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Install Deformetrica into a managed Python environment

Source: R/install-deformetrica.R
install_deformetrica.Rd

deformetricar shells out to the deformetrica (>= 4.3) command-line tool, so you need that tool available once. This is the smooth path: it uses reticulate to create (or reuse) a dedicated Python environment, pip installs Deformetrica into it, verifies the deformetrica console script, and caches its path in options(deformetricar.exe=) so every subsequent find_deformetrica() call resolves it automatically (including in new sessions if you persist the option).

Usage

install_deformetrica(
  envname = "deformetrica",
  method = c("conda", "virtualenv", "auto"),
  python_version = "3.8",
  version = "deformetrica",
  extra_packages = "numpy",
  x86 = NA,
  force = FALSE,
  ...
)

Arguments

envname

Name of the conda env / virtualenv to install into (default "deformetrica"). A dedicated env is recommended because Deformetrica pins specific torch/pykeops versions.

method

One of "conda" (default, recommended - Deformetrica's own install instructions use a conda env), "virtualenv", or "auto" (conda if a conda binary is found, else virtualenv).

python_version

Python for the new environment (default "3.8", which matches the torch==1.6 / pykeops==1.4.1 that Deformetrica 4.3 pins).

version

Package spec passed to pip (default "deformetrica"; pin with e.g. "deformetrica==4.3.0").

extra_packages

Extra packages to co-install (default "numpy", per Deformetrica's install notes).

x86

Build an x86-64 (osx-64) conda env that runs under Rosetta. NA (default) auto-enables this on Apple Silicon and disables it elsewhere. Needed on arm64 macOS because Deformetrica's torch==1.6 pin has no arm64 wheels; the x86-64 wheels install and run fine under Rosetta.

force

Reinstall even if a deformetrica executable is already present in the environment.

...

Passed to reticulate::conda_install() / reticulate::virtualenv_install().

Value

The path to the installed deformetrica executable, invisibly.

Apple Silicon (arm64 macOS)

Deformetrica 4.3 pins torch==1.6, which has no native arm64 wheels, so a plain arm64 pip install fails. This function handles it for you: on an M-series Mac it defaults to x86 = TRUE, building an osx-64 conda env (Python 3.8) whose interpreter runs under Rosetta and pulls the x86-64 wheels - verified end-to-end (estimate + compute) on this hardware. You need Rosetta (softwareupdate --install-rosetta) and a conda binary; the first deformetrica call per process pays a ~45 s Rosetta cold-start to import torch/vtk, then runs normally.

See also

find_deformetrica() to locate an existing install.

Examples

if (FALSE) { # \dontrun{
# One-time setup (needs conda/Miniconda; reticulate::install_miniconda() gets one):
install_deformetrica()
# ... then the rest of the package just works:
find_deformetrica()
} # }