Installs scipion 3 creating a virtual environment for it, for now only for developers.
Project description
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: scipioninstaller [-h] [-conda] [-venv] [-dev] [-noXmipp] [-j J] [-dry]
[-httpsClone] [-noAsk] [-n N]
path
positional arguments:
path Location where you want scipion to be installed.
optional arguments:
-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.
-dev installs components in devel mode
-noXmipp Xmipp is installed in devel mode under xmipp-bundle dir by
default. This flag skips the Xmipp installation.
-j J Number of processors, Xmipp may take a while...
-dry Just shows the commands without running them.
-httpsClone Only when -dev is active, makes git clones using https instead
of ssh
-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 .scipion3env
-sciBranch SCIBRANCH Name of the branch of scipion repos to clone when -dev
is passed.
-xmippBranch XMIPPBRANCH
Name of the branch of xmipp repos to clone when -dev
is passed.
Troubleshooting
Problem
git@github.com: Permission denied (publickey). fatal: Could not read from remote repository.
Solution
Add -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
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.