run in conda environment

.github/workflows/run-unit-tests.yml

@@ -12,33 +12,63 @@ on:
 jobs:
   test:
     runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
         os: [ macos-latest, ubuntu-latest, windows-latest ]
+        python-version: ['3.8', '3.9', '3.10', '3.11']
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+    - uses: actions/checkout@v3  # for the test data
+    - uses: conda-incubator/setup-miniconda@v2
       with:
         python-version: ${{ matrix.python-version }}
+        channels: conda-forge
+        channel-priority: true
+        activate-environment: test
+        mamba-version: "*"
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        python -m pip install flake8 pytest pytest-cov
-        python -m pip install rasterio "opencv-python-headless<4.8" numpy click tqdm pyyaml
-        python -m pip list
-    - 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
-      timeout-minutes: 5
+        mamba info
+        mamba list
+        mamba install -c conda-forge rasterio opencv numpy click tqdm pyyaml pytest pytest-cov
+        mamba list
+    - name: Run unit tests
       run: |
         python -m pytest --cov=simple_ortho --cov-report=term-missing --cov-report=xml:coverage.xml ./tests
+
+#jobs:
+#  test:
+#    runs-on: ${{ matrix.os }}
+#    strategy:
+#      fail-fast: false
+#      matrix:
+#        python-version: ['3.8', '3.9', '3.10', '3.11']
+#        os: [ macos-latest, ubuntu-latest, windows-latest ]
+#    steps:
+#    - uses: actions/checkout@v3
+#    - name: Set up Python ${{ matrix.python-version }}
+#      uses: actions/setup-python@v4
+#      with:
+#        python-version: ${{ matrix.python-version }}
+#    - name: Install dependencies
+#      run: |
+#        python -m pip install --upgrade pip
+#        python -m pip install flake8 pytest pytest-cov
+#        python -m pip install rasterio "opencv-python-headless<4.8" numpy click tqdm pyyaml
+#        python -m pip list
+#    - 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
+#      timeout-minutes: 5
+#      run: |
+#        python -m pytest --cov=simple_ortho --cov-report=term-missing --cov-report=xml:coverage.xml ./tests
 #    - name: Upload coverage
 #      uses: codecov/codecov-action@v3
 #      with:

tests/conftest.py

@@ -298,31 +298,31 @@ def webmerc_egm2008_crs() -> str:
 @pytest.fixture(scope='session')
 def rgb_byte_src_file(tmpdir_factory: pytest.TempdirFactory, im_size: Tuple) -> Path:
     """ An RGB byte checkerboard image with no CRS. """
-    src_filename = Path(tmpdir_factory.mktemp('data').join('rgb_byte_src.tif'))
+    src_filename = Path(tmpdir_factory.mktemp('data')).joinpath('rgb_byte_src.tif')
     create_src(src_filename, im_size, dtype='uint8', count=3)
     return src_filename
 
 
 @pytest.fixture(scope='session')
 def rgb_float_src_file(tmpdir_factory: pytest.TempdirFactory, im_size: Tuple) -> Path:
     """ An RGB float32 checkerboard image with no CRS. """
-    src_filename = Path(tmpdir_factory.mktemp('data').join('rgb_float_src.tif'))
+    src_filename = Path(tmpdir_factory.mktemp('data')).joinpath('rgb_float_src.tif')
     create_src(src_filename, im_size, dtype='float32', count=3)
     return src_filename
 
 
 @pytest.fixture(scope='session')
 def float_src_file(tmpdir_factory: pytest.TempdirFactory, im_size: Tuple) -> Path:
     """ A single band float64 checkerboard image with no CRS. """
-    src_filename = Path(tmpdir_factory.mktemp('data').join('float_src.tif'))
+    src_filename = Path(tmpdir_factory.mktemp('data')).joinpath('float_src.tif')
     create_src(src_filename, im_size, dtype='float32', count=1)
     return src_filename
 
 
 @pytest.fixture(scope='session')
 def rgb_byte_utm34n_src_file(tmpdir_factory: pytest.TempdirFactory, pinhole_camera, utm34n_crs) -> Path:
     """ An RGB byte checkerboard image with UTM zone 34N CRS and bounds 100m below `pinhole_camera`. """
-    src_filename = Path(tmpdir_factory.mktemp('data').join('rgb_byte_src.tif'))
+    src_filename = Path(tmpdir_factory.mktemp('data')).joinpath('rgb_byte_src.tif')
     create_src(src_filename, pinhole_camera._im_size, dtype='uint8', count=3, camera=pinhole_camera, crs=utm34n_crs)
     return src_filename
 
@@ -333,7 +333,7 @@ def float_utm34n_dem_file(tmpdir_factory: pytest.TempdirFactory, pinhole_camera,
     A 2 band float DEM file in UTM zone 34N with no vertical datum.
     Band 1 is a sinusoidal surface, and band 2, a planar surface.
     """
-    filename = Path(tmpdir_factory.mktemp('data').join('float_utm34n_dem.tif'))
+    filename = Path(tmpdir_factory.mktemp('data')).joinpath('float_utm34n_dem.tif')
     create_dem(filename, pinhole_camera, utm34n_crs, resolution=_dem_resolution, dtype='float32')
     return filename
 
@@ -344,7 +344,7 @@ def float_utm34n_wgs84_dem_file(tmpdir_factory: pytest.TempdirFactory, pinhole_c
     A 2 band float DEM file in UTM zone 34N with WGS84 ellipsoid vertical datum.
     Band 1 is a sinusoidal surface, and band 2, a planar surface.
     """
-    filename = Path(tmpdir_factory.mktemp('data').join('float_utm34n_wgs84_dem.tif'))
+    filename = Path(tmpdir_factory.mktemp('data')).joinpath('float_utm34n_wgs84_dem.tif')
     create_dem(filename, pinhole_camera, utm34n_wgs84_crs, resolution=_dem_resolution, dtype='float32')
     return filename
 
@@ -355,7 +355,7 @@ def float_utm34n_egm96_dem_file(tmpdir_factory: pytest.TempdirFactory, pinhole_c
     A 2 band float DEM file in UTM zone 34N with EGM96 geoid vertical datum.
     Band 1 is a sinusoidal surface, and band 2, a planar surface.
     """
-    filename = Path(tmpdir_factory.mktemp('data').join('float_utm34n_egm96_dem.tif'))
+    filename = Path(tmpdir_factory.mktemp('data')).joinpath('float_utm34n_egm96_dem.tif')
     create_dem(filename, pinhole_camera, utm34n_egm96_crs, resolution=_dem_resolution, dtype='float32')
     return filename
 
@@ -366,7 +366,7 @@ def float_wgs84_wgs84_dem_file(tmpdir_factory: pytest.TempdirFactory, pinhole_ca
     A 2 band float DEM file in WGS84 with WGS84 ellipsoid vertical datum.
     Band 1 is a sinusoidal surface, and band 2, a planar surface.
     """
-    filename = Path(tmpdir_factory.mktemp('data').join('float_wgs84_wgs84_dem.tif'))
+    filename = Path(tmpdir_factory.mktemp('data')).joinpath('float_wgs84_wgs84_dem.tif')
     create_dem(
         filename, pinhole_camera, utm34n_wgs84_crs, resolution=_dem_resolution, dtype='float32',
         dem_crs='EPSG:4326+4326'