Fix warnings and raise UserWarning as error in CI (#458)

.github/scripts/generate_yml_env_fixed_py.py

@@ -0,0 +1,54 @@
+from __future__ import annotations
+
+import argparse
+
+import yaml  # type: ignore
+
+
+def environment_yml_nopy(fn_env: str, py_version: str, add_deps: list[str] = None) -> None:
+    """
+    Generate temporary environment-py3.XX.yml files forcing python versions for setup of continuous integration.
+
+    :param fn_env: Filename path to environment.yml
+    :param py_version: Python version to force.
+    :param add_deps: Additional dependencies to solve for directly (for instance graphviz fails with mamba update).
+    """
+
+    # Load the yml as dictionary
+    yaml_env = yaml.safe_load(open(fn_env))
+    conda_dep_env = list(yaml_env["dependencies"])
+
+    # Force python version
+    conda_dep_env_forced_py = ["python=" + py_version if "python" in dep else dep for dep in conda_dep_env]
+
+    # Optionally, add other dependencies
+    if add_deps is not None:
+        conda_dep_env_forced_py.extend(add_deps)
+
+    # Copy back to new yaml dict
+    yaml_out = yaml_env.copy()
+    yaml_out["dependencies"] = conda_dep_env_forced_py
+
+    with open("environment-ci-py" + py_version + ".yml", "w") as outfile:
+        yaml.dump(yaml_out, outfile, default_flow_style=False)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Generate environment files for CI with fixed python versions.")
+    parser.add_argument("fn_env", metavar="fn_env", type=str, help="Path to the generic environment file.")
+    parser.add_argument(
+        "--pyv",
+        dest="py_version",
+        default="3.9",
+        type=str,
+        help="List of Python versions to force.",
+    )
+    parser.add_argument(
+        "--add",
+        dest="add_deps",
+        default=None,
+        type=str,
+        help="List of dependencies to add.",
+    )
+    args = parser.parse_args()
+    environment_yml_nopy(fn_env=args.fn_env, py_version=args.py_version, add_deps=args.add_deps.split(","))

.github/workflows/python-tests.yml

@@ -51,20 +51,16 @@ jobs:
         CACHE_NUMBER: 0 # Increase this value to reset cache if environment.yml has not changed
       id: cache
 
-    # The trick below is necessary because the generic environment file does not specify a Python version, and only
-    # "conda env update" can be used to update with an environment file, which upgrades the Python version
+    # The trick below is necessary because the generic environment file does not specify a Python version, and ONLY
+    # "conda env update" CAN BE USED WITH CACHING, which upgrades the Python version when using the base environment
     # (we add "graphviz" from dev-environment to solve all dependencies at once, at graphviz relies on image
     # processing packages very much like geo-packages; not a problem for docs, dev installs where all is done at once)
     - name: Install base environment with a fixed Python version
       if: steps.cache.outputs.cache-hit != 'true'
       run: |
         mamba install pyyaml python=${{ matrix.python-version }}
-        pkgs_conda_base=`python .github/scripts/get_yml_env_nopy.py "environment.yml" --p "conda"`
-        pkgs_pip_base=`python .github/scripts/get_yml_env_nopy.py "environment.yml" --p "pip"`
-        mamba install python=${{ matrix.python-version }} $pkgs_conda_base graphviz
-        if [[ "$pkgs_pip_base" != "None" ]]; then
-          pip install $pkgs_pip_base
-        fi
+        python .github/scripts/generate_yml_env_fixed_py.py --pyv ${{ matrix.python-version }} --add "graphviz" "environment.yml"
+        mamba env update -n xdem-dev -f environment-ci-py${{ matrix.python-version }}.yml
 
     - name: Install project
       run: pip install -e . --no-dependencies

doc/source/api.md

@@ -60,8 +60,8 @@ documentation.
     Raster.width
     Raster.count
     Raster.count_on_disk
-    Raster.indexes
-    Raster.indexes_on_disk
+    Raster.bands
+    Raster.bands_on_disk
     Raster.res
     Raster.bounds
     Raster.dtypes

geoutils/projtools.py

@@ -244,7 +244,7 @@ def align_bounds(
 
 
 def reproject_points(
-    points: list[list[float]] | tuple[list[float], list[float]] | NDArrayNum, in_crs: CRS, out_crs: CRS
+    points: list[list[float]] | list[float] | tuple[list[float], list[float]] | NDArrayNum, in_crs: CRS, out_crs: CRS
 ) -> tuple[list[float], list[float]]:
     """
     Reproject a set of point from input_crs to output_crs.
@@ -269,7 +269,7 @@ def reproject_points(
 
 
 def reproject_to_latlon(
-    points: list[list[float]] | NDArrayNum, in_crs: CRS, round_: int = 8
+    points: list[list[float]] | list[float] | NDArrayNum, in_crs: CRS, round_: int = 8
 ) -> tuple[list[float], list[float]]:
     """
     Reproject a set of point from in_crs to lat/lon.

geoutils/raster/raster.py

@@ -986,8 +986,8 @@ def raster_equal(self, other: object) -> bool:
         - The raster's transform, crs and nodata values.
         """
 
-        if not isinstance(other, type(self)):  # TODO: Possibly add equals to SatelliteImage?
-            return NotImplemented
+        if not isinstance(other, Raster):  # TODO: Possibly add equals to SatelliteImage?
+            raise NotImplementedError("Equality with other object than Raster not supported by raster_equal.")
         return all(
             [
                 np.array_equal(self.data.data, other.data.data, equal_nan=True),
@@ -2541,7 +2541,7 @@ def save(
             save_data = self.data
 
             # If the raster is a mask, convert to uint8 before saving and force nodata to 255
-            if save_data.dtype == bool:
+            if self.data.dtype == bool:
                 save_data = save_data.astype("uint8")
                 nodata = 255
 
@@ -3744,12 +3744,17 @@ def reproject(
             memory_limit=memory_limit,
         )
 
-        # Transform back to a boolean array
+        # Transform output back to a boolean array
         output._data = output.data.astype(bool)  # type: ignore
 
+        # Transform self back to boolean array
+        self._data = self.data.astype(bool)  # type: ignore
+
         if inplace:
             self._transform = output._transform  # type: ignore
             self._crs = output._crs  # type: ignore
+            # Little trick to force the shape, same as in Raster.reproject()
+            self._data = output._data  # type: ignore
             self.data = output._data  # type: ignore
             return None
         else:
@@ -3820,7 +3825,14 @@ def polygonize(
 
         # Convert to unsigned integer and pass to parent method
         self._data = self.data.astype("uint8")  # type: ignore
-        return super().polygonize(target_values=target_values)
+
+        # Get output from parent method
+        output = super().polygonize(target_values=target_values)
+
+        # Convert array back to boolean
+        self._data = self.data.astype(bool)  # type: ignore
+
+        return output
 
     def proximity(
         self,
@@ -3841,12 +3853,11 @@ def proximity(
         #     warnings.warn("In-value converted to 1 for polygonizing boolean mask.")
         #     target_values = [1]
 
-        # Convert to unsigned integer and pass to parent method
-        self._data = self.data.astype("uint8")  # type: ignore
-
         # Need to cast output to Raster before computing proximity, as output will not be boolean
         # (super() would instantiate Mask() again)
-        raster = Raster({"data": self.data, "transform": self.transform, "crs": self.crs, "nodata": self.nodata})
+        raster = Raster(
+            {"data": self.data.astype("uint8"), "transform": self.transform, "crs": self.crs, "nodata": self.nodata}
+        )
         return raster.proximity(
             vector=vector,
             target_values=target_values,
@@ -3933,6 +3944,10 @@ def proximity_from_vector_or_raster(
     # 1/ First, if there is a vector input, we rasterize the geometry type
     # (works with .boundary that is a LineString (.exterior exists, but is a LinearRing)
     if vector is not None:
+
+        # TODO: Only when using centroid... Maybe we should leave this operation to the user anyway?
+        warnings.filterwarnings("ignore", message="Geometry is in a geographic CRS.*")
+
         # We create a geodataframe with the geometry type
         boundary_shp = gpd.GeoDataFrame(geometry=vector.ds.__getattr__(geometry_type), crs=vector.crs)
         # We mask the pixels that make up the geometry type

pyproject.toml

@@ -16,7 +16,7 @@ fallback_version = "0.0.1"
 target_version = ['py36']
 
 [tool.pytest.ini_options]
-addopts = "--doctest-modules"
+addopts = "--doctest-modules -W error::UserWarning"
 testpaths = [
 	"tests",
 	"geoutils"

tests/test_doc.py

@@ -2,6 +2,7 @@
 import os
 import platform
 import shutil
+import warnings
 
 import sphinx.cmd.build
 
@@ -13,6 +14,11 @@ class TestDocs:
     def test_build(self) -> None:
         """Try building the documentation and see if it works."""
 
+        # Ignore all warnings raised in the documentation
+        # (some UserWarning are shown on purpose in certain examples, so they shouldn't make the test fail,
+        # and most other warnings are for Sphinx developers, not meant to be seen by us; or we can check on RTD)
+        warnings.filterwarnings("ignore")
+
         # Building the doc fails on Windows for the CLI section
         if (platform.system() == "Linux") or (platform.system() == "Darwin"):
 

tests/test_geoviewer.py

@@ -4,6 +4,7 @@
 
 import os
 import sys
+import warnings
 
 import matplotlib.pyplot as plt
 import pytest
@@ -40,9 +41,14 @@ def test_geoviewer_valid_1band(capsys, monkeypatch, filename, option):  # type:
     # To avoid having the plots popping up during execution
     monkeypatch.setattr(plt, "show", lambda: None)
 
+    # The everest example will raise errors when setting a nodata value that exists
+    if "B4" in os.path.basename(filename) and len(option) > 0 and option[0] == "-nodata":
+        warnings.filterwarnings("ignore", category=UserWarning, message="New nodata value found in the data array.*")
+
     # To not get exception when testing generic functions such as --help
     try:
         geoviewer.main([filename, *option])
+        plt.close()
     except SystemExit:
         pass
 
@@ -81,6 +87,10 @@ def test_geoviewer_invalid_1band(capsys, monkeypatch, filename, args):  # type:
     # To avoid having the plots popping up during execution
     monkeypatch.setattr(plt, "show", lambda: None)
 
+    # The everest example will raise errors when setting a nodata value that exists
+    if "B4" in os.path.basename(filename) and len(args) > 0 and args[0] == "-nodata":
+        warnings.filterwarnings("ignore", category=UserWarning, message="New nodata value found in the data array.*")
+
     # To not get exception when testing generic functions such as --help
     option, error = args
     with pytest.raises(error):
@@ -108,9 +118,14 @@ def test_geoviewer_valid_3band(capsys, monkeypatch, filename, option):  # type:
     # To avoid having the plots popping up during execution
     monkeypatch.setattr(plt, "show", lambda: None)
 
+    # The everest RGB example will raise errors when setting a nodata value that exists
+    if "RGB" in os.path.basename(filename) and len(option) > 0 and option[0] == "-nodata":
+        warnings.filterwarnings("ignore", category=UserWarning, message="New nodata value found in the data array.*")
+
     # To not get exception when testing generic functions such as --help
     try:
         geoviewer.main([filename, *option])
+        plt.close()
     except SystemExit:
         pass