=================
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 ***
.. code-block::
python3 -m pip install scipion-installer
python3 -m scipioninstaller where-to-install-scipion
*** Python2 *** (You are going to need python3 anyway)
.. code-block::
python2 -m pip install scipion-installer
python2 -m scipioninstaller where-to-install-scipion
================
Advanced options
================
.. code-block::
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**
git@github.com: Permission denied (publickey).
fatal: Could not read from remote repository.
**Solution**
Add :code:`-httpsClone`
----
**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
----
**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
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