Installation and first run

PharmFlux 0.1.0 is a source release. Start from a checkout of this repository. Rust builds use the pinned Cargo.lock; the first build downloads dependencies. Rust and Cargo are required for the command-line and Python native builds.

Command-line program

From the repository root:

cargo build --release --locked -p pharmflux-cli
./target/release/pharmflux --version
./target/release/pharmflux validate conformance/models/synthetic-one-compartment.pfx
./target/release/pharmflux run \
  conformance/models/synthetic-pbpk-24.pfx \
  conformance/requests/synthetic-pbpk-24.json > simulation.json

The executable writes results to standard output and structured errors to standard error. ./target/release/pharmflux --help lists operations. The model guide explains the request format.

Rust library

This release builds from a workspace; its crates are not published to a Rust registry. In a Rust project, use path dependencies into a checkout:

[dependencies]
pharmflux = { path = "/path/to/pharmflux/crates/pharmflux" }
pharmflux-core = { path = "/path/to/pharmflux/crates/pharmflux-core" }

Replace /path/to/pharmflux with the checkout location. pharmflux-core contains versioned requests and results; pharmflux contains parsing, compilation, simulation, and fitting. See their public Rust APIs and the synthetic conformance cases for examples.

Python package

Python 3.10 or newer is required. From the repository root, in an isolated Python environment:

python -m pip install .
python -c "import pharmflux; print(pharmflux.__version__)"

This builds the native extension from the checked-out Rust source; no wheel is published by these instructions. CompiledModel runs simulations and scalar fits. CompiledSensitivities runs sensitivity and individual or population fits. See fitting for a complete example.

WebAssembly and JavaScript

Install the Rust wasm32-unknown-unknown target and wasm-pack, then build from the repository root:

rustup target add wasm32-unknown-unknown
cd bindings/wasm
wasm-pack build --target web --out-dir pkg/engine

The generated bindings/wasm/pkg/engine/ directory is consumed by the supplied JavaScript worker; generated assets are not committed. Serve the JavaScript module and .wasm file from your application. The package in bindings/wasm/ is marked private and is not published to a JavaScript registry. See browser integration and privacy before embedding it. The direct WASM bindings contain additional operations; the supplied browser worker currently exposes simulation only.

R source package

The source checkout includes the R package and its native Rust workspace. See the R installation instructions and executable guide. It requires R, jsonlite, a compatible C compiler, and Rust/Cargo. No CRAN or R-universe package publication is assumed.

Build the documentation locally

After installing both bindings and the notebook/R Markdown prerequisites:

python -m pip install -r docs/requirements.txt
python scripts/build_user_guide_formats.py
python -m nbconvert --to notebook --execute --inplace docs/PYTHON-USER-GUIDE.ipynb
python -m nbconvert --to html docs/PYTHON-USER-GUIDE.ipynb
Rscript -e 'rmarkdown::render("docs/R-USER-GUIDE.Rmd")'
python scripts/build_quickstart_docs.py

Open docs/_site/index.html to read and search the built site offline. The repository's documentation workflow checks tutorials on pull requests and publishes the site from passing main-branch builds.