fix: pandas applymap change #112

	name: ci

	on:
	push:
	branches:
	- "*"

	pull_request:
	branches:
	- "*"

	# schedule:
	# - cron: '0 0 * * *'

	env:
	CACHE_NUMBER: 1 # increase to reset cache manually

	jobs:
	build:
	strategy:
	matrix:
	include:
	- os: ubuntu-latest
	label: linux-64
	prefix: /usr/share/miniconda3/envs/my-env

	- os: macos-latest
	label: osx-64
	prefix: /Users/runner/miniconda3/envs/my-env

	# - os: windows-latest
	# label: win-64
	# prefix: C:\Miniconda3\envs\my-env

	name: ${{ matrix.label }}
	runs-on: ${{ matrix.os }}
	steps:
	- uses: actions/checkout@v2

	- name: Setup Mambaforge
	uses: conda-incubator/setup-miniconda@v2
	with:
	miniforge-variant: Mambaforge
	miniforge-version: latest
	activate-environment: my-env
	use-mamba: true

	- name: Set cache date
	run: echo "DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV

	- uses: actions/cache@v2
	with:
	path: ${{ matrix.prefix }}
	key: ${{ matrix.label }}-conda-${{ hashFiles('environment.yml') }}-${{ env.DATE }}-${{ env.CACHE_NUMBER }}
	id: cache

	- name: Update environment
	run: \|
	mamba env update -n my-env -f environment.yml && \
	mamba install -n my-env pytest pytest-mock requests-mock types-mock coverage && \
	mamba install -n my-env -c bioconda "samtools>=1.11" "bcftools>=1.11" "htslib>=1.11"
	if: steps.cache.outputs.cache-hit != 'true'

	- name: Coverage and tests
	shell: bash -l {0}
	run: coverage run -m pytest && coverage xml

	- name: Run codacy-coverage-reporter
	uses: codacy/codacy-coverage-reporter-action@v1
	with:
	project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
	coverage-reports: coverage.xml

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