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

1. Clone the git repository locally

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

2. Add git hooks for automatic updates of the current Cytocalc version and commit hash (to save in plots metadata for provenance)

   $ git config --local core.hooksPath .githooks/ && .githooks/post-commit
   

   Note

   Without the hooks, version will not contain commit information, but instead simply return “vX.Y.Z”.

3. Create a python virtual environment for installing the package

   $ python -m venv .venv
   

4. Activate the virtual environment

   $ 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.

5. Install the packages—this may take a while

   (.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 new functionality

6. Cytocalc has been installed! Now you can use scripts (or create them) and analyze code using Cytocalc