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-scipionAdvanced 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
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
1 maintainer
Release files for scipion-installer 2.1.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| scipion_installer-2.1.1.tar.gz | 19.7 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| scipion_installer-2.1.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 40.4 kB
Release files / scipion_installer-2.1.1.tar.gz
| Download URL | scipion_installer-2.1.1.tar.gz |
|---|---|
| Size | 19.7 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
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Release files / scipion_installer-2.1.1-py3-none-any.whl
| Download URL | scipion_installer-2.1.1-py3-none-any.whl |
|---|---|
| Size | 20.7 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.8.18
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