use newer numpy & python

.github/workflows/build-wheel.yml

@@ -12,12 +12,12 @@ jobs:
         uses: actions/setup-python@v3
         with:
           python-version: '3.11'
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install wheel
-      - name: Build bdist_wheel
-        run: python setup.py bdist_wheel
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+      - name: Build wheel
+        run: uv build --wheel
       - uses: actions/upload-artifact@v3
         with:
           path: dist/*.whl

.github/workflows/lint-and-test.yml

@@ -17,7 +17,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.8"
+          python-version: "3.11"
 
       - uses: pre-commit/action@v3.0.0
         with:
@@ -27,21 +27,21 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.8", "3.9", "3.10" ]
+        python-version: [ "3.11", "3.12" ]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
       - name: Install dependencies
         run: |
-          # Keep pip below 23.0.1 (vam.whittaker install fails with higher versions, #84)
-          python -m pip install --upgrade 'pip<23.0.1'
-          pip install flake8 pytest
-          # Workaround for vam.whittaker installation issue https://github.com/WFP-VAM/vam.whittaker/issues/4
-          pip install numpy==1.23.5 cython
-          pip install .[dev]
+          uv pip install --system flake8 pytest cython
+          uv pip install --system .[dev] --index-strategy unsafe-best-match --extra-index-url https://artifactory.vgt.vito.be/artifactory/api/pypi/python-packages-public/simple
       - name: Lint with flake8
         run: |
           # stop the build if there are Python syntax errors or undefined names
@@ -50,4 +50,4 @@ jobs:
           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
       - name: Test with pytest
         run: |
-          pytest
+          pytest

Jenkinsfile

@@ -13,4 +13,6 @@ pythonPipeline {
   wheel_repo = 'python-openeo'
   wheel_repo_dev = 'python-openeo'
   pep440 = true
+  enable_caching = true
+  enable_uv = true
 }

pyproject.toml

@@ -1,13 +1,13 @@
 [build-system]
-requires = ["setuptools>=42", "wheel", "numpy==1.23.5"]
+requires = ["setuptools>=42", "wheel", "numpy>=2.0"]
 build-backend = "setuptools.build_meta"
 
 [tool.black]
 line-length = 120
 
 [tool.ruff]
 line-length = 120
-target-version = "py38"
+target-version = "py311"
 select = ["F401", "I"]
 fix = true
 

setup.cfg

@@ -21,8 +21,10 @@ package_dir =
 packages = find:
 python_requires = >= 3.8
 install_requires =
-    numpy==1.23.5
-    vam.whittaker==2.0.6
+    numpy>=2.0
+    vam_whittaker @ https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp311-cp311-linux_x86_64.whl ; python_version == "3.11" and sys_platform == "linux"
+    vam_whittaker @ https://artifactory.vgt.vito.be/artifactory/python-packages-public/vam_whittaker/2.0.6/vam_whittaker-2.0.6-cp312-cp312-linux_x86_64.whl ; python_version == "3.12" and sys_platform == "linux"
+    vam_whittaker ; sys_platform=="windows"
     xarray>=0.20.2
     lcmap-pyccd==2021.7.19
     openeo
@@ -38,7 +40,7 @@ dev =
     pre-commit
     sphinx>=4.5.0
     myst-parser>=0.17.0
-    h5netcdf
+    h5netcdf[h5py]
     sphinx-autodoc-annotation
     sphinx-autodoc-typehints
     sphinxcontrib-svg2pdfconverter==1.2.0

src/fusets/whittaker.py

@@ -103,7 +103,7 @@ def whittaker(
 
     def callback(timeseries):
         _, _, Zd, XXd = whittaker_f(dates, timeseries, smoothing_lambda, 1)
-        dates_mask = np.in1d(XXd, output_dates)
+        dates_mask = np.isin(XXd, output_dates)
         return Zd[dates_mask]
 
     result = xarray.apply_ufunc(