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Merge pull request #41 from umr-lops/revisit-ci
add workflows and adapt pyproj for pre-commit
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‎.github/workflows/ci.yaml‎

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name: CI
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on:
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push:
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branches: [main]
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pull_request:
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branches: [main]
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workflow_dispatch:
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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detect-skip-ci-trigger:
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name: "Detect CI Trigger: [skip-ci]"
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if: |
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github.repository == 'umr-lops/xarray-safe-s1'
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&& (
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github.event_name == 'push' || github.event_name == 'pull_request'
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)
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runs-on: ubuntu-latest
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outputs:
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triggered: ${{ steps.detect-trigger.outputs.trigger-found }}
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 2
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- uses: xarray-contrib/ci-trigger@v1
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id: detect-trigger
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with:
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keyword: "[skip-ci]"
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ci:
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name: ${{ matrix.os }} py${{ matrix.python-version }}
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runs-on: ${{ matrix.os }}
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needs: detect-skip-ci-trigger
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if: needs.detect-skip-ci-trigger.outputs.triggered == 'false'
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defaults:
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run:
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shell: bash -l {0}
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.10", "3.11", "3.12"]
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os: ["ubuntu-latest", "macos-latest", "windows-latest"]
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steps:
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- name: Checkout the repository
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uses: actions/checkout@v4
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with:
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# need to fetch all tags to get a correct version
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fetch-depth: 0 # fetch all branches and tags
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- name: Setup environment variables
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run: |
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echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
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echo "CONDA_ENV_FILE=ci/requirements/environment.yaml" >> $GITHUB_ENV
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- name: Setup micromamba
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uses: mamba-org/setup-micromamba@v2
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with:
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environment-file: ${{ env.CONDA_ENV_FILE }}
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environment-name: xarray-safe-s1-tests
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cache-environment: true
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cache-environment-key: "${{runner.os}}-${{runner.arch}}-py${{matrix.python-version}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
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create-args: >-
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python=${{matrix.python-version}}
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- name: Install xarray-safe-s1
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run: |
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python -m pip install --no-deps -e .
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- name: Import xarray-safe-s1
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run: |
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python -c "import safe_s1"
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- name: Run tests
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run: |
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python -m pytest --cov=safe_s1

‎.github/workflows/publish.yml‎

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@@ -9,14 +9,14 @@ jobs:
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name: Publish to PyPI
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runs-on: ubuntu-latest
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permissions:
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contents: 'read'
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id-token: 'write'
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contents: "read"
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id-token: "write"
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.x'
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python-version: "3.x"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip build twine
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with:
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password: ${{ secrets.pypi_token }}
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repository_url: https://upload.pypi.org/legacy/
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verify_metadata: true
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verify_metadata: true

‎.github/workflows/upstream-dev.yaml‎

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name: upstream-dev CI
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on:
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push:
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branches: [main]
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pull_request:
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branches: [main]
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schedule:
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- cron: "0 18 * * 0" # Weekly "On Sundays at 18:00" UTC
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workflow_dispatch:
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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detect-test-upstream-trigger:
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name: "Detect CI Trigger: [test-upstream]"
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if: github.event_name == 'push' || github.event_name == 'pull_request'
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runs-on: ubuntu-latest
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outputs:
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triggered: ${{ steps.detect-trigger.outputs.trigger-found }}
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 2
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- uses: xarray-contrib/ci-trigger@v1.2
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id: detect-trigger
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with:
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keyword: "[test-upstream]"
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upstream-dev:
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name: upstream-dev
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runs-on: ubuntu-latest
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needs: detect-test-upstream-trigger
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if: |
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always()
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&& github.repository == 'umr-lops/xarray-safe-s1'
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&& (
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github.event_name == 'schedule'
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|| github.event_name == 'workflow_dispatch'
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|| needs.detect-test-upstream-trigger.outputs.triggered == 'true'
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|| contains(github.event.pull_request.labels.*.name, 'run-upstream')
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)
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defaults:
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run:
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shell: bash -l {0}
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.12"]
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steps:
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- name: checkout the repository
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uses: actions/checkout@v4
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with:
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# need to fetch all tags to get a correct version
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fetch-depth: 0 # fetch all branches and tags
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- name: set up conda environment
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uses: mamba-org/setup-micromamba@v1
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with:
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environment-file: ci/requirements/environment.yaml
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environment-name: tests
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create-args: >-
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python=${{ matrix.python-version }}
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pytest-reportlog
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- name: install upstream-dev dependencies
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run: bash ci/install-upstream-dev.sh
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- name: install the package
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run: python -m pip install --no-deps -e .
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- name: show versions
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run: python -m pip list
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- name: import
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run: |
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python -c 'import safe_s1'
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- name: run tests
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if: success()
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id: status
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run: |
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python -m pytest -rf --report-log=pytest-log.jsonl
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- name: report failures
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if: |
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failure()
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&& steps.tests.outcome == 'failure'
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&& github.event_name == 'schedule'
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uses: xarray-contrib/issue-from-pytest-log@v1
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with:
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log-path: pytest-log.jsonl

‎ci/install-upstream-dev.sh‎

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

‎ci/requirements/environment.yaml‎

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channels:
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- conda-forge
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dependencies:
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- python=3.10
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- python
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# development
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- ipython
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- pre-commit
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# testing
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- pytest
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- pytest-reportlog
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- pytest-cov
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- hypothesis
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- coverage
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# I/O
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- numpy
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- pandas
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- shapely
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- datetime
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- geopandas
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- affine
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- pyproj
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# processing
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- os
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- io
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- lxml
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- jmespath

‎docs/api.rst‎

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.. autoclass:: Sentinel1Reader
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:members:
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‎docs/conf.py‎

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# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
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# ones.
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extensions = [
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'sphinx.ext.autosummary',
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'sphinx.ext.autodoc',
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"sphinx.ext.autosummary",
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"sphinx.ext.autodoc",
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"myst_parser",
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"sphinx.ext.extlinks",
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"sphinx.ext.intersphinx",
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"IPython.sphinxext.ipython_directive",
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"IPython.sphinxext.ipython_console_highlighting",
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'nbsphinx',
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'jupyter_sphinx',
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'sphinx.ext.napoleon'
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"nbsphinx",
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"jupyter_sphinx",
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"sphinx.ext.napoleon",
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]
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extlinks = {
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# Add any paths that contain templates here, relative to this directory.
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templates_path = ["_templates"]
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html_static_path = ['_static']
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html_static_path = ["_static"]
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html_style = 'css/xsar.css'
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html_style = "css/xsar.css"
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# List of patterns, relative to source directory, that match files and
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# directories to ignore when looking for source files.
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"dask": ("https://docs.dask.org/en/latest", None),
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"xarray": ("https://docs.xarray.dev/en/latest/", None),
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"rasterio": ("https://rasterio.readthedocs.io/en/latest/", None),
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"datatree": ("https://xarray-datatree.readthedocs.io/en/latest/", None)
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"datatree": ("https://xarray-datatree.readthedocs.io/en/latest/", None),
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}
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html_theme_options = {
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'navigation_depth': 4, # FIXME: doesn't work as expeted: should expand side menu
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'collapse_navigation': False # FIXME: same as above
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"navigation_depth": 4, # FIXME: doesn't work as expeted: should expand side menu
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"collapse_navigation": False, # FIXME: same as above
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}
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# If true, links to the reST sources are added to the pages.
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html_show_sourcelink = False
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nbsphinx_allow_errors = False
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nbsphinx_execute = 'always'
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nbsphinx_execute = "always"
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nbsphinx_timeout = 300
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today_fmt = '%b %d %Y at %H:%M'
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today_fmt = "%b %d %Y at %H:%M"

‎docs/index.rst‎

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.. _xarray.Dataset: http://xarray.pydata.org/en/stable/generated/xarray.Dataset.html
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.. _`recommended installation`: installing.rst#recommended-packages
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.. _SAFE format: https://sentinel.esa.int/web/sentinel/user-guides/sentinel-1-sar/data-formats
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.. _jupyter notebook: https://jupyter.readthedocs.io/en/latest/running.html#running
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.. _jupyter notebook: https://jupyter.readthedocs.io/en/latest/running.html#running

‎docs/installing.rst‎

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Pytest uses a default configuration file (`config.yml`) in which we can found products paths to test.
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This configuration can be superseded by adding a local config file on the home directory :
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(`~/xarray-safe-s1/localconfig.yml`).
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In this file, testing files can be listed in the var `product_paths`.
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In this file, testing files can be listed in the var `product_paths`.

‎pyproject.toml‎

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float_to_top = true
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default_section = "THIRDPARTY"
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known_first_party = "safe_s1"
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[tool.coverage.report]
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show_missing = true
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exclude_lines = ["pragma: no cover", "if TYPE_CHECKING"]
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[tool.ruff.lint]
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ignore = [
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"E402", # module level import not at top of file
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"E501", # line too long - let black worry about that
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"E731", # do not assign a lambda expression, use a def
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"UP038", # type union instead of tuple for isinstance etc
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]
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select = [
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"F", # Pyflakes
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"E", # Pycodestyle
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"I", # isort
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"UP", # Pyupgrade
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"TID", # flake8-tidy-imports
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"W",
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]
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extend-safe-fixes = [
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"TID252", # absolute imports
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"UP031", # percent string interpolation
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]
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fixable = ["I", "TID252", "UP"]
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[tool.ruff.lint.isort]
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known-first-party = ["safe_s1"]
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known-third-party = ["xarray", "toolz", "construct"]
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[tool.ruff.lint.flake8-tidy-imports]
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# Disallow all relative imports.
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ban-relative-imports = "all"

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