Merge remote-tracking branch 'upstream/main' into pointcloud_class

.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/scripts/generate_pip_deps_from_conda.py

@@ -26,13 +26,7 @@
 
 EXCLUDE = {"python"}
 REMAP_VERSION = {"tzdata": "2022.1"}
-RENAME = {
-    "pytables": "tables",
-    "psycopg2": "psycopg2-binary",
-    "dask-core": "dask",
-    "seaborn-base": "seaborn",
-    "sqlalchemy": "SQLAlchemy",
-}
+RENAME = {}
 
 
 def conda_package_to_pip(package: str):
@@ -108,13 +102,14 @@ def generate_pip_from_conda(conda_path: pathlib.Path, pip_path: pathlib.Path, co
     )
     pip_content = header + "\n".join(pip_deps) + "\n"
 
-    # add setuptools to requirements-dev.txt
-    with open(pathlib.Path(conda_path.parent, "pyproject.toml"), "rb") as fd:
-        meta = tomllib.load(fd)
-    for requirement in meta["build-system"]["requires"]:
-        if "setuptools" in requirement:
-            pip_content += requirement
-            pip_content += "\n"
+    # Add setuptools to requirements-dev.txt
+
+    # with open(pathlib.Path(conda_path.parent, "pyproject.toml"), "rb") as fd:
+    #     meta = tomllib.load(fd)
+    # for requirement in meta["build-system"]["requires"]:
+    #     if "setuptools" in requirement:
+    #         pip_content += requirement
+    #         pip_content += "\n"
 
     if compare:
         with pip_path.open() as file:

.github/workflows/pip-checks.yml

@@ -0,0 +1,48 @@
+# 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: ["3.10", "3.11", "3.12"]
+
+    # 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-version: latest
+          auto-update-conda: true
+          use-mamba: true
+          channel-priority: strict
+          activate-environment: geoutils-pip
+          python-version: ${{ matrix.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 geoutils"

.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

@@ -16,8 +16,8 @@ jobs:
 
     strategy:
       matrix:
-        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.9", "3.10", "3.11"]
+        os: ["ubuntu-latest", "macos-latest"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     defaults:
       run:
@@ -30,7 +30,6 @@ jobs:
     - name: Initiate empty environment
       uses: conda-incubator/setup-miniconda@v3
       with:
-        miniforge-variant: Mambaforge
         miniforge-version: latest
         auto-update-conda: true
         use-mamba: true
@@ -88,7 +87,12 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
 
     - name: Setup pip dependencies
-      run: pip install pytest-cov coveralls coveragepy-lcov
+      run: pip install pytest-cov coveralls coveragepy-lcov 'coverage<7'
+
+    - name: Print conda environment (for debugging)
+      run: |
+        conda info
+        conda list
 
     - name: Test with pytest
       run: pytest -ra --cov=geoutils/

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ ci:
     autoupdate_schedule: quarterly
 repos:
         - repo: https://github.com/pre-commit/pre-commit-hooks
-          rev: v4.3.0
+          rev: v5.0.0
           hooks:
                 - id: check-yaml
                 - id: end-of-file-fixer
@@ -12,10 +12,14 @@ repos:
                 - id: check-merge-conflict
         # Fix common spelling mistakes
         - repo: https://github.com/codespell-project/codespell
-          rev: v2.2.1
+          rev: v2.3.0
           hooks:
                 - id: codespell
-                  args: [--ignore-words-list=alos, --ignore-regex=\bnin\b]
+                  args: [
+                    '--ignore-words-list', 'alos,inout,vor',
+                    '--ignore-regex', '\bnin\b',
+                    '--'
+                  ]
                   types_or: [python, rst, markdown]
                   files: ^(geoutils|doc|tests)/
 
@@ -27,23 +31,24 @@ repos:
 
         # Format the code aggressively using black
         - repo: https://github.com/psf/black
-          rev: 22.10.0
+          rev: 24.10.0
           hooks:
                   - id: black
                     args: [--line-length=120]
 
         # Lint the code using flake8
         - repo: https://github.com/pycqa/flake8
-          rev: 3.9.2
+          rev: 7.1.1
           hooks:
                 - id: flake8
                   args: [
-                          --max-line-length=120,
-                          --extend-ignore=E203,   # flake8 disagrees with black, so this should be ignored.
+                          '--max-line-length', '120',  # we can write dicts however we want
+                          '--extend-ignore', 'E203,B028', # flake8 disagrees with black, so this should be ignored.
+                          '--'
                   ]
                   additional_dependencies:
-                          - flake8-comprehensions==3.1.0
-                          - flake8-bugbear==21.3.2
+                          - flake8-comprehensions
+                          - flake8-bugbear
                   files: ^(geoutils|tests)
         # Lint the code using mypy
         - repo: https://github.com/pre-commit/mirrors-mypy
@@ -63,26 +68,26 @@ repos:
                         --disable-error-code=var-annotated,
                         --disable-error-code=no-any-return
                   ]
-                  additional_dependencies: [tokenize-rt==3.2.0, numpy==1.22]
+                  additional_dependencies: [tokenize-rt==3.2.0, numpy==1.26]
                   files: ^(geoutils|tests)
 
         # Sort imports using isort
         - repo: https://github.com/PyCQA/isort
-          rev: 5.12.0
+          rev: 5.13.2
           hooks:
                   - id: isort
                     args: [ "--profile", "black" ]
 
   # Automatically upgrade syntax to a minimum version
         - repo: https://github.com/asottile/pyupgrade
-          rev: v3.1.0
+          rev: v3.19.0
           hooks:
                 - id: pyupgrade
                   args: [--py37-plus]
 
         # Various formattings
         - repo: https://github.com/pre-commit/pygrep-hooks
-          rev: v1.9.0
+          rev: v1.10.0
           hooks:
                 # Single backticks should apparently not be used
                 - id: rst-backticks
@@ -101,7 +106,7 @@ repos:
 
         # Add custom regex lints (see .relint.yml)
         - repo: https://github.com/codingjoe/relint
-          rev: 2.0.0
+          rev: 3.3.1
           hooks:
                 - id: relint
         - repo: local

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
 

bin/geoviewer.py

@@ -181,12 +181,16 @@ def main(test_args: Sequence[str] = None) -> None:
         vmax = None
 
     # color map
+    # Get the list of existing color maps, including reversed maps
+    mpl_cmap_list = list(plt.cm.datad.keys())
+    mpl_cmap_list.extend([cmap + "_r" for cmap in mpl_cmap_list])
+
     if args.cmap == "default":
         cmap = plt.rcParams["image.cmap"]
-    elif args.cmap in plt.cm.datad.keys():
+    elif args.cmap in mpl_cmap_list:
         cmap = args.cmap
     else:
-        raise ValueError("Wrong cmap, must be in: {}".format(",".join(str(elem) for elem in plt.cm.datad.keys())))
+        raise ValueError("Wrong cmap, must be in: {}".format(",".join(str(elem) for elem in mpl_cmap_list)))
 
     # Figsize
     if args.figsize == "default":

dev-environment.yml

@@ -2,16 +2,17 @@ name: geoutils-dev
 channels:
   - conda-forge
 dependencies:
-  - python>=3.9,<3.12
-  - geopandas>=0.12.0,<0.14
+  - python>=3.10,<3.13
+  - geopandas>=0.12.0
   - matplotlib=3.*
   - pyproj=3.*
   - rasterio>=1.3,<2
-  - pandas>=1,<2.2
+  - pandas>=1,<3
   - numpy=1.*
   - scipy=1.*
   - tqdm
   - xarray
+  - dask
   - rioxarray=0.*
   - python-pdal
 
@@ -22,12 +23,16 @@ dependencies:
   - scikit-image
 
   # Test dependencies
+  - gdal  # To test functionalities against GDAL
   - pytest=7.*
   - pytest-xdist
   - pytest-lazy-fixture
   - pyyaml
   - flake8
   - pylint
+  - netcdf4  # To write synthetic data with chunksizes
+  - dask-memusage
+  - pre-commit
 
   # Doc dependencies
   - sphinx

doc/source/_static/css/custom.css

@@ -0,0 +1,8 @@
+/*  Work around to wrong dark-mode for toggle button: https://github.com/executablebooks/MyST-NB/issues/523 */
+div.cell details.hide > summary {
+    background-color: var(--pst-color-surface);
+}
+
+div.cell details[open].above-input div.cell_input {
+    border-top: None;
+}

doc/source/about_geoutils.md

@@ -38,7 +38,7 @@ In particular, GeoUtils:
 - Strives to rely on **lazy operations** under-the-hood to avoid unnecessary data loading,
 - Allows for **match-reference operations** to facilitate geospatial handling,
 - Re-implements **several of [GDAL](https://gdal.org/)'s features** missing in other packages (e.g., proximity, gdalDEM),
-- Naturally handles **different `dtypes` and `nodata`** values through its NumPy masked-array interface.
+- Naturally handles **different `dtype` and `nodata`** values through its NumPy masked-array interface.
 
 
 ```{note}
@@ -90,13 +90,13 @@ header-rows: 1
 * - ```{eval-rst}
     .. literalinclude:: code/about_geoutils_sidebyside_raster_geoutils.py
         :language: python
-        :lines: 12-29
+        :lines: 15-30
     ```
 
   - ```{eval-rst}
     .. literalinclude:: code/about_geoutils_sidebyside_raster_rasterio.py
         :language: python
-        :lines: 10-62
+        :lines: 11-57
     ```
 `````
 
@@ -112,13 +112,13 @@ header-rows: 1
 * - ```{eval-rst}
     .. literalinclude:: code/about_geoutils_sidebyside_vector_geoutils.py
         :language: python
-        :lines: 10-25
+        :lines: 11-26
     ```
 
   - ```{eval-rst}
     .. literalinclude:: code/about_geoutils_sidebyside_vector_geopandas.py
         :language: python
-        :lines: 10-40
+        :lines: 11-34
     ```
 
 `````