Modernize package

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# See https://docs.github.com/en/code-security/supply-chain-security/keeping-your-dependencies-updated-automatically/keeping-your-actions-up-to-date-with-dependabot
+
+version: 2
+updates:
+
+ - package-ecosystem: "github-actions"
+ directory: "/"
+ schedule:
+ interval: "daily"
+ labels:
+ - "Bot"

.github/workflows/deploy-docs.yml

@@ -0,0 +1,51 @@
+
+name: Documentation
+
+on:
+ pull_request:
+ push:
+ branches: [master, main]
+ release:
+ types:
+ - published
+
+jobs:
+ build-docs:
+ runs-on: ubuntu-latest
+
+ steps:
+ - name: checkout
+ uses: actions/checkout@v3
+ with:
+ fetch-depth: 0
+
+ - name: Setup Micromamba
+ uses: mamba-org/setup-micromamba@v1
+ with:
+ environment-name: TEST
+ init-shell: bash
+ create-args: >-
+ python=3 pip
+ --file requirements.txt
+ --file requirements-dev.txt
+ --channel conda-forge
+
+ - name: Install utide
+ shell: bash -l {0}
+ run: |
+ pip install -e . --no-deps --force-reinstall
+
+ - name: Build documentation
+ shell: bash -l {0}
+ run: |
+ set -e
+ pushd docs
+ make clean html linkcheck
+ popd
+
+ - name: Deploy
+ if: success() && github.event_name == 'release'
+ uses: peaceiris/actions-gh-pages@v3
+ with:
+ github_token: ${{ secrets.GITHUB_TOKEN }}
+ publish_dir: docs/build/html

.github/workflows/pre-commit.yml

@@ -8,17 +8,7 @@ on:
 jobs:
  pre-commit:
  runs-on: ubuntu-latest
- env:
- FORCE_COLOR: "1"
  steps:
- - uses: actions/checkout@v2
- - uses: actions/setup-python@v2
- with:
- python-version: '3.x'
- - id: file_changes
- uses: trilom/[email protected]
- with:
- output: ' '
- - uses: pre-commit/[email protected]
- with:
- extra_args: --files ${{ steps.file_changes.outputs.files}}
+ - uses: actions/checkout@v3
+ - uses: actions/setup-python@v4
+ - uses: pre-commit/[email protected]

.github/workflows/publish.yml → .github/workflows/pypi.yml

@@ -1,47 +1,53 @@
 name: Publish to PyPI
 
 on:
+ pull_request:
+ push:
+ branches: [master, main]
  release:
  types:
  - published
 
+defaults:
+ run:
+ shell: bash
+
 jobs:
  packages:
  runs-on: ubuntu-latest
  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: Get tags
  run: git fetch --depth=1 origin +refs/tags/*:refs/tags/*
- shell: bash
 
  - name: Install build tools
  run: |
- python -m pip install --upgrade pip wheel setuptools setuptools_scm build twine pytest numpy scipy
-
- shell: bash
+ python -m pip install --upgrade pip build
 
- - name: Build binary wheel
+ - name: Build sdist and binary wheel
  run: python -m build --sdist --wheel . --outdir dist
 
  - name: CheckFiles
  run: |
  ls dist
- shell: bash
+ python -m pip install --upgrade check-manifest
+ check-manifest --verbose
 
  - name: Test wheels
  run: |
- cd dist && python -m pip install UTide*.whl
+ cd dist && python -m pip install *.whl
+ python -m pip install --upgrade twine
  python -m twine check *
- shell: bash
 
  - name: Publish a Python distribution to PyPI
- uses: pypa/gh-action-pypi-publish@master
+ if: success() && github.event_name == 'release'
+ uses: pypa/gh-action-pypi-publish@release/v1
  with:
  user: __token__
  password: ${{ secrets.PYPI_PASSWORD }}

.github/workflows/tests.yml

@@ -10,41 +10,40 @@ jobs:
  runs-on: ${{ matrix.os }}
  strategy:
  matrix:
- python-version: [ "3.7", "3.8", "3.9", "3.10"]
+ python-version: ["3.8", "3.9", "3.10", "3.11"]
  os: [windows-latest, ubuntu-latest, macos-latest]
  # Oldest one based on NEP-29 and latest one.
  # See https://numpy.org/neps/nep-0029-deprecation_policy.html
- numpy-version: ["1.19", "1.22"]
+ numpy-version: ["1.21", "1.25"]
  exclude:
- - python-version: "3.10"
- numpy-version: "1.19"
+ - python-version: "3.11"
+ numpy-version: "1.21"
+ - python-version: "3.8"
+ numpy-version: "1.25"
  fail-fast: false
 
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
 
- - name: Setup
- uses: mamba-org/provision-with-micromamba@main
+ - name: Setup Micromamba Python ${{ matrix.python-version }}
+ uses: mamba-org/setup-micromamba@v1
  with:
- environment-file: false
+ environment-name: TEST
+ init-shell: bash
+ create-args: >-
+ python=${{ matrix.python-version }} pip
+ --file requirements.txt
+ --file requirements-dev.txt
+ --channel conda-forge
 
- - name: Python ${{ matrix.python-version }} numpy ${{ matrix.numpy-version }}
+ - name: Install utide
  shell: bash -l {0}
- run: |
- micromamba create --name TEST python=${{ matrix.python-version }} --file requirements.txt --file requirements-dev.txt --channel conda-forge
- micromamba activate TEST
- micromamba install numpy=${{ matrix.numpy-version }}
- pip install -e . --no-deps --force-reinstall
-
- - name: Debug Info
- shell: bash -l {0}
- run: |
- micromamba activate TEST
- micromamba info --all
- micromamba list
+ run: >
+ python -m pip install -e . --no-deps --force-reinstall
+ && micromamba install numpy=${{ matrix.numpy-version }}
+ && pip install -e . --no-deps --force-reinstall
 
- - name: Tests
+ - name: Run tests
  shell: bash -l {0}
  run: |
- micromamba activate TEST
- pytest -n 2 -rxs --cov=utide tests
+ pytest -rxs --cov=utide tests

.gitignore

@@ -73,3 +73,4 @@ doc/_build/
 .project
 .pydevproject
 .vscode/
+utide/_version.py

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v4.2.0
+ rev: v4.4.0
  hooks:
  - id: check-ast
  - id: end-of-file-fixer
@@ -14,34 +14,44 @@ repos:
  - id: trailing-whitespace
  - id: debug-statements
 
-- repo: https://gitlab.com/pycqa/flake8
- rev: 3.9.2
+- repo: https://github.com/psf/black
+ rev: 23.3.0
  hooks:
- - id: flake8
- exclude: docs/source/conf.py
- args: [--max-line-length=105]
+ - id: black
+ language_version: python3
 
-- repo: https://github.com/pre-commit/mirrors-isort
- rev: v5.10.1
+- repo: https://github.com/asottile/add-trailing-comma
+ rev: v2.5.1
  hooks:
- - id: isort
- additional_dependencies: [toml]
- args: [--project=utide, --multi-line=3, --lines-after-imports=2, --lines-between-types=1, --trailing-comma, --force-grid-wrap=0, --use-parentheses, --line-width=88]
+ - id: add-trailing-comma
 
-- repo: https://github.com/psf/black
- rev: 22.3.0
+- repo: https://github.com/keewis/blackdoc
+ rev: v0.3.8
  hooks:
- - id: black
- language_version: python3
+ - id: blackdoc
 
-- repo: https://github.com/asottile/pyupgrade
- rev: v2.32.0
+- repo: https://github.com/codespell-project/codespell
+ rev: v2.2.5
  hooks:
- - id: pyupgrade
+ - id: codespell
+ exclude: >
+ (?x)^(
+ .*\.yaml
+ )$
  args:
- - --py36-plus
+ - --ignore-words-list=fo,htmp
 
 - repo: https://github.com/asottile/add-trailing-comma
- rev: v2.2.3
+ rev: v2.5.1
  hooks:
  - id: add-trailing-comma
+
+- repo: https://github.com/charliermarsh/ruff-pre-commit
+ rev: v0.0.272
+ hooks:
+ - id: ruff
+
+- repo: https://github.com/tox-dev/pyproject-fmt
+ rev: 0.12.0
+ hooks:
+ - id: pyproject-fmt

MANIFEST.in

@@ -1,5 +1,5 @@
 include *.txt
-include README.rst
+include README.md
 include pyproject.toml
 
 graft utide
@@ -11,6 +11,6 @@ prune *.egg-info
 
 global-exclude *.mat
 
-exclude *.yml
-exclude *.enc
+exclude *.yaml
 exclude .gitignore
+exclude utide/_version.py