Fix pip install and add new tests (#559)

.github/workflows/pip-checks.yml

@@ -0,0 +1,49 @@
+# This workflow checks that pip installation works to import the package (tests are in python-tests.yml)
+
+name: pip-install
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  test:
+    name: ${{ matrix.os }}, python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.9", "3.10", "3.11"]
+
+    # Run all shells using bash (including Windows)
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      # We initiate the environment empty
+      - name: Initiate empty environment
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          auto-update-conda: true
+          use-mamba: true
+          channel-priority: strict
+          activate-environment: xdem-pip
+          python-version:
+
+      # Use pip install
+      - name: Install project
+        run: |
+          mamba install pip
+          pip install -e .
+
+      # Check import works
+      - name: Check import works with base environment
+        run: python -c "import xdem"

dev-environment.yml

@@ -13,7 +13,7 @@ dependencies:
   - tqdm
   - scikit-image=0.*
   - scikit-gstat>=1.0,<1.1
-  - geoutils=0.1.7
+  - geoutils=0.1.8
 
   # Development-specific, to mirror manually in setup.cfg [options.extras_require].
   - pip

environment.yml

@@ -13,7 +13,7 @@ dependencies:
   - tqdm
   - scikit-image=0.*
   - scikit-gstat>=1.0,<1.1
-  - geoutils=0.1.7
+  - geoutils=0.1.8
   - pip
 
    # To run CI against latest GeoUtils

requirements.txt

@@ -11,5 +11,5 @@ scipy>=1.0,<1.13
 tqdm
 scikit-image==0.*
 scikit-gstat>=1.0,<1.1
-geoutils==0.1.7
+geoutils==0.1.8
 pip

tests/test_misc.py

@@ -118,8 +118,8 @@ def useless_func() -> int:
     def test_diff_environment_yml(self, capsys) -> None:  # type: ignore
 
         # Test with synthetic environment
-        env = {"dependencies": ["python==3.9", "numpy", "fiona"]}
-        devenv = {"dependencies": ["python==3.9", "numpy", "fiona", "opencv"]}
+        env = {"dependencies": ["python==3.9", "numpy", "pandas"]}
+        devenv = {"dependencies": ["python==3.9", "numpy", "pandas", "opencv"]}
 
         # This should print the difference between the two
         xdem.misc.diff_environment_yml(env, devenv, input_dict=True, print_dep="conda")
@@ -134,8 +134,8 @@ def test_diff_environment_yml(self, capsys) -> None:  # type: ignore
         captured = capsys.readouterr().out
         assert captured == "opencv\nNone\n"
 
-        env2 = {"dependencies": ["python==3.9", "numpy", "fiona"]}
-        devenv2 = {"dependencies": ["python==3.9", "numpy", "fiona", "opencv", {"pip": ["geoutils", "-e ./"]}]}
+        env2 = {"dependencies": ["python==3.9", "numpy", "pandas"]}
+        devenv2 = {"dependencies": ["python==3.9", "numpy", "pandas", "opencv", {"pip": ["geoutils", "-e ./"]}]}
 
         # The diff function should not account for -e ./ that is the local install for developers
         xdem.misc.diff_environment_yml(env2, devenv2, input_dict=True, print_dep="both")
@@ -155,13 +155,13 @@ def test_diff_environment_yml(self, capsys) -> None:  # type: ignore
 
         # When the dependencies are not defined in dev-env but in env, it should raise an error
         # For normal dependencies
-        env3 = {"dependencies": ["python==3.9", "numpy", "fiona", "lol"]}
-        devenv3 = {"dependencies": ["python==3.9", "numpy", "fiona", "opencv", {"pip": ["geoutils"]}]}
+        env3 = {"dependencies": ["python==3.9", "numpy", "pandas", "lol"]}
+        devenv3 = {"dependencies": ["python==3.9", "numpy", "pandas", "opencv", {"pip": ["geoutils"]}]}
         with pytest.raises(ValueError, match="The following dependencies are listed in env but not dev-env: lol"):
             xdem.misc.diff_environment_yml(env3, devenv3, input_dict=True, print_dep="pip")
 
         # For pip dependencies
-        env4 = {"dependencies": ["python==3.9", "numpy", "fiona", {"pip": ["lol"]}]}
-        devenv4 = {"dependencies": ["python==3.9", "numpy", "fiona", "opencv", {"pip": ["geoutils"]}]}
+        env4 = {"dependencies": ["python==3.9", "numpy", "pandas", {"pip": ["lol"]}]}
+        devenv4 = {"dependencies": ["python==3.9", "numpy", "pandas", "opencv", {"pip": ["geoutils"]}]}
         with pytest.raises(ValueError, match="The following pip dependencies are listed in env but not dev-env: lol"):
             xdem.misc.diff_environment_yml(env4, devenv4, input_dict=True, print_dep="pip")

xdem/coreg/base.py

@@ -18,11 +18,11 @@
 )
 
 import affine
-import fiona
 import geopandas as gpd
 import geoutils as gu
 import numpy as np
 import pandas as pd
+import pyogrio
 import rasterio as rio
 import rasterio.warp  # pylint: disable=unused-import
 import scipy
@@ -272,8 +272,8 @@ def _mask_as_array(reference_raster: gu.Raster, mask: str | gu.Vector | gu.Raste
         # First try to load it as a Vector
         try:
             mask = gu.Vector(mask)
-        # If the format is unsopported, try loading as a Raster
-        except fiona.errors.DriverError:
+        # If the format is unsupported, try loading as a Raster
+        except pyogrio.errors.DataSourceError:
             try:
                 mask = gu.Raster(mask)
             # If that fails, raise an error