Release 0.1.8

[j-c-gibson]

Description of the PR

New PyGOM release with the primary goal to provide complete and up to date documentation.

There are a few minor changes to the code too: In the process of writing the documentation, it was decided that the SimulateOde class should be used for all (deterministic and stochastic) simulations. There is also a bug fix in the tau leap safety algorithm.

Checks

This is an itemised checklist for the QA process within UKHSA and represents the bare minimum a QA should be.

Full instructions on reviewing work can be found at Confluence on the ONS QA of code guidance page.

To the reviewer: Check the boxes once you have completed the checks below.

• [x] It runs
  • Can you get the code run to completion in a new instance and from top to bottom in the case of notebooks, or in a new R session?
  • Can original analysis results be accurately & easily reproduced from the code?
• [] tests pass
• [] CI is successful This is a basic form of Smoke Testing
• [x] Data and security
  • Use nbstripout to prevent Jupyter notebook output being committed to git repositories
  • Files containing individual user's secret files and config files are not in repo, however examples of these files and setup instructions are included in the repo.
  • Secrets include s3 bucket names, login credentials, and organisation information. These can be handled using secrets.yml
  • If you are unsure whether an item should be secret please discuss with repo owner
  • The changes do not include unreleased policy or official information.
• [x] Sensible
  • Does the code execute the task accurately? This is a subjective challenge.
  • Does the code do what the comments and readme say it does*?
  • Is the code robust enough to handle missing or challenging data?
• [x] Documentation
  • The purpose of the code is clearly defined, whether in a markdown chunk at the top of a notebook or in a README
  • Assumptions of the analysis & input data are clearly displayed to the reader, whether in a markdown chunk at the top of a notebook or in a README
  • Comments are included in the code so the reader can follow why the code behaves in the way it does
  • Teams with high quality documentation are better able to implement technical practices more readily and perform better as a whole (DORA, 2021).
  • Is the code written in a standard way? (In a hurry this may be a nice to have, but if at all possible, this standard from the beginning can cut long term costs dramatically)
  • Code is modular, storing functions & classes in the src and being imported into a notebook or script
  • Projects should be based on the UKHSA repo template developed to work with cookiecutter
  • Variable, function & module names should be intuitive to the reader
  • For example, intuitive names include df_geo_lookup & non-intuitive names include foobar
  • Common and useful checks for coding we use broadly across UKHSA include:
  • Rstyler
  • lintr
  • black
  • flake8
• [x] Pair coding review completed (optional, but highly recommended for QA in a hurry)
  • Pair programming is a way of working and reviewing that can result in the same standard of work being completed 40%-50% faster (Williams et al., 2000, Nosek, 1998) and is better than solo programming for tasks involving efficient knowledge transferring and for working on highly connected systems (Dawande et al., 2008).
  • Have the assignee and reviewer been on a video call or in person together during the code development in a line by line writing and review process?

* If the comments or readme do not have enough information, this check fails.

How to QA this PR

Before accepting the PR and merging to main or master, please follow these steps on a terminal in your development instance:

• git status check what branch you are on and if you have any uncommitted changes.
• Handle the work on your current branch:
  • git commit if you would like to keep the changes you have made on your current branch.
  • git stash if you do not want to keep these changes, although you can recover these later.
• git checkout main or git checkout master to go to the branch that will be merged to.
• git pull origin main or git pull origin master fetches the most up to date git info on this branch.
• git branch -a lists all the available branches.
• git checkout BRANCHNAME-FOR-PR moves you into the branch to QA.
• git pull origin BRANCHNAME-FOR-PR ensures you have the most recent changes for the PR.
• Run the notebooks or code.
• Run pre-commit. This runs some automated checks to check the code is well formatted and does not contain data.
  • Are there any small changes that can be made to get it to run?
  • Yes: make annotations on github and notify code creator to correct them
  • No, it runs: done!
  • No, and it looks like it would need a lot of work: note major points in Github PR chat and discuss with author.
• Carefully read through the code or documentation and make sure it makes sense.