Add comprehensive CONTRIBUTING.md guide for new contributors#860
Add comprehensive CONTRIBUTING.md guide for new contributors#860jonbrenas merged 4 commits intomalariagen:masterfrom
Conversation
- Add structured contributor onboarding guide - Document development workflow and testing - Clarify contribution and PR process
adilraza99
force-pushed
the
docs/add-contributing-md
branch
from
af69461 to
b69d587
Compare
|
@jonbrenas I’ve opened this PR adding the CONTRIBUTING.md guide. The documentation focuses on contributor workflow, development setup, testing, and review expectations, and is aligned with the current repository structure. Could you please review and let me know if anything should be adjusted? |
|
Hi @jonbrenas, Just a gentle follow-up on this PR whenever you have time. I’ve addressed the earlier feedback and ensured the guide aligns with the current repository structure and contributor workflow. Please let me know if any further adjustments are needed. Thanks again! |
jonbrenas
left a comment
jonbrenas
left a comment
There was a problem hiding this comment.
Thanks, @adilraza99! This looks great. There are some minor changes (which mostly lie with me) that would make but this makes a lot of things much clearer.
It would probably be worth modifying the README as well (as it is the first block of text that anyone sees) to refer to CONTRIBUTING and to remove the parts that are superseded by it.
CONTRIBUTING.md
Outdated
|
|
||
| ## About the project | ||
|
|
||
| This package provides Python tools for accessing and analyzing genomic data from [MalariaGEN](https://www.malariagen.net/), a global research network studying the genomic epidemiology of malaria and its vectors. The package supports multiple data releases (Ag3, Af1, Amin1, Adir1, Pf7, Pf8, Pv4) and provides functionality for variant analysis, haplotype clustering, population genetics, and visualization. |
There was a problem hiding this comment.
I think it would be better to focus on the data instead of the release (e.g., access to the Anopheles gambiae s.l. data instead of Ag3). The range of functionality is also quite different between vector and parasite. I'll try to think more deeply on this subject soon.
|
|
||
| ```bash | ||
| poetry install | ||
| poetry shell |
There was a problem hiding this comment.
Not your fault, we haven't updated the README either but poetry shell has been moved to a different plugin: https://python-poetry.org/docs/cli/#shell. TLDR: there is an additional step for it to work now.
|
|
||
| ## Development workflow | ||
|
|
||
| ### Creating a new feature or fix |
There was a problem hiding this comment.
I think a step is missing around generating issues if they do not exist. In either case, we generally favour branches being named 'GH{#issue}-{branch description}' where {#issue} is the number/identifier of the issue and {PR description} describes the content of the branch (more important when the branch only addresses part of the issue).
| - Address review feedback by pushing new commits to your branch | ||
| - Once approved, a maintainer will merge your PR | ||
|
|
||
| ## AI-assisted contributions |
There was a problem hiding this comment.
I need to discuss what our policy is around AI-use with @cclarkson and @ahernank, but this looks like a great start.
- focus project description on supported data types
- replace deprecated poetry shell workflow
- document GH{issue-number}-{description} branch convention
- improve contributor workflow clarity
|
@jonbrenas Thank you for the helpful review and guidance. I’ve incorporated the suggested updates: Please let me know if anything further should be adjusted. I appreciate your time and feedback. |
|
Thank you @adilraza99. It looks like you completely removed the 'poetry shell' part instead of updating it with the new version. |
|
@jonbrenas Thanks for the clarification and guidance. I’ve updated the development environment section to keep Please let me know if this aligns with what you had in mind or if any further adjustments would be helpful. |
2 participants
Summary
Add a comprehensive CONTRIBUTING.md guide to standardize the contribution workflow and improve onboarding for new contributors.
This guide includes:
This is a documentation-only change. No application code was modified.
Fixes #859