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
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 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 3.8 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
Some of the utilities in cellpy
have additional dependencies:
Using the
ocv_rlx
utilities requireslmfit
andmatplotlib
.For using the
batch
utilities efficiently,holoviews
is needed, as well asbokeh
andmatplotlib
for plotting.
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
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.
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).