Merge pull request #2 from amullen01/refactor

Refactor

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/custom.md

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+---
+name: Custom issue template
+about: Describe this issue template's purpose here.
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/build-docs.yml

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+name: Publish Docs
+
+on:
+  push:
+    branches:
+      - 'main'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}
+  cancel-in-progress: true
+
+env:
+  SM_FRAMEWORK: "tf.keras"
+
+jobs:
+  docs:
+    name: Publish Docs
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          persist-credentials: false
+
+      - name: Setup Conda
+        uses: s-weigand/setup-conda@v1
+        with:
+          python-version: 3.9
+          conda-channels: conda-forge
+
+      - name: Install and Build
+        shell: bash
+        run: |
+          conda config --prepend channels conda-forge
+          conda config --set channel_priority strict
+          conda create -n docs python=3.9 rasterio xarray scipy pyproj pandoc sphinx sphinx-autodoc-typehints jupyter_sphinx sphinx_rtd_theme sphinx-click nbsphinx autodocsumm
+          source activate docs
+          python -m pip install -e .[doc]
+          sphinx-build -b html docs/ docs/_build/
+          #cd docs/
+          #make html
+
+      - name: Deploy 🚀
+        uses: JamesIves/github-pages-deploy-action@v4
+        if: ${{ github.event_name == 'release' }}
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          branch: gh-pages
+          folder: docs/_build/
+          #folder: docs/_build/html
+          clean: false
+          target-folder: ${{ github.ref }}
+
+      - name: Deploy 🚀
+        uses: JamesIves/github-pages-deploy-action@v4
+        if: ${{ github.event_name == 'push' }}
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          branch: gh-pages
+          folder: docs/_build/
+          #folder: docs/_build/html
+          clean: false
+          target-folder: latest

.github/workflows/ci.yml

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+name: CI Regression
+
+on: [push, pull_request]
+
+env:
+  SM_FRAMEWORK: "tf.keras"
+
+jobs:
+
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 4
+      matrix:
+        # 3.6 will reach EoL in December 2021
+        # https://devguide.python.org/#status-of-python-branches
+        python-version: [ "3.8", "3.9" ]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Setup python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: x64
+      - name: Install test dependencies
+        run: |
+          sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable
+          sudo apt-get update
+          sudo apt-get install -y gdal-bin libgdal-dev build-essential
+          python -m pip install --upgrade pip
+          pip install https://github.com/rasterio/rasterio/archive/master.zip
+          pip install .[test]
+          pip install coveralls
+      - name: Run tests
+        run: coverage run -m pytest -v
+      - name: Submit coveralls
+        if: github.event_name != 'pull_request'
+        run: coveralls --service=github
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/codeql-analysis.yml

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+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "main" ]
+  schedule:
+    - cron: '29 15 * * 2'
+
+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: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v2
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+    #   If the Autobuild fails above, remove it and uncomment the following three lines. 
+    #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+    # - run: |
+    #   echo "Run, Build Application using script"
+    #   ./location_of_script_within_repo/buildscript.sh
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2
+      with:
+        category: "/language:${{matrix.language}}"

.github/workflows/dockerhub-dev.yml

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+name: Dev - CI to Docker Hub 
+
+on:
+  push:
+    branches:
+      - 'develop'
+  schedule:
+    - cron: '30 5 * * 1,3'
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Checkout
+        uses: actions/checkout@v3
+      -
+        name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+      -
+        name: Login to Docker Hub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - 
+        name: Lower github-runner storage
+        run: |
+          sudo rm -rf /usr/share/dotnet
+          sudo rm -rf /opt/ghc
+          sudo rm -rf "/usr/local/share/boost"
+          sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+
+      -
+        name: Build and push
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          file: ./requirements/Dockerfile.dev
+          push: true
+          tags: nasanccs/vhr-cloudmask:dev

.github/workflows/dockerhub.yml

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+name: Prod - CI to Docker Hub
+
+on:
+  push:
+    branches:
+      - 'main'
+  schedule:
+    - cron: '30 5 * * 1,3'
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Checkout
+        uses: actions/checkout@v3
+      -
+        name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+      -
+        name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+      -
+        name: Login to Docker Hub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - 
+        name: Lower github-runner storage
+        run: |
+          sudo rm -rf /usr/share/dotnet
+          sudo rm -rf /opt/ghc
+          sudo rm -rf "/usr/local/share/boost"
+          sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+
+      -
+        name: Build and push
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          file: ./requirements/Dockerfile
+          push: true
+          tags: nasanccs/vhr-cloudmask:latest

.github/workflows/lint.yml

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+name: Code style - PEP8
+
+on: [push, pull_request]
+
+jobs:
+
+  flake8-lint:
+    runs-on: ubuntu-latest
+    name: Lint
+    steps:
+      - name: Check out source repository
+        uses: actions/checkout@v2
+      - name: Set up Python environment
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.8"
+      - name: flake8 Lint
+        uses: py-actions/flake8@v2

.github/workflows/pypi-publish.yml

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+name: Publish to PyPI.org
+on:
+  workflow_dispatch:
+  release:
+    types: [published]
+jobs:
+  pypi:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - run: python3 -m pip install --upgrade build && python3 -m build
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

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+.DS_Store/
+.ipynb_checkpoints/
+__pycache__/
+.DS_Store