CI: make CI run

.ci/37.yaml → .ci/310.yaml

@@ -2,7 +2,7 @@ name: test
 channels:
   - conda-forge
 dependencies:
-  - python=3.7
+  - python=3.10
   - libpysal
   - numpy>=1.3
   - pandas>=1

.ci/39-DEV.yaml → .ci/311-DEV.yaml

@@ -2,7 +2,7 @@ name: test
 channels:
   - conda-forge
 dependencies:
-  - python=3.9
+  - python=3.11
   - libpysal
   - shapely
   - numpy>=1.3

.ci/38.yaml → .ci/311.yaml

@@ -2,7 +2,7 @@ name: test
 channels:
   - conda-forge
 dependencies:
-  - python=3.8
+  - python=3.11
   - libpysal
   - numpy>=1.3
   - pandas>=1

.github/workflows/unittest.yml

@@ -15,47 +15,38 @@
      timeout-minutes: 90
      strategy:
        matrix:
-         os: ['macos-latest', 'ubuntu-latest', 'windows-latest']
-         environment-file: [.ci/37.yaml, .ci/38.yaml, .ci/39.yaml]
+         os: ['ubuntu-latest']
+         environment-file: [.ci/39.yaml, .ci/310.yaml, .ci/311.yaml, .ci/311-DEV.yaml]
          include:
-           - environment-file: .ci/39-DEV.yaml
-             os: ubuntu-latest
-
+           - environment-file: .ci/311.yaml
+             os: macos-latest
+           - environment-file: .ci/311.yaml
+             os: windows-latest
+       fail-fast: false
+     defaults:
+       run:
+         shell: bash -l {0}
+
      steps:
        - name: checkout repo
-         uses: actions/checkout@v2
-       
+         uses: actions/checkout@v4
+
        - name: setup micromamba
-         uses: mamba-org/provision-with-micromamba@main
+         uses: mamba-org/setup-micromamba@v1
          with:
            environment-file: ${{ matrix.environment-file }}
            micromamba-version: 'latest'
        - name: install spglm via pip
-         shell: bash -l {0}
-         run: pip install --upgrade git+https://github.com/pysal/spglm.git@master
-
+         run: pip install --upgrade --no-deps git+https://github.com/pysal/spglm.git@main
+
        - name: install spreg via pip
-         shell: bash -l {0}
-         run: pip install spreg 
-
+         run: pip install spreg
+
        - name: install bleeding edge libpysal (only Ubuntu / Python 3.9)
-         shell: bash -l {0}
-         run: pip install git+https://github.com/pysal/libpysal.git@master
+         run: pip install git+https://github.com/pysal/libpysal.git@main
          if: matrix.os == 'ubuntu-latest' && contains(matrix.environment-file, 'DEV')
-       
+
        - name: run tests - bash
-         shell: bash -l {0}
          run: pytest -v mgwr --cov=mgwr --cov-report=xml --timeout=300
-         if: matrix.os != 'windows-latest'
-
-       - name: run tests - powershell
-         shell: powershell
-         run: pytest -v mgwr --cov=mgwr --cov-report=xml --timeout=300
-         if: matrix.os == 'windows-latest'
-
-       - name: codecov
-         uses: codecov/codecov-action@v2
-         with:
-           token: ${{ secrets.CODECOV_TOKEN }}
-           file: ./coverage.xml
-           name: spot-codecov
+
+       - uses: codecov/codecov-action@v3

mgwr/tests/test_gwr.py

@@ -299,12 +299,12 @@ def test_MGWR(self):
         np.testing.assert_allclose(rslt_hat.R, rslt_hat_2.R, atol=1e-07)
         np.testing.assert_allclose(
             rslt_hat.S.dot(std_y).flatten(), self.MGWR.predy, atol=1e-07)
-            
+
         exact_rslt = model.exact_fit()
-        
+
         np.testing.assert_allclose(exact_rslt.R, rslt_hat.R,atol=1e-04)
         np.testing.assert_allclose(exact_rslt.params, rslt_hat.params,atol=1e-04)
-        
+
         varnames = ['X0', 'X1', 'X2', 'X3']
 
         # def suffixed(x):
@@ -366,13 +366,13 @@ def test_MGWR(self):
             rslt.filter_tvals(),
             self.MGWR[[s + "_filter_tvalues" for s in varnames]].values,
             atol=1e-07)
-            
+
         np.testing.assert_allclose(rslt.get_bws_intervals(selector),
                                    [(92.0, 99.0), (99.0, 101.0), (99.0, 136.0), (122.0, 158.0)])
-        
+
         np.testing.assert_allclose(rslt.local_collinearity()[0].flatten(),
                                    self.MGWR.local_collinearity, atol=1e-07)
-    
+
     def test_Prediction(self):
         coords = np.array(self.coords)
         index = np.arange(len(self.y))
@@ -502,7 +502,7 @@ class TestGWRPoisson(unittest.TestCase):
     def setUp(self):
         data_path = os.path.join(
             os.path.dirname(__file__), 'tokyo/Tokyomortality.csv')
-        data = io.open(data_path, mode='Ur')
+        data = io.open(data_path, mode='r')
         self.coords = list(
             zip(data.by_col('X_CENTROID'), data.by_col('Y_CENTROID')))
         self.y = np.array(data.by_col('db2564')).reshape((-1, 1))

mgwr/tests/test_parallel.py

@@ -396,7 +396,7 @@ class TestGWRPoissonPool(unittest.TestCase):
     def setUp(self):
         data_path = os.path.join(
             os.path.dirname(__file__), 'tokyo/Tokyomortality.csv')
-        data = io.open(data_path, mode='Ur')
+        data = io.open(data_path, mode='r')
         self.coords = list(
             zip(data.by_col('X_CENTROID'), data.by_col('Y_CENTROID')))
         self.y = np.array(data.by_col('db2564')).reshape((-1, 1))

mgwr/tests/test_sel_bw.py

@@ -189,7 +189,7 @@ class TestGWRSelBWPoisson(unittest.TestCase):
     def setUp(self):
         data_path = os.path.join(
             os.path.dirname(__file__), 'tokyo/Tokyomortality.csv')
-        data = io.open(data_path, mode='Ur')
+        data = io.open(data_path, mode='r')
         self.coords = list(
             zip(data.by_col('X_CENTROID'), data.by_col('Y_CENTROID')))
         self.y = np.array(data.by_col('db2564')).reshape((-1, 1))