Merge branch 'master' into shebang

.coveragerc

@@ -0,0 +1,10 @@
+[run]
+branch = true
+omit = */BOUT-dev/*
+
+[report]
+exclude_lines =
+    if __name__ == .__main__.:
+omit =
+    */tests/*
+    */docs/*

.github/workflows/lint.yml

@@ -0,0 +1,42 @@
+name: Lint
+
+on:
+  # Run each time we push and pull requests
+  push:
+  pull_request:
+  # Cron job
+  # https://help.github.com/en/actions/automating-your-workflow-with-github-actions/events-that-trigger-workflows#scheduled-events-schedule
+  schedule:
+    # https://crontab.guru/#0_0_1_*_*
+    - cron: "0 0 1 * *"
+
+jobs:
+  linting:
+    runs-on: ubuntu-latest
+
+    steps:
+      # Use the v2 tag of: https://github.com/actions/checkout
+      - name: Checkout repo
+        uses: actions/checkout@v2
+
+      - name: Set up Python 3.x
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      - name: Set up Python ${{ matrix.python-version }}
+        # Use the v2 tag of: https://github.com/actions/setup-python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        # https://github.com/PyCQA/pylint/issues/352
+        # pylint need the requirements to do the checks as the pre-commit repo is local
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install --upgrade pre-commit
+          pip install .
+
+      - name: Lint
+        run: pre-commit run --all-files

.github/workflows/python_publish.yml

@@ -9,19 +9,19 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v1
-    - name: Set up Python
-      uses: actions/setup-python@v1
-      with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+      - uses: actions/checkout@v1
+      - name: Set up Python
+        uses: actions/setup-python@v1
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools wheel twine
+      - name: Build and publish
+        env:
+          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: |
+          python setup.py sdist bdist_wheel
+          twine upload dist/*

.github/workflows/test.yml

@@ -0,0 +1,51 @@
+name: Test
+
+on:
+  # Run each time we push and pull requests
+  push:
+  pull_request:
+  # Cron job
+  # https://help.github.com/en/actions/automating-your-workflow-with-github-actions/events-that-trigger-workflows#scheduled-events-schedule
+  schedule:
+    # https://crontab.guru/#0_0_1_*_*
+    - cron: "0 0 1 * *"
+
+jobs:
+  # As we are running on different environments, we are splitting the jobs
+  # https://docs.github.com/en/free-pro-team@latest/actions/reference/workflow-syntax-for-github-actions#jobs
+  local:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: true
+      matrix:
+        python-version: [3.7, 3.8]
+        os: [ubuntu-latest]
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Setup prerequisites
+        run:
+          sudo apt update && sudo apt install -y libhdf5-serial-dev netcdf-bin
+          libnetcdf-dev libsm6 libxext6 libxrender-dev libxt6 libgl1-mesa-glx
+          libfontconfig libxkbcommon-x11-0
+
+      - name: Install dependencies
+        run: |
+          pip install setuptools_scm pytest-cov
+          pip install .
+
+      - name: Test local run
+        run: |
+          pytest --cov=./
+
+      - name: Upload to codecov
+        run: |
+          pip install codecov
+          codecov

.gitignore

@@ -126,4 +126,3 @@ dmypy.json
 .DS_Store
 .idea/
 *.sw[po]
-

.pre-commit-config.yaml

@@ -0,0 +1,29 @@
+# NOTE: The versions can be updated by calling
+#        pre-commit autoupdate
+repos:
+  - repo: https://github.com/psf/black
+    rev: 20.8b1
+    hooks:
+      - id: black
+
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 3.8.4
+    hooks:
+      - id: flake8
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+
+  - repo: https://github.com/prettier/pre-commit
+    rev: 57f39166b5a5a504d6808b87ab98d41ebf095b46
+    hooks:
+      - id: prettier
+        args: [--prose-wrap=always, --print-width=88]
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.7.0
+    hooks:
+      - id: isort

README.md

@@ -7,25 +7,21 @@
 [![PEP8](https://img.shields.io/badge/code%20style-PEP8-brightgreen.svg)](https://www.python.org/dev/peps/pep-0008/)
 [![License](https://img.shields.io/badge/license-LGPL--3.0-blue.svg)](https://github.com/boutproject/boututils/blob/master/LICENSE)
 
-pip-package of what was previously found in
-`BOUT-dev/tools/pylib/boututils`
-Note that `BOUT-dev/tools/pylib/boututils` will likely be replaced by this repo
-in `BOUT++ v4.3.0`.
-See [this issue](https://github.com/boutproject/BOUT-dev/issues/1347),
+pip-package of what was previously found in `BOUT-dev/tools/pylib/boututils` Note that
+`BOUT-dev/tools/pylib/boututils` will likely be replaced by this repo in
+`BOUT++ v4.3.0`. See [this issue](https://github.com/boutproject/BOUT-dev/issues/1347),
 [this pull request](https://github.com/boutproject/BOUT-dev/pull/1766) and
 [this pull request](https://github.com/boutproject/BOUT-dev/pull/1740) for details.
 
 > **NOTE**: This package will likely be superseded by
-  [`xBOUT`](https://github.com/boutproject/xBOUT) in the near future
+> [`xBOUT`](https://github.com/boutproject/xBOUT) in the near future
 
 # Dependencies
 
-`boututils` depends on
-[`netcfd4`](https://github.com/Unidata/netcdf4-python) which requires
-[`HDF5`](https://www.h5py.org) and
-[`netcdf-4`](https://github.com/Unidata/netcdf-c/releases) are
-installed, and that the `nc-config` utility is in your `PATH`. This
-can be install with
+`boututils` depends on [`netcfd4`](https://github.com/Unidata/netcdf4-python) which
+requires [`HDF5`](https://www.h5py.org) and
+[`netcdf-4`](https://github.com/Unidata/netcdf-c/releases) are installed, and that the
+`nc-config` utility is in your `PATH`. This can be install with
 
 ```
 sudo apt-get install libhdf5-serial-dev netcdf-bin libnetcdf-dev
@@ -36,4 +32,3 @@ in ubuntu
 # Install
 
 `pip install boututils`
-