FlatGFA: Optimize GFA parsing a bit #40

	name: build

	on:
	push:
	branches:
	- main
	pull_request:
	branches:
	- main

	jobs:
	test-py:
	name: test Python tools
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4

	- uses: actions/setup-python@v4
	with:
	python-version: '3.11'
	cache: pip
	cache-dependency-path: \|
	mygfa/pyproject.toml
	pollen_data_gen/pyproject.toml
	pollen_py/pyproject.toml
	slow_odgi/pyproject.toml

	- name: Install Flit
	run: pip install flit

	- name: Install mygfa
	run: cd mygfa ; flit install --symlink
	- name: Install pollen_data_gen
	run: cd pollen_data_gen ; flit install --symlink
	- name: Install pollen_py
	run: cd pollen_py ; flit install --symlink
	- name: Install slow_odgi
	run: cd slow_odgi ; flit install --symlink

	- name: Install Turnt
	run: pip install turnt

	- name: Problem matcher
	run: echo '::add-matcher::.github/tap-matcher.json'

	- name: Fetch test data
	run: make fetch SMALL=1

	- name: Pull odgi container
	run: \|
	docker pull quay.io/biocontainers/odgi:0.8.3--py310h6cc9453_0
	docker tag quay.io/biocontainers/odgi:0.8.3--py310h6cc9453_0 odgi

	- name: Install odgi alias
	run: \|
	mkdir -p $HOME/.local/bin
	cp .github/odgi.sh $HOME/.local/bin/odgi
	chmod a+x $HOME/.local/bin/odgi

	# Test slow_odgi.
	- name: Set up for slow_odgi tests
	run: make slow-odgi-setup SMALL=1
	- name: Test slow_odgi
	run: make test-slow-odgi SMALL=1

	test-parser:
	name: test DSL parser
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- uses: actions-rust-lang/setup-rust-toolchain@v1
	- run: cargo install runt
	- run: cargo build
	working-directory: ./pollen
	- run: runt -v
	working-directory: ./pollen

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