[CI] Update codecov action #90

	name: Tests

	on:
	push:
	branches: [ master, dev ]
	paths-ignore:
	- 'docs/**'
	pull_request:
	branches: [ master ]

	jobs:
	build:
	runs-on: ${{ matrix.os }}
	env:
	CYTHON_LINETRACE: true
	strategy:
	matrix:
	python-version: [3.9]
	os: [macos-latest]
	# exclude: # Temporarily disable release for macos and python 3.8 as there is a bug with openblas
	# - os: macos-latest
	# python-version: 3.8
	fail-fast: false

	steps:
	- uses: actions/checkout@v3
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}
	- name: Add OpenMP flags (macOS)
	if: runner.os == 'macOS'
	run: \|
	brew info libomp
	echo "LDFLAGS=${LDFLAGS} -L$(brew --prefix libomp)/lib" >> "$GITHUB_ENV"
	echo "CPPFLAGS=${CPPFLAGS} -I$(brew --prefix libomp)/include" >> "$GITHUB_ENV"
	- name: Show python info
	shell: bash -e {0}
	run: \|
	which python
	python --version
	- name: Build
	shell: bash -e {0}
	run: \|
	python -m pip install . -vv
	- name: Install test dependencies
	shell: bash -e {0}
	run: \|
	python -m pip install -q pytest pylint pytest-pylint pytest-cov codecov pytest-mock pyteomics cython
	- name: Install xvfb (Linux)
	shell: bash -e {0}
	run: python -m pip install pytest-xvfb
	if: runner.os == 'Linux'
	- name: Test with pytest
	shell: bash -e {0}
	run: \|
	cd tests
	pytest --cov=libmetgem --cov-report=xml
	- name: Upload coverage
	if: success()
	uses: codecov/codecov-action@v3
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	file: ./coverage.xml
	name: ${{ runner.os }} Python ${{ matrix.python-version }}

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