From bc0a663b052616e3b2359a2397fc5dd0b8ccb8a6 Mon Sep 17 00:00:00 2001
From: "Karl N. Kappler" <magnetotellurics@gmail.com>
Date: Fri, 16 Aug 2024 15:22:54 -0700
Subject: [PATCH] Add gh actions tests

These were suppresed during manuscript development to conserve energy.
We are re-enabling them so that the `joss` release can be shown
to pass tests with the current mt_metadata, and mth5 releases.

The tests.yml pins mt_metadata to 0.3.7, and mth5 to 0.4.4

- also updated path to ipynb moved from example to tutorial in yml
  - (and updated the filename)
---
 .github/workflows/tests.yml                   | 103 ++++++++++++++++++
 ...ynb => process_cas04_single_station.ipynb} |   0
 2 files changed, 103 insertions(+)
 create mode 100644 .github/workflows/tests.yml
 rename docs/tutorials/{process_cas04_single_station_h5.ipynb => process_cas04_single_station.ipynb} (100%)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
new file mode 100644
index 00000000..5bd03033
--- /dev/null
+++ b/.github/workflows/tests.yml
@@ -0,0 +1,103 @@
+name: Testing
+
+on:
+  push:
+    branches:
+      - '*'
+  pull_request:
+    branches:
+      - '*'
+jobs:
+  setup-build:
+    name: Ex1 (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version: [3.8, 3.9, "3.10", "3.11"]
+#        python-version: ["3.10", ] 
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Setup Miniconda
+      uses: conda-incubator/setup-miniconda@v2.1.1
+      with:
+        activate-environment: aurora-test
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install Env
+      run: |
+        python --version
+        conda install -c conda-forge pytest pytest-cov certifi">=2017.4.17" pandoc
+        pip install -r requirements-dev.txt
+        pip install mt_metadata==0.3.7
+        pip install mth5==0.4.4
+
+    - name: Install Our Package
+      run: |
+        pip install -e .
+        conda list
+        
+    - name: Install Jupyter and dependencies
+      run: |
+        pip install jupyter
+        pip install ipykernel
+        python -m ipykernel install --user --name aurora-test
+        # Install any other dependencies you need
+
+    - name: Execute Jupyter Notebooks
+      run: |
+        jupyter nbconvert --to notebook --execute docs/examples/dataset_definition.ipynb
+        jupyter nbconvert --to notebook --execute docs/examples/operate_aurora.ipynb
+        jupyter nbconvert --to notebook --execute docs/tutorials/pole_zero_fitting/lemi_pole_zero_fitting_example.ipynb
+        jupyter nbconvert --to notebook --execute docs/tutorials/processing_configuration.ipynb
+        jupyter nbconvert --to notebook --execute docs/tutorials/process_cas04_single_station.ipynb
+        jupyter nbconvert --to notebook --execute docs/tutorials/synthetic_data_processing.ipynb
+        jupyter nbconvert --to notebook --execute tests/test_run_on_commit.ipynb
+        # Replace "notebook.ipynb" with your notebook's filename
+
+#    - name: Commit changes (if any)
+#      run: |
+#        git config --local user.email "action@github.com"
+#        git config --local user.name "GitHub Action"
+#        git commit -a -m "Execute Jupyter notebook"
+#        git push
+#      if: ${{ success() }}
+
+
+    - name: Run Tests
+      run: |
+        # pytest -s -v tests/synthetic/test_fourier_coefficients.py
+        # pytest -s -v tests/test_general_helper_functions.py 
+        pytest -s -v --cov=./ --cov-report=xml --cov=aurora
+
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        fail_ci_if_error: false
+
+
+    - name: Build Doc
+      if: ${{ (github.ref == 'refs/heads/main') && (matrix.python-version == '3.8')}}
+      run: |
+        cd docs
+        make html
+        cd ..
+
+    - name: GitHub Pages
+      if: ${{ (github.ref == 'refs/heads/main') && (matrix.python-version == '3.8')}}
+      uses: crazy-max/ghaction-github-pages@v2.5.0
+      with:
+        build_dir: docs/_build/html
+        # Write the given domain name to the CNAME file
+        # fqdn: aurora.simpeg.xyz
+        # Allow Jekyll to build your site
+        jekyll: false # optional, default is true
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/docs/tutorials/process_cas04_single_station_h5.ipynb b/docs/tutorials/process_cas04_single_station.ipynb
similarity index 100%
rename from docs/tutorials/process_cas04_single_station_h5.ipynb
rename to docs/tutorials/process_cas04_single_station.ipynb