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MRG: update the CLI docs and help for search --containment and prefetch #4405

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MRG: update the CLI docs and help for search --containment and prefetch

MRG: update the CLI docs and help for search --containment and prefetch #4405

Workflow file for this run

.github/workflows/rust.yml at 5f9d47a
name: Rust checks
on:
push:
branches: [latest]
pull_request:
schedule:
- cron: "0 0 * * *" # daily
jobs:
check:
name: Check
runs-on: ubuntu-latest
steps:
- name: Checkout sources
uses: actions/checkout@v4
- name: Install stable toolchain
uses: actions-rs/toolchain@v1
with:
profile: minimal
toolchain: stable
override: true
- name: Run cargo check
uses: actions-rs/cargo@v1
with:
command: check
test:
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
build: [beta, stable, windows, macos]
include:
- build: macos
os: macos-latest
rust: stable
continue: false
- build: windows
os: windows-latest
rust: stable
continue: true
- build: beta
os: ubuntu-latest
rust: beta
continue: false
- build: stable
os: ubuntu-latest
rust: stable
continue: false
steps:
- uses: actions/checkout@v4
- uses: actions-rs/toolchain@v1
with:
toolchain: ${{ matrix.rust }}
override: true
- name: Run tests
uses: actions-rs/cargo@v1
with:
command: test
args: --no-fail-fast
test_all_features:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions-rs/toolchain@v1
with:
toolchain: stable
override: true
- uses: actions-rs/[email protected]
with:
crate: cargo-all-features
version: latest
use-tool-cache: true
- name: Run tests for all feature combinations
run: cargo test-all-features --no-fail-fast --all
coverage:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions-rs/toolchain@v1
with:
toolchain: stable
override: true
- name: Install cargo-binstall
run: |
wget https://github.com/ryankurte/cargo-binstall/releases/latest/download/cargo-binstall-x86_64-unknown-linux-gnu.tgz
tar xf cargo-binstall-x86_64-unknown-linux-gnu.tgz
chmod +x cargo-binstall
mv cargo-binstall "$HOME/.cargo/bin"
- name: Install cargo-tarpaulin
run: cargo binstall --no-confirm cargo-tarpaulin
- name: Coverage with tarpaulin
run: cargo tarpaulin --all --all-features --timeout 600 --out xml -- --test-threads 1
- name: Upload Rust coverage to codecov
uses: codecov/codecov-action@v3
with:
flags: rust
fail_ci_if_error: true
lints:
name: Lints
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
build: [beta, stable]
include:
- build: beta
rust: beta
- build: stable
rust: stable
steps:
- name: Checkout sources
uses: actions/checkout@v4
- name: Install Rust toolchain
uses: actions-rs/toolchain@v1
with:
profile: minimal
toolchain: ${{ matrix.rust }}
override: true
components: rustfmt, clippy
- name: Run cargo fmt
uses: actions-rs/cargo@v1
with:
command: fmt
args: --all -- --check
- name: Run cargo clippy
uses: actions-rs/cargo@v1
with:
command: clippy
args: --all -- -D warnings
wasm-pack:
name: Check if wasm-pack builds a valid package for the sourmash crate
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions-rs/toolchain@v1
with:
toolchain: stable
target: wasm32-unknown-unknown
- name: Install wasm-pack
run: "curl https://rustwasm.github.io/wasm-pack/installer/init.sh -sSf | sh"
- name: Prepare node for running tests
uses: actions/setup-node@v4
with:
node-version: 16
registry-url: https://registry.npmjs.org/
- name: run wasm tests
continue-on-error: true ## TODO: remove this when tests works again...
run: wasm-pack test --node src/core
- name: run wasm-pack build
run: wasm-pack build src/core -d ../../pkg
- name: Prepare package for NPM publishing
working-directory: pkg
run: npm pack
- uses: actions/upload-artifact@v4
with:
path: 'pkg/sourmash*.tgz'
wasm32-wasi:
name: Run tests under wasm32-wasi
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Install wasm32-wasi target
uses: actions-rs/toolchain@v1
with:
toolchain: stable
target: wasm32-wasi
- name: Install wasmtime
run: "curl https://wasmtime.dev/install.sh -sSf | bash"
- name: Add wasmtime to PATH
run: echo "$HOME/.wasmtime/bin" >> $GITHUB_PATH
- name: Install cargo-wasi command
uses: actions-rs/cargo@v1
with:
command: install
args: --force cargo-wasi
- name: Build code with cargo-wasi
uses: actions-rs/cargo@v1
continue-on-error: true ## TODO: remove this when build works...
with:
command: wasi
args: build
- name: Run tests under wasm32-wasi
uses: actions-rs/cargo@v1
continue-on-error: true ## TODO: remove this when tests work...
with:
command: wasi
args: test
publish:
name: Publish (dry-run)
runs-on: ubuntu-latest
steps:
- name: Checkout sources
uses: actions/checkout@v4
- name: Install stable toolchain
uses: actions-rs/toolchain@v1
with:
profile: minimal
toolchain: stable
override: true
- name: Check semver
uses: obi1kenobi/cargo-semver-checks-action@v2
with:
crate-name: sourmash
version-tag-prefix: r
feature-group: default-features
features: branchwater
- name: Make sure we can publish the sourmash crate
uses: actions-rs/cargo@v1
with:
command: publish
args: --dry-run --manifest-path src/core/Cargo.toml
minimum_rust_version:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions-rs/toolchain@v1
with:
toolchain: "1.65.0"
override: true
- name: check if README matches MSRV defined here
run: grep '1.65.0' src/core/README.md
- name: Check if it builds properly
uses: actions-rs/cargo@v1
with:
command: build
args: --all-features --tests
check_cbindgen:
name: "Check if cbindgen runs cleanly for generating the C headers"
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions-rs/toolchain@v1
with:
toolchain: stable
override: true
- uses: actions-rs/[email protected]
with:
crate: cbindgen
version: 0.20.0
use-tool-cache: true
- run: make include/sourmash.h
- name: check if headers have the same content
run: |
git update-index --refresh
git diff
git diff-index --quiet HEAD -- include/sourmash.h || echo "::error file=include/sourmash.h::Header doesn't match committed file, did you forget to rerun cbindgen?"