Merge branch 'ARM-DOE:main' into master

.coveragerc

@@ -1,2 +1,6 @@
 [run]
-omit =./act/tests/*, ./act/*version*py
+omit =
+    *tests*
+    act/*version*py
+    versioneer.py
+    setup.py

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,15 @@
+* ACT version:
+* Python version:
+* Operating System:
+
+### Description
+
+Describe what you were trying to get done.
+Tell us what happened, what went wrong, and what you expected to happen.
+
+### What I Did
+
+```
+Paste the command(s) you ran and the output.
+If there was a crash, please include the traceback here.
+```

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,7 @@
+<!-- Please remove check-list items that aren't relevant to your changes -->
+
+- [ ] Closes #xxxx
+- [ ] Tests added
+- [ ] Documentation reflects changes
+- [ ] PEP8 Standards or use of linter
+- [ ] Xarray Dataset or DataArray variable naming follows 'ds' or 'da' naming

.github/workflows/antivirus.yml

@@ -0,0 +1,14 @@
+on:
+  pull_request:
+    types: [assigned, opened, synchronize, reopened, closed]
+
+jobs:
+  gitavscan:
+    runs-on: ubuntu-latest
+    name: AV scan
+    steps:
+    - uses: actions/checkout@v3
+    - name: Git AV Scan
+      uses: djdefi/gitavscan@main
+      with:
+        full: '--full'

.github/workflows/build-docs.yml

@@ -0,0 +1,52 @@
+name: build-docs
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+# This job installs dependencies, build the website, and pushes it to `gh-pages`
+jobs:
+  deploy-website:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v3
+
+      # Install dependencies
+      - name: Setup Conda Environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: docs/environment_docs.yml
+          environment-name: act-docs
+          cache-downloads: true
+
+      - name: Install ACT
+        run: |
+          pip install -e . --no-deps --force-reinstall
+      # Build the website
+      - name: Build the site
+        run: |
+          cd docs
+          make html
+        env:
+          ARM_USERNAME: ${{ secrets.ARM_USERNAME }}
+          ARM_PASSWORD: ${{ secrets.ARM_PASSWORD }}
+          AIRNOW_API: ${{ secrets.AIRNOW_API }}
+      # Push the book's HTML to github-pages
+      - name: GitHub Pages action
+        uses: peaceiris/[email protected]
+        if: github.ref == 'refs/heads/main'
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/build/html
+          cname: https://arm-doe.github.io/ACT/

.github/workflows/ci.yml

@@ -0,0 +1,73 @@
+name: Run Unit Tests CI
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+# Cancel concurrent runs
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  ARM_USERNAME: ${{ secrets.ARM_USERNAME }}
+  ARM_PASSWORD: ${{ secrets.ARM_PASSWORD }}
+  AIRNOW_API: ${{ secrets.AIRNOW_API }}
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  COVERALLS_TOKEN: ${{ secrets.COVERLALLS_REPO_TOKEN }}
+
+jobs:
+  build:
+    name: ${{ matrix.os }}-${{ matrix.python-version }}
+    if: github.repository == 'ARM-DOE/ACT'
+    runs-on: ${{ matrix.os }}-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        os: [macOS, ubuntu, Windows]
+        inlcude:
+          - os: macos-latest
+            PLAT: arm64
+            INTERFACE64: ""
+            platform: [x64]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Setup Conda Environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          create-args: python=${{ matrix.python-version }}
+          environment-file: ./continuous_integration/environment_actions.yml
+          environment-name: act_env
+
+      - name: Install ACT
+        run: |
+          python -m pip install -e . --no-deps --force-reinstall
+
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          # flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+          # Switching back to original flake
+          python -m flake8 --max-line-length=127 --ignore=F401,E402,W504,W605,F403
+      - name: Test with pytest
+        run: |
+          python -m pytest -v --mpl --cov=./ --cov-report=xml
+
+      - name: Upload code coverage to Codecov
+        uses: codecov/[email protected]
+        with:
+          file: ./coverage.xml
+          flags: unittests
+          env_vars: OS,PYTHON
+          name: codecov-umbrella
+          fail_ci_if_error: false

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,74 @@
+# 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: '42 7 * * 5'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+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://git.io/codeql-language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      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.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+    # 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/pypi-release.yml

@@ -0,0 +1,74 @@
+name: Build and Upload ACT Release to PyPI
+on:
+  release:
+    types:
+      - published
+
+jobs:
+  build-artifacts:
+    runs-on: ubuntu-latest
+    if: github.repository == 'ARM-DOE/ACT'
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v4
+        name: Install Python
+        with:
+          python-version: 3.11
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install setuptools setuptools-scm wheel twine check-manifest
+      - name: Build tarball and wheels
+        run: |
+          git clean -xdf
+          git restore -SW .
+          python -m build --sdist --wheel .
+      - name: Check built artifacts
+        run: |
+          python -m twine check dist/*
+          pwd
+          if [ -f dist/act-atmos-0.0.0.tar.gz ]; then
+            echo "❌ INVALID VERSION NUMBER"
+            exit 1
+          else
+            echo "✅ Looks good"
+          fi
+      - uses: actions/upload-artifact@v3
+        with:
+          name: releases
+          path: dist
+
+  test-built-dist:
+    needs: build-artifacts
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/setup-python@v4
+        name: Install Python
+        with:
+          python-version: "3.x"
+      - uses: actions/download-artifact@v3
+        with:
+          name: releases
+          path: dist
+      - name: List contents of built dist
+        run: |
+          ls -ltrh
+          ls -ltrh dist
+  upload-to-pypi:
+    needs: test-built-dist
+    if: github.event_name == 'release'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: releases
+          path: dist
+      - name: Publish package to PyPI
+        uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}
+          verbose: true

.gitignore

@@ -81,3 +81,23 @@ target/
 
 # Files on local computer
 *.xml
+
+# Test files downloaded locally
+**/bck_Radar_FMCW_Bright_Band/
+**/bck_Radar_FMCW_Moment/
+**/ctd_449RWP_Bright_Band/
+**/ctd_449RWP_Sub-Hour_Temp/
+**/ctd_449RWP_Sub-Hour_Wind/
+**/ctd_449RWP_Wind/
+**/ctd_915RWP_Sub-Hour_Temp/
+**/ctd_915RWP_Sub-Hour_Wind/
+**/ctd_915RWP_Temp/
+**/ctd_915RWP_Wind/
+**/ctd_GpsTrimble/
+**/ctd_Pressure/
+**/ctd_Radar_S-band_Bright_Band/
+**/ctd_Radar_S-band_Moment/
+**/kps_Radar_FMCW_Moment/
+**/BARR_DP1.00002.001/
+data/*ctd
+act/tests/data/*stats*

.pre-commit-config.yaml

@@ -0,0 +1,35 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-docstring-first
+      - id: check-json
+      - id: check-yaml
+      - id: double-quote-string-fixer
+      - id: debug-statements
+      - id: mixed-line-ending
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.3.1
+    hooks:
+      - id: pyupgrade
+        args:
+          - '--py38-plus'
+
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+      - id: black
+      - id: black-jupyter
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort