🚚 reshuffle for lfs

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

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+name: Python Package using Conda
+on: [push]
+
+jobs:
+  test:
+    name: Test python ${{ matrix.python-version }} on ${{ matrix.os }}
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macOS-latest]
+        python-version: [3.7]
+    steps:
+      - uses: actions/checkout@v2
+        with:
+         submodules: recursive
+      - name: install mamba
+        uses: mamba-org/provision-with-micromamba@main
+        with:
+          environment-file: CNN.yml
+          environment-name: CNN
+      - name: Install test packages
+        shell: bash -l {0}
+        run: |
+          pip install pytest nbconvert nbformat
+      - name: which python
+        shell: bash -l {0}
+        run: |
+          which python
+      - name: Test with pytest
+        shell: bash -l {0}
+        run: |
+          pytest .github/workflows/test_CNN_notebooks.py

.github/workflows/test_CNN_notebooks.py

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+"""
+Tests for checking that all Jupyter notebooks in repository execute without errors.
+Based on https://github.com/mcullan/jupyter-actions/blob/master/test/test_notebooks.py
+Leif Denby - MIT License 2021
+"""
+import os
+import subprocess
+import pytest
+from pathlib import Path
+
+import nbformat
+from nbconvert.preprocessors import ExecutePreprocessor
+
+TEST_DIR = os.path.dirname(os.path.abspath(__file__))
+PARENT_DIR = os.path.join(TEST_DIR, "../")
+
+
+def _find_notebooks():
+    # Get all files included in the git repository
+    git_files = (
+        subprocess.check_output(
+            "git ls-tree --full-tree --name-only -r HEAD", shell=True
+        )
+        .decode("utf-8")
+        .splitlines()
+    )
+
+    # Get just the notebooks from the git files
+    notebooks_files = [Path(fn) for fn in git_files if fn.endswith("CNN_Volcanic_deformation_test.ipynb")]
+
+    # remove all notebooks that haven't been checked
+    notebooks_files = [p for p in notebooks_files if p.parent.name != "unchecked"]
+    return [str(p) for p in notebooks_files]
+
+
+@pytest.mark.parametrize("notebook_filename", _find_notebooks())
+def test_notebook(notebook_filename, html_directory="notebook-html"):
+    """
+    Checks if an IPython notebook runs without error from start to finish.
+    """
+    with open(notebook_filename) as f:
+        nb = nbformat.read(f, as_version=4)
+
+    ep = ExecutePreprocessor(timeout=600)
+
+    # Check that the notebook runs
+    ep.preprocess(nb, {"metadata": {"path": Path(notebook_filename).parent }})

.github/workflows/windows_python_package.yml

@@ -0,0 +1,33 @@
+name: Python Package using Conda
+on: [push]
+
+jobs:
+  test:
+    name: Test python ${{ matrix.python-version }} on ${{ matrix.os }}
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [windows-latest]
+        python-version: [3.7]
+    steps:
+      - uses: actions/checkout@v2
+        with:
+         submodules: recursive
+      - name: install mamba
+        uses: mamba-org/provision-with-micromamba@main
+        with:
+          environment-file: CNN_windows.yml
+          environment-name: CNN
+      - name: Install test packages
+        shell: bash -l {0}
+        run: |
+          pip install pytest nbconvert nbformat
+      - name: which python
+        shell: bash -l {0}
+        run: |
+          which python
+      - name: Test with pytest
+        shell: bash -l {0}
+        run: |
+          pytest .github/workflows/test_CNN_notebooks.py

.gitignore

@@ -0,0 +1,7 @@
+ConvolutionalNeuralNetworks/**/*.npz
+**/.ipynb_checkpoints/
+**/__pycache__
+ConvolutionalNeuralNetworks/data/real/
+ConvolutionalNeuralNetworks/data/train_full_model/
+ConvolutionalNeuralNetworks/data/train_fully_connected_model/
+ConvolutionalNeuralNetworks/vgg16_2head.png