Merge pull request #843 from MiraGeoscience/GEOPY-2661

GEOPY-2661: Update minimum requirement to python >=3.12, <3.15 and numpy 2.*

Author: sebhmg

.github/workflows/python_analysis.yml

@@ -33,7 +33,7 @@ jobs:
     with:
       package-manager: 'poetry'
       app-name: 'geoh5py'
-      python-version: '3.10'
+      python-version: '3.12'
   call-workflow-pytest:
     name: Pytest
     uses: MiraGeoscience/CI-tools/.github/workflows/reusable-python-pytest.yml@v2
@@ -42,10 +42,10 @@ jobs:
       pull-requests: read
     with:
       package-manager: 'poetry'
-      python-versions: '["3.10", "3.11", "3.12"]'
+      python-versions: '["3.12", "3.13", "3.14"]'
       os: '["ubuntu-latest", "windows-latest"]'
       cache-number: 1
-      codecov-reference-python-version: '3.10'
+      codecov-reference-python-version: '3.12'
       codecov-reference-os: '["windows-latest"]'
     secrets:
       CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/python_deploy_dev.yml

@@ -19,7 +19,7 @@ jobs:
       contents: write
     with:
       package-name: 'geoh5py'
-      python-version: '3.10'
+      python-version: '3.12'
       source-repo-names: '["public-noremote-conda-dev"]'
       conda-channels: '["conda-forge"]'
       publish-repo-names: '["public-noremote-conda-dev"]'
@@ -35,7 +35,7 @@ jobs:
       package-manager: 'poetry'
       package-name: 'geoh5py'
       version-tag: ${{ github.ref_name }}
-      python-version: '3.10'
+      python-version: '3.12'
       virtual-repo-names: '["public-pypi-dev", "test-pypi"]'
     secrets:
       JFROG_ARTIFACTORY_URL: ${{ secrets.JFROG_ARTIFACTORY_URL }}

.pre-commit-config.yaml

@@ -36,7 +36,7 @@ repos:
     -   id: mypy
         additional_dependencies: [
 #            numpy==1.26.*,  # TODO: fix mypy errors related to numpy
-            pydantic==2.5.*,
+            pydantic==2.12.*,
             tomli, # to read config from pyproject.toml
             types-toml,
             types-PyYAML,

geoh5py/data/referenced_data.py

@@ -212,3 +212,10 @@ def add_data_map(self, name: str, values: np.ndarray | dict, public: bool = True
         """
         data = self.parent.add_data_map(self, name, values, public)
         return data
+
+    @property
+    def nan_value(self):
+        """
+        Nan-Data-Value
+        """
+        return 0

poetry.lock

@@ -13,7 +13,7 @@ build-backend = "poetry_dynamic_versioning.backend"
 
 [project]
 name = "geoh5py"
-requires-python = ">=3.10,<4.0"
+requires-python = ">=3.12,<3.15"
 
 
 description = "Python API for geoh5, an open file format for geoscientific data"
@@ -63,10 +63,10 @@ include = [
 version = "0.0.0.dev0"
 
 [tool.poetry.dependencies]
-h5py = "^3.2.1"
-numpy = "~1.26.0"
-Pillow = "~10.3.0"
-pydantic = "^2.12.0"
+h5py = "^3.15.0"
+numpy = "~2.4.0"
+Pillow = "~12.1.0"
+pydantic = "~2.12.0"
 
 [tool.poetry.group.dev.dependencies]
 lockfile = "^0.12.2"
@@ -76,11 +76,10 @@ pylint = "*"
 pytest = "*"
 pytest-cov = "*"
 pyyaml = '*'
-scipy = "~1.14.0"
+scipy = "~1.17.0"
 sphinx = "^3.0"
 sphinx-autodoc-typehints = "^1.10"
 sphinx-rtd-theme = "^0.4.3"
-h5py = "^3.14.0"
 
 [tool.poetry.requires-plugins]
 poetry-dynamic-versioning = { version = ">=1.9.1,<2.0.0", extras = ["plugin"] }

pyproject.toml

@@ -3,7 +3,7 @@ schema_version: 1
 context:
   name: "geoh5py"
   version: "0.0.0.dev0"  # This will be replaced by the actual version in the build process
-  python_min: "3.10"
+  python_min: "3.12"
   module_name: ${{ name|lower|replace("-", "_") }}
 
 package:
@@ -27,10 +27,10 @@ requirements:
     - pip
   run:
     - python >=${{ python_min }}
-    - h5py >=3.2.1, 3.*
-    - numpy >=1.26.0, 1.26.*
-    - pillow >=10.3.0, 10.3.*
-    - pydantic >=2.12.0, 2.*
+    - h5py >=3.15.0, 3.*
+    - numpy 2.4.*
+    - pillow 12.1.*
+    - pydantic 2.12.*
 
 tests:
   - python:
@@ -42,7 +42,7 @@ tests:
     requirements:
       run:
         - pytest
-        - scipy >= 1.14.0, <1.15.dev
+        - scipy 1.17.*
     files:
       source:
         - tests/

recipe.yaml

@@ -52,7 +52,7 @@ def test_coordinate_system(tmp_path):
 
     # create and save a tiff
     image = Image.fromarray(
-        np.random.randint(0, 255, (128, 128, 3)).astype("uint16"), "RGB"
+        np.random.randint(0, 255, (128, 128, 3)).astype("uint8"), "RGB"
     )
 
     for id_ in tag.items():

tests/coordinate_system_test.py

@@ -375,9 +375,7 @@ def test_georeference_image(tmp_path):
         assert isinstance(geoimage.image_georeferenced, Image.Image)
 
         # test grid2d errors
-        with pytest.raises(
-            ValueError, match="conversion from RGB to bidon not supported"
-        ):
+        with pytest.raises(ValueError, match="image has wrong mode"):
             geoimage.to_grid2d(new_name="RGB", mode="bidon")
 
         # test save_as