Modernize dependencies and CI, add Python 3.13 support, and fix NumPy 2 compatibility issues

.github/ci-environment.yml

@@ -0,0 +1,5 @@
+name: ci
+channels:
+  - conda-forge
+dependencies:
+  - gdal

.github/workflows/install-methods.yml

@@ -0,0 +1,57 @@
+name: Install Methods
+
+on:
+  schedule:
+    - cron: '0 6 * * 1'
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+jobs:
+  conda-pip:
+    name: conda + pip
+    runs-on: ubuntu-24.04
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v6
+      - uses: conda-incubator/setup-miniconda@v4
+        with:
+          python-version: "3.12"
+          activate-environment: install-test
+          channels: conda-forge
+          channel-priority: strict
+          conda-remove-defaults: true
+      - run: conda install -y gdal
+      - run: pip install .[implementations]
+      - run: python -c "import openeo_processes_dask; print('OK')"
+
+  micromamba-pip:
+    name: micromamba + pip
+    runs-on: ubuntu-24.04
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v6
+      - uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-name: install-test
+          create-args: python=3.12 gdal
+      - run: pip install .[implementations]
+      - run: python -c "import openeo_processes_dask; print('OK')"
+
+  system-pip:
+    name: system packages + pip
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v6
+      - run: sudo apt-get update && sudo apt-get install -y gdal-bin libgdal-dev
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+      - run: pip install "gdal==$(gdal-config --version)" .[implementations]
+      - run: python -c "import openeo_processes_dask; print('OK')"

.github/workflows/main.yml

@@ -14,8 +14,7 @@ on:
   workflow_dispatch:
 
 env:
-  POETRY_VERSION: 1.5.1
-
+  POETRY_VERSION: 2.3.3
 
 jobs:
   tests:
@@ -24,77 +23,83 @@ jobs:
     strategy:
       matrix:
         os: [Ubuntu]
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
         include:
           - os: Ubuntu
-            image: ubuntu-24.04   # switch to Noble (24.04)
+            image: ubuntu-24.04
       fail-fast: false
     defaults:
       run:
-        shell: bash
+        shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v6
         with:
           submodules: recursive
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+      # --- Conda env with GDAL from conda-forge ---
+      - name: Set up Miniforge + Python ${{ matrix.python-version }}
+        uses: conda-incubator/setup-miniconda@v4
         with:
+          miniforge-version: latest
           python-version: ${{ matrix.python-version }}
+          activate-environment: ci
+          channels: conda-forge
+          channel-priority: strict
+          environment-file: .github/ci-environment.yml
+          use-mamba: true
+          conda-remove-defaults: true
+
+      # Cache downloaded conda tarballs (NOT the resolved environment)
+      - name: Cache conda package downloads
+        uses: actions/cache@v5
+        with:
+          path: ~/conda_pkgs_dir
+          key: conda-pkgs-${{ runner.os }}-py${{ matrix.python-version }}-${{ hashFiles('.github/ci-environment.yml') }}
+          restore-keys: |
+            conda-pkgs-${{ runner.os }}-py${{ matrix.python-version }}-
 
-      - name: Install system GDAL 3.11.3 (UbuntuGIS)
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y software-properties-common
-          sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable -y
-          sudo apt-get update
-          # Install GDAL from the PPA (brings matching libgdal)
-          sudo apt-get install -y libgdal-dev gdal-bin
-          gdalinfo --version
-          # Show where libgdal comes from (should be /usr/lib/* from UbuntuGIS)
-          apt-cache policy libgdal-dev | sed -n '1,20p'
+      - name: Configure conda pkg cache directory
+        run: conda config --add pkgs_dirs ~/conda_pkgs_dir
 
-      - name: Get full Python version
-        id: full-python-version
-        run: echo version=$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))") >> $GITHUB_OUTPUT
+      # Always do a full solve + install — never skip, so dependency breakage is caught
+      - name: Install GDAL via conda-forge
+        run: |
+          mamba install -y gdal
+          conda clean --all -f -y
 
-      - name: Bootstrap poetry
-        run: curl -sSL https://install.python-poetry.org | python3 - -y --version $POETRY_VERSION
+      - name: Verify GDAL
+        run: |
+          gdalinfo --version
+          python -c "from osgeo import gdal; print('GDAL Python:', gdal.__version__)"
 
-      - name: Update PATH
-        run: echo "$HOME/.local/bin" >> $GITHUB_PATH
+      # --- Poetry ---
+      - name: Install Poetry
+        run: |
+          curl -sSL https://install.python-poetry.org | python3 - -y --version $POETRY_VERSION
+          echo "$HOME/.local/bin" >> $GITHUB_PATH
 
-      - name: Configure poetry
-        run: poetry config virtualenvs.in-project true
+      - name: Configure Poetry to use conda env
+        run: poetry config virtualenvs.create false
 
-      - name: Set up cache
-        uses: actions/cache@v3
-        id: cache
+      # Cache downloaded pip wheels (NOT installed packages)
+      - name: Cache pip downloads
+        uses: actions/cache@v5
         with:
-          path: .venv
-          key: venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/poetry.lock') }}
+          path: ~/.cache/pip
+          key: pip-${{ runner.os }}-py${{ matrix.python-version }}-${{ hashFiles('**/poetry.lock') }}
+          restore-keys: |
+            pip-${{ runner.os }}-py${{ matrix.python-version }}-
 
-      - name: Ensure cache is healthy
-        if: steps.cache.outputs.cache-hit == 'true'
-        run: |
-          [ "$(command -v timeout)" ] || function timeout() { perl -e 'alarm shift; exec @ARGV' "$@"; }
-          timeout 10s poetry run pip --version || rm -rf .venv
-
-      # Important: make Poetry resolve GDAL against system libgdal=3.11
-      # If you explicitly pin GDAL in pyproject, set it to "==3.11.3".
       - name: Install dependencies
-        run: |
-          ver="$(gdal-config --version)"
-          poetry add "gdal==${ver}"          # adds to main group
-          poetry install --with dev --all-extras
+        run: poetry install --with dev --all-extras
 
       - name: Pre-commit hooks
-        run: poetry run pre-commit run --all-files
+        run: pre-commit run --all-files
 
       - name: Run pytest
-        run: poetry run pytest --cov=openeo_processes_dask --cov-report=xml
+        run: pytest --cov=openeo_processes_dask --cov-report=xml
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v6
         with:
           files: ./coverage.xml

.github/workflows/release.yml

@@ -6,29 +6,53 @@ on:
       - '*.*.*'
 
 env:
-  POETRY_VERSION: 1.5.1
+  POETRY_VERSION: 2.3.3
 
 jobs:
   release:
     name: Release
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v6
         with:
           submodules: recursive
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+      - name: Set up Miniforge + Python 3.12
+        uses: conda-incubator/setup-miniconda@v4
         with:
-          python-version: "3.11"
+          miniforge-version: latest
+          python-version: "3.12"
+          activate-environment: release
+          channels: conda-forge
+          channel-priority: strict
+          environment-file: .github/ci-environment.yml
+          use-mamba: true
+          conda-remove-defaults: true
 
-      - name: Bootstrap poetry
+      - name: Install GDAL via conda-forge
         run: |
-          curl -sL https://install.python-poetry.org | python - -y
+          mamba install -y gdal
+          conda clean --all -f -y
 
-      - name: Update PATH
-        run: echo "$HOME/.local/bin" >> $GITHUB_PATH
+      - name: Verify GDAL
+        run: |
+          gdalinfo --version
+          python -c "from osgeo import gdal; print('GDAL Python:', gdal.__version__)"
+
+      - name: Install Poetry
+        run: |
+          curl -sSL https://install.python-poetry.org | python3 - -y --version $POETRY_VERSION
+          echo "$HOME/.local/bin" >> $GITHUB_PATH
+
+      - name: Configure Poetry to use conda env
+        run: poetry config virtualenvs.create false
+
+      - name: Install dependencies
+        run: poetry install
 
       - name: Build project for distribution
         run: poetry build

.pre-commit-config.yaml

@@ -1,38 +1,39 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 default_language_version:
-    python: python3
+  python: python3
+
 repos:
--   repo: https://github.com/asottile/pyupgrade
-    rev: v3.10.1
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.21.2 # upgrading to 3.21.2 from 3.10.1 to accomodate py3.14 in test_matrix
     hooks:
       - id: pyupgrade
         args:
           - --keep-runtime-typing
           - --py39-plus
 
--   repo: https://github.com/python-poetry/poetry
-    rev: 1.5.1
+  - repo: https://github.com/python-poetry/poetry
+    rev: 2.3.3
     hooks:
       - id: poetry-check
 
--   repo: https://github.com/pycqa/isort
+  - repo: https://github.com/pycqa/isort
     rev: 5.12.0
     hooks:
       - id: isort
         name: isort (python)
         args: ["--profile", "black"]
 
--   repo: https://github.com/pre-commit/pre-commit-hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-yaml
-    -   id: check-added-large-files
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
 
--   repo: https://github.com/psf/black
+  - repo: https://github.com/psf/black
     rev: 23.7.0
     hooks:
-    -   id: black
+      - id: black
         exclude: ^specs/openeo-processes/