Agents updated to try to reduce copilot errors #194

	name: Continuous integration tests

	on:
	push:
	branches: [main]
	pull_request:
	branches: [main]

	jobs:
	ci:
	name: "CI setup"

	strategy:
	fail-fast: false
	matrix:
	python-version:
	- "3.12"
	- "3.11"
	- "3.10"

	os:
	- "ubuntu-latest"

	runs-on: "${{ matrix.os }}"

	# use bash everywhere
	defaults:
	run:
	shell: "bash -l {0}"

	steps:
	- name: "Checkout code"
	uses: "actions/checkout@v4"

	- name: Install opencv dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install -y libgl1 and libglx-mesa0

	- name: Install ipynb dependencies (pandoc)
	run: \|
	sudo apt-get update
	sudo apt-get install -y pandoc

	- name: Install uv
	uses: astral-sh/setup-uv@v5
	with:
	python-version: ${{ matrix.python-version }}

	- name: Set up Python
	run: uv python install

	- name: Install package
	run: uv sync --all-extras --dev

	- name: Run pytest with coverage
	run: uv run pytest -v --cov=src/deepforest --cov-report=xml --cov-report=term-missing

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v4
	with:
	file: ./coverage.xml
	flags: unittests
	name: codecov-umbrella
	fail_ci_if_error: false

	- name: Check predict script
	run: uv run deepforest predict src/deepforest/data/OSBS_029.png

	- name: Check train script
	run: uv run deepforest train train.csv_file=src/deepforest/data/OSBS_029.csv train.root_dir=src/deepforest/data train.fast_dev_run=True

	- name: Test Docs
	run: \|
	cd docs && uv run make clean && uv run make html SPHINXOPTS="-W"

	- name: Test and check build artifacts
	run: \|
	uv pip install build && uv run python -m build && uv run twine check dist/*

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