sciunit2 0.2.post21.dev236407654

Sciunit command line

sciunit is a command-line tool that answers the call for a reusable research object that containerizes and stores applications simply and efficiently, facilitates sharing and collaboration, and eases the task of executing, understanding, and building on shared work.

Installing

[ Note This section introduces the binary distributions of sciunit. –end note ]

Requires: pip>=8.1.1, glibc>=2.17, python2.7 with headers and compiler

Platform: amd64-pc-linux-gnu

Ensure that ~/.local/bin is in your PATH environment variable, and then, run

pip install --user sciunit2

Add --upgrade to the command line arguments to upgrade an existing sciunit installation.

Verify the installation with

sciunit --version

In the following per-distro instructions, if you see a command-line in the form of

export PATH=~/.local/bin:$PATH

, it merely means that you will need the aforementioned binary path in PATH before proceeding; normally you should adjust it according to your login shell and write it to a shell configuration such as ~/.profile.

Ubuntu 16.04

sudo apt update
sudo apt install python-dev python-pip
pip install --user sciunit2

Ubuntu 14.04

sudo apt update
sudo apt install python-dev python-pip
pip install --user -U pip
export PATH=~/.local/bin:$PATH
pip install --user sciunit2

Arch Linux

sudo pacman -S python2-pip
export PATH=~/.local/bin:$PATH
pip2 install --user sciunit2

Fedora 26

sudo dnf install python2-pip python2-devel gcc redhat-rpm-config
pip install --user sciunit2

CentOS 7

sudo yum install -y epel-release
sudo yum install python2-pip python-devel gcc
pip install --user sciunit2

RHEL 7

sudo yum install -y https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
sudo yum install python2-pip python-devel gcc
pip install --user sciunit2

Debian 9

sudo apt update
sudo apt install python-dev python-pip
export PATH=~/.local/bin:$PATH
pip install --user sciunit2

Debian 8

sudo apt update
sudo apt install python-dev python-pip
pip install --user -U pip
export PATH=~/.local/bin:$PATH
pip install --user sciunit2

OpenSUSE 42

Note that OpenSUSE defaults user-binary path to ~/bin rather than ~/.local/bin, so you may want to symlink one to the other.

sudo zypper install python-pip python-devel gcc
pip install --user -U pip
export PATH=~/.local/bin:$PATH
pip install --user sciunit2

Known Issues

If your environment is not listed, or you missed some prerequisites before issuing pip, you may observe the following error when running sciunit:

ImportError: No module named _bsddb

Fortunately, there are more than one ways to fulfill this dependency. Try to find and install a package often named “python-bsddb” or “python-bsddb3” with your system package manager. In Anaconda, you will need a port called “bsddb.”

Using

Checkout our tutorial and manpage. The manpage is available as

man sciunit

after a successful installation.