merge

.github/workflows/python-package.yml

@@ -13,31 +13,63 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: [3.9]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install system dependencies
-      run: |
-        sudo apt-get update && sudo apt-get install -y libproj-dev proj-data proj-bin libgeos-dev
-    - name: Install python dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
-        python -m pip install cython numpy
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
-      run: |
-        pytest
+
+      - uses: actions/checkout@v2
+
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniconda-version: "latest"
+          channels: bioconda, conda-forge, defaults
+          use-only-tar-bz2: true  # IMPORTANT: This needs to be set for caching to work properly!
+          auto-update-conda: true
+          auto-activate-base: true
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update && sudo apt-get install -y libproj-dev proj-data proj-bin libgeos-dev
+
+      - name: Create conda environment
+        run: |
+          conda init bash
+          conda create -n myenv python=${{ matrix.python-version }}
+
+      - name: Activate conda environment
+        run: |
+          conda activate myenv
+          conda config --set always_yes yes --set changeps1 no
+          
+      - name: Update conda environment
+        run: |
+          conda update --name base -q conda
+
+      - name: Install Python dependencies with Conda
+        run: |
+          conda install cartopy
+
+      - name: Install python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install flake8 pytest
+          python -m pip install cython numpy
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
+      - name: Lint with flake8
+        run: |
+          # 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
+        run: |
+          pytest

requirements.txt

@@ -9,7 +9,7 @@ scipy
 Shapely
 seaborn
 setuptools
-cartopy<0.20.0
+cartopy
 typing_extensions
 tables
 pydantic

test/test_model.py

@@ -140,7 +140,7 @@ def test_minimal_example(self):
         p_global = np.full(shape=(1, n_features, n_states), fill_value=0.5)
         source = np.zeros((n_objects, n_features, 2), dtype=bool)
         sample = Sample.from_numpy_arrays(
-            clusters=np.ones((1, n_objects),  dtype=np.bool),
+            clusters=np.ones((1, n_objects),  dtype=bool),
             weights=broadcast_weights([0.5, 0.5], n_features),
             cluster_effect=p_cluster,
             confounding_effects={"universal": p_global},