scipion-installer 1.0.8

Installs scipion 3 creating a virtual environment for it, for now only for developers.

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

[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