Merge pull request #52 from ocefpaf/fix_cis

Use pixi for CIs

.gitattributes

@@ -0,0 +1,2 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML linguist-generated=true

.github/workflows/deploy-docs.yml

@@ -10,41 +10,18 @@ on:
       - published
 
 jobs:
-  build-docs:
+  run:
     runs-on: ubuntu-latest
 
     steps:
-    - name: checkout
-      uses: actions/checkout@v4
+    - uses: actions/checkout@v4
+    - name: Setup Pixi
+      uses: prefix-dev/setup-pixi@v0.8.1
       with:
-        fetch-depth: 0
+        manifest-path: pyproject.toml
 
-    - name: Setup Micromamba
-      uses: mamba-org/setup-micromamba@v1
-      with:
-        environment-name: TEST
-        init-shell: bash
-        create-args: >-
-          python=3 pip
-          --file requirements.txt
-          --file requirements-dev.txt
-          --channel conda-forge
-
-    - name: Install ciso
-      shell: bash -l {0}
-      run: |
-        python -m pip install -e . --no-deps --force-reinstall
-
-    - name: Build documentation
-      shell: bash -l {0}
-      run: |
-        set -e
-        jupyter nbconvert --to notebook --execute notebooks/ciso_unstructure.ipynb --output=ciso_unstructure-output.ipynb
-        jupyter nbconvert --to notebook --execute notebooks/ciso_c_grid.ipynb --output=ciso_c_grid-output.ipynb
-        mv notebooks/*output.ipynb docs/source/
-        pushd docs
-        make clean html linkcheck
-        popd
+    - name: Run Tests
+      run: pixi run --environment py312 docs
 
     - name: Deploy
       if: success() && github.event_name == 'release'

.github/workflows/tests.yml

@@ -3,48 +3,28 @@ name: Tests
 on:
   pull_request:
   push:
-    branches: [main]
+    branches:
+      - main
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   run:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
-        os: [windows-latest, ubuntu-latest, macos-latest]
-        experimental: [false]
-        include:
-          - python-version: "3.12"
-            os: "ubuntu-latest"
-            experimental: true
+        pixi-environment: [ py310, py311,  py312 ]
+        os: [ windows-latest, ubuntu-latest, macos-latest ]
       fail-fast: false
-    defaults:
-      run:
-        shell: bash -l {0}
 
     steps:
     - uses: actions/checkout@v4
-
-    - name: Setup Micromamba ${{ matrix.python-version }}
-      uses: mamba-org/setup-micromamba@v1
+    - name: Setup Pixi
+      uses: prefix-dev/setup-pixi@v0.8.1
       with:
-        environment-name: TEST
-        init-shell: bash
-        create-args: >-
-          python=${{ matrix.python-version }} pip
-          --file requirements.txt
-          --file requirements-dev.txt
-          --channel conda-forge
-
-    - name: Install unstable dependencies
-      if: matrix.experimental == true
-      run: |
-        micromamba install conda-forge/label/numpy_dev::numpy
-
-    - name: Install ciso
-      run: |
-        python -m pip install -e . --no-deps --force-reinstall
+        manifest-path: pyproject.toml
 
-    - name: Tests
-      run: |
-        python -m pytest -rxs ciso/tests
+    - name: Run Tests
+      run: pixi run --environment ${{ matrix.pixi-environment }} test

.gitignore

@@ -7,3 +7,6 @@ _ciso*.so
 build/
 ciso/_version.py
 dist/
+# pixi environments
+.pixi
+*.egg-info

pyproject.toml

@@ -3,8 +3,7 @@ requires = [
   "setuptools>=41.2",
   "setuptools-scm",
   "cython>=3",
-  "oldest-supported-numpy ; python_version < '3.9'",
-  "numpy>=2.0.0rc1 ; python_version >= '3.9'",
+  "numpy>=2",
   "wheel",
 ]
 build-backend = "setuptools.build_meta"
@@ -18,11 +17,10 @@ authors = [
   {email = "hetland@tamu.edu"},
   {name = "Robert Hetland"}
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 license = {text = "BSD-2-Clause"}
 dependencies = [
-    "oldest-supported-numpy ; python_version < '3.9'",
-    "numpy>=2.0.0rc1 ; python_version >= '3.9'",
+    "numpy",
 ]
 
 [project.optional-dependencies]
@@ -79,3 +77,48 @@ exclude = ["setup.py", "docs", "tests"]
 verbose = 1
 quiet = false
 color = true
+
+[tool.pixi.project]
+channels = ["conda-forge"]
+platforms = ["win-64", "linux-64", "osx-64"]
+
+[tool.pixi.environments]
+default = { features = ["py312"], solve-group = "py312" }
+py312 = { features = ["py312"], solve-group = "py312" }
+py311 = ["py311"]
+py310 = ["py310"]
+
+[tool.pixi.tasks]
+install-pre-commit = "pre-commit install"
+pre-commit = "pre-commit run --all-files"
+test = "pip install -e . --no-deps --force-reinstall && pytest -rxs ciso/tests"
+docs = """\
+pip install -e . --no-deps --force-reinstall
+&& jupyter nbconvert --to notebook --execute notebooks/ciso_unstructure.ipynb --output=ciso_unstructure-output.ipynb
+&& jupyter nbconvert --to notebook --execute notebooks/ciso_c_grid.ipynb --output=ciso_c_grid-output.ipynb
+&& mv notebooks/*output.ipynb docs/source/
+&& cd docs
+&& make clean html linkcheck
+"""
+
+[tool.pixi.feature.py312.dependencies]
+python = "3.12.*"
+
+[tool.pixi.feature.py311.dependencies]
+python = "3.11.*"
+
+[tool.pixi.feature.py310.dependencies]
+python = "3.10.*"
+
+[tool.pixi.dependencies]
+cython = ">=3.0.11,<4"
+numpy = ">1.19"
+pytest = ">=8.3.3,<9"
+pre-commit = ">=3.8.0,<4"
+gridgeo = ">=1.5.2,<2"
+jupyter = ">=1.1.1,<2"
+nbsphinx = ">=0.9.5,<0.10"
+sphinx = ">=8.0.2,<9"
+pip = ">=24.2,<25"
+scitools-iris = ">=3.9.0,<4"
+nbclassic = ">=1.1.0,<2"