make utils a subpackage of snmachine

[heather999]

IMPORTANT: Please create an issue first before opening a Pull Request.
Linked to issue(s): #258

Type of change

Please delete options that are not relevant.

• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

What changes were proposed in this pull request?

Making the utils package a subpackage of snmachine.

How is the issue this PR is referenced against solved with this PR?

The utils directory has been moved under snmachine and corresponding code has been updated to reference snmachine.utils where appropriate.

How was this patch tested?

Locally, I modified my copies of the example notebooks to use snmachine.utils and ran through the first 3 notebooks. It is necessary for someone to go through all the notebooks and rerun them to make sure things are ok.

Final Checklist:

• My code follows the style guidelines of this project
• I have made corresponding changes to the documentation
• I have added tests that prove my fix is effective or that my feature works
• I am up to date with dev branch of snmachine at the time of this PR

[Catarina-Alves]

@heather999 I find it strange that I have no issues running the notebooks because in their imports they have

from snmachine import gps, sndata
from utils.plasticc_pipeline import create_folder_structure, get_directories, load_dataset

With this PR, I assumed that the second line had to be modified to

from snmachine.utils.plasticc_pipeline import ....

however, this modification returns an error and keeping the same does not.

Moreover, the tests didn't run for this PR and I have no way to re-run them, which is strange because for all other PRs I had no issues.

[Catarina-Alves]

It seems that there is a space between . and utils that should not be here. However, I find no issues running the notebooks.

[heather999]

I just updated this to from snmachine.utils and that works for me - but it would be great if you could test it too

[Catarina-Alves]

@heather999 did you have the time to look at my comments regarding this PR?

[heather999]

@Catarina-Alves I think this is ready for testing by others. I did the following:

• Created a new installation of Miniconda with python 3.8
• Cloned this repo and checked out this branch `general/issue/258/utils-subpackage
• pip installed snmachine by doing: pip install -e ./snmachine
• pip install pytest
• Unpacked the SPCC_SUBSET.tar.gz in the snmachine/example_data directory
• entered the test directory and ran the tests: py.test -m "not slow" and they passed.

Does that work for you?

[Catarina-Alves]

@Catarina-Alves I think this is ready for testing by others. I did the following:

• Created a new installation of Miniconda with python 3.8
• Cloned this repo and checked out this branch `general/issue/258/utils-subpackage
• pip installed snmachine by doing: pip install -e ./snmachine
• pip install pytest
• Unpacked the SPCC_SUBSET.tar.gz in the snmachine/example_data directory
• entered the test directory and ran the tests: py.test -m "not slow" and they passed.

Does that work for you?

Yes, thank you. I will now repeat the tests on my local machine. Once they pass, I will merge the PR and update the pip package.

[Catarina-Alves]

I had to update a few libraries in the setup to make all the tests run. I will now merge the PR, and update the version of snmachine in pip