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Countoscope (Python) ####################

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

Installation (users)

Clone the repository using:

.. code:: bash

Install all the required Python packages using:

.. code:: bash

pip install -r requirements.txt

Then, type:

.. code:: bash

pip install .

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

.. code:: bash

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

Install all the required Python packages using:

.. code:: bash

pip install -r requirements.txt

Then, type:

.. code:: bash

pip install -e .

See examples/example_xyz.py

Go to the tests/ repository, then type:

.. code:: bash

pytest .

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

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: