Clean repo for test.pypi release

.github/workflows/main.yml

@@ -0,0 +1,81 @@
+name: Test and publish to PyPI
+
+on:
+  push:
+    branches: [ main ]
+    tags: [ 'v*.*.*' ]
+  pull_request:
+    branches: [ main ]
+  release:
+    types: [ created ]
+
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: 'Set up Python ${{matrix.python-version}}'
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{matrix.python-version}}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+
+    - name: Install my package
+      run: |
+        python -m pip install .
+
+    - name: Install test dependencies
+      run: |
+        pip install flake8 pytest coverage
+
+    - name: Test with pytest
+      run: |
+        coverage run -m pytest
+
+    - name: Clean up coverage data
+      run: |
+        # This is a workaround for the fact that the `[coverage:paths]` section
+        # of `setup.cfg` is not actually applies until we run `combine`; so we
+        # rename the report such that we can then "combine" it.
+        mv .coverage .coverage.hack
+        coverage combine
+        coverage report
+  
+    - uses: codecov/codecov-action@v1
+
+  deploy:
+    needs: test
+    runs-on: ubuntu-latest
+    name: deploy
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python '3.9'
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.9'
+    - name: "Install"
+      run: |
+        python -m pip install --upgrade pip;
+        python -m pip install build
+        pip install setuptools wheel twine
+        python setup.py sdist bdist_wheel
+    - uses: actions/upload-artifact@v2
+      with:
+        name: dist
+        path: dist
+
+    - name: Publish to PyPI (on tag)
+      if: startsWith(github.ref, 'refs/tags/v')
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.pypi_token }}

.gitignore

@@ -1,13 +1,12 @@
 .DS_Store
 __pycache__
-GEOROC_minerals/
-backup/
-working/
-Validation_Data/LEPR_Penny/
-Validation_Data/GEOROC_validationdata.csv
-MIN_ML_Cluster/scs76-31450.log
-MIN_ML_Cluster/scs76-31497.log
-MIN_ML_Cluster/nn_parametermatrix/nkfcv_test_saveall_test_reports.pkl
-MIN_ML_Cluster/nn_parametermatrix/nkfcv_test_saveall_train_reports.pkl
-MIN_ML_Cluster/nkfcv_test_saveall_results.npz
-georoc_err.csv
+*.ipynb
+*.icloud
+/GEOROC_minerals/
+/backup/
+/working/
+/Validation_Data/LEPR_Penny/
+/Validation_Data/GEOROC_validationdata.csv
+/Training_Data/Mineral/
+/MIN_ML_Cluster/t
+/parametermatrix_autoencoder/features/

.readthedocs.yaml

@@ -0,0 +1,18 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+# Build documentation in the "docs/" directory with Sphinx
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "mambaforge-22.9"
+
+sphinx:
+  configuration: docs/conf.py
+  # Fail on all warnings to avoid broken references
+  fail_on_warning: true
+
+conda: 
+  environment: docs/rtd_environment.yml