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Installation for macOS

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Hiromichi Yokoyama edited this page Aug 5, 2026 · 6 revisions

Installation for macOS

MoleditPy supports Python 3.9 through 3.14 (requires-python = ">=3.9, <3.15"). On Python 3.9 specifically, PyQt6 is pinned to <6.10 (all other supported versions use <6.12); pip resolves this automatically.

There are two supported ways to install MoleditPy on macOS:

  • Recommended: moleditpy-installer — installs the moleditpy package for you and creates a MoleditPy.app launcher (in ~/Applications or /Applications) plus the .pmeprj file association. See Method A below.
  • Conda-based install — a manually managed environment. See Method B.

Method A: moleditpy-installer (recommended)

  1. Install the Python package

    pip install moleditpy-installer

    This automatically installs the moleditpy package as a dependency.

  2. Run the installer

    moleditpy-installer

    In an interactive terminal this opens a TUI where you pick the components (Desktop shortcut, .pmeprj file association) and scope (per-user ~/Applications or system-wide /Applications), then press Install. For scripted use: moleditpy-installer --no-tui (defaults), moleditpy-installer --desktop (also add a Desktop copy), or sudo moleditpy-installer --system (system-wide).

    The generated MoleditPy.app pairs the moleditpy script with the Python interpreter of its own environment (detected from the adjacent interpreter or the script's shebang), and is ad-hoc code-signed after configuration — required for the app to launch on Apple Silicon. MoleditPy always opens inside a Terminal window so Python output and errors stay visible; the first launch shows a one-time macOS consent prompt ("MoleditPy wants access to control Terminal") — click OK.

  3. Launch

    Double-click MoleditPy.app in Applications, or from the terminal:

    moleditpy

  4. Upgrade

    pip install --upgrade moleditpy moleditpy-installer
moleditpy-installer          # re-run to refresh the app bundle/signature if needed

  5. Uninstall

    moleditpy-installer --uninstall
pip uninstall moleditpy

See the moleditpy-installer README for the full option list, or Shortcut (macOS) to build the .app launcher manually with Automator.

Method B: Conda environment

This procedure is designed to ensure library compatibility, which can often be an issue with GUI applications.

Prerequisites

  • Anaconda or Miniconda must be installed on your Mac.

Step 1: create and activate a new Conda environment

First, create a clean virtual environment dedicated to moleditpy.

  1. Open Terminal
  2. Create a New Environment
    Create an environment named moleditpy-env specifying a compatible Python version (e.g., 3.12). 
    conda create -n moleditpy-env python=3.12
    • If prompted with Proceed ([y]/n)?, type y and press Enter.
  3. Activate the Created Environment
    All subsequent operations will be performed within this new environment. 
    conda activate moleditpy-env
    Confirm that the terminal prompt now starts with (moleditpy-env).

Step 2: install moleditpy

With all the necessary dependencies in place, install moleditpy itself using pip.

  1. Install moleditpy with pip
    Run the following command in the activated conda environment. 
    pip install moleditpy
    If you want to install specific versions that are confirmed to be compatible, run this command: 
    pip install numpy==2.3.3 openbabel-wheel==3.1.1.22 PyQt6==6.9.1 QtPy==2.4.3 rdkit==2025.3.6 vtk==9.5.2 pyvista==0.46.3 pyvistaqt==0.11.3 moleditpy

Step 3: launch moleditpy

Once the installation is complete, launch moleditpy as a GUI application.

  1. Run the Launch Command
    In the terminal (with moleditpy-env activated), execute the following:

    moleditpy

    If the moleditpy GUI window appears, the environment setup is successful. Confirm the installed version with moleditpy --version.

Upgrading and uninstalling (Conda method)

conda activate moleditpy-env
pip install --upgrade moleditpy

To remove the environment entirely:

conda deactivate
conda env remove -n moleditpy-env

See also

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