Installation

Use automesh from one of the following interfaces:

command line interface,
Rust interface, or
Python interface.

All interfaces are independent from each other:

The Rust interfaces can be used without the Python interface.
The Python interface can be used without the Rust interfaces.

For macOS and Linux, use a terminal. For Windows, use a Command Prompt (CMD) or PowerShell.

Some macOS users have encountered a build error with the netcdf-src crate. See Troubleshooting for a solution to this error.

Step 1: Install Prerequisites

The command line interface and Rust interface depend on Rust and Cargo.
- Cargo is the Rust package manager.
- Cargo is included with the Rust installation.
The Python interface depends on Python and pip.
- pip is the Python package installer.
- pip is included with the standard installation of Python starting from Python 3.4.

Rust Prerequisites

It is recommended to install Rust using Rustup, which is an installer and version management tool.

Python Prerequisites

macOS

Install Homebrew (if you don't have it already). Open the Terminal and run:

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

Install Python. After Homebrew is installed, run:

brew install python

Verify Python and pip are installed:

python3 --version
pip3 --version

Linux

Update Package List. Open a terminal and run:

sudo apt update

Install Python and pip. For Ubuntu or Debian-based systems, run:

sudo apt install python3 python3-pip

Verify Python and pip are installed:

python3 --version
pip3 --version

Windows

Download Python. Go to the official Python website and download the latest version of Python for Windows.
Run the Installer. During installation, make sure to check the box that says "Add Python to PATH."
Verify Python and pip are installed:

python --version
pip --version

All Environments

On all environments, a virtual environment is recommended, but not required. Create a virtual environment:

python3 -m venv .venv  # venv, or
uv venv .venv          # using uv

uv is a fast Python package manager, written in Rust. It is an alternative to pip.

Activate the virtual environment:

source .venv/bin/activate       # for bash shell
source .venv/bin/activate.csh   # for c shell
source .venv/bin/activate.fish  # for fish shell
.\.venv\Scripts\activate        # for powershell

Step 2: Install `automesh`

Install the desired interface.

Command Line Interface

cargo install automesh

Rust Interface

cargo add automesh

Python Interface

pip install automesh     # using pip, or
uv pip install automesh  # using uv

Step 3: Verify Installation

Rust Interfaces

Run the command line help:

automesh

which should display the following:


     @@@@@@@@@@@@@@@@
      @@@@  @@@@@@@@@@
     @@@@  @@@@@@@@@@@
    @@@@  @@@@@@@@@@@@    automesh: Automatic mesh generation
      @@    @@    @@      v0.3.6 build 05acfd9 linux x86_64
      @@    @@    @@      Chad B. Hovey <chovey@sandia.gov>
    @@@@@@@@@@@@  @@@     Michael R. Buche <mrbuche@sandia.gov>
    @@@@@@@@@@@  @@@@
    @@@@@@@@@@ @@@@@ @
     @@@@@@@@@@@@@@@@

Usage: automesh [COMMAND]

Commands:
  convert    Converts between mesh or segmentation file types
  defeature  Defeatures and creates a new segmentation
  diff       Show the difference between two segmentations
  extract    Extracts a specified range of voxels from a segmentation
  mesh       Creates a finite element mesh from a tessellation or segmentation
  metrics    Quality metrics for an existing finite element mesh
  remesh     Applies isotropic remeshing to an existing mesh
  segment    Creates a segmentation or voxelized mesh from an existing mesh
  smooth     Applies smoothing to an existing mesh
  help       Print this message or the help of the given subcommand(s)

Options:
  -h, --help     Print help
  -V, --version  Print version

Python Interface

python

# In Python, import the module
>>> import automesh

# List all attributes and methods of the module
>>> dir(automesh)

# Get help on the module
>>> help(automesh)

Troubleshooting

`ZLIB` target not found

Some users have encountered an error when trying to build the netcdf crate, e.g.,

...
error: failed to run custom build command for `netcdf-src v0.4.3`
...
The link interface of target "hdf5-static" contains:

  ZLIB::ZLIB

but the target was not found.  Possible reasons include:

  * There is a typo in the target name.
  * A find_package call is missing for an IMPORTED target.
  * An ALIAS target is missing.
...

HDF5 is looking for ZLIB::ZLIB as a CMake target, but it's not being found even though ZLIB is present.

A solution is to use a dynamically-linked netcdf from Homebrew instead of trying to build it statically. This should avoid the CMake ZLIB::ZLIB target issue entirely.

Update the Cargo.toml for automesh to avoid static linking:

...
# netcdf = { version = "=0.11.1", features = ["ndarray", "static"] }
netcdf = { version = "=0.11.1", features = ["ndarray"] }
...

Then,

# Make sure netcdf is installed via Homebrew
brew install netcdf

# Set the environment variable to use system netcdf
export NETCDF_DIR=/opt/homebrew

# Clean and build
cargo clean
cargo build

If you still encounter errors about netcdf not being found, also try:

export PKG_CONFIG_PATH=/opt/homebrew/lib/pkgconfig
export DYLD_LIBRARY_PATH=/opt/homebrew/lib

Keyboard shortcuts

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