gmpavanlab/dynsight

maintainers:	andrewtarzia
documentation:	https://dynsight.readthedocs.io

Installation

To get dynsight, you can install it with pip:

$ pip install dynsight

Examples

There are examples available in the examples/ directory of this repository.

There are also examples available in the cpctools repository here <https://github.com/GMPavanLab/cpctools/tree/main/Examples>

How To Cite

If you use dynsight please cite

https://github.com/GMPavanLab/dynsight

Publications

• people need to add PRs to mention these.

Acknowledgements

We developed this code when working in the Pavan group, https://www.gmpavanlab.com/, whose members often provide very valuable feedback, which we gratefully acknowledge.

Much of the original code in cpctools was written by Daniele Rapetti (Iximiel).

The work was funded by the European Union and ERC under projects DYNAPOL and the NextGenerationEU project, CAGEX.

dynsight's Issues

Update all .rst files for modules to include explanations of methods. #8

• data_processing.rst
• timesoap.rst
• hd5fer.rst
• soapify.rst
• lens.rst

all in docs/source/

Fix doc strings and type hints for all saponify. #7

I am not fully aware of how the saponify functions work. So someone should go through and set the type hints and doc strings correctly.

Add dev install instructions to README

Fix math in timesoapsimple

Similar to #22

Typo in LICENSE

There is a typo in the LICENSE file, it says

iCopyright

instead of

Copyright

Clean up LENS example #3

Maybe add clustering and more analysis to lens and time soap examples.

• lens example
• timesoap example

Like in cpctools examples, if appropriate!

Consider the issues here: GMPavanLab/cpctools#83

Speed up install times that are slowed down by dscribe #14

Use of a simple example for running SOAPify in examples. #6

Currently, the examples are too heavyweight to run in tests, so it would be good if someone could generate a very cheap (millisecond calculation) test case.

Partly handled with #17 but with a test. Should be converted to an example.

Check for typos in all of docs. Replace all instances of "words" #10

Includes:
in the index.html there is "The main dependancies are for SOAP analysis:". is it dependancies or dependencies?

background color of onion documentation figures

The documentation has dark background, but the figures have white background...

Someone to write the overview and information into docs. #4

Someone with more expertise in this code should write this.

Fix RUFF format check in github workflows

Fix all mentions of authors and maintainers in docs and doc strings #11

The math in timeSOAP doc strings updates #5

Doc strings in saponify.py.

Error in onion documentation

In the last paragraph of docs/build/html/onion.html from docs/source/onion.rst, the example of how to call the multi-dimensional clustering is wrong. Instead of

The code for performing clustering on multi time-series can be found in examples/onion_multi.py. The only difference in the usage is that when you run the script you have to specify all the input files, each one containing a different variable:
python3 onion_multi.py path/to/input/file_0.npy path/to/input/file_1.npy

it should be

The code for performing clustering on multi time-series can be found in examples/onion_multi.py. The only differences that the input file has to be an .npy or .npz containing a numpy.ndarray with shape (D, N, T), where D is the number of variables (2 or 3). Is is then called with
python3 onion_multi.py path/to/input/file.npy