Make this repo a working Python package

[yonatank93]

Here is the TODO list I had for this process:

• [ ] Convert the geodesic/MBAM into a Python package
  • [X] setup.py
  • [ ] Work on the organization of the package (check with Mark)
• [X] Documentation for each functions (numpydoc style)
  • [X] Rename class/functions according to PEP8
• [X] README
  • [X] Installation - pip and source
  • [X] Example - Refer to example folder
  • [X] Attribution - How to cite the papers
  • [X] Licence - MIT
• [X] A wrapper to compute jacobian and Avv using autograd/JAX.
• [X] Unit test
  • [X] Derivative: Compare analytic to finite difference, jacobian, Avv, jax
  • [X] Geodesic: Use a linear model. Compare the geodesic vector to eigenvector.

[yonatank93]

@mktranstrum Do we need to specify M and N when instantiating Geodesic? M is not used anywhere in the calculation, and N can be retrieved from the initial parameters (self.N = len(x)).

[yonatank93]

@mktranstrum I have addressed your comments. Can you take a look at it?

[mktranstrum]

Did you see the comment about the initial_velocity function? It doesn't look like you have made those changes yet.

---

From: Yonatan Kurniawan @.> Sent: Wednesday, July 6, 2022 5:35 PM To: mktranstrum/MBAM @.> Cc: mktranstrum @.>; Mention @.> Subject: Re: [mktranstrum/MBAM] WIP: Make this repo a working Python package (PR #1)

@mktranstrumhttps://github.com/mktranstrum I have addressed your comments. Can you take a look at it?

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[yonatank93]

I made those changes. I added 2 optional arguments in initial_velocity: i and forward. See this commit.