wl-utilities 2022.0.4

Utility code to perform QAG and SV analysis

Utility code to be used in the WEAVE-QAG/SV environment

This package is called wl-utilities on PyPI and can be installed with pip install wl-utilities and then imported with import wl_utilities This package is a collaborative effort and will comprise the scientific code that allows the QAG tests and SV to run. wl_utilities will be a dependency of those projects. wl_utilities should not use weaveio or qag packages.

Please see setup for setting up github

Workflow

There will be 2 branches in use on this repository:

• main - where the production-ready version exists and which is uploaded automatically to PyPI for use by everyone.
• develop - where changes and merges all take place before merging into the main branch

Setup git

To setup git to deal with collaboration. This will allow you to use our custom git aliases, shortcuts that make your life easier.

1. On github click Fork. This creates a copy of wl_utilities for you to work on (WARNING: make sure your repo is called "wl_utilities" and not "utilities")
2. Check that your machine can use ssh key authentication with github
3. On the pc where you develop QAG tests, cd somewhere for development on this wl_utiltities repository. There is no need to create a wl_utilities directory.
4. git clone [e-mail]:YOURUSERNAME/wl-utilities.git (the link can be found under the green code button on your github page)
5. cd wl_utilities on your local machine.
6. Activate your development environment (maybe: conda activate weaveio or similar)
7. Install helper aliases chmod +x setup.sh && ./setup.sh

To add/modify this repository with your own changes and improvements please use this workflow:

0. Activate your development environment (maybe: conda activate weaveio or similar)
1. Pull the latest updates: git sync-fork
2. Create a new branch for your changes to live on: git fork-branch my-clever edit
3. Make your changes on this branch
4. View what has happened: git status
5. Add your changes to be commited: git add <file1> <file2> ...
6. View what has changed: git status
7. Save your changes: git commit -m "description of changes"
8. Wait for automated checks to complete (and then commit again if necessary: git commit -m "description of changes")
9. Push changes to your fork only: git push
10. Open a pull request on your github page (https://github.com/USERNAME/wl-utilities), click contribute->open pull request, and check "allow edits by maintainer"

You can also use gh pr create --fill to open a pull request on command line. This requires the github cli utility which can be installed with apt-get or conda

In general we should be writing code like this:

* Play with code in jupyter notebook (all weaveio queries, new functions, plotting)
* Refactor this notebook and the wl_utilities module to move new functions/plotting to wl_utilities
* Run notebook to make sure its still doing what you want

All changes therefore end up in the develop branch of the weave-lofar shared repo.

All pull requests will be reviewed before merging, so we can limit mistakes.

Structure

The structure of this package will be:

wl_utilities/
  misc/  # for random short but useful snippets
  spectrum/  # for anything that processes spectra
    e.g. cross-correlation.py
    e.g. reduction.py
  stats/  # for anything that looks like a statistical test
    e.g. zscores.py

We will not use separate folders for individual's code since the objective is to put them together and not repeat.

Rules:

• This repo will be autoformatted according to black on server-side
• No change is merged with the main branch until approved by "enough" people
• Keep the code as modular as possible