Update CI workflows

.flake8

@@ -0,0 +1,10 @@
+[flake8]
+exclude = docs, build, .nox
+ignore =
+  E203
+  E501
+  W503
+  W605
+max-line-length = 88
+max-complexity = 18
+select = B,C,E,F,W,T4,B9

.github/workflows/docs.yml

@@ -2,6 +2,10 @@ name: Documentation
 
 on: [push, pull_request]
 
+concurrency:
+  group: ${{ github.ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
 
   build:
@@ -13,9 +17,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-version: latest
           python-version: 3.11

.github/workflows/format.yml → .github/workflows/lint.yml

@@ -1,7 +1,11 @@
-name: Format
+name: Lint
 
 on: [push, pull_request]
 
+concurrency:
+  group: ${{ github.ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
 jobs:
 
   format:
@@ -12,9 +16,9 @@ jobs:
 
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-version: latest
           python-version: 3.11
@@ -24,4 +28,4 @@ jobs:
         run: pip install nox
 
       - name: Format code
-        run: nox -s format -- --check --verbose --diff
+        run: nox -s lint

.github/workflows/test-notebooks.yml

@@ -0,0 +1,44 @@
+name: Notebooks
+
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
+jobs:
+  test-notebooks:
+    name: Check notebooks
+    if:
+      github.event_name == 'push' || github.event.pull_request.head.repo.full_name !=
+      github.repository
+
+    runs-on: ${{ matrix.os }}
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+          miniforge-variant: Miniforge3
+          miniforge-version: latest
+          auto-update-conda: true
+
+      - name: Install nox
+        run: pip install nox
+
+      - name: Test Jupyter notebooks
+        env:
+          MPLBACKEND: "Agg"
+        run: |
+          nox --verbose -s test-notebooks --force-pythons="${{ matrix.python-version }}"

.github/workflows/build-test-ci.yml → .github/workflows/test.yml

@@ -1,11 +1,14 @@
-name: Build/Test CI
+name: Test
 
 on: [push, pull_request]
 
-jobs:
+concurrency:
+  group: ${{ github.ref }}-${{ github.workflow }}
+  cancel-in-progress: true
 
-  build-and-test:
+jobs:
 
+  test:
     if:
       github.event_name == 'push' || github.event.pull_request.head.repo.full_name !=
       github.repository
@@ -28,18 +31,10 @@ jobs:
         with:
           miniforge-variant: Mambaforge
           miniforge-version: latest
-          environment-file: environment.yml
-          activate-environment: geotiff
           python-version: ${{ matrix.python-version }}
-          auto-activate-base: false
-
-      - name: Show conda installation info
-        run: |
-          conda info
-          conda list
 
-      - name: Install package
-        run: pip install -e .
+      - name: Install nox
+        run: pip install nox
 
       - name: Test
         run: |

.pre-commit-config.yaml

@@ -0,0 +1,98 @@
+repos:
+- repo: local
+  hooks:
+    - id: unnecessary_doctest_directives
+      name: Check for redundant doctest directives
+      description:
+        "Check for inline doctest directives that are specified globally through pyproject.toml"
+      types: [python]
+      entry: >
+        (?x)(
+          \+IGNORE_EXCEPTION_DETAIL|
+          \+NORMALIZE_WHITESPACE
+        )
+      language: pygrep
+
+- repo: https://github.com/psf/black
+  rev: 24.4.0
+  hooks:
+  - id: black
+    name: black
+    description: "Black: The uncompromising Python code formatter"
+    entry: black
+    language: python
+    language_version: python3
+    minimum_pre_commit_version: 2.9.2
+    require_serial: true
+    types_or: [python, pyi]
+  - id: black-jupyter
+    name: black-jupyter
+    description:
+      "Black: The uncompromising Python code formatter (with Jupyter Notebook support)"
+    entry: black
+    language: python
+    minimum_pre_commit_version: 2.9.2
+    require_serial: true
+    types_or: [python, pyi, jupyter]
+    additional_dependencies: [".[jupyter]"]
+
+- repo: https://github.com/keewis/blackdoc
+  rev: v0.3.9
+  hooks:
+  - id: blackdoc
+    description: "Black for doctests"
+    additional_dependencies: ["black==24.4.0"]
+  - id: blackdoc-autoupdate-black
+
+- repo: https://github.com/pycqa/flake8
+  rev: 7.0.0
+  hooks:
+  - id: flake8
+    additional_dependencies:
+    # - flake8-bugbear!=24.4.21
+    # - flake8-comprehensions
+    - flake8-simplify
+
+- repo: https://github.com/nbQA-dev/nbQA
+  rev: 1.8.5
+  hooks:
+    - id: nbqa-pyupgrade
+      args: ["--py310-plus"]
+    # - id: nbqa-isort
+    - id: nbqa-flake8
+      args: ["--extend-ignore=E402"]
+
+- repo: https://github.com/kynan/nbstripout
+  rev: 0.7.1
+  hooks:
+    - id: nbstripout
+      description: Strip output from jupyter notebooks
+      args: [--drop-empty-cells]
+
+- repo: https://github.com/asottile/pyupgrade
+  rev: v3.15.2
+  hooks:
+  - id: pyupgrade
+    args: [--py310-plus]
+
+- repo: https://github.com/PyCQA/isort
+  rev: 5.13.2
+  hooks:
+  - id: isort
+    name: isort (python)
+    # args: [--force-single-line-imports]
+    types: [python]
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.6.0
+  hooks:
+    - id: check-builtin-literals
+    - id: check-added-large-files
+    - id: check-case-conflict
+    - id: check-toml
+    - id: check-yaml
+    - id: debug-statements
+    - id: end-of-file-fixer
+    - id: forbid-new-submodules
+    - id: mixed-line-ending
+    - id: trailing-whitespace

README.md

@@ -1,7 +1,7 @@
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.8327418.svg)](https://doi.org/10.5281/zenodo.8327418)
 [![PyPI](https://img.shields.io/pypi/v/bmi-geotiff)](https://pypi.org/project/bmi-geotiff)
 [![Conda Version](https://img.shields.io/conda/vn/conda-forge/bmi-geotiff.svg)](https://anaconda.org/conda-forge/bmi-geotiff)
-[![Build/Test CI](https://github.com/csdms/bmi-geotiff/actions/workflows/build-test-ci.yml/badge.svg)](https://github.com/csdms/bmi-geotiff/actions/workflows/build-test-ci.yml)
+[![Test](https://github.com/csdms/bmi-geotiff/actions/workflows/test.yml/badge.svg)](https://github.com/csdms/bmi-geotiff/actions/workflows/test.yml)
 [![Documentation Status](https://readthedocs.org/projects/bmi-geotiff/badge/?version=latest)](https://bmi-geotiff.readthedocs.io/en/latest/?badge=latest)
 
 # bmi-geotiff

docs/source/conf.py

@@ -28,7 +28,7 @@
 version = pkg_resources.get_distribution("bmi_geotiff").version
 release = version
 this_year = datetime.date.today().year
-copyright = "{}, {}".format(this_year, author)
+copyright = f"{this_year}, {author}"
 
 
 # -- General configuration ---------------------------------------------------

examples/bmi-geotiff.ipynb

@@ -140,7 +140,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ls"
+    "!ls"
    ]
   },
   {
@@ -150,7 +150,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "cat config.yaml"
+    "!cat config.yaml"
    ]
   },
   {

noxfile.py

@@ -49,19 +49,28 @@ def test_bmi(session: nox.Session) -> None:
     )
 
 
-@nox.session
-def format(session: nox.Session) -> None:
-    """Clean lint and assert style."""
-    session.install(".[dev]")
+@nox.session(name="test-notebooks", python=PYTHON_VERSIONS[-1])
+def test_notebooks(session: nox.Session) -> None:
+    """Test the notebooks."""
+    session.install(".[testing,examples]")
+    session.install("nbmake")
 
-    if session.posargs:
-        black_args = session.posargs
-    else:
-        black_args = []
+    args = [
+        "examples",
+        "--nbmake",
+        "--nbmake-kernel=python3",
+        "--nbmake-timeout=3000",
+        "-vvv",
+    ] + session.posargs
 
-    session.run("black", *black_args, *PATHS)
-    session.run("isort", *PATHS)
-    session.run("flake8", *PATHS)
+    session.run("pytest", *args)
+
+
+@nox.session
+def lint(session: nox.Session) -> None:
+    """Clean lint and assert style."""
+    session.install("pre-commit")
+    session.run("pre-commit", "run", "--all-files")
 
 
 @nox.session(name="prepare-docs")

pyproject.toml

@@ -46,9 +46,6 @@ Changelog = "https://github.com/csdms/bmi-geotiff/blob/main/CHANGES.md"
 
 [project.optional-dependencies]
 dev = [
-  "black",
-  "flake8",
-  "isort",
   "nox",
 ]
 build = [
@@ -95,6 +92,7 @@ addopts = """
   --durations 16
   --doctest-modules
   -vvv
+  --ignore-glob=examples/*.py
 """
 doctest_optionflags = [
   "NORMALIZE_WHITESPACE",