Merge pull request #130 from ajdawson/develop-2.0

Work towards a 2.0 release

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# See https://docs.github.com/en/code-security/supply-chain-security/keeping-your-dependencies-updated-automatically/keeping-your-actions-up-to-date-with-dependabot
+
+version: 2
+updates:
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    labels:
+      - "bot"

.github/workflows/deploy-docs.yml

@@ -0,0 +1,50 @@
+
+name: Documentation
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: checkout
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Setup Micromamba
+      uses: mamba-org/setup-micromamba@v2
+      with:
+        environment-name: TEST
+        init-shell: bash
+        create-args: >-
+          python=3 pip pyspharm iris xarray sphinx sphinx-issues --channel conda-forge
+
+    - name: Install windspharm
+      shell: bash -l {0}
+      run: |
+        python -m pip install -e . --no-deps --force-reinstall
+
+    - name: Build documentation
+      shell: bash -l {0}
+      run: |
+        set -e
+        micromamba activate TEST
+        pushd docs
+        make clean html linkcheck
+        popd
+
+    - name: Deploy
+      if: success() && github.event_name == 'release'
+      uses: peaceiris/actions-gh-pages@v4
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: docs/_build/html

.github/workflows/pypi.yml

@@ -0,0 +1,65 @@
+name: Publish to PyPI
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  build_wheels:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Get tags
+      run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+
+    - name: Setup Micromamba Python
+      uses: mamba-org/setup-micromamba@v2
+      with:
+        environment-name: PYPI
+        init-shell: bash
+        create-args: >-
+          python
+          pip
+          pytest
+          numpy
+          pyspharm
+          --channel conda-forge
+
+    - name: Install build tools
+      shell: bash -l {0}
+      run: |
+        python -m pip install --upgrade build check-manifest twine
+
+    - name: Build binary wheel
+      shell: bash -l {0}
+      run: |
+        python -m build --sdist --wheel . --outdir dist
+
+    - name: Check manifest
+      shell: bash -l {0}
+      run: |
+        ls dist
+        check-manifest --verbose
+
+    - name: Test wheels
+      shell: bash -l {0}
+      run: |
+        cd dist && python -m pip install *.whl
+        python -m twine check *
+
+    - name: Publish a Python distribution to PyPI
+      if: success() && github.event_name == 'release'
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/tests-standard.yml

@@ -0,0 +1,37 @@
+name: Standard Tests
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  run:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        os: [ubuntu-latest, macos-latest]
+      fail-fast: false
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Setup Micromamba Python ${{ matrix.python-version }}
+      uses: mamba-org/setup-micromamba@v2
+      with:
+        environment-name: TEST
+        init-shell: bash
+        create-args: >-
+          python=${{ matrix.python-version }} pip pytest numpy pyspharm --channel conda-forge
+
+
+    - name: Install windspharm
+      shell: bash -l {0}
+      run: |
+        python -m pip install -e . --no-deps --force-reinstall
+
+    - name: Tests
+      shell: bash -l {0}
+      run: |
+        python -m pytest -vrsx windspharm/tests

.github/workflows/tests.yml

@@ -0,0 +1,36 @@
+name: Full Tests
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  run:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        os: [ubuntu-latest, macos-latest]
+      fail-fast: false
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Setup Micromamba Python ${{ matrix.python-version }}
+      uses: mamba-org/setup-micromamba@v2
+      with:
+        environment-name: TEST
+        init-shell: bash
+        create-args: >-
+          python=${{ matrix.python-version }} pip pytest numpy pyspharm iris xarray --channel conda-forge
+
+    - name: Install windspharm
+      shell: bash -l {0}
+      run: |
+        python -m pip install -e . --no-deps --force-reinstall
+
+    - name: Tests
+      shell: bash -l {0}
+      run: |
+        python -m pytest -vrsx windspharm/tests

.gitignore

@@ -1,5 +1,7 @@
 # Created by https://www.gitignore.io/api/vim,code,emacs,python
 
+windspharm/_version.py
+
 ### Code ###
 # Visual Studio Code - https://code.visualstudio.com/
 .settings/
@@ -193,4 +195,4 @@ tags
 [._]*.un~
 
 
-# End of https://www.gitignore.io/api/vim,code,emacs,python
+# End of https://www.gitignore.io/api/vim,code,emacs,python

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+repos:
+- repo: https://github.com/tox-dev/pyproject-fmt
+  rev: v2.5.0
+  hooks:
+    - id: pyproject-fmt
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.7.3
+  hooks:
+    - id: ruff

MANIFEST.in

@@ -1,4 +1,15 @@
+includ pyproject.toml
 include README.md
 include license.txt
-include versioneer.py
-include lib/windspharm/_version.py
+
+graft windspharm
+
+recursive-include examples *.py
+recursive-include  windspharm *.nc
+
+prune .github
+prune *.egg-info
+prune docs
+
+exclude *.yaml
+exclude windspharm/_version.py

README.md

@@ -1,7 +1,7 @@
 windspharm - spherical harmonic vector wind analysis in Python
 ==============================================================
 
-[![Build Status](https://api.travis-ci.org/repositories/ajdawson/windspharm.svg?branch=master)](https://travis-ci.org/ajdawson/windspharm) [![DOI (paper)](https://img.shields.io/badge/DOI%20%28paper%29-10.5334%2Fjors.129-blue.svg)](http://doi.org/10.5334/jors.129) [![DOI (latest release)](https://zenodo.org/badge/20448/ajdawson/windspharm.svg)](https://zenodo.org/badge/latestdoi/20448/ajdawson/windspharm)
+[![DOI (paper)](https://img.shields.io/badge/DOI%20%28paper%29-10.5334%2Fjors.129-blue.svg)](http://doi.org/10.5334/jors.129) [![DOI (latest release)](https://zenodo.org/badge/4715033.svg)](https://zenodo.org/records/1401190)
 
 Overview
 --------
@@ -17,9 +17,7 @@ windspharm provides a replacement for the windfield package from CDAT.
 Requirements
 ------------
 
-`windspharm` only requires [`numpy`](http://numpy.org) and [`pyspharm`](https://github.com/jswhit/pyspharm) (version 1.0.8 or higher), but for full functionality (meta-data interfaces) one or more of [`iris`](http://scitools.org.uk/iris/), [`xarray`](http://xarray.pydata.org) or the `cdms2` module (from [UV-CDAT](http://uvcdat.llnl.gov) is required.
-The setuptools package is required for installation.
-windspharm runs on Python 2 and 3.
+`windspharm` only requires [`numpy`](http://numpy.org) and [`pyspharm`](https://github.com/jswhit/pyspharm) (version 1.0.9 or higher), but for full functionality (meta-data interfaces) one or both of [`iris`](http://scitools.org.uk/iris/) and/or [`xarray`](http://xarray.pydata.org) are required.
 
 
 Documentation
@@ -39,8 +37,8 @@ You can additionally cite the [Zenodo DOI](https://zenodo.org/badge/latestdoi/20
 Frequently asked questions
 --------------------------
 
-* **Do I need UV-CDAT/iris/xarray to use windspharm?**
-  No. All the computation code uses numpy only. The iris, xarray and  cdms2 modules are only required for the meta-data preserving interfaces.
+* **Do I need iris/xarray to use windspharm?**
+  No. All the computation code uses numpy only. The iris and/or xarray modules are only required for the meta-data preserving interfaces.
 * **Is windspharm a drop in replacement for windfield?**
   No. Because windspharm was written from scratch the naming conventions for methods
   are different. Some new methods have been added compared to windfield, and some
@@ -54,7 +52,9 @@ The easiest way to install is via [conda](http://conda.pydata.org):
 
     conda install -c conda-forge windspharm
 
-You can also install from the source distribution.
-Download the archive, unpack it, then enter the source directory and use:
+You can also install with pip::
 
-    python setup.py install
+    python -m pip install windspharm
+
+> [!CAUTION]
+> Make sure you already have pyspharm dependency installed, as it may fail to install if pip tries to do it.

docs/api/index.rst

@@ -10,7 +10,6 @@ Full documentation
    :maxdepth: 1
 
    windspharm.standard
-   windspharm.cdms
    windspharm.iris
    windspharm.xarray
    windspharm.tools