Update unifrac to 1.5 #14656

Workflow file for this run

	name: PR Check
	on:
	pull_request:
	types: [opened, synchronize, reopened]
	concurrency:
	group: build-${{ github.event.pull_request.number \|\| github.head_ref }}
	cancel-in-progress: true
	jobs:
	lint:
	name: Lint
	runs-on: ubuntu-22.04
	strategy:
	fail-fast: true
	max-parallel: 13
	steps:
	- uses: actions/checkout@v4

	- name: Fetch commits through the merge base
	uses: fulcrumgenomics/fetch-through-merge-base@v1
	with:
	base-ref: ${{ env.GITHUB_BASE_REF }}
	head-ref: ${{ github.sha }}
	fallback-base-ref: master
	fallback-fetch-all: true

	- name: set path
	run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH

	- name: Fetch conda install script
	run: \|
	wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh

	- name: Restore cache
	id: cache
	uses: actions/cache@v4
	with:
	path: /opt/mambaforge
	key: ${{ runner.os }}--master--${{ hashFiles('install-and-set-up-conda.sh', 'common.sh', 'configure-conda.sh') }}

	- name: Set up bioconda-utils
	if: steps.cache.outputs.cache-hit != 'true'
	run: bash install-and-set-up-conda.sh

	# This script can be used to reconfigure conda to use the right channel setup.
	# This has to be done after the cache is restored, because
	# the channel setup is not cached as it resides in the home directory.
	# We could use a system-wide (and therefore cached) channel setup,
	# but mamba does not support that at the time of implementation
	# (it ignores settings made with --system).
	- name: Configure conda
	run: bash configure-conda.sh

	- name: Perform lint
	env:
	# Mimic circleci
	OSTYPE: "linux-gnu"
	CI: "true"
	run: \|
	set -e
	eval "$(conda shell.bash hook)"
	conda activate bioconda
	source common.sh
	echo '============'
	conda info --all
	conda config --show-sources
	python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")'
	echo '============'
	bioconda-utils lint --loglevel debug --full-report --git-range origin/"$GITHUB_BASE_REF" HEAD
	conda clean -y --all

	build-linux:
	name: Linux Tests
	runs-on: ubuntu-22.04
	strategy:
	fail-fast: true
	max-parallel: 13
	needs: lint
	steps:
	- name: Free space
	# HACK fixes 'No space left on device'
	# see:
	# - https://github.com/orgs/community/discussions/25678#discussioncomment-5242449
	# - https://github.com/galaxyproteomics/tools-galaxyp/blob/master/.github/workflows/pr.yaml#L293
	# NOTE we don't use those, bioconda-utils run everything inside conda environment, anyway
	run: \|
	sudo rm -rf \
	/opt/hostedtoolcache \
	/opt/google/chrome \
	/opt/microsoft/msedge \
	/opt/microsoft/powershell \
	/opt/pipx \
	/usr/local/julia* \
	/usr/local/lib/android \
	/usr/local/lib/node_modules \
	/usr/local/share/chromium \
	/usr/local/share/powershell \
	/usr/share/dotnet \
	/usr/share/swift

	- uses: actions/checkout@v4

	- name: Fetch commits through the merge base
	uses: fulcrumgenomics/fetch-through-merge-base@v1
	with:
	base-ref: ${{ env.GITHUB_BASE_REF }}
	head-ref: ${{ github.sha }}
	fallback-base-ref: master
	fallback-fetch-all: true

	- name: set path
	run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH

	- name: Fetch conda install script
	run: \|
	wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh

	- name: Restore cache
	id: cache
	uses: actions/cache@v4
	with:
	path: /opt/mambaforge
	key: ${{ runner.os }}--master--${{ hashFiles('install-and-set-up-conda.sh', 'common.sh', 'configure-conda.sh') }}

	- name: Set up bioconda-utils
	if: steps.cache.outputs.cache-hit != 'true'
	run: bash install-and-set-up-conda.sh

	# This script can be used to reconfigure conda to use the right channel setup.
	# This has to be done after the cache is restored, because
	# the channel setup is not cached as it resides in the home directory.
	# We could use a system-wide (and therefore cached) channel setup,
	# but mamba does not support that at the time of implementation
	# (it ignores settings made with --system).
	- name: Configure conda
	run: bash configure-conda.sh

	- name: Build and test
	env:
	# Mimic circleci
	OSTYPE: "linux-gnu"
	CI: "true"
	run: \|
	set -e

	# Clean up lingering build artifacts
	for n in linux-64 osx-64 noarch; do
	rm -f /opt/mambaforge/envs/bioconda/conda-bld/$n/*.tar.bz2
	rm -f /opt/mambaforge/envs/bioconda/conda-bld/$n/*.conda
	done

	eval "$(conda shell.bash hook)"
	conda activate bioconda
	source common.sh

	bioconda-utils build recipes config.yml \
	--docker --mulled-test \
	--git-range origin/"$GITHUB_BASE_REF" HEAD

	- name: Prepare artifacts
	run: \|
	(
	rm -rf /tmp/artifacts
	mkdir -p /tmp/artifacts/packages
	cd /opt/mambaforge/envs/bioconda/conda-bld \|\| exit 0
	find -name .cache \| xargs rm -rf \|\| true
	for n in index.html channeldata.json linux-64 osx-64 noarch; do
	cp -rv $n /tmp/artifacts/packages \|\| true
	done
	if command -V docker >/dev/null; then
	mkdir -p /tmp/artifacts/images
	cd /tmp/artifacts/images
	docker image ls --format='{{.Repository}}:{{.Tag}}' \| \
	{ grep biocontainers \|\| true ; } \| \
	xargs -n1 -P4 bash -c '
	test -n "${1+x}" \|\| exit 0
	echo "Start compressing docker image ${1} ..."
	docker save "${1}" \| gzip -c > "${1##*/}.tar.gz"
	echo "Finished compressing docker image ${1} ."
	' --
	# There's no : allowed in artifact names, replace it with ---
	for f in /tmp/artifacts/images/: ; do mv -- "$f" "${f//:/---}"; done
	fi
	) \|\| true

	- name: Archive packages
	uses: actions/upload-artifact@v4
	with:
	name: linux-packages
	path: \|
	/tmp/artifacts


	build-osx-64:
	name: OSX-64 Tests
	runs-on: macos-13
	strategy:
	fail-fast: true
	max-parallel: 4
	# Limited concurrency for osx, so first make sure linux can pass
	needs: build-linux
	steps:
	- uses: actions/checkout@v4

	- name: Fetch commits through the merge base
	uses: fulcrumgenomics/fetch-through-merge-base@v1
	continue-on-error: true
	with:
	base-ref: ${{ env.GITHUB_BASE_REF }}
	head-ref: ${{ github.sha }}
	fallback-base-ref: master
	fallback-fetch-all: true

	- name: set path
	run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH

	- name: Fetch conda install script
	run: \|
	wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh

	# This is required so actions/cache below will restore properly
	# See: https://github.com/actions/cache/issues/629#issuecomment-1189184648
	- name: Make gtar SUDO
	run: \|
	echo -e '#!/bin/sh\nexec sudo /usr/local/bin/gtar.orig "$@"\n' > gtar;
	cat gtar;
	sudo mv -v /usr/local/bin/gtar /usr/local/bin/gtar.orig;
	sudo cp -v gtar /usr/local/bin/gtar;
	sudo chmod +x /usr/local/bin/gtar;

	- name: Restore cache
	id: cache
	uses: actions/cache@v4
	with:
	path: /opt/mambaforge
	key: ${{ runner.os }}--master--${{ hashFiles('install-and-set-up-conda.sh', 'common.sh', 'configure-conda.sh') }}

	- name: Set up bioconda-utils
	if: steps.cache.outputs.cache-hit != 'true'
	run: bash install-and-set-up-conda.sh

	# This script can be used to reconfigure conda to use the right channel setup.
	# This has to be done after the cache is restored, because
	# the channel setup is not cached as it resides in the home directory.
	# We could use a system-wide (and therefore cached) channel setup,
	# but mamba does not support that at the time of implementation
	# (it ignores settings made with --system).
	- name: Configure conda
	run: bash configure-conda.sh

	- name: Build and Test
	env:
	# Mimic circleci
	OSTYPE: "darwin"
	CI: "true"
	run: \|
	set -e
	eval "$(conda shell.bash hook)"
	conda activate bioconda
	source common.sh
	# Sets up OSX SDK
	run_conda_forge_build_setup

	# Clean up lingering build artifacts
	for n in linux-64 osx-64 noarch; do
	rm -f /opt/mambaforge/envs/bioconda/conda-bld/$n/*.tar.bz2
	done

	bioconda-utils build recipes config.yml \
	--git-range origin/"$GITHUB_BASE_REF" HEAD

	- name: Prepare artifacts
	run: \|
	(
	rm -rf /tmp/artifacts
	mkdir -p /tmp/artifacts/packages
	cd /opt/mambaforge/envs/bioconda/conda-bld \|\| exit 0
	find -name .cache \| xargs rm -rf \|\| true
	for n in index.html channeldata.json linux-64 osx-64 noarch; do
	cp -rv $n /tmp/artifacts/packages \|\| true
	done
	) \|\| true

	- name: Archive packages
	uses: actions/upload-artifact@v4
	with:
	name: osx-packages
	path: \|
	/tmp/artifacts

	# Disabled due to concurrency limits on GHA for OSX. osx-arm64 builds are on CircleCI.
	# build_and_test-osx-arm64:
	# name: OSX-ARM64 Tests
	# runs-on: macOS-14 # M1
	# strategy:
	# fail-fast: true
	# max-parallel: 4
	# needs: build-linux
	# steps:
	# - uses: actions/checkout@v4

	# # bail if there's no osx-arm64 recipes
	# - name: Check for Additional Platforms
	# id: additional_platforms
	# run: \|
	# result=$(./scripts/check-for-additional-platforms.sh "origin/master...HEAD" "build_and_test" "${GITHUB_JOB}")
	# if [[ ${result} != "build" ]]
	# then
	# echo "No recipes using this platform, skipping rest of job."
	# echo "skip_build=true" >> $GITHUB_OUTPUT
	# fi

	# - name: set path
	# run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH

	# - name: Fetch conda install script
	# if: steps.additional_platforms.outputs.skip_build != 'true'
	# run: \|
	# wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh

	# - name: Set up bioconda-utils
	# if: steps.additional_platforms.outputs.skip_build != 'true'
	# run: bash install-and-set-up-conda.sh

	# - name: Configure conda
	# if: steps.additional_platforms.outputs.skip_build != 'true'
	# run: bash configure-conda.sh

	# - name: Build and Test
	# if: steps.additional_platforms.outputs.skip_build != 'true'
	# env:
	# # Mimic circleci
	# OSTYPE: "darwin"
	# CI: "true"
	# run: \|
	# set -xe
	# eval "$(conda shell.bash hook)"
	# conda activate bioconda
	# source common.sh
	# # Sets up OSX SDK
	# run_conda_forge_build_setup

	# if [ -z "$GITHUB_BASE_REF" ] ; then
	# export GITHUB_BASE_REF="master"
	# fi
	# git fetch origin "$GITHUB_BASE_REF"

	# bioconda-utils build recipes config.yml \
	# --lint --git-range origin/"$GITHUB_BASE_REF" HEAD

	# - name: Prepare artifacts
	# if: steps.additional_platforms.outputs.skip_build != 'true'
	# run: \|
	# (
	# rm -rf /tmp/artifacts
	# mkdir -p /tmp/artifacts/packages
	# cd /opt/mambaforge/envs/bioconda/conda-bld \|\| exit 0
	# find -name .cache \| xargs rm -rf \|\| true
	# for n in index.html channeldata.json osx-arm64 noarch; do
	# cp -rv $n /tmp/artifacts/packages \|\| true
	# done
	# ) \|\| true

	# - name: Archive packages
	# if: steps.additional_platforms.outputs.skip_build != 'true'
	# uses: actions/upload-artifact@v4
	# with:
	# name: osx-arm64-packages
	# path: \|
	# /tmp/artifacts

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Update unifrac to 1.5 #14656

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Update unifrac to 1.5 #14656

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Workflow file for this run