Rust

chore(semver): bump #137

Workflow file for this run

	name: Rust

	on: push

	env:
	CARGO_TERM_COLOR: always

	jobs:
	ci:
	needs: [build, test, integration-tests]
	name: CI
	runs-on: "ubuntu-latest"
	steps:
	- name: Done
	run: exit 0

	build:
	name: Build
	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	os: ["ubuntu-latest", "macos-latest"]
	steps:
	- uses: actions/checkout@v3
	- name: Build
	run: cargo build --verbose
	- name: Build no default
	run: cargo build --verbose --no-default-features

	test:
	name: Test
	runs-on: "ubuntu-latest"
	steps:
	- uses: actions/checkout@v3
	- name: Test
	run: cargo test

	integration-tests:
	needs:
	[
	test-fastx,
	test-interleaved,
	test-multiline-fasta,
	test-read-write,
	test-htslib,
	test-parallel,
	test-paired-parallel,
	test-naive,
	test-reloading,
	test-reloading-parallel,
	test-multi,
	test-multi-interleaved,
	test-url,
	]
	name: Integration Tests
	runs-on: "ubuntu-latest"
	steps:
	- name: Done
	run: echo "Done"

	build-fastx:
	name: Build FASTX
	runs-on: "ubuntu-latest"
	steps:
	- uses: actions/checkout@v3
	- name: Build target
	run: cargo build --release --example fastx
	- name: Upload binary artifact
	uses: actions/upload-artifact@v4
	with:
	name: fastx-binary
	path: target/release/examples/fastx
	retention-days: 1

	test-fastx:
	name: Test FASTX
	runs-on: "ubuntu-latest"
	needs: build-fastx
	strategy:
	matrix:
	input_format: [fasta, fastq]
	output_format: [fasta, fastq]
	steps:
	- uses: actions/checkout@v3
	- name: Download binary artifact
	uses: actions/download-artifact@v4
	with:
	name: fastx-binary
	path: .
	- name: Make binary executable
	run: chmod +x fastx
	- name: Run test (from file)
	run: ./fastx data/sample.${{ matrix.input_format }} -f ${{ matrix.output_format }}
	- name: Run test (from stdin)
	run: /bin/cat data/sample.${{ matrix.input_format }} \| ./fastx -f ${{ matrix.output_format }}

	test-url:
	name: Test URL
	runs-on: "ubuntu-latest"
	steps:
	- uses: actions/checkout@v3
	- name: run test
	run: cargo run --release --example url

	build-multi:
	name: Build Multi
	runs-on: "ubuntu-latest"
	steps:
	- uses: actions/checkout@v3
	- name: build target
	run: cargo build --release --example multi_parallel
	- name: upload binary artifact
	uses: actions/upload-artifact@v4
	with:
	name: multi-binary
	path: ./target/release/examples/multi_parallel

	test-multi:
	name: Test Multi
	runs-on: "ubuntu-latest"
	needs: build-multi
	strategy:
	matrix:
	threads: [1, 4]
	steps:
	- uses: actions/checkout@v3
	- name: download binary artifact
	uses: actions/download-artifact@v4
	with:
	name: multi-binary
	path: .
	- name: make executable
	run: chmod +x ./multi_parallel
	- name: test arity-2
	run: ./multi_parallel -T ${{ matrix.threads }} ./data/r1.fastq ./data/r2.fastq
	- name: test arity-3
	run: ./multi_parallel -T ${{ matrix.threads }} ./data/r1.fastq ./data/r2.fastq ./data/r3.fastq
	- name: test arity-4
	run: ./multi_parallel -T ${{ matrix.threads }} ./data/r1.fastq ./data/r2.fastq ./data/r3.fastq ./data/r4.fastq

	build-multi-interleaved:
	name: Build Multi Interleaved
	runs-on: "ubuntu-latest"
	steps:
	- uses: actions/checkout@v3
	- name: build target
	run: cargo build --release --example multi_interleaved
	- name: upload binary artifact
	uses: actions/upload-artifact@v4
	with:
	name: multi-interleaved-binary
	path: ./target/release/examples/multi_interleaved

	test-multi-interleaved:
	name: Test Multi Interleaved
	runs-on: "ubuntu-latest"
	needs: build-multi-interleaved
	strategy:
	matrix:
	threads: [1, 4]
	steps:
	- uses: actions/checkout@v3
	- name: download binary artifact
	uses: actions/download-artifact@v4
	with:
	name: multi-interleaved-binary
	path: .
	- name: make executable
	run: chmod +x ./multi_interleaved
	- name: test arity-2
	run: ./multi_interleaved -T ${{ matrix.threads }} ./data/interleaved.fastq --arity 2
	- name: test arity-3
	run: ./multi_interleaved -T ${{ matrix.threads }} ./data/r123.fastq --arity 3

	build-read-write:
	name: Build Read Write
	runs-on: "ubuntu-latest"
	steps:
	- uses: actions/checkout@v3
	- name: build target
	run: cargo build --release --example read_write
	- name: upload binary artifact
	uses: actions/upload-artifact@v4
	with:
	name: read-write-binary
	path: ./target/release/examples/read_write

	test-read-write:
	name: Test Read Write
	runs-on: "ubuntu-latest"
	needs: build-read-write
	strategy:
	matrix:
	input_format: [fasta, fastq]
	input_compression: ["", ".gz", ".zst"]
	output_format: [fasta, fastq]
	steps:
	- uses: actions/checkout@v3
	- name: download binary artifact
	uses: actions/download-artifact@v4
	with:
	name: read-write-binary
	path: .
	- name: make executable
	run: chmod +x ./read_write
	- name: test io from file
	run: ./read_write -f ${{ matrix.output_format }} data/sample.${{ matrix.input_format }}${{ matrix.input_compression }}
	- name: test io from stdin
	run: ./read_write ./data/sample.${{ matrix.input_format }}${{ matrix.input_compression }} -f ${{ matrix.output_format }} \| ./read_write

	build-htslib:
	name: Build Htslib
	runs-on: "ubuntu-latest"
	steps:
	- uses: actions/checkout@v3
	- name: build target
	run: cargo build --release --example htslib
	- name: upload binary artifact
	uses: actions/upload-artifact@v4
	with:
	name: htslib-binary
	path: ./target/release/examples/htslib

	test-htslib:
	name: Test Htslib Read
	runs-on: "ubuntu-latest"
	needs: build-htslib
	strategy:
	matrix:
	input_format: [sam, bam, cram]
	output_format: [fasta, fastq]
	steps:
	- uses: actions/checkout@v3
	- name: download binary artifact
	uses: actions/download-artifact@v4
	with:
	name: htslib-binary
	path: .
	- name: make executable
	run: chmod +x ./htslib
	- name: test io from file
	run: ./htslib -f ${{ matrix.output_format }} data/sample.${{ matrix.input_format }}
	- name: test io from stdin
	run: /bin/cat ./data/sample.${{ matrix.input_format }} \| ./htslib -f ${{ matrix.output_format }}
	- name: test io from file (paired)
	run: ./htslib -f ${{ matrix.output_format }} data/paired.${{ matrix.input_format }} --paired
	- name: test io from stdin (paired)
	run: /bin/cat ./data/paired.${{ matrix.input_format }} \| ./htslib -f ${{ matrix.output_format }} --paired

	test-interleaved:
	name: Test Interleaved
	runs-on: "ubuntu-latest"
	steps:
	- uses: actions/checkout@v3
	- name: Test interleaved example
	run: cargo run --release --example interleaved -- data/interleaved.fastq

	test-multiline-fasta:
	name: Test Multiline FASTA
	runs-on: "ubuntu-latest"
	steps:
	- uses: actions/checkout@v3
	- name: Test multiline FASTA example
	run: cargo run --release --example multiline_fasta -- data/multiline.fasta

	test-parallel:
	name: Test Parallel
	runs-on: "ubuntu-latest"
	steps:
	- uses: actions/checkout@v3
	- name: Test parallel example with FASTQ (1 thread)
	run: cargo run --release --example parallel -- data/sample.fastq 1
	- name: Test parallel example with FASTQ (2 threads)
	run: cargo run --release --example parallel -- data/sample.fastq 2
	- name: Test parallel example with FASTQ (2 threads) alternative batch size
	run: cargo run --release --example parallel -- data/sample.fastq 2 48
	- name: Test parallel example with FASTA (1 thread)
	run: cargo run --release --example parallel -- data/sample.fasta 1
	- name: Test parallel example with FASTA (2 threads)
	run: cargo run --release --example parallel -- data/sample.fasta 2
	- name: Test parallel example with FASTA (2 threads) alternative batch size
	run: cargo run --release --example parallel -- data/sample.fasta 2 48

	test-paired-parallel:
	name: Test Paired Parallel
	runs-on: "ubuntu-latest"
	steps:
	- uses: actions/checkout@v3
	- name: Test paired parallel example with FASTQ (1 thread)
	run: cargo run --release --example paired_parallel -- data/r1.fastq data/r2.fastq 1
	- name: Test paired parallel example with FASTQ (2 threads)
	run: cargo run --release --example paired_parallel -- data/r1.fastq data/r2.fastq 2

	test-naive:
	runs-on: "ubuntu-latest"
	steps:
	- uses: actions/checkout@v3
	- name: Test naive example with FASTQ
	run: cargo run --release --example naive -- data/sample.fastq
	- name: Test naive example with FASTA
	run: cargo run --release --example naive -- data/sample.fasta

	test-reloading:
	runs-on: "ubuntu-latest"
	steps:
	- uses: actions/checkout@v3
	- name: Test reloading example with FASTQ
	run: cargo run --release --example reloading -- data/sample.fastq
	- name: Test reloading example with FASTA
	run: cargo run --release --example reloading -- data/sample.fasta

	test-reloading-parallel:
	runs-on: "ubuntu-latest"
	steps:
	- uses: actions/checkout@v3
	- name: Test reloading parallel example with FASTQ (1 thread)
	run: cargo run --release --example reloading_parallel -- data/sample.fastq 1
	- name: Test reloading parallel example with FASTQ (2 threads)
	run: cargo run --release --example reloading_parallel -- data/sample.fastq 2
	- name: Test reloading parallel example with FASTA (1 thread)
	run: cargo run --release --example reloading_parallel -- data/sample.fasta 1
	- name: Test reloading parallel example with FASTA (2 threads)
	run: cargo run --release --example reloading_parallel -- data/sample.fasta 2

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chore(semver): bump #137

Workflow file

chore(semver): bump #137

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Workflow file for this run