Cutsite pairs rebased #199

manulera · 2024-02-05T17:50:32Z

Implements #157, and few bug fixes (see commit text)

* fix Dseq.apply_cut and minor error in Dseqrecord.apply_cut * WIP * return error on overlapping cuts, add tests for it * #180 solved for features on + strand, but not all * fixes #180

* implemented and tests pass * added cutsite_is_valid to check that the cutting site and recognition site are double stranded * finished notebook new cut implementation * extra function documentation and tests * fix small error

manulera · 2024-02-05T17:55:06Z

Big merge is ready 🚀🚀🚀🚀🚀🚀🚀🚀

codecov · 2024-02-05T17:56:40Z

Codecov Report

Attention: 6 lines in your changes are missing coverage. Please review.

Comparison is base (f17e73e) 92.95% compared to head (c9b003d) 93.01%.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #199      +/-   ##
==========================================
+ Coverage   92.95%   93.01%   +0.06%     
==========================================
  Files          39       39              
  Lines        3688     3739      +51     
  Branches      553      562       +9     
==========================================
+ Hits         3428     3478      +50     
- Misses        214      216       +2     
+ Partials       46       45       -1

Files	Coverage Δ
src/pydna/amplify.py	`98.65% <100.00%> (+0.01%)`	⬆️
src/pydna/utils.py	`93.08% <97.61%> (+1.15%)`	⬆️
src/pydna/dseq.py	`97.01% <97.33%> (+0.80%)`	⬆️
src/pydna/dseqrecord.py	`95.19% <90.32%> (-0.83%)`	⬇️

BjornFJohansson

This seems fine to me. I have tested it using the web form (Pydnaweb) locally and everything seems to work.

manulera added 23 commits February 2, 2024 12:51

working for Dseq

88287b8

WIP

d9883fa

Fixed itertools issue and modified tests , see #78

3e2535b

more WIP

339e862

closes #160

b38f5c4

working

4b8d0ec

remove old cut2

aeeec00

extra docs

af6140c

removed more_itertools deps

d6359e2

switch to alternative representation

0a58133

update docs

11a5668

Cutsite pairs bugs (#184)

bb547cc

* fix Dseq.apply_cut and minor error in Dseqrecord.apply_cut * WIP * return error on overlapping cuts, add tests for it * #180 solved for features on + strand, but not all * fixes #180

Simpler cut representation (#187)

2307ab7

* implemented and tests pass * added cutsite_is_valid to check that the cutting site and recognition site are double stranded * finished notebook new cut implementation * extra function documentation and tests * fix small error

Update utils.py

6fa6d84

closes #194

e3255f2

closes #195

830889d

closes #180 for all cases I could think of

c62f8a7

closes #161

a2c7dec

closes #197, but two tests still fail

becec35

Try to fix dependencies

cf75eb8

fix typing syntax to be compatible with python 3.8

7deba11

closes #198

8932fd2

all tests passing

c9b003d

BjornFJohansson approved these changes Feb 5, 2024

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BjornFJohansson merged commit 4fd760d into master Feb 5, 2024
35 checks passed

manulera mentioned this pull request Feb 6, 2024

Revise getitem in Dseqrecord #182

Closed

manulera deleted the cutsite_pairs_rebased branch February 6, 2024 08:42

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Cutsite pairs rebased #199

Cutsite pairs rebased #199

manulera commented Feb 5, 2024 •

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manulera commented Feb 5, 2024

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BjornFJohansson left a comment

Cutsite pairs rebased #199

Cutsite pairs rebased #199

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manulera commented Feb 5, 2024 •

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