Prepare v0.17 (numpy>=2.0) (#310)

* Build extensions with numpy 2 * Build extensions with numpy 2 * Update metapackage * Rebuild with numpy 2.0.2 * Update readme * Update for numpy 2 * Update C files * Update for numpy 2 * Cleanup
TUW-GEO · Nov 13, 2024 · 25e8dfa · 25e8dfa
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -4,7 +4,7 @@
 # For more information see:
 # https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: Automated Tests
+name: CI/CD
 
 on:
   push:
@@ -19,24 +19,24 @@ jobs:
         # as we build C extension for users to download, we want to include as many python versions
         # and OS versions as possible (especially windows to create .whl packages,
         # see step "Create wheel and dist package")
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
-        os: ["ubuntu-latest", "windows-latest"]
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+        os: ["ubuntu-latest", "windows-latest", "macos-latest"]
     name: py${{ matrix.python-version }} @ ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
 
     steps:
       - uses: actions/checkout@v4
         with:
-          submodules: true # does not work with self-hosted testdata
+          submodules: true
           fetch-depth: 0
       - uses: conda-incubator/setup-miniconda@v3
         with:
            miniconda-version: "latest"
            auto-update-conda: true
            python-version: ${{ matrix.python-version }}
            environment-file: environment.yml
-           activate-environment: pytesmo # todo: must match with name in environment.yml
-           mamba-version: "*"
+           activate-environment: pytesmo
+           channel-priority: flexible
            auto-activate-base: false
       - name: Print Infos
         shell: bash -l {0}
@@ -54,11 +54,22 @@ jobs:
           mkdir -p artifacts
           filename=env_py${{ matrix.python-version }}_${{ matrix.os }}.yml
           conda env export --no-builds | grep -v "prefix" > artifacts/$filename
-      - name: Install package and test
+      - name: Install package and dependencies
         shell: bash -l {0}
         run: |
           pip install -e .[testing]
+      - name: Run unit tests
+        shell: bash -l {0}
+        run: |
           pytest --cache-clear
+      - name: Create wheel and dist package
+        shell: bash -l {0}
+        run: |
+          pip install setuptools_scm twine wheel
+          python setup.py sdist --dist-dir artifacts/dist
+          python setup.py bdist_wheel --dist-dir artifacts/dist
+          ls artifacts/dist
+          twine check artifacts/dist/*
       - name: Upload Coverage
         shell: bash -l {0}
         run: |
@@ -67,27 +78,13 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COVERALLS_FLAG_NAME: ${{ matrix.python-version }}
           COVERALLS_PARALLEL: true
-      - name: Create wheel and dist package
-        shell: bash -l {0}
-        run: |
-          git status
-          pip install setuptools_scm twine
-          if [ ${{ matrix.os }} == "windows-latest" ]
-          then
-            # build whls on windows
-            pip install wheel
-            python setup.py bdist_wheel --dist-dir artifacts/dist
-          else
-            # build dist on linux
-            python setup.py sdist --dist-dir artifacts/dist
-          fi
-          ls artifacts/dist
-          twine check artifacts/dist/*
+
       - name: Upload Artifacts
         uses: actions/upload-artifact@v4
         with:
           name: Artifacts-${{ matrix.python-version }}-${{ matrix.os }}
           path: artifacts/*
+
   coveralls:
     name: Submit Coveralls 👚
     needs: build
@@ -99,6 +96,7 @@ jobs:
           pip3 install --upgrade coveralls && coveralls --service=github --finish
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
   publish:
     name: Upload to PyPI
     if: |
@@ -127,4 +125,4 @@ jobs:
           verify_metadata: true
           packages_dir: Artifacts/dist/
           user: __token__
-          password: ${{ secrets.PYPI_API_TOKEN }} # this needs to be uploaded to github actions secrets
+          password: ${{ secrets.PYPI_API_TOKEN }}  # this needs to be uploaded to github actions secrets
diff --git a/README.rst b/README.rst
@@ -1,17 +1,19 @@
 pytesmo - a Python Toolbox for the Evaluation of Soil Moisture Observations
 ***************************************************************************
 
-.. image:: https://github.com/TUW-GEO/pytesmo/workflows/Automated%20Tests/badge.svg?branch=master
+|ci| |cov| |pip| |doc|
+
+.. |ci| image:: https://github.com/TUW-GEO/pytesmo/actions/workflows/ci.yml/badge.svg?branch=master
    :target: https://github.com/TUW-GEO/pytesmo/actions
 
-.. image:: https://coveralls.io/repos/TUW-GEO/pytesmo/badge.png?branch=master
+.. |cov| image:: https://coveralls.io/repos/TUW-GEO/pytesmo/badge.png?branch=master
   :target: https://coveralls.io/r/TUW-GEO/pytesmo?branch=master
 
-.. image:: https://badge.fury.io/py/pytesmo.svg
+.. |pip| image:: https://badge.fury.io/py/pytesmo.svg
     :target: https://badge.fury.io/py/pytesmo
 
-.. image:: https://readthedocs.org/projects/pytesmo/badge/?version=latest
-    :target: https://pytesmo.readthedocs.io/en/latest/?badge=latest
+.. |doc| image:: https://readthedocs.org/projects/pytesmo/badge/?version=latest
+   :target: https://pytesmo.readthedocs.io/en/latest/
 
 pytesmo, the Python Toolbox for the Evaluation of Soil Moisture Observations, is
 a package/python toolbox which aims to provide a library that can be used for
@@ -45,35 +47,34 @@ If you want to contribute, take a look at the `developers guide
 Installation
 ============
 
-This package should be installable through `pip
+This package can be installed through `pip
 <https://pip.pypa.io/en/latest/installing.html>`__ which downloads the package
 from the `python package repository Pypi <https://pypi.python.org/>`__.
-However, pytesmo also needs some packages that depend on C or Fortran libraries (like ``netCDF4``).
-They should be installed first with conda or mamba. We recommend installing `Mambaforge <https://github.com/conda-forge/miniforge#mambaforge>`__.
-Then the following command should install all dependencies:
-
-.. code-block:: bash
-
-    mamba install -c conda-forge 'numpy<2.0.0' scipy pandas netCDF4 cython pyresample
-
-Afterwards ``pytesmo`` can be installed via pip.
 
 .. code-block:: bash
 
     pip install pytesmo
 
+Note that ``pytesmo>=0.17`` will only work with ``numpy>=2.0`` and ``python>=3.9``.
+If you still require a version compatible with numpy v1, install ``pytesmo<0.17``.
+
+Compiled C extensions are available as wheels for Windows and Linux for
+python 3.9 to 3.12.
 
-As an alternative (e.g. if you want to contribute to the package), you can
-clone the Github repository and install from source:
+For other operating systems and/or python versions, it might be necessary
+to compile the binaries yourself. This should
+happen automatically, if you have a C compiler installed (e.g.
+`GCC <https://gcc.gnu.org/>`_ ).
 
 .. code::
 
     git clone https://github.com/TUW-GEO/pytesmo.git --recursive
     cd pytesmo
-    mamba create -n pytesmo python=3.10 # or any supported python version
+    mamba create -n pytesmo python=3.12 # or any supported python version
     conda activate pytesmo
-    mamba env update -f environment.yml -n pytesmo
-    pip install -e .
+    pip install -e .[testing]  # install source package
+    python setup.py build_ext --inplace --cythonize  # optional compile cython C extensions
+    pytest  # Run tests to check if everything works
 
 Supported Products
 ==================

diff --git a/docs/examples/validation_framework.ipynb b/docs/examples/validation_framework.ipynb
@@ -70,8 +70,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
-   "metadata": {},
+   "execution_count": null,
+   "metadata": {
+    "is_executing": true
+   },
    "outputs": [],
    "source": [
     "import os\n",

diff --git a/environment.yml b/environment.yml
@@ -7,7 +7,7 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - numpy<2.0.0
+  - numpy>=2.0.0
   - numba
   - scipy>=0.12
   - pandas>=0.23.0

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,5 +1,5 @@
 [build-system]
-requires = ["Cython >= 0.29.23", "setuptools>=46.1.0", "wheel", "setuptools_scm[toml]>=5", "oldest-supported-numpy"]
+requires = ["Cython >= 0.29.23", "setuptools>=46.1.0", "wheel", "setuptools_scm[toml]>=5", "numpy>=2,<3"]
 build-backend = "setuptools.build_meta"
 [tool]
 [tool.setuptools_scm]

diff --git a/setup.cfg b/setup.cfg
@@ -31,20 +31,19 @@ package_dir =
 # Add here dependencies of your project (semicolon/line-separated), e.g.
 install_requires =
     importlib-metadata; python_version<"3.8"
-    numpy>=1.7.0,<2.0.0
+    numpy>=2.0
+    numba
     scipy>=0.12
     pandas>=0.23.0
-    matplotlib>=1.2.0
     netCDF4>=1.0.1,!=1.6.2
     pygeogrids
     pygeobase>=0.6.0
     pynetcf>=0.4.0
     configparser
     pykdtree
-    repurpose>=0.7.1
+    repurpose>=0.13.1
     cadati>=0.0.2
     Cython>=0.29.21
-    numba
     scikit-learn
 # The usage of test_requires is discouraged, see `Dependency Management` docs
 # tests_require = pytest; pytest-cov
@@ -62,13 +61,18 @@ exclude =
 # PDF = ReportLab; RXP
 # Add here test requirements (semicolon/line-separated)
 testing =
+    ascat==2.4.3
+    ismn==1.5.1
+    nbconvert
+    ipykernel
+    sphinx_rtd_theme
+    matplotlib
     pytest
     pytest-cov
     pytest-mpl
-    nbconvert
-    ipykernel
-    ascat>=2.0
-    ismn==1.3.4
+    pre-commit
+    flake8
+    yapf
 
 [options.entry_points]
 # Add here console scripts like: