Installation

If you are (relatively) new to installing python packages, please jump to the getting started tutorial (The getting started with cellpy tutorial (opinionated version)) for an opinionated step-by-step procedure.

Stable release

Conda

Usually, the easiest way to install cellpy is by using conda:

$ conda install cellpy --channel conda-forge

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

Pip

If you would like to install only cellpy, you should install using pip. A small warning if you are on Windows: cellpy uses several packages that are a bit cumbersome to install on windows (e.g. scipy, numpy and pytables ).

Install cellpy by running this command in your terminal:

$ python -m 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:

$ python -m pip install pyodbc

or:

$ conda install -c conda-forge pyodbc

Some of the utilities in cellpy have additional dependencies:

• Using the ocv_rlx utilities requires lmfit and matplotlib.

• For using the batch utilities efficiently, you should install bokeh, plotly, and matplotlib for plotting. Also, holoviews is a good tool to have.

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). Feel free to edit this to fit your needs.

If you are OK with letting cellpy select your settings, you can omit the -i (interactive mode).

Hint

Since cellpy uses several packages that are a bit cumbersome to install on windows, you circumvent this by install one of the anaconda python packages (python 3.9 or above) before installing cellpy. Remark, that if you chose miniconda, you need to manually install scipy, numpy and pytables using conda:

$ conda install scipy numpy pytables

Hint

It is recommended to run the cellpy setup command also after each time you upgrade cellpy. It will keep the settings you already have in your prms-file and, if the newer version has introduced some new parameters, it will add those too.

Hint

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

Caution

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 ‘The getting started with cellpy tutorial (opinionated version)’.