Installation

If you are (relatively) new to installing python packages, please jump to the getting started tutorial (Tutorials/getting_started_tutorial) for an opinionated step-by-step procedure.

Stable release

The preferred way to install cellpy is by using conda:

$ conda install cellpy --channel conda-forge

This will also install all of the dependencies, as well as jupyter that comes in handy when working with cellpy.

If you would like to install only cellpy, you should install using pip. You also need to take into account that cellpy uses several packages that are a bit cumbersome to install on windows. It is therefore recommended to install one of the anaconda python packages (python 3.6 or above) before installing cellpy. If you chose miniconda, you should install scipy, numpy and pytables using conda:

$ conda install scipy numpy pytables

Then install cellpy, by running this command in your terminal:

$ pip install cellpy

You can install pre-releases by adding the --pre flag.

If you are on Windows and plan to work with Arbin files, we recommend that you try to install pyodbc (Python ODBC bridge). Either by using pip or from conda-forge:

$ pip install pyodbc

or:

$ conda install -c conda-forge pyodbc

If this is the first time you install cellpy, it is recommended that you run the setup script:

$ cellpy setup -i

This will install a .cellpy_prms_USER.conf file in your home directory (USER = your user name) for posix systems and the documents folder in windows. Feel free to edit this to fit your needs.

(It is probably best to run the command also if you are upgrading cellpy)

You can restore your prms-file by running cellpy setup if needed (i.e. get a copy of the default file copied to your user folder).

Note

Since Arbin (at least some versions) uses access database files, you will need to install pyodbc, a python ODBC bridge that can talk to database files. On windows, at least if you don´t have a newer version of office 365, you most likely need to use Microsoft’s dll for handling access database formats, and you might run into 32bit vs. 64bit issues. The simplest solution is to have the same “bit” for python and the access dll (or office). More advanced options are explained in more details in the getting-started tutorial. For Posix-type systems, you will need to download and install mdbtools. If you are on Windows and you cannot get your pyodbc to work, you can try the same there also (search for Windows binaries and set the appropriate settings in your cellpy config file).

From sources

The sources for cellpy can be downloaded from the Github repo.

You can clone the public repository by:

$ git clone git://github.com/jepegit/cellpy

Once you have a copy of the source, you can install in development mode using pip:

$ pip install -e .

(assuming that you are in the project folder, i. e. the folder that contains the setup.py file)

Further reading

You can find more information in the Tutorials, particularly in Tutorials/getting_started_tutorial.