BjornFJohansson / pydna

Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.
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Primerdesignbug #300

Closed manulera closed 1 month ago

manulera commented 1 month ago

Hi @BjornFJohansson I have been fixing the history of dev_bjorn to be properly grafted into master. I have also fixed the history of the primerdesignbug branch and create this one that contains the same code, but has the right commit history. You can keep working on this one, or merge if the fix is finished.

Best, Manu

manulera commented 1 month ago

I added an extra commit to re-run the notebook, since the output was wrong due to the bug from #279 (now fixed).

I actually have included a similar example that is now in the README, with a matching notebook at docs/notebooks/readme_example.ipynb

codecov[bot] commented 1 month ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 93.60%. Comparing base (f063c40) to head (c11bee7). Report is 6 commits behind head on dev_bjorn.

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/BjornFJohansson/pydna/pull/300/graphs/tree.svg?width=650&height=150&src=pr&token=8gKFpo7HAl&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Bj%C3%B6rn+Johansson)](https://app.codecov.io/gh/BjornFJohansson/pydna/pull/300?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Bj%C3%B6rn+Johansson) ```diff @@ Coverage Diff @@ ## dev_bjorn #300 +/- ## ========================================== Coverage 93.60% 93.60% ========================================== Files 40 40 Lines 3922 3922 Branches 588 588 ========================================== Hits 3671 3671 Misses 199 199 Partials 52 52 ``` | [Files with missing lines](https://app.codecov.io/gh/BjornFJohansson/pydna/pull/300?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Bj%C3%B6rn+Johansson) | Coverage Δ | | |---|---|---| | [src/pydna/design.py](https://app.codecov.io/gh/BjornFJohansson/pydna/pull/300?src=pr&el=tree&filepath=src%2Fpydna%2Fdesign.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Bj%C3%B6rn+Johansson#diff-c3JjL3B5ZG5hL2Rlc2lnbi5weQ==) | `97.51% <100.00%> (ø)` | |
BjornFJohansson commented 1 month ago

Thanks! This seems to be ok. The example.ipynb is now correct.