Merge pull request #138 from rcjackson/nightly_build

ADD: Nightly builds

Author: rcjackson

.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@v5
+    - name: Git AV Scan
+      uses: djdefi/gitavscan@main
+      with:
+        full: '--full'

.github/workflows/build-docs.yml

@@ -16,27 +16,28 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v5
 
       # Install dependencies
       - name: Setup Conda Environment
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           environment-file: doc/environment_docs.yml
           activate-environment: pydda-docs
           auto-activate-base: false
           mamba-version: '*'
           use-mamba: true
-          miniforge-variant: Mambaforge
 
       - name: Install PyDDA
         run: |
           pip install -e .
+
       # Build the website
       - name: Build the site
         run: |
           cd doc
           make html
+
       # Push the book's HTML to github-pages
       - name: GitHub Pages action
         uses: peaceiris/[email protected]

.github/workflows/codeql.yml

@@ -0,0 +1,77 @@
+# 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: '39 13 * * 2'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    timeout-minutes: ${{ (matrix.language == 'swift' && 120) || 360 }}
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: ['python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby', 'swift' ]
+        # Use only 'java' to analyze code written in Java, Kotlin or both
+        # Use only 'javascript' to analyze code written in JavaScript, TypeScript or both
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v5
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, Go, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v3
+
+    # ℹ️  Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+    #   If the Autobuild fails above, remove it and uncomment the following three lines.
+    #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+    # - run: |
+    #     echo "Run, Build Application using script"
+    #     ./location_of_script_within_repo/buildscript.sh
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:${{matrix.language}}"

.github/workflows/linting.yml

@@ -23,9 +23,9 @@ jobs:
     if: ${{ needs.pre-job.outputs.should_skip != 'true' }}
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.9.1
+        uses: styfle/cancel-workflow-action@0.12.1
         with:
           access_token: ${{ github.token }}
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
-      - uses: pre-commit/action@v2.0.3
+      - uses: actions/checkout@v5
+      - uses: actions/setup-python@v6
+      - uses: pre-commit/action@v3.0.1

.github/workflows/python-package-conda.yml

@@ -5,6 +5,8 @@ on:
     branches: [ main ]
   pull_request:
     branches: [ main ]
+  schedule:
+    - cron: '0 2 * * *'  # Runs at 2:00 AM UTC every day
 
 jobs:
    build:
@@ -17,7 +19,7 @@ jobs:
      strategy:
         fail-fast: false
         matrix:
-          python-version: ["3.10", "3.11", "3.12"]
+          python-version: ["3.10", "3.11", "3.12", "3.13"]
           os: [macOS, ubuntu]
           inlcude:
             - os: macos-latest
@@ -26,25 +28,40 @@ jobs:
               platform: [x64]
 
      steps:
-      - uses: actions/checkout@v2
-      - name: Setup Conda Environment
-        uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v5
+      - name: Install Conda environment with Micromamba
+        uses: mamba-org/setup-micromamba@v2.0.6
         with:
-          python-version: ${{ matrix.python-version }}
-          environment-file: ./continuous_integration/environment-actions.yml
-          activate-environment: pydda_env
-          auto-activate-base: False
-          mamba-version: '*'
-          use-mamba: true
-          miniforge-variant: Mambaforge
+          environment-file: continuous_integration/environment-actions.yml
+          micromamba-version: '2.0.0-0'
+          environment-name: pydda-env
+          cache-downloads: false
+
+      - name: Install PyDDA
+        shell: bash -l {0}
+        run: |
+          python -m pip install -e . --no-deps --force-reinstall
+
       - name: Lint with flake8
+        shell: bash -l {0}
         run: |
-           conda install flake8
+           pip install flake8
            # 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
+
       - name: Test with pytest
+        shell: bash -l {0}
         run: |
-           conda install pytest
-           pytest
+           pip install pytest
+           python -m pytest -v --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

doc/environment_docs.yml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python>=3.10
+  - python
   - pip
   - arm_pyart
   - cython
@@ -12,7 +12,6 @@ dependencies:
   - pytest-mpl
   - pytest-cov
   - cartopy
-  - pyproj=3.3
   - cfgrib
   - eccodes
   - sphinx