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

Issue 237 optimisation #250

Merged
merged 4 commits into from
Aug 8, 2024
Merged

Issue 237 optimisation #250

merged 4 commits into from
Aug 8, 2024

Conversation

manulera
Copy link
Collaborator

@manulera manulera commented Jul 25, 2024

  • Adds tm_neb to pydna.tm (uses NEB's API). It calls it using browser-like headers, which hopefully will work most of the time.
  • Adds the possibility to use an estimate function as first attempt to design the primer, then calls the actual function to ge the result. This is useful when using NEB, which is pretty slow. To use that:
primer_design(dseqr, target_tm=55, tm_func=tm_neb, estimate_function=tm_default)

Copy link

codecov bot commented Jul 25, 2024

Codecov Report

Attention: Patch coverage is 95.91837% with 2 lines in your changes missing coverage. Please review.

Project coverage is 93.92%. Comparing base (7747787) to head (7e4f306).
Report is 2 commits behind head on dev_bjorn.

Files Patch % Lines
src/pydna/tm.py 87.50% 1 Missing and 1 partial ⚠️
Additional details and impacted files

Impacted file tree graph

@@              Coverage Diff              @@
##           dev_bjorn     #250      +/-   ##
=============================================
+ Coverage      93.66%   93.92%   +0.25%     
=============================================
  Files             40       40              
  Lines           3867     4080     +213     
  Branches         576      666      +90     
=============================================
+ Hits            3622     3832     +210     
- Misses           196      200       +4     
+ Partials          49       48       -1     
Files Coverage Δ
src/pydna/design.py 97.51% <100.00%> (+0.31%) ⬆️
src/pydna/tm.py 96.92% <87.50%> (-3.08%) ⬇️

... and 2 files with indirect coverage changes

@manulera
Copy link
Collaborator Author

Tests are missing here, I will add them. Don't merge yet!

@manulera manulera requested a review from BjornFJohansson July 31, 2024 11:25
@manulera
Copy link
Collaborator Author

@hiyama341 this is ready and tested, have a look at the description to see how to use it!

@manulera
Copy link
Collaborator Author

@BjornFJohansson please have a look, I think this can be safely merged

@BjornFJohansson BjornFJohansson merged commit f156549 into dev_bjorn Aug 8, 2024
34 checks passed
@manulera manulera deleted the issue_237_optimisation branch October 8, 2024 10:58
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