Merge pull request #115 from ocefpaf/modernize_package

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/file-changes-action@v1.2.3
-      with:
-        output: ' '
-    - uses: pre-commit/action@v2.0.0
-      with:
-        extra_args: --files ${{ steps.file_changes.outputs.files}}
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+    - uses: pre-commit/action@v3.0.0

.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