Testing updates (#133)

update the environment file, break up testing

.github/workflows/tests.yml

@@ -11,29 +11,33 @@ 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]
+        python-version: ["3.10"]
+        test_file: ["tests/test_dcip.py", "tests/test_em.py", "tests/test_gpr.py", "tests/test_mag.py", "tests/test_seismic.py"]
 
     steps:
     - uses: actions/checkout@v2
     - name: Setup Conda
-      uses: s-weigand/setup-conda@v1
+      uses: conda-incubator/setup-miniconda@v2
       with:
-        update-conda: true
-        conda-channels: conda-forge
+        auto-update-conda: true
+        activate-environment: geosci-labs
+        channels: conda-forge
+        environment-file: environment.yml
         python-version: ${{ matrix.python-version }}
-
     - name: Install Env
-      shell: bash
       run: |
-        python --version
-        conda env create -f environment-dev.yml
-
+        conda info
+        conda config --show
+        conda install -y pytest
+        pip install testipynb
+        conda list
     - name: Run Tests
-      shell: bash
       run: |
-        source activate geosci-labs
-        pytest .
+        pytest -v ${{ matrix.test_file }}

environment.yml

@@ -1,37 +1,23 @@
-name: e350
+name: geosci-labs
 
 channels:
   - conda-forge
 dependencies:
-  - mamba
-  - notebook
-  - jupyterhub
-  - jupyterlab
-  - bokeh
-  - conda-lock
-  - ghp-import
-  - git
-  - jupytext
-  - jupyter-resource-usage
-  - matplotlib=3.4.3
-  - numpy=1.21
-  - nbgitpuller
-  - pandas
-  - pip
-  - pillow
-  - python=3.9
+  - cvxopt
+  - deepdish
   - discretize
-  - empymod
-  - ipykernel
-  - ipywidgets=7.7.1
-  - mkl
-  - nb_conda_kernels 
+  - empymod=2.0.0
+  - ipywidgets>=0.6.0
+  - jupyter
+  - matplotlib<3.5
+  - mkl>=2021.3.0
+  - numpy
+  - Pillow
+  - pip
   - pymatsolver
-  - qtconsole
-  - qtpy
+  - python=3.10
+  - requests
   - scipy
-  - scikit-learn
-  - discretize=0.8.0
-  - SimPEG=0.17.0
+  - SimPEG
   - pip:
     - git+https://github.com/geoscixyz/geosci-labs

setup.sh

@@ -9,7 +9,7 @@ mamba env create -f environment.yml --prefix ./envs
 
 # activate enviornment
 mamba activate ./envs
-python -m ipykernel install --user --name=e350
+python -m ipykernel install --user --name=geosci
 
 # success
 echo "Success!"

tests/test_dcip.py

@@ -0,0 +1,28 @@
+import unittest
+import os
+import testipynb
+
+TESTDIR = os.path.abspath(__file__)
+
+NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "dcip"])
+Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+TestsDC = Test.get_tests()
+
+# NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "em"])
+# Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+# TestsEM = Test.get_tests()
+
+# NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "gpr"])
+# Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+# TestsGPR = Test.get_tests()
+
+# NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "mag"])
+# Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+# TestsMag = Test.get_tests()
+
+# NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "seismic"])
+# Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+# TestsSeis = Test.get_tests()
+
+if __name__ == "__main__":
+    unittest.main()

tests/test_em.py

@@ -0,0 +1,28 @@
+import unittest
+import os
+import testipynb
+
+TESTDIR = os.path.abspath(__file__)
+
+# NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "dcip"])
+# Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+# TestsDC = Test.get_tests()
+
+NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "em"])
+Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+TestsEM = Test.get_tests()
+
+# NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "gpr"])
+# Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+# TestsGPR = Test.get_tests()
+
+# NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "mag"])
+# Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+# TestsMag = Test.get_tests()
+
+# NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "seismic"])
+# Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+# TestsSeis = Test.get_tests()
+
+if __name__ == "__main__":
+    unittest.main()

tests/test_gpr.py

@@ -0,0 +1,28 @@
+import unittest
+import os
+import testipynb
+
+TESTDIR = os.path.abspath(__file__)
+
+# NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "dcip"])
+# Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+# TestsDC = Test.get_tests()
+
+# NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "em"])
+# Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+# TestsEM = Test.get_tests()
+
+NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "gpr"])
+Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+TestsGPR = Test.get_tests()
+
+# NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "mag"])
+# Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+# TestsMag = Test.get_tests()
+
+# NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "seismic"])
+# Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+# TestsSeis = Test.get_tests()
+
+if __name__ == "__main__":
+    unittest.main()

tests/test_mag.py

@@ -0,0 +1,28 @@
+import unittest
+import os
+import testipynb
+
+TESTDIR = os.path.abspath(__file__)
+
+# NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "dcip"])
+# Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+# TestsDC = Test.get_tests()
+
+# NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "em"])
+# Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+# TestsEM = Test.get_tests()
+
+# NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "gpr"])
+# Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+# TestsGPR = Test.get_tests()
+
+NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "mag"])
+Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+TestsMag = Test.get_tests()
+
+# NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "seismic"])
+# Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+# TestsSeis = Test.get_tests()
+
+if __name__ == "__main__":
+    unittest.main()

tests/test_seismic.py

@@ -0,0 +1,28 @@
+import unittest
+import os
+import testipynb
+
+TESTDIR = os.path.abspath(__file__)
+
+# NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "dcip"])
+# Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+# TestsDC = Test.get_tests()
+
+# NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "em"])
+# Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+# TestsEM = Test.get_tests()
+
+# NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "gpr"])
+# Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+# TestsGPR = Test.get_tests()
+
+# NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "mag"])
+# Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+# TestsMag = Test.get_tests()
+
+NBDIR = os.path.sep.join(TESTDIR.split(os.path.sep)[:-2] + ["notebooks", "seismic"])
+Test = testipynb.TestNotebooks(directory=NBDIR, timeout=2100)
+TestsSeis = Test.get_tests()
+
+if __name__ == "__main__":
+    unittest.main()