.github.com/articles/fork-a-repo/) and
+[creating a pull request](https://help.github.com/articles/creating-a-pull-request/).
+
+
+## Finding contributions to work on
+Looking at the existing issues is a great way to find something to contribute on. As our projects, by default, use the default GitHub issue labels (enhancement/bug/duplicate/help wanted/invalid/question/wontfix), looking at any 'Call for Contribution' or 'good first issue' issues is a great place to start.
+
+
+## Code of Conduct
+This project has adopted the [Amazon Open Source Code of Conduct](https://aws.github.io/code-of-conduct).
+For more information see the [Code of Conduct FAQ](https://aws.github.io/code-of-conduct-faq) or contact
+opensource-codeofconduct@amazon.com with any additional questions or comments.
+
+
+## Security issue notifications
+If you discover a potential security issue in this project we ask that you notify AWS/Amazon Security via our [vulnerability reporting page](http://aws.amazon.com/security/vulnerability-reporting/). Please do **not** create a public github issue.
+
+
+## Licensing
+
+See the [LICENSE](LICENSE) file for our project's licensing. We will ask you to confirm the licensing of your contribution.
+
+We may ask you to sign a [Contributor License Agreement (CLA)](http://en.wikipedia.org/wiki/Contributor_License_Agreement) for larger changes.