Bundle the gen CLI client in the Python wheel

.github/workflows/python-wheels.yaml

@@ -27,13 +27,23 @@ jobs:
       - name: Install capnp (Windows)
         if: runner.os == 'Windows'
         run: choco install capnproto
+      - name: Stage bundled client (macOS)
+        if: runner.os == 'macOS'
+        run: make stage-python-client
+      - name: Stage bundled client (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          $ErrorActionPreference = 'Stop'
+          cargo build --release --locked --bin gen
+          New-Item -ItemType Directory -Force "gen.gen.data/scripts"
+          Copy-Item "target/release/gen.exe" "gen.gen.data/scripts/gen.exe"
       - name: Build wheels (Linux)
         if: runner.os == 'Linux'
         uses: PyO3/maturin-action@v1
         with:
           command: build
           args: --release --manifest-path gen-python/Cargo.toml --features extension-module --interpreter python${{ matrix.python-version }} --out gen-python/target/wheels
-          sccache: true
           manylinux: auto
           container: quay.io/pypa/manylinux_2_28_x86_64:latest
           before-script-linux: |
@@ -45,6 +55,7 @@ jobs:
             mkdir -p gen-capnp-schemas/src/generated
             (cd gen-capnp-schemas && capnp compile -I . -orust:src/generated gen-core.capnp gen-models.capnp gen-schema.capnp)
             ls -la gen-capnp-schemas/src/generated
+            make stage-python-client
           working-directory: .
         env:
           CAPNP: /usr/bin/capnp
@@ -58,6 +69,31 @@ jobs:
           args: --release --manifest-path gen-python/Cargo.toml --features extension-module --interpreter ${{ steps.setup-python.outputs.python-path }} --out gen-python/target/wheels
           sccache: true
           working-directory: .
+      - name: Verify wheel contents (macOS, Linux)
+        if: runner.os != 'Windows'
+        run: python gen-python/scripts/verify_wheel.py gen-python/target/wheels/*.whl
+      - name: Verify wheel contents (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          $ErrorActionPreference = 'Stop'
+          $wheel = Get-ChildItem "gen-python/target/wheels/*.whl"
+          python gen-python/scripts/verify_wheel.py "$($wheel.FullName)"
+      - name: Smoke test wheel (macOS, Linux)
+        if: runner.os != 'Windows'
+        run: |
+          python -m pip install --force-reinstall --no-deps gen-python/target/wheels/*.whl
+          python -c "import gen; print(gen.__version__)"
+          gen --version
+      - name: Smoke test wheel (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          $ErrorActionPreference = 'Stop'
+          $wheel = Get-ChildItem "gen-python/target/wheels/*.whl"
+          python -m pip install --force-reinstall --no-deps "$($wheel.FullName)"
+          python -c "import gen; print(gen.__version__)"
+          gen --version
       - name: Upload wheels to releases
         if: runner.os != 'Windows'
         env:

.gitignore

@@ -40,6 +40,7 @@ gen-r/vignettes/*.html
 # Python bindings
 **/__pycache__/
 gen-python/python/gen/*.so
+/gen.gen.data/
 
 # R package extension built from Rust
 gen-r/src/genr.so

Cargo.toml

@@ -25,6 +25,11 @@ members = [".", "gen-core", "gen-models", "gen-graph", "gen-diff", "gen-tui", "g
 default-members = [".", "gen-core", "gen-models", "gen-graph", "gen-diff", "gen-capnp-schemas", "gen-annotations"]
 exclude = ["gen-python", "gen-r/src/rust"]
 
+[patch.crates-io]
+# TEMPORARY: verifying the Windows MSVC build fix in CI before it's published
+# to crates.io. Revert this patch before merging.
+rusqdoltlite = { git = "https://github.com/bobvh/rusqdoltlite", rev = "d1ef39b" }
+
 [features]
 benchmark = []
 default = ["models", "cli", "diff", "remote"]

Makefile

@@ -1,8 +1,17 @@
-.PHONY: python jupyter r r-test release-check-js clean build clippy-fix docker-build gif
+.PHONY: python python-wheel stage-python-client jupyter r r-test release-check-js clean build clippy-fix docker-build gif
 python:
 	@[ -d .venv ] || python -m venv .venv
 	@.venv/bin/pip show maturin >/dev/null 2>&1 || .venv/bin/pip install maturin
 	.venv/bin/maturin develop --release --manifest-path gen-python/Cargo.toml --features extension-module
+stage-python-client:
+	cargo build --release --locked --bin gen
+	mkdir -p gen.gen.data/scripts
+	cp target/release/gen gen.gen.data/scripts/gen
+	chmod +x gen.gen.data/scripts/gen
+python-wheel: stage-python-client
+	@[ -d .venv ] || python -m venv .venv
+	@.venv/bin/pip show maturin >/dev/null 2>&1 || .venv/bin/pip install maturin
+	.venv/bin/maturin build --release --manifest-path gen-python/Cargo.toml --features extension-module
 # The jupyter widget requires a bundled JS file compiled from the TypeScript sources in gen-python/js/.
 # We check in the compiled jupyter_widget.js alongside the TS so npm is not required to build the widget.
 jupyter: python

README.md

@@ -8,19 +8,33 @@ Gen brings version control to genetic sequences. With it, you can track variants
 
 ## Install
 
-**Gen client**: prebuilt binaries for macOS and Linux are on the [releases page](https://github.com/genhub-bio/gen/releases): [macOS (.pkg)](https://github.com/genhub-bio/gen/releases/download/nightly/gen.macos.pkg), [Linux x86_64 (.zip)](https://github.com/genhub-bio/gen/releases/download/nightly/gen.linux-x86_64.zip), [Linux arm64 (.zip)](https://github.com/genhub-bio/gen/releases/download/nightly/gen.linux-arm64.zip). Gen is built primarily for Unix-like systems; on Windows, you can install [WSL](https://learn.microsoft.com/en-us/windows/wsl/) to get a Linux environment, then use the Linux binary above from inside it.
+Install Gen with pip:
 
-**Python package**: install on macOS, Linux, or Windows using:
 ```sh
 pip install gen
 ```
 
-Install the `jupyter` extra to include an interactive graph widget for Jupyter and other anywidget-compatible notebooks:
+Or install CLI in an isolated environment with uv:
+
+```sh
+uv tool install gen
+```
+
+It is also available from crates.io:
+
+```sh
+cargo install gen
+```
+
+Prebuilt binaries and installers are available on the [releases page](https://github.com/genhub-bio/gen/releases) for [macOS](https://github.com/genhub-bio/gen/releases/download/nightly/gen.macos.pkg) and Linux ([x64](https://github.com/genhub-bio/gen/releases/download/nightly/gen.linux-x86_64.zip) / [arm64](https://github.com/genhub-bio/gen/releases/download/nightly/gen.linux-arm64.zip)). Gen is built primarily for Unix-like systems; on Windows, you can install [WSL](https://learn.microsoft.com/en-us/windows/wsl/) to get a Linux environment, then use the Linux binary above from inside it.
+
+**Python package**: Installing Gen with pip also installs the Python package. Install the `jupyter` extra to include an interactive graph widget for Jupyter and other anywidget-compatible notebooks:
+
 ```sh
 pip install gen[jupyter]
 ```
 
-**R package**: install on macOS (Apple silicon) using the `remotes` package:
+**R package**: Install on macOS (Apple silicon) using the `remotes` package:
 ```r
 install.packages("remotes")
 remotes::install_url(

gen-python/README.md

@@ -2,9 +2,10 @@
 
 Python bindings to the Gen version control system for genetic sequences.
 
-The bindings expose the full Gen data model — repositories, sequence graphs,
-import/export pipelines — from Python and Jupyter notebooks. An optional Jupyter
-widget provides interactive graph visualization.
+The package installs the `gen` command-line client and exposes the full Gen data
+model — repositories, sequence graphs, import/export pipelines — from Python and
+Jupyter notebooks. An optional Jupyter widget provides interactive graph
+visualization.
 
 ## Quick start
 
@@ -29,6 +30,12 @@ sample.plot()  # or sg.plot()
 
 The package is built from three layers:
 
+### Client (`src/main.rs`)
+
+The existing Rust command-line client is compiled separately and staged in
+maturin's wheel data `scripts` directory. Package installers place that executable
+on `PATH` as `gen` on macOS and Linux or `gen.exe` on Windows.
+
 ### Rust (`src/python_api/`)
 
 The core of the package. [PyO3](https://pyo3.rs) + [maturin](https://www.maturin.rs)
@@ -72,6 +79,7 @@ Loaded by anywidget directly in the browser. Responsible for:
 
 ```sh
 make          # from the project root — builds the native extension via maturin
+make python-wheel  # builds a wheel containing the extension and client
 make jupyter  # also builds the JS widget bundle and installs the `jupyter` extras
 ```
 

gen-python/scripts/verify_wheel.py

@@ -0,0 +1,47 @@
+#!/usr/bin/env python3
+"""Verify that a Gen wheel contains the Python package and bundled client."""
+
+import sys
+import zipfile
+from pathlib import Path
+
+
+def fail(message: str) -> None:
+    raise SystemExit(message)
+
+
+def verify_wheel(wheel_path: Path) -> None:
+    client_name = "gen.exe" if "-win" in wheel_path.name else "gen"
+
+    with zipfile.ZipFile(wheel_path) as wheel:
+        names = {entry.filename for entry in wheel.infolist()}
+
+        if not any(name.endswith(f".data/scripts/{client_name}") for name in names):
+            fail(f"{wheel_path} should contain the bundled {client_name}")
+
+        extension_suffixes = (".pyd", ".so")
+        if not any(
+            name.startswith("gen/") and name.endswith(extension_suffixes)
+            for name in names
+        ):
+            fail(f"{wheel_path} should contain the compiled gen extension")
+
+        if "gen/static/jupyter_widget.js" not in names:
+            fail(f"{wheel_path} should contain the Jupyter widget asset")
+
+    print(f"Verified bundled client and Python package in {wheel_path}")
+
+
+def main() -> None:
+    if len(sys.argv) != 2:
+        fail(f"usage: {Path(sys.argv[0]).name} WHEEL")
+
+    wheel_path = Path(sys.argv[1])
+    if not wheel_path.is_file():
+        fail(f"wheel does not exist: {wheel_path}")
+
+    verify_wheel(wheel_path)
+
+
+if __name__ == "__main__":
+    main()