Merge pull request #218 from halomod/warnings-tests

Warnings tests

.flake8

@@ -1,21 +1,36 @@
 [flake8]
 ignore =
-    E203  # No space before colon
+    # No space before colon
+    E203
     W503
-    D107  # Missing docstring in __init__ (we do it in the class)
-    D401  # "First line should be in imperative mood" -- this doesn't work for properties, see https://github.com/PyCQA/pydocstyle/issues/301
-    A003  # allow method names to be the same as python builtins
-    RST210  # inline strong start-string without end-string. This is OK in the case of **kwargs in parameters.
-    D102  # Ignore public methods without docstrings, because it doesn't check for inheritance :/
-    D200  # TODO: remove. (one-line docstring should fit on one line with quotes)
-    D400  # TODO: remove. (first line should end with a period)
-    E501  # TODO: remove (line too long)
-    D105  # TODO: remove
-    D204  # TODO: remove
-    D202  # TODO: remove
-    D205  # TODO: remove
-    G004  # logging statement uses f-string
-    B028  # stuff manually surrounded by quotes.
+    # Missing docstring in __init__ (we do it in the class)
+    D107
+    # "First line should be in imperative mood" -- this doesn't work for properties, see https://github.com/PyCQA/pydocstyle/issues/301
+    D401
+    # allow method names to be the same as python builtins
+    A003
+    # inline strong start-string without end-string. This is OK in the case of **kwargs in parameters.
+    RST210
+    # Ignore public methods without docstrings, because it doesn't check for inheritance :/
+    D102
+    # TODO: remove. (one-line docstring should fit on one line with quotes)
+    D200
+    # TODO: remove. (first line should end with a period)
+    D400
+    # TODO: remove (line too long)
+    E501
+    # TODO: remove
+    D105
+    # TODO: remove
+    D204
+    # TODO: remove
+    D202
+    # TODO: remove
+    D205
+    # logging statement uses f-string
+    G004
+    # No explicit stacklevel keyword argument in warn calls
+    B028
 max-line-length = 88
 # Should be 18.
 max-complexity = 25

.github/workflows/check-build.yml

@@ -0,0 +1,27 @@
+name: Check Distribution Build
+
+on: push
+
+jobs:
+  check-build:
+    name: Twine Check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@master
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install Build Tools
+        run: pip install build twine
+
+      - name: Build a binary wheel
+        run: |
+          python -m build .
+
+      - name: Check Distribution
+        run: |
+          twine check dist/*

.github/workflows/publish-to-pypi.yaml

@@ -1,42 +1,30 @@
-name: Deploy to PyPI
+name: Publish Python distributions to PyPI
 
-on: push
+on:
+  release:
+    types: [published]
 
 jobs:
   build-n-publish:
-    name: Deploy
-    runs-on: ubuntu-22.04
+    name: Make Release on PyPI and Github
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@master
-      # https://github.com/ansible/pylibssh/blob/1e7b17f/.github/workflows/build-test-n-publish.yml#L146-L151
-      - name: Get history and tags for SCM versioning to work
-        run: |
-          git fetch --prune --unshallow
-          git fetch --depth=1 origin +refs/tags/*:refs/tags/*
-          git describe --tags
-          git describe --tags $(git rev-list --tags --max-count=1)
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v4
         with:
-          python-version: "3.10"
-      - name: Install pep517
-        run: |
-          python -m pip install pep517 --user
-          python -m pip install setuptools_scm
-          python setup.py --version
-      - name: Create setuptools_scm env variable
-        if: startsWith(github.ref, 'refs/tags/') != true
-        shell: bash
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install Build Tools
+        run: pip install build
+
+      - name: Build a binary wheel
         run: |
-          wget https://gist.github.com/plaplant/0902f09e59166bac742bbd554f3cd2f9/raw/make_dev_version.sh -O ../make_dev_version.sh
-          version=$(bash ../make_dev_version.sh)
-          echo "SETUPTOOLS_SCM_PRETEND_VERSION=$version" >> $GITHUB_ENV
-      - name: Build a binary wheel and a source tarball
-        run: python -m pep517.build --binary --source --out-dir dist .
-      # deploy to actual PyPI only when a tag is pushed (which should happen only
-      # automatically on master)
-      - name: Publish distribution 📦 to PyPI
-        if: startsWith(github.ref, 'refs/tags')
-        uses: pypa/gh-action-pypi-publish@release/v1
+          python -m build .
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@master
         with:
           password: ${{ secrets.pypi_password }}

.github/workflows/test_suite.yaml

@@ -5,12 +5,9 @@ name: Tests
 # Also, only test on pull requests into master/dev.
 on:
   push:
-    tags-ignore:
-      - 'v*'
   pull_request:
     branches:
-      - 'master'
-      - 'dev'
+      - 'main'
 
 jobs:
   tests:
@@ -34,8 +31,11 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Setup GNU Fortran
-        uses: modflowpy/[email protected]
+      - uses: fortran-lang/setup-fortran@v1
+        id: setup-fortran
+        with:
+          compiler: gcc
+          version: 13
       - name: Install
         run:  pip install .[dev]
       - name: Run Tests

.github/workflows/warnings-tests.yaml

@@ -0,0 +1,49 @@
+name: Warnings Tests
+
+# Test on all pushes, except when the push is literally just a tag (because we
+# tag automatically via CI, and therefore there's no extra code in that push).
+# Also, only test on pull requests into master/dev.
+on:
+  push:
+  pull_request:
+    branches:
+      - 'main'
+
+jobs:
+  tests:
+    env:
+      ENV_NAME: tests
+      PYTHON: ${{ matrix.python-version }}
+      OS: ${{ matrix.os }}
+    name: Testing
+    #    needs: [linter]
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.11"]
+    steps:
+      - uses: actions/checkout@master
+        with:
+          fetch-depth: 1
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - uses: fortran-lang/setup-fortran@v1
+        id: setup-fortran
+        with:
+          compiler: gcc
+          version: 13
+      - name: Install
+        run:  pip install .[dev]
+      - name: Run Tests
+        run: |
+          python -m pytest -Werror --cov=hmf --cov-config=.coveragerc --cov-report xml:./coverage.xml --durations=25
+      - uses: codecov/codecov-action@v3
+        if: matrix.os == 'ubuntu-latest' && success()
+        with:
+          file: ./coverage.xml # optional
+          fail_ci_if_error: true
+          verbose: true
+          token: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ exclude: '^docs/conf.py'
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.3.0
+  rev: v4.6.0
   hooks:
   - id: trailing-whitespace
   - id: check-added-large-files
@@ -18,35 +18,35 @@ repos:
   - id: mixed-line-ending
     args: ['--fix=no']
 -   repo: https://github.com/PyCQA/flake8
-    rev: '5.0.4'  # pick a git hash / tag to point to
+    rev: '7.0.0'  # pick a git hash / tag to point to
     hooks:
     -   id: flake8
         additional_dependencies:
           - flake8-rst-docstrings
           - flake8-docstrings
           - flake8-builtins
-          - flake8-logging-format
           - flake8-rst-docstrings
           - flake8-rst
           - flake8-markdown
           - flake8-bugbear
           - flake8-comprehensions
           - flake8-print
--   repo: https://github.com/psf/black
-    rev: 22.10.0
-    hooks:
+# Using this mirror lets us use mypyc-compiled black, which is about 2x faster
+- repo: https://github.com/psf/black-pre-commit-mirror
+  rev: 24.4.2
+  hooks:
     - id: black
--   repo: https://github.com/pre-commit/pygrep-hooks
-    rev: v1.9.0
-    hooks:
-      - id: rst-backticks
+- repo: https://github.com/pre-commit/pygrep-hooks
+  rev: v1.10.0
+  hooks:
+  - id: rst-backticks
 - repo: https://github.com/PyCQA/isort
-  rev: 5.10.1
+  rev: 5.13.2
   hooks:
   - id: isort
 
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.2.0
+  rev: v3.16.0
   hooks:
   - id: pyupgrade
     args: [--py38-plus]