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.
The preferred 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
that comes in handy when working with
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
python packages (python 3.8 or above) before installing
If you chose
miniconda, you should install
$ conda install scipy numpy pytables
cellpy, by running this command in your terminal:
$ pip install cellpy
You can install pre-releases by adding the
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
$ conda install -c conda-forge pyodbc
Some of the utilities in
cellpy have additional dependencies:
For using the
holoviewsis needed, as well as
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).
It is recommended to run the 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.
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).
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
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).
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)
You can find more information in the Tutorials, particularly in The getting started with cellpy tutorial (opinionated version).