.github/PULL_REQUEST_TEMPLATE.md

@@ -2,5 +2,6 @@
 
  - [ ] Resolves #xxx,
  - [ ] Tests added, otherwise issue #xxx opened,
- - [ ] New optional dependencies added to both `dev-environment.yml` and `setup.cfg`,
  - [ ] Fully documented, including `api/*.md` for new API.
+ - [ ] New optional dependencies or Python version support added to both `dev-environment.yml` and `setup.cfg`,
+ - [ ] If contributor workflow (test, doc, linting) or Python version support changed, update `CONTRIBUTING.md`.

.github/workflows/pip-checks.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     # Run all shells using bash (including Windows)
     defaults:
@@ -36,7 +36,7 @@ jobs:
           use-mamba: true
           channel-priority: strict
           activate-environment: geoutils-pip
-          python-version:
+          python-version: ${{ matrix.python-version }}
 
       # Use pip install
       - name: Install project

.github/workflows/python-publish.yml

@@ -25,7 +25,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: '3.12'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/python-tests.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     defaults:
       run:

CONTRIBUTING.md

@@ -14,7 +14,7 @@ For more details, see the rest of this document.
 
 ## Development environment
 
-GeoUtils currently supports only Python versions of 3.9 and higher, see `environment.yml` for detailed dependencies.
+GeoUtils currently supports only Python versions of 3.10 to 3.12, see `environment.yml` for detailed dependencies.
 
 ### Setup
 

dev-environment.yml

@@ -2,7 +2,7 @@ name: geoutils-dev
 channels:
   - conda-forge
 dependencies:
-  - python>=3.9,<3.12
+  - python>=3.10,<3.13
   - geopandas>=0.12.0
   - matplotlib=3.*
   - pyproj=3.*
@@ -22,6 +22,7 @@ dependencies:
   - scikit-image
 
   # Test dependencies
+  - gdal  # To test functionalities against GDAL
   - pytest=7.*
   - pytest-xdist
   - pytest-lazy-fixture

doc/source/conf.py

@@ -9,6 +9,7 @@
 sys.path.append(os.path.abspath("../.."))
 sys.path.append(os.path.abspath("../../geoutils/"))
 sys.path.append(os.path.abspath(".."))
+sys.path.insert(0, os.path.dirname(__file__))
 
 from sphinx_gallery.sorting import ExampleTitleSortKey, ExplicitOrder
 
@@ -104,6 +105,11 @@
     "backreferences_dir": "gen_modules/backreferences",
     "doc_module": ("geoutils"),  # Which function/class levels are used to create galleries
     "remove_config_comments": True,  # To remove comments such as sphinx-gallery-thumbnail-number (only works in code, not in text)
+    "reset_modules": (
+        "matplotlib",
+        "sphinxext.reset_mpl",
+    ),
+    # To reset matplotlib for each gallery (and run custom function that fixes the default DPI)
 }
 
 extlinks = {

doc/source/index.md

@@ -26,7 +26,7 @@ GeoUtils is a Python package for **accessible**, **efficient** and **reliable**
 
 ```{important}
 :class: margin
-GeoUtils ``v0.1`` is released, with most features drafted 3 years ago now finalized 🎉! We are working on an **Xarray accessor** and a few other features for 2024.
+GeoUtils ``v0.1`` is released, with most features drafted 3 years ago now finalized 🎉! We are working on an **Xarray accessor** and a few other features for 2025.
 ```
 
 GeoUtils is built on top of core geospatial packages (Rasterio, GeoPandas, PyProj) and numerical packages

doc/source/sphinxext.py

@@ -0,0 +1,8 @@
+"""Functions for documentation configuration only, importable by sphinx"""
+# To reset resolution setting for each sphinx-gallery example
+def reset_mpl(gallery_conf, fname):
+    # To get a good resolution for displayed figures
+    from matplotlib import pyplot
+
+    pyplot.rcParams["figure.dpi"] = 600
+    pyplot.rcParams["savefig.dpi"] = 600

environment.yml

@@ -2,7 +2,7 @@ name: geoutils
 channels:
   - conda-forge
 dependencies:
-  - python>=3.9,<3.12
+  - python>=3.10,<3.13
   - geopandas>=0.12.0
   - matplotlib=3.*
   - pyproj=3.*

geoutils/raster/multiraster.py

@@ -165,26 +165,30 @@ def stack_rasters(
             return_rio_bbox=True,
         )
 
-    # Make a data list and add all of the reprojected rasters into it.
+    # Make a data list and add all the reprojected rasters into it.
     data: list[NDArrayNum] = []
 
     for raster in tqdm(rasters, disable=not progress):
         # Check that data is loaded, otherwise temporarily load it
         if not raster.is_loaded:
             raster.load()
 
-        nodata = reference_raster.nodata or gu.raster.raster._default_nodata(reference_raster.data.dtype)
+        nodata = reference_raster.nodata if not None else gu.raster.raster._default_nodata(reference_raster.data.dtype)
         # Reproject to reference grid
         reprojected_raster = raster.reproject(
             bounds=dst_bounds,
             res=reference_raster.res,
             crs=reference_raster.crs,
             dtype=reference_raster.data.dtype,
-            nodata=reference_raster.nodata,
+            nodata=nodata,
             resampling=resampling_method,
             silent=True,
         )
-        reprojected_raster.set_nodata(nodata)
+        # If the georeferenced grid was the same, reproject() will have returned self with a warning (silenced here),
+        # and we want to copy the raster and just modify its nodata (or would modify raster inputs of this function)
+        if reprojected_raster.georeferenced_grid_equal(raster):
+            reprojected_raster = reprojected_raster.copy()
+            reprojected_raster.set_nodata(nodata)
 
         # Optionally calculate difference
         if diff:

geoutils/raster/raster.py

@@ -3304,6 +3304,7 @@ def plot(
             cbar = None
 
         plt.sca(ax0)
+        plt.tight_layout()
 
         # If returning axes
         if return_axes:

pyproject.toml

@@ -13,7 +13,7 @@ version_file = "geoutils/_version.py"
 fallback_version = "0.0.1"
 
 [tool.black]
-target_version = ['py36']
+target_version = ['py310']
 
 [tool.pytest.ini_options]
 addopts = "--doctest-modules -W error::UserWarning"

setup.cfg

@@ -1,7 +1,7 @@
 [metadata]
 author = The GlacioHack Team
 name = geoutils
-version = 0.1.9
+version = 0.1.10
 description = Analysis and handling of georeferenced rasters and vectors
 keywords = raster, vector, geospatial, gis, xarray
 long_description = file: README.md
@@ -34,7 +34,7 @@ packages = find:
 scripts = bin/geoviewer.py
 zip_safe = False # https://mypy.readthedocs.io/en/stable/installed_packages.html
 include_package_data = True
-python_requires = >=3.9
+python_requires = >=3.10,<3.13
 # Avoid pinning dependencies in requirements.txt (which we don't do anyways, and we rely mostly on Conda)
 # (https://caremad.io/posts/2013/07/setup-vs-requirement/, https://github.com/pypa/setuptools/issues/1951)
 install_requires = file: requirements.txt

tests/test_raster/test_multiraster.py

@@ -14,11 +14,12 @@
 import geoutils as gu
 from geoutils import examples
 from geoutils.raster import RasterType
+from geoutils.raster.raster import _default_nodata
 
 
-class StackMergeImages:
+class RealImageStack:
     """
-    Test cases for stacking and merging images
+    Real test cases for stacking and merging images
     Split an image with some overlap, then stack/merge it, and validate bounds and shape.
     Param `cls` is used to set the type of the output, e.g. gu.Raster (default).
     """
@@ -67,24 +68,93 @@ def __init__(
         )
 
 
+class SyntheticImageStack:
+    """
+    Synthetic image stack for tests
+
+    Create a small synthetic example, where one can specify nodata value, values in second image (and potentially more
+    in the future).
+    """
+
+    def __init__(self, nodata: int | float, img2_value: int | float):
+
+        shape = (10, 10)
+        data_int = np.ones(shape).astype(np.uint16)
+        data_mask = np.zeros(shape).astype(bool)
+        data_masked = np.ma.masked_array(data=data_int, mask=data_mask, fill_value=nodata)
+        img = gu.Raster.from_array(
+            data=data_masked,
+            transform=rio.transform.Affine(
+                1000.0,
+                0.0,
+                1_000_000.0,
+                0.0,
+                -1000.0,
+                1_000_000.0,
+            ),
+            crs=pyproj.CRS.from_string("EPSG:3857"),
+            nodata=nodata,
+        )
+        self.img = img
+
+        # Find the easting midpoint of the img
+        x_midpoint = np.mean([self.img.bounds.right, self.img.bounds.left])
+        x_midpoint -= (x_midpoint - self.img.bounds.left) % self.img.res[0]
+
+        # Cut the img into two imgs that slightly overlap each other.
+        self.img1 = img.copy()
+        self.img1.crop(
+            rio.coords.BoundingBox(
+                right=x_midpoint + img.res[0] * 3, left=img.bounds.left, top=img.bounds.top, bottom=img.bounds.bottom
+            ),
+            inplace=True,
+        )
+        self.img2 = img.copy()
+        self.img2.crop(
+            rio.coords.BoundingBox(
+                left=x_midpoint - img.res[0] * 3, right=img.bounds.right, top=img.bounds.top, bottom=img.bounds.bottom
+            ),
+            inplace=True,
+        )
+
+        # Define a second raster with only 5s and the value defined above
+        self.img2[:5, :5] = img2_value
+
+        self.img3 = self.img1.copy()
+        self.img3.crop(
+            rio.coords.BoundingBox(
+                left=x_midpoint - self.img.res[0] * 3,
+                right=self.img.bounds.right - self.img.res[0] * 2,
+                top=self.img.bounds.top,
+                bottom=self.img.bounds.bottom,
+            ),
+            inplace=True,
+        )
+
+
 @pytest.fixture
 def images_1d():  # type: ignore
-    return StackMergeImages("everest_landsat_b4")
+    return RealImageStack("everest_landsat_b4")
 
 
 @pytest.fixture
 def images_different_crs():  # type: ignore
-    return StackMergeImages("everest_landsat_b4", different_crs=4326)
+    return RealImageStack("everest_landsat_b4", different_crs=4326)
 
 
 @pytest.fixture
 def sat_images():  # type: ignore
-    return StackMergeImages("everest_landsat_b4", cls=gu.SatelliteImage)
+    return RealImageStack("everest_landsat_b4", cls=gu.SatelliteImage)
 
 
 @pytest.fixture
 def images_3d():  # type: ignore
-    return StackMergeImages("everest_landsat_rgb")
+    return RealImageStack("everest_landsat_rgb")
+
+
+@pytest.fixture
+def images_nodata_zero():  # type: ignore
+    return SyntheticImageStack(nodata=0, img2_value=65534)
 
 
 class TestMultiRaster:
@@ -95,6 +165,7 @@ class TestMultiRaster:
             pytest.lazy_fixture("sat_images"),
             pytest.lazy_fixture("images_different_crs"),
             pytest.lazy_fixture("images_3d"),
+            pytest.lazy_fixture("images_nodata_zero"),
         ],
     )  # type: ignore
     def test_stack_rasters(self, rasters) -> None:  # type: ignore
@@ -105,6 +176,7 @@ def test_stack_rasters(self, rasters) -> None:  # type: ignore
             "ignore", category=UserWarning, message="New nodata value cells already exist in the data array.*"
         )
         warnings.filterwarnings("ignore", category=UserWarning, message="For reprojection, nodata must be set.*")
+        warnings.filterwarnings("ignore", category=UserWarning, message="Unmasked values equal to*")
 
         # Merge the two overlapping DEMs and check that output bounds and shape is correct
         if rasters.img1.count > 1:
@@ -139,6 +211,7 @@ def test_stack_rasters(self, rasters) -> None:  # type: ignore
         )
         assert merged_bounds == stacked_img.bounds
 
+        nodata_ref = rasters.img1.nodata
         # Check that reference works with input Raster
         stacked_img = gu.raster.stack_rasters([rasters.img1, rasters.img2], reference=rasters.img, use_ref_bounds=True)
         assert rasters.img.bounds == stacked_img.bounds
@@ -170,6 +243,16 @@ def test_stack_rasters(self, rasters) -> None:  # type: ignore
         stacked_img = gu.raster.stack_rasters([rasters.img1, rasters.img2], resampling_method="bilinear")
         assert not np.array_equal(np.unique(stacked_img.data.compressed()), np.array([1, 5]))
 
+        # Check input nodata is not modified inplace (issue 609)
+        new_nodata_ref = rasters.img1.nodata
+        assert nodata_ref == new_nodata_ref
+
+        # Check nodata value output is consistent with reference input
+        if nodata_ref is not None:
+            assert stacked_img.nodata == nodata_ref
+        else:
+            assert stacked_img.nodata == _default_nodata(rasters.img1.dtype)
+
     @pytest.mark.parametrize(
         "rasters",
         [
@@ -187,6 +270,7 @@ def test_merge_rasters(self, rasters) -> None:  # type: ignore
             "ignore", category=UserWarning, message="New nodata value cells already exist in the data array.*"
         )
         warnings.filterwarnings("ignore", category=UserWarning, message="For reprojection, nodata must be set.*")
+        warnings.filterwarnings("ignore", category=UserWarning, message="Unmasked values equal to*")
 
         # Ignore warning already checked in test_stack_rasters
         if rasters.img1.count > 1: