Installation
=============

.. note::
   The following instructions are for installing the project directly from the git repository. Once it is available on pypi.org, it can be installed as a regular package

#. Clone the git repository locally

   .. code-block:: sh

      $ git clone https://gitlab.gwdg.de/vadakkeputha/csmparser
      $ cd csmparser

#. Create a python virtual environment for installing the package

   .. code-block:: sh

      $ python -m venv .venv

#. Activate the virtual environment

   .. code-block:: sh

      $ source .venv/bin/activate

   .. note::
      For other shells like ``csh``, ``fish`` or ``ps1``, use corresponding ``activate.[csh,fish,ps1]`` file. The virtual environment can be deactivated using ``deactive``.

#. Install the packages---this may take a while

   .. code-block:: sh

      (.venv) $ pip install -r requirements.txt
      (.venv) $ pip install -e .
   
   Using the ``-e`` flag automatically updates the package if it has been edited, or when adding :doc:`new functionality</extending_cytocalc>`

#. ``Cytocalc`` has been installed! Now you can :doc:`use scripts</scripts>` (or :doc:`create them</creating_scripts>`) and analyze code using ``Cytocalc``