Update pytest coverage command to specify source directory and add te… #16

	# FILE: .github/workflows/test.yaml
	name: Run software tests

	on:
	push:
	pull_request:
	branches:
	- main

	jobs:
	test:
	name: Run tests
	runs-on: ubuntu-latest
	steps:
	- name: Checkout repository
	uses: actions/checkout@v4

	- name: Setup Conda
	uses: conda-incubator/setup-miniconda@v3
	with:
	miniforge-variant: Miniforge3
	miniforge-version: latest
	activate-environment: test_env
	use-mamba: true
	python-version: "3.9"
	channels: conda-forge,nodefaults
	channel-priority: strict
	auto-activate-base: false
	conda-remove-defaults: true

	- name: Cache conda env
	uses: actions/cache@v3
	with:
	path: \|
	/usr/share/miniconda/pkgs
	/usr/share/miniconda/envs
	key: conda-${{ runner.os }}-py${{ matrix.python-version }}-${{ github.sha }}
	restore-keys: \|
	conda-${{ runner.os }}-py${{ matrix.python-version }}-
	conda-${{ runner.os }}-

	- name: Install dependencies
	shell: bash -l {0}
	run: \|
	# Install tomlkit and sh first to run the installation script
	mamba install -y -c conda-forge tomlkit sh

	# Run the installation script
	python install_dev_deps.py

	- name: Install package
	shell: bash -l {0}
	run: \|
	pip install -e .

	- name: Run tests
	shell: bash -l {0}
	run: \|
	pytest --cov=src/planetarypy --cov-report=xml --cov-report=term

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v3
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	files: ./coverage.xml
	fail_ci_if_error: true

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