Add Python 3.13 support (#719)

Author: rhugonnet

.github/workflows/pip-checks.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
       - uses: actions/checkout@v4

.github/workflows/python-tests.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest", "macos-latest"]
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     # Run all shells using bash (including Windows)
     defaults:

CONTRIBUTING.md

@@ -20,11 +20,11 @@ The technical steps to contributing to xDEM are:
 
 ## Development environment
 
-xDEM currently supports Python versions of 3.10 to 3.12 (see `dev-environment.yml` for detailed dependencies), which are
+xDEM currently supports Python versions of 3.10 to 3.13 (see `dev-environment.yml` for detailed dependencies), which are
 tested in a continuous integration (CI) workflow running on GitHub Actions.
 
 When you open a PR on xDEM, a single linting action and 9 test actions will automatically start, corresponding to all
-supported Python versions (3.10, 3.11 and 3.12) and OS (Ubuntu, Mac, Windows). The coverage change of the tests will also
+supported Python versions (3.10, 3.11, 3.12 and 3.13) and OS (Ubuntu, Mac, Windows). The coverage change of the tests will also
 be reported by CoverAlls.
 
 ### Setup
@@ -46,8 +46,6 @@ cd xdem
 make install
 ```
 
-Please note: pip installation is currently only possible under python3.10.
-
 ### Tests
 
 At least one test per feature (in the associated `tests/test_*.py` file) should be included in the PR, using `pytest` (see existing tests for examples).

Makefile

@@ -14,7 +14,7 @@ endif
 # Python global variables definition
 PYTHON_VERSION_MIN = 3.10
 # Set PYTHON if not defined in command line
-# Example: PYTHON="python3.10" make venv to use python 3.10 for the venv
+# Example: PYTHON="python3.13" make venv to use python 3.13 for the venv
 # By default the default python3 of the system.
 ifndef PYTHON
 	PYTHON = "python3"

dev-environment.yml

@@ -2,7 +2,7 @@ name: xdem-dev
 channels:
   - conda-forge
 dependencies:
-  - python>=3.10,<3.13
+  - python>=3.10,<3.14
   - geopandas>=0.12.0
   - numba=0.*
   - numpy>=1,<3
@@ -11,7 +11,6 @@ dependencies:
   - rasterio>=1.3,<2
   - scipy=1.*
   - tqdm
-  - scikit-gstat>=1.0.18,<1.1
   - geoutils=0.1.17
   - affine
   - pandas
@@ -25,7 +24,6 @@ dependencies:
   - pytransform3d
   - pyyaml
   - scikit-learn
-  - scikit-gstat>=1.0.18
 
   # Test dependencies
   - pytest
@@ -48,7 +46,11 @@ dependencies:
   - numpydoc
 
   - pip:
-    - -e ./
+      # Optional dependencies with Pip
+      # SciKit-GStat temporarily here until Conda version supports Python 3.13
+      - scikit-gstat>=1.0.18
+
+      - -e ./
 
     # To run CI against latest GeoUtils
 #    - git+https://github.com/rhugonnet/geoutils.git

doc/source/quick_start.md

@@ -1,5 +1,7 @@
 ---
 file_format: mystnb
+mystnb:
+  execution_timeout: 60
 jupytext:
   formats: md:myst
   text_representation:

environment.yml

@@ -2,7 +2,7 @@ name: xdem
 channels:
   - conda-forge
 dependencies:
-  - python>=3.10,<3.13
+  - python>=3.10,<3.14
   - geopandas>=0.12.0
   - numba=0.*
   - numpy>=1,<3

setup.cfg

@@ -22,6 +22,7 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Programming Language :: Python :: 3
     Topic :: Software Development :: Libraries :: Python Modules
     Typing :: Typed
@@ -32,7 +33,7 @@ download_url = https://pypi.org/project/xdem/
 packages = find:
 zip_safe = False # https://mypy.readthedocs.io/en/stable/installed_packages.html
 include_package_data = True
-python_requires = >=3.10,<3.13
+python_requires = >=3.10,<3.14
 # 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

xdem/misc.py

@@ -21,6 +21,7 @@
 
 import copy
 import functools
+import sys
 import warnings
 from typing import Any, Callable
 
@@ -125,14 +126,27 @@ def decorator(decorated: Callable) -> Callable:  # type: ignore
         # Replace argument description of dem and resolution (not used in the DEM class, only in terrain)
         if remove_dem_res_params:
 
+            # Get Python version (spaces of docstring are not handled the same way after Python 3.13)
+            pyv = Version(".".join(str(getattr(sys.version_info, v)) for v in ["major", "minor", "micro"]))
+
             # Find and remove them if they exist
             if ":param dem:" in other_doc:
-                dem_section = "\n    :param dem:" + other_doc.split("\n    :param dem:")[1].split("\n")[0]
+                if pyv >= Version("3.13"):
+                    dem_section = "\n:param dem:" + other_doc.split("\n:param dem:")[1].split("\n")[0]
+                else:
+                    dem_section = "\n    :param dem:" + other_doc.split("\n    :param dem:")[1].split("\n")[0]
+
                 other_doc = other_doc.replace(dem_section, "")
             if ":param resolution:" in other_doc:
-                resolution_section = (
-                    "\n    :param resolution:" + other_doc.split("\n    :param resolution:")[1].split("\n")[0]
-                )
+                if pyv >= Version("3.13"):
+                    resolution_section = (
+                        "\n:param resolution:" + other_doc.split("\n:param resolution:")[1].split("\n")[0]
+                    )
+                else:
+                    resolution_section = (
+                        "\n    :param resolution:" + other_doc.split("\n    :param resolution:")[1].split("\n")[0]
+                    )
+
                 other_doc = other_doc.replace(resolution_section, "")
 
         # Remove docstring examples