@casperdcl could you have a quick look at formatting of comments at the start? Not sure what the recommended way of doing this is. (I'd rather avoid docopt).

Codacy flags up some issues at https://app.codacy.com/gh/UCL/STIR/pull-requests/1593/issues.

• some unused variables
• some formatting. Probably best is to do pip install black; black Vision_files_preprocessing.py
• quite a few warnings about unknown escape sequences. However, the script works... Maybe @casperdcl can recommend something.

Thanks @casperdcl. These suggestions look good to me. @NicoleJurjew how do you want to do this? Easiest might be to let @casperdcl commit them, and then you try it out (after MIC deadline!). If it doesn't work, we either remove the commit, or fix it...

Hi both,

thanks for your help, I'll have a look at it next week then!

Nicole

The remaining issues should be v. easy to fix :)

Hi both,

Thanks for your help, I've fixed most of the codacy issues now.

At first I was surprised by the trailing whitespace issues codacy flagged because I'm using pre-commit, but I'm guessing they occur because there is no rule for python code in the .pre-commit-config.yaml file. I've tried adding it, such that pre-commit fixes my white-space errors automatically:

- repo: https://github.com/pre-commit/pre-commit-hooks rev: v4.4.0 hooks: - id: trailing-whitespace

But it ended up modifying 468 files across the repo, so I decided not to include it. I'm afraid I don't know how to fix that, but I thought I'd bring it to your attention in case you want to prioritise it.

Nicole

I've tried adding it, such that pre-commit fixes my white-space errors automatically:

- repo: https://github.com/pre-commit/pre-commit-hooks rev: v4.4.0 hooks: - id: trailing-whitespace

But it ended up modifying 468 files across the repo, so I decided not to include it. I'm afraid I don't know how to fix that, but I thought I'd bring it to your attention in case you want to prioritise it.

yes, this is on our list. I'm a bit surprised that that particular hook modifies so many files (all C++ files should have been handled already) but fine. As before, I think we will need to create those hooks in 2 stages, such that we can let "git blame" ignore these automatic changes.

thanks!

By the way, I see VS Code reformatted the html as well. @casperdcl if you know about a good hook for that...

@NicoleJurjew can I delete the branch?