Merge branch 'master' into read-wtime-stats

.github/workflows/black.yml

@@ -0,0 +1,37 @@
+name: black
+
+on:
+  pull_request:
+    paths:
+      - '**.py'
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  black:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        ref: ${{ github.head_ref }}
+    - name: Setup Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.x
+    - name: Install black
+      run: |
+        python -m pip install --upgrade pip
+        pip install black
+    - name: Version
+      run: |
+        python --version
+        black --version
+    - name: Run black
+      run: |
+        black xbout
+        black docs
+    - uses: stefanzweifel/git-auto-commit-action@v4
+      with:
+        commit_message: "Apply black formatting"

.github/workflows/master.yml

@@ -20,94 +20,51 @@ jobs:
     if: always()
     strategy:
       matrix:
-        python-version: [3.8, 3.9, '3.10', 3.x]
-        pip-packages:
-          - "setuptools pip pytest pytest-cov coverage codecov boutdata xarray numpy>=1.16.0"
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.x"]
       fail-fast: false
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         sudo apt-get update && sudo apt-get install libhdf5-dev libnetcdf-dev
         python -m pip install --upgrade pip
-        pip install --upgrade ${{ matrix.pip-packages }}
-        pip install -e .
+    - name: Install package
+      run: |
+        pip install -e .[calc,tests]
     - name: Test with pytest
       run: |
-        pip install pytest
-        pytest -v --long --cov
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v1
+        pytest -vv --long --cov
 
 
-  pytest-min-versions:
+  # test with oldest supported version of packages
+  pytest-oldest-xarray:
 
     runs-on: ubuntu-latest
     if: always()
     strategy:
       matrix:
-        python-version: [3.8]
-        pip-packages:
-          - "setuptools pip pytest pytest-cov coverage codecov boutdata==0.1.4 xarray==0.18.0 dask==2.10.0 numpy==1.18.0 natsort==5.5.0 matplotlib==3.1.1 animatplot==0.4.2 netcdf4==1.4.2 Pillow==6.1.0" # test with oldest supported version of packages. Note, using numpy==1.18.0 as a workaround because numpy==1.17.0 is not supported on Python-3.7, even though we should currently support numpy==1.17.0.
+        python-version: ["3.8"]
       fail-fast: false
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         sudo apt-get update && sudo apt-get install libhdf5-dev libnetcdf-dev
         python -m pip install --upgrade pip
-        pip install --upgrade ${{ matrix.pip-packages }}
-        pip install -e .
-    - name: Test with pytest
+        pip install xarray~=0.18.0 pandas~=1.4.0
+    - name: Install package
       run: |
-        pip install pytest
-        pytest -v --long --cov
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v1
-
-
-  # Need to tidy up the things that flake8 finds before we activate this
-  #flake8:
-
-  #  runs-on: ubuntu-latest
-  #  if: always()
-
-  #  steps:
-  #  - uses: actions/checkout@v2
-  #  - name: Set up Python
-  #    uses: actions/setup-python@v1
-  #  - name: Install dependencies
-  #    run: |
-  #      python -m pip install --upgrade pip
-  #  - name: Lint with flake8
-  #    run: |
-  #      pip install flake8
-  #      flake8
-
-
-  black:
-
-    runs-on: ubuntu-latest
-    if: always()
-
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v1
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-    - name: Check formatting with black
+        pip install -e .[tests]
+    - name: Test with pytest
       run: |
-        pip install black
-        black --check .
+        pytest -vv --long --cov

.github/workflows/pythonpackage.yml

@@ -20,94 +20,51 @@ jobs:
     if: always()
     strategy:
       matrix:
-        python-version: [3.8, 3.9, '3.10', 3.x]
-        pip-packages:
-          - "setuptools pip pytest pytest-cov coverage codecov boutdata xarray numpy>=1.16.0"
+        python-version: ["3.8", "3.9", "3.10", "3.x"]
       fail-fast: false
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         sudo apt-get update && sudo apt-get install libhdf5-dev libnetcdf-dev
         python -m pip install --upgrade pip
-        pip install --upgrade ${{ matrix.pip-packages }}
-        pip install -e .
+    - name: Install package
+      run: |
+        pip install -e .[calc,tests]
     - name: Test with pytest
       run: |
-        pip install pytest
-        pytest -v --long --cov
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v1
+        pytest -vv --long --cov
 
 
-  pytest-min-versions:
+  # test with oldest supported version of packages
+  pytest-oldest-xarray:
 
     runs-on: ubuntu-latest
     if: always()
     strategy:
       matrix:
-        python-version: [3.8]
-        pip-packages:
-          - "setuptools pip pytest pytest-cov coverage codecov boutdata==0.1.4 xarray==0.18.0 dask==2.10.0 numpy==1.18.0 natsort==5.5.0 matplotlib==3.1.1 animatplot==0.4.2 netcdf4==1.4.2 Pillow==7.2.0" # test with oldest supported version of packages. Note, using numpy==1.18.0 as a workaround because numpy==1.17.0 is not supported on Python-3.7, even though we should currently support numpy==1.17.0.
+        python-version: ["3.8"]
       fail-fast: false
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         sudo apt-get update && sudo apt-get install libhdf5-dev libnetcdf-dev
         python -m pip install --upgrade pip
-        pip install --upgrade ${{ matrix.pip-packages }}
-        pip install -e .
-    - name: Test with pytest
+        pip install xarray~=0.18.0 pandas~=1.4.0
+    - name: Install package
       run: |
-        pip install pytest
-        pytest -v --long --cov
-    - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v1
-
-
-  # Need to tidy up the things that flake8 finds before we activate this
-  #flake8:
-
-  #  runs-on: ubuntu-latest
-  #  if: always()
-
-  #  steps:
-  #  - uses: actions/checkout@v2
-  #  - name: Set up Python
-  #    uses: actions/setup-python@v1
-  #  - name: Install dependencies
-  #    run: |
-  #      python -m pip install --upgrade pip
-  #  - name: Lint with flake8
-  #    run: |
-  #      pip install flake8
-  #      flake8
-
-
-  black:
-
-    runs-on: ubuntu-latest
-    if: always()
-
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v1
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-    - name: Check formatting with black
+        pip install -e .[tests]
+    - name: Test with pytest
       run: |
-        pip install black
-        black --check .
+        pytest -vv --long --cov

.github/workflows/pythonpublish.yml

@@ -5,125 +5,26 @@ name: Upload Python Package
 
 on:
   release:
-    types: [created]
+    types: [published]
 
 jobs:
-  pytest:
-
-    runs-on: ubuntu-latest
-    if: always()
-    strategy:
-      matrix:
-        python-version: [3.8, 3.9, '3.10', 3.x]
-        pip-packages:
-          - "setuptools pip pytest boutdata xarray numpy>=1.16.0"
-      fail-fast: true
-
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        sudo apt-get update && sudo apt-get install libhdf5-dev libnetcdf-dev
-        python -m pip install --upgrade pip
-        pip install --upgrade ${{ matrix.pip-packages }}
-        pip install -e .
-    - name: Test with pytest
-      run: |
-        pip install pytest
-        pytest -v --long
-
-
-  pytest-min-versions:
-
-    runs-on: ubuntu-latest
-    if: always()
-    strategy:
-      matrix:
-        python-version: [3.8]
-        pip-packages:
-          - "setuptools pip pytest boutdata==0.1.4 xarray==0.18.0 dask==2.10.0 numpy==1.18.0 natsort==5.5.0 matplotlib==3.1.1 animatplot==0.4.2 netcdf4==1.4.2 Pillow==7.2.0" # test with oldest supported version of packages. Note, using numpy==1.18.0 as a workaround because numpy==1.17.0 is not supported on Python-3.7, even though we should currently support numpy==1.17.0.
-      fail-fast: true
-
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        sudo apt-get update && sudo apt-get install libhdf5-dev libnetcdf-dev
-        python -m pip install --upgrade pip
-        pip install --upgrade ${{ matrix.pip-packages }}
-        pip install -e .
-    - name: Test with pytest
-      run: |
-        pip install pytest
-        pytest -v --long
-
-
-  # Need to tidy up the things that flake8 finds before we activate this
-  #flake8:
-
-  #  runs-on: ubuntu-latest
-  #  if: always()
-
-  #  steps:
-  #  - uses: actions/checkout@v2
-  #  - name: Set up Python
-  #    uses: actions/setup-python@v1
-  #  - name: Install dependencies
-  #    run: |
-  #      python -m pip install --upgrade pip
-  #  - name: Lint with flake8
-  #    run: |
-  #      pip install flake8
-  #      flake8
-
-
-  black:
-
-    runs-on: ubuntu-latest
-    if: always()
-
-    steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v1
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-    - name: Check formatting with black
-      run: |
-        pip install black
-        black --check .
-
   deploy:
-
+    name: Upload release to PyPI
     runs-on: ubuntu-latest
-    needs: [pytest, pytest-min-versions, black]
-
+    environment: release
+    permissions:
+      id-token: write
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
     - name: Install dependencies
       run: |
         sudo apt-get update && sudo apt-get install libhdf5-dev libnetcdf-dev
-        python -m pip install --upgrade pip
-        pip install --upgrade setuptools wheel twine
-        pip install -e .
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      run: |
-        git fetch --tags --unshallow
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+        python -m pip install --upgrade pip build
+    - name: Build package
+      run: python -m build --sdist --wheel
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1