scipion-installer 2.1.1

Installs scipion 3 creating a virtual environment for it anc creates a launcher.

Scipion installer

Scipion installer is a python module to install scipion 3 (already in alfa) and not ready for production.

This installer is python2-python3 compatible and is a very lightweight package. It will create a python3 virtual environment (conda or virtualenv) with scipion in it.

The entire collection is licensed under the terms of the GNU Public License, version 3 (GPLv3).

Installation

It is a 2 lines’ installation: First to install the installer, second to use the installer (to install scipion).

* Python 3 *

python3 -m pip install scipion-installer
python3 -m scipioninstaller where-to-install-scipion

* Python2 * (You are going to need python3 anyway)

python2 -m pip install scipion-installer
python2 -m scipioninstaller where-to-install-scipion

Advanced options

usage: installscipion [-h] [-conda] [-venv] [-dry] [-noAsk] [-n N] [-scratchPath SCRATCHPATH] [-python PYTHON] path

     Installs scipion3 in a conda or virtualenv environment. Check all parameters bellow for a custom installation. If there are issues initializing conda you
     can set CONDA_ACTIVATION_CMD variable and it will be used instead of guessing. Typical values are . "/path/to/miniconda3/etc/profile.d/conda.sh" or eval
     "$(/path/to/miniconda3/bin/conda shell.bash hook)"

 positional arguments:
   path                  Location where you want scipion to be installed.

 options:
   -h, --help            show this help message and exit
   -conda                Force conda as environment manager, otherwise will use conda anyway if found in the path, else: virtualenv.
   -venv                 Force virtualenv as environment manager, otherwise will use conda if found in the path, otherwise: virtualenv.
   -dry                  Just shows the commands without running them.
   -noAsk                try to install scipion ignoring some control questions in that process. You must make sure to write the correct path where Scipion
                         will be installed
   -n N                  Name of the virtual environment. By default, if this parameter is not passed, the name will be scipion3
   -scratchPath SCRATCHPATH
                         Path to a folder working at high speed(like SSDs) to be used temporarily during processing.
   -python PYTHON        Python version to use in the environment. For virtualenv, default value will become "python3", otherwise argument will be
                         literally passed to virtualenv.Default value is 3.8 but up to 3.11 may work as well.

Bundle installation

Checkout Jesper L. Karlsen’s script to make a full installation –> https://github.com/jelka71/scipion_auto_install.git

Troubleshooting

Problem

[e-mail]: Permission denied (publickey). fatal: Could not read from remote repository.

Solution Add -httpsClone

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Problem

pip/pip3 is needed to get the installer.

Solution

For ubuntu/debian you might need root access to run

sudo apt-get install python-pip

No root access?: You can try pip install –user scipion-installer to install it locally

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Problem

Missing dependencies: scipion needs python3-tkinter to work and an existing python3 installation.

Solution

For ubuntu/debian you might need root access to run

sudo apt-get install python3-tk

If Error: “pkg_resources.DistributionNotFound: The ‘zipp>=0.5’ is raised when launching installscipion, try to install zipp by

pip install zipp