add 2 workflows and script/conf associated + define style linter

.github/workflows/ci.yaml

@@ -0,0 +1,85 @@
+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/xradarsat2'
+      && (
+          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@v2
+        with:
+          environment-file: ${{ env.CONDA_ENV_FILE }}
+          environment-name: xradarsat2-tests
+          cache-environment: true
+          generate-run-shell: true
+          cache-environment-key: "${{runner.os}}-${{runner.arch}}-py${{matrix.python-version}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
+          create-args: >-
+            python=${{matrix.python-version}}
+
+      - name: Install xradarsat2
+        run: |
+          python -m pip install --no-deps -e .
+
+      - name: Import xradarsat2
+        run: |
+          python -c "import xradarsat2"
+
+      - name: Run tests
+        run: |
+          python -m pytest --cov=xradarsat2

.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: ${{ steps.detect-trigger.outputs.trigger-found }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 2
+      - uses: xarray-contrib/[email protected]
+        id: detect-trigger
+        with:
+          keyword: "[test-upstream]"
+
+  upstream-dev:
+    name: upstream-dev
+    runs-on: ubuntu-latest
+    needs: detect-test-upstream-trigger
+
+    if: |
+      always()
+      && github.repository == 'umr-lops/xradarsat2'
+      && (
+        github.event_name == 'schedule'
+        || github.event_name == 'workflow_dispatch'
+        || needs.detect-test-upstream-trigger.outputs.triggered == 'true'
+        || contains(github.event.pull_request.labels.*.name, 'run-upstream')
+      )
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+      - name: checkout the repository
+        uses: actions/checkout@v4
+        with:
+          # need to fetch all tags to get a correct version
+          fetch-depth: 0 # fetch all branches and tags
+
+      - name: set up conda environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: ci/requirements/environment.yaml
+          environment-name: tests
+          create-args: >-
+            python=${{ 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 xradarsat2'
+
+      - 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

.gitignore

@@ -129,4 +129,4 @@ tmp/
 /.idea/
 
 dask-worker-space/
-localxradarsat2-config.yaml
+localxradarsat2-config.yaml

ci/install-upstream-dev.sh

@@ -0,0 +1,14 @@
+#!/usr/bin/env bash
+
+conda remove -y --force cytoolz numpy xarray toolz python-dateutil rioxarray
+python -m pip install \
+  -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple \
+  --no-deps \
+  --pre \
+  --upgrade \
+  numpy \
+  rioxarray \
+  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: xradarsat2-docs
+channels:
+  - conda-forge
+dependencies:
+  - python=3.11
+  - sphinx>=4
+  - sphinx_book_theme
+  - ipython

ci/requirements/environment.yaml

@@ -0,0 +1,26 @@
+name: xradarsat2-tests
+channels:
+  - conda-forge
+dependencies:
+  - python
+  - ipython
+  - pre-commit
+  - pytest
+  - pytest-reportlog
+  - pytest-cov
+  - numpy
+  - toolz
+  - cytoolz
+  - python-dateutil
+  - construct
+  - xarray
+  - rioxarray>=0.17.0
+  - aiohttp
+  - fsspec
+  - dask
+  - opencv
+  - pyyaml
+  - affine
+  - h5netcdf
+  - scipy
+  - xmltodict

docs/doc_xradarsat2.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "03cfc89b-5ee1-49c2-8bc9-ca88c00eb63b",
+   "id": "0",
    "metadata": {},
    "source": [
     "# examples"
@@ -11,7 +11,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9f901d61-adf5-4ad2-a721-b92fb8555642",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -23,7 +23,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "84c1a31d-c27c-4614-8a39-f4dca2801bf6",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -36,7 +36,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "90fb68ff-2c19-4432-8d95-98159ee546a8",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -48,7 +48,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ff1730a0-caeb-4c53-8fa0-85c79adfb5a6",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -59,7 +59,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "6f74bb35-b8d0-4a17-82d2-4b151e3044fb",
+   "id": "5",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -74,11 +74,6 @@
   }
  ],
  "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
@@ -88,8 +83,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.11.0"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,