Installation

AutoZyme ships as two packages: autozyme (Python, on PyPI) and autozyme (R, from the GitHub repository; CRAN release pending). Both have no hard dependencies on any upstream package; each patch activates only when its upstream is importable.

Python

pip install autozyme

Requires Python 3.10 or newer. Prebuilt wheels cover Linux (x86_64 + aarch64, manylinux + musllinux), macOS (arm64 + x86_64), and Windows (x86_64) for CPython 3.10–3.14, so there is nothing to compile. The wheel has no runtime dependencies (no scanpy, no torch, no tensorflow).

Optional: install upstream packages

autozyme is useless without something to accelerate. Install whichever upstream(s) you actually use:

pip install scanpy           # for autozyme.activate("scanpy")
pip install cell2location    # for autozyme.activate("cell2location")
pip install scvelo           # for autozyme.activate("scvelo")
pip install MDAnalysis       # for autozyme.activate("mdanalysis_rmsd")
# ...

See the patch catalog for the full list and which upstream version each patch is pinned against.

Confirm the install

import autozyme
autozyme.list_patches()                 # all 16 patches discovered
autozyme.list_patches(installed=True)   # only those whose upstream is importable

Or from the shell:

python -m autozyme

prints a one-screen dashboard of every patch and its upstream availability.

R

# from GitHub (CRAN release pending); the R package lives in the autozyme_r/ subdir
remotes::install_github("ElliotXie/autozyme", subdir = "autozyme_r")

# once published to CRAN
install.packages("autozyme")

The R package compiles C++ (Rcpp) kernels at install. This only really trips up Windows (no built-in compiler): install Rtools matching your R version first, or the build fails. macOS (Xcode Command Line Tools) and Linux (gcc) normally already have a compiler.

Requires R 4.0 or newer. Depends: is empty — Suggests: lists every upstream the lifted patches recognize, but installing autozyme doesn’t pull any of them in.

Confirm the install

library(autozyme)
list_patches()                         # all shipped patches
list_patches(installed = TRUE)         # only those whose upstream is installed
dashboard()                            # one-screen status of patches + upstream availability

Platform support

Python ships prebuilt wheels (nothing to compile). The R package compiles from source, which only needs setup on Windows (Rtools).

All patches are tested across Linux + Windows in CI; macOS is tested by maintainers but not on every PR.

Updating

pip install --upgrade autozyme

The R package installs from GitHub (CRAN pending), so re-run the install to pull the latest:

remotes::install_github("ElliotXie/autozyme", subdir = "autozyme_r", force = TRUE)

Releases follow PEP 440 / semver. Breaking API changes (e.g. a register_patch kwarg rename) bump the minor version and are gated by the API signature snapshot test — you’ll see the change in the changelog before it can land.

Uninstall

pip uninstall autozyme

remove.packages("autozyme")

autozyme makes no system-wide changes outside its own package directory. Removing it leaves your scanpy / Seurat / etc. installs untouched.