Skip to content
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
54 changes: 2 additions & 52 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -350,70 +350,20 @@ jobs:
name: oxo-call-${{ matrix.target }}
path: dist/*.zip

# ─── Build WebAssembly binary (always, release artifacts only on tags) ──────
build-wasm:
name: Build WebAssembly (wasm32-wasip1)
runs-on: ubuntu-latest
needs: [test]
# always() breaks the skip-cascade from sync-version through test.
if: always() && needs.test.result == 'success'

steps:
- uses: actions/checkout@v6
with:
ref: ${{ (github.event_name == 'workflow_dispatch' && inputs.tag != '') && format('refs/tags/{0}', inputs.tag) || github.ref }}

- name: Install Rust (stable) with wasm32-wasip1
uses: dtolnay/rust-toolchain@stable
with:
targets: wasm32-wasip1

- name: Cache cargo
uses: actions/cache@v5
with:
path: |
~/.cargo/registry
~/.cargo/git
target
key: ${{ runner.os }}-cargo-wasm32-wasip1-${{ hashFiles('**/Cargo.lock') }}

- name: Build release (wasm32-wasip1)
run: cargo build --release --target wasm32-wasip1

- name: Package binary
if: startsWith(github.ref, 'refs/tags/v') || (github.event_name == 'workflow_dispatch' && inputs.tag != '')
shell: bash
run: |
set -euxo pipefail
BIN_NAME="oxo-call"
TARGET_DIR="target/wasm32-wasip1/release"
mkdir -p dist
tar -C "${TARGET_DIR}" -czvf \
"dist/${BIN_NAME}-${RELEASE_TAG}-wasm32-wasip1.tar.gz" \
"${BIN_NAME}.wasm"

- name: Upload artifact
if: startsWith(github.ref, 'refs/tags/v') || (github.event_name == 'workflow_dispatch' && inputs.tag != '')
uses: actions/upload-artifact@v7
with:
name: oxo-call-wasm32-wasip1
path: dist/*.tar.gz

# ─── GitHub Release (attach all binary artifacts) ─────────────────────────
release:
permissions:
contents: write
name: GitHub Release
needs: [sync-version, build-linux, build-macos, build-windows, build-wasm]
needs: [sync-version, build-linux, build-macos, build-windows]
runs-on: ubuntu-latest
if: >-
always() &&
(startsWith(github.ref, 'refs/tags/v') || (github.event_name == 'workflow_dispatch' && inputs.tag != '')) &&
(needs.sync-version.result == 'success' || needs.sync-version.result == 'skipped') &&
needs.build-linux.result == 'success' &&
needs.build-macos.result == 'success' &&
needs.build-windows.result == 'success' &&
needs.build-wasm.result == 'success'
needs.build-windows.result == 'success'

steps:
- uses: actions/checkout@v6
Expand Down
7 changes: 0 additions & 7 deletions Cargo.toml
Original file line number Diff line number Diff line change
Expand Up @@ -34,20 +34,13 @@ tracing = "0.1"
regex = "1.12.3"
lru = "0.12"
hex = "0.4"

# ── Native-only dependencies (not available on wasm32) ────────────────────────
[target.'cfg(not(target_arch = "wasm32"))'.dependencies]
tokio = { version = "1", features = ["full"] }
reqwest = { version = "0.13", features = ["json", "rustls"], default-features = false }
directories = "6.0"
which = "8.0"
indicatif = "0.18"
termimad = "0.34"

# ── WebAssembly dependencies ──────────────────────────────────────────────────
[target.'cfg(target_arch = "wasm32")'.dependencies]
tokio = { version = "1", features = ["rt", "macros"] }

[dev-dependencies]
tempfile = "3"
wiremock = "0.6.5"
Expand Down
185 changes: 159 additions & 26 deletions docs/guide/src/reference/architecture.md

Large diffs are not rendered by default.

1 change: 0 additions & 1 deletion docs/guide/src/tutorials/installation.md
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,6 @@ Pre-built binaries are the easiest way to get started. Download from the [Releas
| macOS | aarch64 (Apple Silicon) | `oxo-call-vX.Y.Z-aarch64-apple-darwin.tar.gz` |
| Windows | x86_64 | `oxo-call-vX.Y.Z-x86_64-pc-windows-msvc.zip` |
| Windows | aarch64 | `oxo-call-vX.Y.Z-aarch64-pc-windows-msvc.zip` |
| WebAssembly | wasm32-wasip1 | `oxo-call-vX.Y.Z-wasm32-wasip1.tar.gz` (advanced) |

2. Extract and move to your PATH:

Expand Down
26 changes: 3 additions & 23 deletions docs/index.html
Original file line number Diff line number Diff line change
Expand Up @@ -603,19 +603,9 @@
.community-links { grid-template-columns: 1fr; }
}

/* ── Wasm note ──────────────────────────────────────────────────────── */
/* ── Wasm note (removed) ──────────────────────────────────────────── */
.wasm-badge {
display: inline-flex;
align-items: center;
gap: 0.4rem;
padding: 0.2rem 0.7rem;
background: rgba(88,166,255,0.1);
border: 1px solid rgba(88,166,255,0.3);
border-radius: 20px;
font-family: 'JetBrains Mono', monospace;
font-size: 0.72rem;
color: var(--accent);
margin-bottom: 1rem;
display: none;
}
.pulse {
width: 6px; height: 6px;
Expand Down Expand Up @@ -902,7 +892,6 @@
<span class="badge">🦀 Rust 2024</span>
<span class="badge">🧬 Bioinformatics</span>
<span class="badge">🤖 LLM-powered</span>
<span class="badge">⚡ WebAssembly</span>
</div>
<h1>Model-intelligent<br/>orchestration for<br/><em>CLI bioinformatics</em></h1>
<p>
Expand Down Expand Up @@ -1413,7 +1402,7 @@ <h2 class="section-title">Get started in 60 seconds</h2>
tar xzf oxo-call-*-x86_64-unknown-linux-gnu.tar.gz
sudo mv oxo-call /usr/local/bin/

<span class="c"># Available for: Linux (x86_64/aarch64), macOS (Intel/Apple Silicon), Windows, WASM</span></pre>
<span class="c"># Available for: Linux (x86_64/aarch64), macOS (Intel/Apple Silicon), Windows</span></pre>
</div>

<div class="code-block">
Expand Down Expand Up @@ -1481,15 +1470,6 @@ <h2 class="section-title">Get started in 60 seconds</h2>
--input-list samples.txt --jobs 4</pre>
</div>

<div class="code-block">
<div class="code-block-header">
<span>WASI binary (requires wasmtime)</span>
<button class="copy-btn" data-copy="wasmtime oxo-call.wasm -- dry-run samtools &quot;sort input.bam by coordinate&quot;">copy</button>
</div>
<pre><span class="c"># Download the .wasm binary from the GitHub Releases page, then:</span>
wasmtime oxo-call.wasm -- dry-run samtools <span class="s">"sort input.bam by coordinate"</span></pre>
</div>

<div class="code-block">
<div class="code-block-header">
<span>Quick test license (copy & paste to get started)</span>
Expand Down
Loading
Loading