pyomeca / biosiglive Goto Github PK

I see that you have a lot of tests, which is great! However, to make sure that the tests continue to pass you should also set up some continuous integration that runs the tests on every push and pull request to the main branch, see e.g https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

This is related to openjournals/joss-reviews#5091

The list of authors needs clarification. Three authors are listed in the paper, but only one (or maybe two) author(s) seems to have committed to repository. The command git shortlog --summary yields

107  Amedeo
1  Pariterre
19  aceglia
72  ceglia

Can you please explain the contribution of the other authors?

This is related to openjournals/joss-reviews#5091

When running the EMG_streaming.py example I get the following error

python EMG_streaming.py
Traceback (most recent call last):
  File "/Users/finsberg/local/src/biosiglive/examples/EMG_streaming.py", line 22, in <module>
    from examples.custom_interface import MyInterface
ModuleNotFoundError: No module named 'examples'

Changing the line

from examples.custom_interface import MyInterface

to

from custom_interface import MyInterface

fixes the problem. Perhaps I am doing something wrong?

This is related to openjournals/joss-reviews#5091

I would clean up the setup script so that it is straight forward to install this package without having to read the documentation.

It looks like you have some required dependencies, e.g matplotlib, numpy , scipy. You can read how to specify these in setup.py here: https://setuptools.pypa.io/en/latest/userguide/dependency_management.html#declaring-required-dependency.

For the optional dependencies you should also consider to add these to extras_require, see https://setuptools.pypa.io/en/latest/userguide/dependency_management.html#optional-dependencies

I would also not pin the dependencies to any exact version (like you do in requirements.txt) unless you absolutely need a specific version of a package.
That just makes it hard to combine you library with other libraries. Also, if you specify the dependencies in setup.py, then you don't need the requirements.txt anymore.

It is also not clear to my why you need to have this line

Finally, using a pure setup.py file is considered legacy, and you should consider to use a more modern way of specifying the metadata for your project, e.g using pyproject.toml

This is related to openjournals/joss-reviews#5091

The only documentation I could find about this project is within the README file.

I think this project deserves a proper documentation hosted at e.g GitHub pages or Read the docs. This would make the project much more digestible for more users. Furthermore, you could also host API documentation which you could generate using Sphinx API doc on this page.

On such a documentation page, you should also add separate pages with the examples.

This is related to openjournals/joss-reviews#5091

As an open source project you should make sure to add some documentation on how to contribute to the project, see https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/setting-guidelines-for-repository-contributors

This is related to openjournals/joss-reviews#5091

I think it is great that you have added biosiglive to conda-forge, but for user that don't use conda it would also be great if you could add it to pypi

This is related to openjournals/joss-reviews#5091

For example, in a loop for N muscles, when the condition is respected for one muscle (enough activation), update, else don't update

When running the custom_interface.py demo I get the following error

custom_interface.py
Traceback (most recent call last):
  File "/Users/finsberg/local/src/biosiglive/examples/custom_interface.py", line 221, in <module>
    print(interface.get_kinematics_from_markers("My markers", get_markers_data=True))
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/local/src/biosiglive/examples/custom_interface.py", line 201, in get_kinematics_from_markers
    return self.marker_sets[marker_set_idx].get_kinematics(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/mambaforge/envs/biosiglive/lib/python3.11/site-packages/biosiglive/interfaces/param.py", line 279, in get_kinematics
    self.kin_data = self.msk_class.compute_inverse_kinematics(
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/mambaforge/envs/biosiglive/lib/python3.11/site-packages/biosiglive/processing/msk_functions.py", line 94, in compute_inverse_kinematics
    ik = biorbd.InverseKinematics(self.model, markers)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/finsberg/mambaforge/envs/biosiglive/lib/python3.11/site-packages/biorbd/rigid_body.py", line 218, in __init__
    raise ValueError(f"The standard dimension of the NumPy array should be (nb_dim, nb_marker, nb_frame)")
ValueError: The standard dimension of the NumPy array should be (nb_dim, nb_marker, nb_frame)

I installed biosiglive from conda-forge on Mac ARM64.

This is related to openjournals/joss-reviews#5091

When asked which data to plot after a trial or after sating yes to plotting again, if you do not use the "plot raw only" option, it will become impossible to "plot raw only" for this trial and the next ones unless you reload the module.

This is a simple fix, the "plot raw only" option was missed in /processing/compute_mvc.py line 357 if statement :

if plot != "c":
    if plot == "p":
        data = processed_data
        legend = ["Processed"]
    elif plot == "b":
        data = [raw_data, processed_data]
        legend = ["Raw data", "Processed"]

just add

elif plot == "pr":
    data = raw_data
    legend = ["Raw data"]

I see you have a lot of examples in the examples folder but it is very hard to know what these examples are doing. It would be good to have proper text explaining each example. One way could be to add each example to a separate folder and add readme file in each folder. Another way could by to embed the documentation directly in the python files. In the latter case I would recommend check out jupytext where you can convert the documentation to markdown (or jupyter notebooks), and then you can host the documentation for these examples online (see #6).

This is related to openjournals/joss-reviews#5091