Virtual environment

[rmndrs89]

Hi @masoudabedinifar and @hansencl and @JuliusWelzel,

we still need to look at that cross-platform conda or pip environment file. I have just pulled the main branch to update the dataset definitions, and I get the following:

No module named 'pywt'
  File "/home/robbin/Projects/NGMT/ngmt/modules/gsd/GSDA.py", line 7, in <module>
    import pywt
  File "/home/robbin/Projects/NGMT/test.py", line 5, in <module>
    from ngmt.modules.gsd import GSDA
ModuleNotFoundError: No module named 'pywt'

Obviously, I can just intall pip install PyWavelets or conda install pywavelets, but it is also not clear from the environment.yml that this packages is required.

Best, Robbin

[JuliusWelzel]

Thanks for pointing this out you can sign me to resolve the issue

[rmndrs89]

My suggestion is that this may work:

(ngmt) username@host:~/Projects/NGMT$ conda env export --from-history

but it may need testing :)

[JuliusWelzel]

I gave pipreqs a try which scans the folder and checks all relevant packages used. These are than exported to a requirement.txt file. for a pip install. Is there a reason, we are installing some packages via conda and some via pip? In a venv, I think all can be run through pip. Ideally, we can move to poerty and use pyproject.toml in the future. This is what gaitmap and other recent packages do :) Let's discuss tomorrow

[rmndrs89]

@JuliusWelzel please have a look at pyproject, then @rmndrs89 will take a look at poetry

[rmndrs89]

I have looked a bit at poetry, see, e.g.:

• https://www.freecodecamp.org/news/how-to-build-and-publish-python-packages-with-poetry/
• https://realpython.com/dependency-management-python-poetry/

Especially, the first source I found very useful, as it also includes writing some test functions. Could be something for @masoudabedinifar to checkout in a lightweight version of the NGMT package? For example, if we create a demo package that only performs the following steps:

1. resample to 40 Hz
2. compute the signal norm

With a few commands the package can then be build poetry build and published to PyPI poetry publish.

I am, however, still not sure how this works across Windows, MacOS and Linux operating systems.

[JuliusWelzel]

I was able to easily create an venv using poerty. @rmndrs89 could you, please try for Linux.

Just install poerty, clone the repo and cd to the clone. I updated the install instructions in https://github.com/neurogeriatricskiel/NGMT/commit/0486575b3d9b53d9d9ca5802b58239bd3f7d77dc

[rmndrs89]

Hi @JuliusWelzel,

apart from some typos in the installation guideline, I have managed to clone the repo and install the environment:

$ git clone https://github.com/neurogeriatricskiel/NGMT.git
$ cd NGMT
$ poetry install

However, when trying to run the example for gait sequence detection in VS Code, I encountered already two missing libraries, ipykernel and matplotlib.

Did you not include these libraries on purpose, or were they omitted when creating the poetry virtual environment?

[JuliusWelzel]

I added the required packages in 94134b0b42f79d5a91b159a4a9d128e49ea87fd3.

Closing now 💯 If you encounter new problems, please open a new issue!