Installation

SEAMM Manager is the one tool you install by hand; it installs everything else.

1. Install uv if you do not have it. It is a single binary with no dependencies:

   $ curl -LsSf https://astral.sh/uv/install.sh | sh
   

   then open a new shell (or source ~/.local/bin/env) so uv is on your path. On a cluster, do this in your own account; no administrator access is needed.

2. Install the manager as a uv tool, i.e. in its own small environment, outside the one it will manage:

   $ uv tool install seamm-manager
   

3. Install SEAMM:

   $ seamm-manager install --all
   

   This creates the SEAMM root (~/SEAMM by default; --root chooses another), installs Python 3.12 and a virtual environment ~/SEAMM/venv inside it, and installs SEAMM with all the MolSSI plug-ins from PyPI, constrained to the published lock file so the versions are a tested set. Add --third-party for the third-party plug-ins, or name individual plug-ins instead of --all.

The installation also creates the jobs database (the datastore) under ~/SEAMM/Jobs with an administrator account admin whose password is admin; change it from the web interface once that is running. Running a flowchart locally with run_flowchart needs no account at all.

Optional: seamm-manager services create jobserver sets up the JobServer to run in the background, seamm-manager install seamm-webui and ... services create webui the web interface, and seamm-manager apps create desktop apps for the flowchart editor.

Updating

$ seamm-manager update --all

updates the manager itself, every installed SEAMM package (to the versions in the current lock file), and restarts the JobServer if it needs to be. --no-constraints ignores the lock and takes the newest releases. --latest also asks PyPI directly, so a release made today is picked up rather than waiting for the nightly list.

The environment

Everything Python lives in ~/SEAMM/venv. If it is ever damaged,

$ seamm-manager environment recreate

deletes and rebuilds it and reinstalls the packages that were in it, in well under a minute. environment show describes it. You never need to activate it; the manager, the services and the apps all use its interpreter directly.

Conda

Conda is not needed for SEAMM itself. The plug-ins for external codes – MOPAC, Psi4, DFTB+, LAMMPS, xTB, Packmol, … – install the code into a conda environment of its own, so conda (Miniforge is recommended) is needed on a machine where you install one of those. The plug-in’s installer tells you if it is missing.

When a plug-in updates its code environment from its environment file, pip packages named without a version (torch) are installed only if missing and otherwise left as they are, while those with a version specifier are kept current within it. So a torch build you installed by hand for your GPU driver survives updates; to change it, reinstall it by hand in that environment.

Migrating from seamm-installer

seamm-installer managed SEAMM in a conda environment. Such an installation keeps working, but it reads a frozen package list and no longer receives updates. To move to the manager: follow the three steps above, then

$ seamm-manager services create jobserver     # if you ran the JobServer
$ seamm-manager apps create                   # if you had desktop apps

so they use the new environment. Jobs, ~/SEAMM/*.ini configuration and the codes’ conda environments are shared and untouched. Once satisfied, remove the old conda environment (conda env remove -n seamm).

Development installation

$ seamm-manager --development install --all development

uses ~/SEAMM_DEV and adds the development tooling. Its services and apps carry the installation’s name (jobserver-SEAMM_DEV, SEAMM (SEAMM_DEV).app); see Several installations in the usage guide. To work on a package, install your checkout into the environment with ~/SEAMM_DEV/venv/bin/pip install -e . or the package’s make install with that environment activated.