Countoscope (Python)

This is the repository containing the Python code of the Countoscope.

Installation (users)

Clone the repository using:

git clone https://github.com/Countoscope/countoscope.git

Install all the required Python packages using:

pip install -r requirements.txt

Then, type:

pip install .

Installation (developers)

Clone the repository with its submodule (containing datasets for testing) using:

git clone https://github.com/Countoscope/countoscope.git --recurse-submodules

You will need Git LFS installed (https://git-lfs.com/)

Install all the required Python packages using:

pip install -r requirements.txt

Then, type:

pip install -e .

Use

See examples/example_xyz.py

Run the tests

Go to the tests/ repository, then type:

pytest .

Note that the repository must have been cloned with its submodules for the tests to work.

To-do list

• allow the user to input his/her own grid with specific box ?
• allow group selection (for trajectory with different type of particles)
• test if numba helps making the code faster
• allow for inputing data in a numpy array
• allow for inputing data pandas dataframe,
• make an extra tool for converting automatically data into a regular format (like XYZ) --> done, see tools.py
• re-add the features from countoscope_old, like the automated system-size detection
• allow for cross correlation between neighbor boxes

When the repository is public:

• have the GitHub runners automatically launch the tests
• integrate the python modules into the public documentation
• have branch protection