Merge pull request #81 from umr-lops/migrate2pyproject.toml

Migrate from `setup.py` to `pyproject.toml`

.github/release.yml

@@ -0,0 +1,5 @@
+changelog:
+  exclude:
+    authors:
+      - dependabot
+      - pre-commit-ci

.github/workflows/ci.yaml

@@ -0,0 +1,84 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  detect-skip-ci-trigger:
+    name: "Detect CI Trigger: [skip-ci]"
+    if: |
+      github.repository == 'umr-lops/xsarsea'
+      && (
+          github.event_name == 'push' || github.event_name == 'pull_request'
+      )
+    runs-on: ubuntu-latest
+    outputs:
+      triggered: ${{ steps.detect-trigger.outputs.trigger-found }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 2
+      - uses: xarray-contrib/ci-trigger@v1
+        id: detect-trigger
+        with:
+          keyword: "[skip-ci]"
+
+  ci:
+    name: ${{ matrix.os }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    needs: detect-skip-ci-trigger
+
+    if: needs.detect-skip-ci-trigger.outputs.triggered == 'false'
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+
+    steps:
+      - name: Checkout the repository
+        uses: actions/checkout@v4
+        with:
+          # need to fetch all tags to get a correct version
+          fetch-depth: 0 # fetch all branches and tags
+
+      - name: Setup environment variables
+        run: |
+          echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
+
+          echo "CONDA_ENV_FILE=ci/requirements/environment.yaml" >> $GITHUB_ENV
+
+      - name: Setup micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: ${{ env.CONDA_ENV_FILE }}
+          environment-name: xsarsea-tests
+          cache-environment: true
+          cache-environment-key: "${{runner.os}}-${{runner.arch}}-py${{matrix.python-version}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
+          create-args: >-
+            python=${{matrix.python-version}}
+
+      - name: Install xsarsea
+        run: |
+          python -m pip install --no-deps -e .
+
+      - name: Import xsarsea
+        run: |
+          python -c "import xsarsea"
+
+      - name: Run tests
+        run: |
+          python -m pytest --cov=xsarsea

.github/workflows/conda-feedstock-check.yml

@@ -0,0 +1,65 @@
+name: Conda feedstock test
+
+# this workflow generate the documentation, using conda-feedstock
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '00 23 * * 0'
+
+
+jobs:
+  dynamic-matrix:
+# from https://michaelheap.com/dynamic-matrix-generation-github-actions/
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - id: get-matrix
+        run: |
+          echo "get matrix for event ${{ github.event_name }}"
+          echo "::echo::on"
+          python .github/actions/dynamic_matrix.py ${{ github.event_name }}
+    outputs:
+      os_matrix: ${{ steps.get-matrix.outputs.os_matrix }}
+      python_version_matrix: ${{ steps.get-matrix.outputs.python_version_matrix }}
+
+  build:
+    needs: dynamic-matrix
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ${{ fromJson(needs.dynamic-matrix.outputs.os_matrix) }}
+        python-version: ${{ fromJson(needs.dynamic-matrix.outputs.python_version_matrix) }}
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
+    name: python ${{ matrix.python-version }} on ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Strip python version
+        run: cat environment.yml | egrep -vw python > environment-nopython.yml
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          activate-environment: xsarsea
+          environment-file: environment-nopython.yml
+          condarc-file: condarc.yml
+          python-version: ${{ matrix.python-version }}
+
+      - name: install xsarsea from feedstock
+        run: | 
+          conda install -c conda-forge xsarsea
+          (cd docs ; pip install -r ../requirements.txt)
+
+      - name: List Packages
+        run: |
+          python -V
+          conda info
+          conda list
+
+      - name: Documentation test
+        run: |
+          cd docs
+          make html
+

.github/workflows/upstream-dev.yaml

@@ -0,0 +1,98 @@
+name: upstream-dev CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  schedule:
+    - cron: "0 18 * * 0" # Weekly "On Sundays at 18:00" UTC
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  detect-test-upstream-trigger:
+    name: "Detect CI Trigger: [test-upstream]"
+    if: github.event_name == 'push' || github.event_name == 'pull_request'
+    runs-on: ubuntu-latest
+    outputs:
+      triggered: ${{ steps.detect-trigger.outputs.trigger-found }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 2
+      - uses: xarray-contrib/ci-trigger@v1.2
+        id: detect-trigger
+        with:
+          keyword: "[test-upstream]"
+
+  upstream-dev:
+    name: upstream-dev
+    runs-on: ubuntu-latest
+    needs: detect-test-upstream-trigger
+
+    if: |
+      always()
+      && github.repository == 'umr-lops/xsarsea'
+      && (
+        github.event_name == 'schedule'
+        || github.event_name == 'workflow_dispatch'
+        || needs.detect-test-upstream-trigger.outputs.triggered == 'true'
+        || contains(github.event.pull_request.labels.*.name, 'run-upstream')
+      )
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+      - name: checkout the repository
+        uses: actions/checkout@v4
+        with:
+          # need to fetch all tags to get a correct version
+          fetch-depth: 0 # fetch all branches and tags
+
+      - name: set up conda environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: ci/requirements/environment.yaml
+          environment-name: tests
+          create-args: >-
+            python=${{ matrix.python-version }}
+            pytest-reportlog
+
+      - name: install upstream-dev dependencies
+        run: bash ci/install-upstream-dev.sh
+
+      - name: install the package
+        run: python -m pip install --no-deps -e .
+
+      - name: show versions
+        run: python -m pip list
+
+      - name: import
+        run: |
+          python -c 'import xsarsea'
+
+      - name: run tests
+        if: success()
+        id: status
+        run: |
+          python -m pytest -rf --report-log=pytest-log.jsonl
+
+      - name: report failures
+        if: |
+          failure()
+          && steps.tests.outcome == 'failure'
+          && github.event_name == 'schedule'
+        uses: xarray-contrib/issue-from-pytest-log@v1
+        with:
+          log-path: pytest-log.jsonl

.pre-commit-config.yaml

@@ -1,39 +1,41 @@
 ci:
-  autoupdate_schedule: weekly
+  autoupdate_schedule: monthly
 
 # https://pre-commit.com/
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-docstring-first
-      - id: check-yaml
-      - id: check-toml
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
   - repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 24.10.0
     hooks:
       - id: black
-      - id: black-jupyter
   - repo: https://github.com/keewis/blackdoc
-    rev: v0.3.8
+    rev: v0.3.9
     hooks:
       - id: blackdoc
-  - repo: https://github.com/pycqa/flake8
-    rev: 6.0.0
+        additional_dependencies: ["black==24.10.0"]
+      - id: blackdoc-autoupdate-black
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.7.1
     hooks:
-      - id: flake8
+      - id: ruff
+        args: [--fix]
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
+    rev: 0.7.1
     hooks:
       - id: nbstripout
         args: [--extra-keys=metadata.kernelspec metadata.language_info.version]
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0-alpha.4
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: v3.3.3
+    hooks:
+      - id: prettier
+  - repo: https://github.com/ComPWA/taplo-pre-commit
+    rev: v0.9.3
     hooks:
-      - id: prettier
+      - id: taplo-format
+      - id: taplo-lint
+        args: [--no-schema]

ci/install-upstream-dev.sh

@@ -0,0 +1,14 @@
+#!/usr/bin/env bash
+
+conda remove -y --force cytoolz numpy xarray toolz python-dateutil pandas
+python -m pip install \
+  -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple \
+  --no-deps \
+  --pre \
+  --upgrade \
+  numpy \
+  pandas \
+  xarray
+python -m pip install --upgrade \
+  git+https://github.com/pytoolz/toolz \
+  git+https://github.com/dateutil/dateutil

ci/requirements/docs.yaml

@@ -0,0 +1,8 @@
+name: xsarsea-docs
+channels:
+  - conda-forge
+dependencies:
+  - python=3.11
+  - sphinx>=4
+  - sphinx_book_theme
+  - ipython

ci/requirements/environment.yaml

@@ -0,0 +1,17 @@
+name: xsarsea-tests
+channels:
+  - conda-forge
+dependencies:
+  - ipython
+  - pre-commit
+  - pytest
+  - pytest-reportlog
+  - pytest-cov
+  - numpy
+  - toolz
+  - cytoolz
+  - python-dateutil
+  - construct
+  - xarray
+  - pandas
+  - aiohttp