Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

V2.0.0 dev #4

Merged
merged 11 commits into from
Jun 7, 2024
Merged

V2.0.0 dev #4

merged 11 commits into from
Jun 7, 2024

Conversation

isabelrem
Copy link
Contributor

@isabelrem isabelrem commented May 13, 2024

This change is Reviewable

isabelrem and others added 8 commits March 18, 2024 13:24
…o be build 38 coordinates. Using broad institute liftover online tool
… allows patient sample to be tested using make test_sample
made a note of how the genomic coordinates used are now for build 38
Removed notes to self. Added note in PRS(object) docstring that notes the paper this class was based on originally used build 37 genomic coordinates for the SNPs, whereas the v2.0.0 version of this script uses build 38 genomic coordinates.
Copy link
Contributor

@RachelDuffin RachelDuffin left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Reviewed 6 of 6 files at r1, all commit messages.
Reviewable status: all files reviewed, 3 unresolved discussions (waiting on @isabelrem)


-- commits line 20 at r1:
Suggestion for future work - it is best practice to use the imperative voice in your commit messages


Makefile line 23 at r1 (raw file):

build:
	docker build -t $(IMG_VERSIONED) .
	#docker buildx build --platform linux/amd64 -t $(IMG_VERSIONED) .

Is this required?


README line 1 at r1 (raw file):

# FH-PRS v2.0.0

Suggestion to not include version numbers in the readme - this is denoted in the release information and tags. It can easily get out of date when written manually in documentation like this

Copy link
Contributor Author

@isabelrem isabelrem left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I've cleaned up the things you pointed out (version number in readme, a comment in the make file) and I've also swapped out the 'docker build -t fhprs .' in the readme file to 'make build', since the make file will do the same thing with less input required from the user and therefore less opportunity for mistake.

Thanks!

Reviewable status: 4 of 6 files reviewed, 3 unresolved discussions (waiting on @RachelDuffin)


-- commits line 20 at r1:

Previously, RachelDuffin wrote…

Suggestion for future work - it is best practice to use the imperative voice in your commit messages

Thanks for this tip - I'll do my best to remember this in the future. I have also used the imperative voice in the commit messages I've written since.


Makefile line 23 at r1 (raw file):

Previously, RachelDuffin wrote…

Is this required?

If you're referring to the comment, no it is not - I've now removed this. Good catch!


README line 1 at r1 (raw file):

Previously, RachelDuffin wrote…

Suggestion to not include version numbers in the readme - this is denoted in the release information and tags. It can easily get out of date when written manually in documentation like this

Thanks for the tip, I've since removed the version number from the readme.

Copy link
Contributor

@RachelDuffin RachelDuffin left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This Looks great - well done Isabel!

Reviewed 2 of 2 files at r2, all commit messages.
Reviewable status: :shipit: complete! all files reviewed, all discussions resolved (waiting on @isabelrem)

@RachelDuffin RachelDuffin merged commit 0394332 into main Jun 7, 2024
3 checks passed
@RachelDuffin RachelDuffin deleted the v2.0.0_dev branch June 7, 2024 12:15
isabelrem pushed a commit that referenced this pull request Nov 18, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants