Update perturbIC.py

[leoberhelman]

This is a draft of a pull request to keep track of comments and questions I will have during refactoring and testing. Nothing yet but I am creating my unit tests.

[MartinDix]

I can't work out why I specified it this way. In any case RandomState is no longer the recommended generator and the more up to date way of doing it would be

from numpy.random import Generator, PCG64
rg = Generator(PCG64(seed))
.. .rg.random(...)

This will give different results to the current implementation but will be stable in the future. PCG64 is currently the default bit generator but that could change so it's used explicitly here.

[leoberhelman]

Fixes Issue #8 #4 #6

[atteggiani]

Fixes Issue #8 #4 #6

I think this would not work. You will have to write the issues in separate lines, e.g.:

Fixes #8
Fixes #4
Fixes #6

Also, I would write them in the main text of the PR to be more visible (I'm also not sure if they would even work within a comment).

[atteggiani]

Thank you for this PR @leoberhelman!

Overall I think you did a pretty good job restructuring and refactoring the code into functional portions that can be easily tested! Well done!

I left many comments, but please don't get scared by their amount:

• Many of them are minor corrections to docstrings or function/variable names that I think would make the code clearer
• Some are related to the python environment and CI, which have good structures but might be restructured a bit
• Some are related to the structure and performance of some functions and of the overall main function

I have not reviewed the unit-testing file (perturbIC_test.py), because I believe some tests will need modifications after the suggested restructuring.
Therefore, I think it might be better you to address the comments first, and change the tests accordingly. Then, I can re-review everything including the tests.

I tried to leave comments and explain most of my suggestions, but feel free to comment back for further explanations, or ask me directly.

[leoberhelman]

I made the changes and a few more to correct some errors. Still need to update the unit tests

[atteggiani]

Thank you @leoberhelman for the amazing work restructuring this after my extensive review!

I added a few other minor suggestions. Please refer to the specific comments.

Two important points:

• I am going to open up a PR with a revision of the testing suite. That can also serve as a guideline an example for future testing suites.
  As a consequence, there is no need to address the specific comment I left regarding the test_create_default_outname function. I will include that part in my testing-suite PR. The test_create_default_outname comment should be viewed as an example of a testing approach.
• With the restructuring of the repo and creation of the original branch, I think the main branch should now only include the portions of the codebase we are restructuring, and potentially be in a "releasable" state (in the not-too-far future). Therefore, I would delete all the scripts that we are not using from this branch.
  Namely, I would only keep the perturbIC.py script (moving it inside the umfile_utils folder, along with the already present _version.py and __init__.py files) while movind the README.md at the top-level of the repo.
  Note that, after this restructure, some minor modifications might be needed with the imports (from perturbIC import ... should become from umfile_utils.perturbIC for example). Also, in the pyproject.toml file the following lines should be added to ensure pytest works correctly:

  [tool.pytest.ini_options]
  pythonpath = "src"

[atteggiani]

Just added another comment

[atteggiani]

Looks good!

Thank you @leoberhelman for your great work on this!

[atteggiani]

I have another comment that I thought about when reviewing the subset function.

[atteggiani]

LGTM!

[atteggiani]

Thank you so much for the work on this @leoberhelman!
Merged.