set standard python package structure

[aremazeilles]

I propose to use a standard package structure, which ease the installation, and also the use of the entry point, run_protocol_1. I had to change a bit run_pi_mocap_metrics.py, as you are opening local files, which needed to be a bit more generic: if we installe the python package, the script run_protool_1could be launched from anywhere.

You can see the suggested changes through the "Files changes" area above

[dborro]

Hi, I guess all instructions in readme file are for Linux, isn't it? I say this because I tried in Windows and I have the following issues:

• Using venv: this instruction is for Linux "source venv/bin/activate". In windows is without "source"
• The line of usage doesn't work for me "run_protocol_1 pi_algo/pi_algo/tests/data/protocol_1/input/data/test.csv out" Instead, I have to run "python script/run_protocol_1 pi_algo/tests/data/protocol_1/input/data/test.csv pi_algo/tests/data/protocol_1/output" (i.e., specify completely the paths of run_protocol_1 file and input/output folders

[aremazeilles]

effectively the command I suggested to add is for Linux, which is the target platform onto which development will be run. Actually, the docker image is for such environment as well. If you want I can add a comment on this aspect in the readme.

The good part of the python package structure proposed is that, by installing it (and using the virtual environment), the python script run_protocol_1 is then accessible from anywhere. The fact that you have to state the full relative path indicates that the package is not installed. Might be an equivalent command existing from an anaconda space.

If you want I can adjust doc to state commands from windows (through conda), and from linux. But I cannot state how to install the package from conda in windows, as I am not using such tools to run scripts.

[dborro]

Ok. Don’t worry Anthony. As you say, if your platform is based on Linux, go head. There is no need to change the doc/readme. I just told you for your knowledge, just in case. Regards, Diego

From: Anthony Remazeilles notifications@github.com Sent: miércoles, 24 de febrero de 2021 16:19 To: STEPbySTEPproj/Protocol_biomechanics Protocol_biomechanics@noreply.github.com Cc: Borro, Diego dborro@ceit.es; State change state_change@noreply.github.com Subject: Re: [STEPbySTEPproj/Protocol_biomechanics] set standard python package structure (#5)

effectively the command I suggested to add is for Linux, which is the target platform onto which development will be run. Actually, the docker image is for such environment as well. If you want I can add a comment on this aspect in the readme.

The good part of the python package structure proposed is that, by installing it (and using the virtual environment), the python script run_protocol_1 is then accessible from anywhere. The fact that you have to state the full relative path indicates that the package is not installed. Might be an equivalent command existing from an anaconda space.

If you want I can adjust doc to state commands from windows (through conda), and from linux. But I cannot state how to install the package from conda in windows, as I am not using such tools to run scripts.

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