Added a noxfile and removed lint (#83)

* add a noxfile * add a pre-commit config file * remove all the lint * update requirements; add requirements.py to extract requirements * update path to the docs * update readthedocs config file * move black workflow into lint workflow * add a workflow to test that the docs build * add session to build the languages and test them * add make and pip to the external requirements * remove old and deprecated wrap module * install pydocstyl[toml] * require coverage[toml] * simplify calls to subprocess.run using partial * fix typos * run tests with nox * add pytest-xdist as a requirement for testing * require setuptools < 60 for the build system * use python -m pip * clean up noxfile.py, parametrize python versions * specify the python version * use setup-python action * remove conda backend from regular tests * run the language tests in a separate step * use --python option * fix typos * ignore nox virtual envs in the .nox folder * print some debugging messages * run with --verbose * run setup.py build_ext * print more debugging messages * run the language tests with nox, not pytest * install tomli for ci tests * more debugging messages * limit to just c * forget linux for now * reinstall the compilers * install compilers before running nox * test on linux again; clean up the nox file * print the environment before compiling * disable linux again * install cmake along with compilers * try linux again * try an older version of gfortran * try to install gcc9 on linux * try gcc less than 10 * try installing older version of all the compilers * try native compilers on linux * install bmi-fortran along with the fortran compiler * try the new build of bmi-fortran * add towncrier as a dev requirement * add news fragments * auto-generate the api documentation * move the cli doc page out of the api docs * update extension settings in conf.py * move the tomli import * add a GitHub action to check for news fragments * update requirements file * remove the makefile * install cmake to build the examples
csdms · Nov 28, 2022 · 56ce18b · 56ce18b
1 parent 5c40eaa
commit 56ce18b
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diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml
diff --git a/.github/workflows/build-test-ci.yml b/.github/workflows/build-test-ci.yml
@@ -20,12 +20,16 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10"]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           submodules: true
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
 
       - uses: conda-incubator/setup-miniconda@v2
         with:
@@ -36,60 +40,16 @@ jobs:
           channel-priority: true
 
       - name: Install dependencies
-        run: |
-          pip install coverage[toml]
-          mamba install --file=requirements.txt --file=requirements-testing.txt --file=external/requirements.txt
-          conda list
-
-      - name: Install build system
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.8'
-        run: |
-          mamba install cython numpy setuptools wheel
-
-      - name: Install babelizer
-        run: |
-          pip install .
-
-      - name: Run diagnostics
-        run: |
-          babelize --version
-          babelize --help
-          babelize init --help
-          babelize update --help
-          babelize generate --help
-          babelize generate
-          python -c 'import babelizer; print(babelizer.__version__)'
-
-      - name: Make C example
-        run: |
-          mkdir buildc && pushd buildc
-          cmake ../external/bmi-example-c -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX
-          make install
-          popd
-
-      - name: Make C++ example
-        run: |
-          mkdir buildcxx && pushd buildcxx
-          cmake ../external/bmi-example-cxx -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX
-          make install
-          popd
+        run: python -m pip install nox tomli
 
-      - name: Make Fortran example
-        run: |
-          mkdir buildf && pushd buildf
-          cmake ../external/bmi-example-fortran -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX
-          make install
-          popd
+      - name: Install compilers
+        run: mamba install c-compiler cxx-compiler fortran-compiler cmake
 
-      - name: Make Python example
-        run: |
-          pushd ./external/bmi-example-python
-          make install
-          popd
+      - name: Run the tests
+        run: nox --session test test-cli --python ${{ matrix.python-version }} --verbose
 
-      - name: Test babelizer + language examples and generate coverage report
-        run: |
-          pytest --cov=babelizer --cov-report=xml:./coverage.xml -vvv babelizer tests external/tests
+      - name: Run the language tests
+        run: nox --non-interactive --error-on-missing-interpreter --session test-langs --python ${{ matrix.python-version }} --verbose
 
       - name: Coveralls
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.9'

diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml
@@ -0,0 +1,25 @@
+name: Check
+
+on:
+  pull_request:
+    types: [labeled, unlabeled, opened, reopened, synchronize]
+
+jobs:
+  check-changelog-entry:
+    name: changelog entry
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          # `towncrier check` runs `git diff --name-only origin/main...`, which
+          # needs a non-shallow clone.
+          fetch-depth: 0
+
+      - name: Check changelog
+        if: "!contains(github.event.pull_request.labels.*.name, 'Skip Changelog')"
+        run: |
+          if ! pipx run towncrier check --compare-with origin/${{ github.base_ref }}; then
+          echo "Please see https://landlab.readthedocs.io/en/master/development/contribution/index.html?highlight=towncrier#news-entries for guidance."
+            false
+          fi
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -26,9 +26,9 @@ jobs:
         if:
           github.event_name == 'push' || github.event.pull_request.head.repo.full_name !=
           github.repository
-    
+
         runs-on: ubuntu-latest
-        
+
         defaults:
           run:
             shell: bash -l {0}
@@ -43,16 +43,11 @@ jobs:
               channel-priority: true
 
           - name: Show conda installation info
-            run: |
-              conda info
-              conda list
+            run: conda info
 
           - name: Install dependencies
             run: |
-              conda install mamba
-              mamba install --file=requirements.txt
-              pip install -r requirements-docs.txt
-              pip install -e .
+              pip install nox
 
           - name: Build documentation
-            run: make -C docs clean html
+            run: nox -s build-docs
diff --git a/.github/workflows/flake8.yml → .github/workflows/lint.yml b/.github/workflows/flake8.yml → .github/workflows/lint.yml
@@ -1,10 +1,11 @@
-name: Flake8
+name: Lint
 
 on: [push, pull_request]
 
 jobs:
 
   lint:
+    name: Check for lint
     # We want to run on external PRs, but not on our own internal PRs as they'll be run
     # by the push to the branch. Without this if check, checks are duplicated since
     # internal PRs match both the push and pull_request events.
@@ -15,12 +16,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python 3.8
+      - name: Set up Python 3.9
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - name: Lint
         run: |
-          pip install flake8
-          flake8
+          pip install nox tomli
+          nox -s lint
diff --git a/.gitignore b/.gitignore
@@ -99,3 +99,6 @@ ENV/
 
 # mypy
 .mypy_cache/
+
+# nox virtual envs
+.nox/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,84 @@
+repos:
+- repo: https://github.com/psf/black
+  rev: 22.3.0
+  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]
+    exclude: ^babelizer/data
+  - 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]"]
+    exclude: ^babelizer/data
+
+- repo: https://github.com/pycqa/flake8
+  rev: 4.0.1
+  hooks:
+  - id: flake8
+    additional_dependencies:
+    - flake8-bugbear
+    - flake8-comprehensions
+    - flake8-simplify
+    exclude: ^babelizer/data
+
+- repo: https://github.com/asottile/pyupgrade
+  rev: v2.34.0
+  hooks:
+  - id: pyupgrade
+    args: [--py38-plus]
+    exclude: ^babelizer/data
+
+- repo: https://github.com/PyCQA/isort
+  rev: 5.10.1
+  hooks:
+  - id: isort
+    files: \.py$
+    exclude: ^babelizer/data
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.3.0
+  hooks:
+    - id: check-builtin-literals
+      exclude: ^babelizer/data
+    - id: check-added-large-files
+    - id: check-case-conflict
+    - id: check-toml
+      exclude: ^babelizer/data
+    - id: check-yaml
+      exclude: ^babelizer/data
+    - id: debug-statements
+      exclude: ^babelizer/data
+    - id: end-of-file-fixer
+    - id: forbid-new-submodules
+    - id: trailing-whitespace
+
+- repo: https://github.com/PyCQA/pydocstyle
+  rev: 6.1.1
+  hooks:
+  - id: pydocstyle
+    files: babelizer/.*\.py$
+    args:
+    - --convention=numpy
+    - --add-select=D417
+    exclude: ^babelizer/data
+    additional_dependencies: [".[toml]"]
+
+- repo: https://github.com/pre-commit/mirrors-mypy
+  rev: v0.982
+  hooks:
+  - id: mypy
+    additional_dependencies: [types-all]
+    exclude: ^babelizer/data
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -9,7 +9,6 @@ formats:
   - htmlzip
 
 python:
-  version: 3.8
   install:
     - requirements: requirements-docs.txt
     - requirements: requirements.txt
@@ -18,4 +17,9 @@ python:
   system_packages: false
 
 build:
-  image: latest
+  os: ubuntu-22.04
+  tools:
+    python: "3.9"
+  jobs:
+    pre_build:
+      - sphinx-apidoc -e -force --no-toc --module-first -o docs/source/api babelizer
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,13 +1,9 @@
 Changelog
 =========
 
-.. towncrier release notes start
-
-0.3.10 (unreleased)
--------------------
-
-- Nothing changed yet.
+.. towncrier-draft-entries:: Not yet released
 
+.. towncrier release notes start
 
 0.3.9 (2022-03-04)
 ------------------
@@ -242,4 +238,3 @@ Improved Documentation
 ------------------
 
 - Initial release
-
diff --git a/LICENSE.rst b/LICENSE.rst
@@ -23,4 +23,3 @@ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
 WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
 OTHER DEALINGS IN THE SOFTWARE.
-