Code

User cloning#314

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dgruano wants to merge 91 commits intopydna-group:dev_bjornpydna-group/pydna:dev_bjornfrom dgruano:user_cloningdgruano/pydna:user_cloningCopy head branch name to clipboard

+91,259-11,106

Commits

Commits on Oct 8, 2024

• added new translation function

  

  BjornFJohansson

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  manulera

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  15f17ff

• new orfs method for Seq based on three_frame_orfs function

  

  BjornFJohansson

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  d333558

• new orfs_to_features method for Dseqrecord

  

  BjornFJohansson

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  5717dc0

• new extract_from_text functions that also returns the intervening text between sequences

  

  BjornFJohansson

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  37cbe3e

• bugfix orfs for Seq and Dsecrecord

  

  BjornFJohansson

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  1fc277d

• added crispr tests

  

  BjornFJohansson

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  c27e762

• added pairwise for older Python versions

  

  BjornFJohansson

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  4c4e4cc

• older type hint

  

  BjornFJohansson

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  f948b8c

• Deploying to gh-pages from @ pydna-group/pydna@da3e7e9 🚀

  

  BjornFJohansson

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  4d84231

• Deploying to gh-pages from @ pydna-group/pydna@5be4f9d 🚀

  

  BjornFJohansson

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  46f9d2c

• Deploying to gh-pages from @ pydna-group/pydna@b37a17c 🚀

  

  BjornFJohansson

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  64f531b

• Deploying to gh-pages from @ pydna-group/pydna@11aae3c 🚀

  

  BjornFJohansson

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  00795cd

• Deploying to gh-pages from @ pydna-group/pydna@0f95223 🚀

  

  BjornFJohansson

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  d0fef14

• try to build docs locally on gh-pages

  

  BjornFJohansson

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  80834d1

• try to build gh pages

  

  BjornFJohansson

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  806f20e

• try to build gh pages

  

  BjornFJohansson

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  1464e63

• fix

  

  BjornFJohansson

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  e13a009

• added sphinx ext

  

  BjornFJohansson

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  94f6eb0

• Deploying to gh-pages from @ pydna-group/pydna@bc08a36 🚀

  

  BjornFJohansson

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  0f947ea

• try fix docs

  

  BjornFJohansson

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  1c3f678

• build docs

  

  BjornFJohansson

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  1864101

• clean

  

  BjornFJohansson

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  4cfbdb7

• redirect docs badge to action

  

  BjornFJohansson

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  255aa46

• redirect docs badge to action

  

  BjornFJohansson

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  96c1de5

• fix readme links

  

  BjornFJohansson

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  6ddec81

• fix readme

  

  BjornFJohansson

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  7f013bd

• fix

  

  BjornFJohansson

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  23a6a2d

• try to fix test error

  

  BjornFJohansson

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  0c43349

• fix bug that recognized parts of re enzyme names as other enzymes

  

  BjornFJohansson

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  6a72988

• added comment with number of enzymes

  

  BjornFJohansson

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  3222075

• changed number of expected enzymes to the correct number 621

  

  BjornFJohansson

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  c61afff

• more informative error msg

  

  BjornFJohansson

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  afac39c

• closes pydna-group#216 (2)

  manulera

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  444e9fb

• closes pydna-group#196

  manulera

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  205ed7d

• vscode and poetry settings added

  manulera

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  ac81427

• fix test

  manulera

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  88c56da

• add locations_overlap to utils

  manulera

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  9b8986b

• Issue 238 (pydna-group#239)

  Show description for 8c1ebb8
  manulera

  committed
  8c1ebb8

• closes pydna-group#240

  

  JeffXiePL

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  2be88fb

• atomically write default config

  

  jxu10

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  17a1ed1

• optimisation for pydna-group#237

  manulera

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  2c92f13

• fix python 3.8 typing

  manulera

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  47bc08e

• include neb calculator and its tests

  manulera

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  d133461

• fix design and add tests

  manulera

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  12508a7

• example commit for pydna-group#176

  manulera

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  019013e

• Documentation notebooks 2 (pydna-group#272)

  Show description for 3514427
  

  manulera

  and

  JeffXiePL

  committed
  3514427

• update contribution guidelines (pydna-group#274)

  manulera

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  31b3322

• update CI action to enforce hooks (pydna-group#277)

  Show description for 09199a9
  manulera

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  09199a9

• update: Added google badge to all notebooks issue pydna-group#266 (pydna-group#275)

  Show description for 2cd9d38
  

  hiyama341

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  2cd9d38

• added seguid stamp to Genbank sequence files

  

  BjornFJohansson

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  1d36eeb

• fix test sequence file

  

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  610d3f6

• dependabot monthly

  

  BjornFJohansson

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  277f61a

• New CRISPR example notebook (pydna-group#260) (pydna-group#284)

  Show description for 26bb292
  

  hiyama341

  and

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  26bb292

• Updated notebooks (pydna-group#295)

  Show description for d46b3d9
  

  manulera

  and

  JeffXiePL

  committed
  d46b3d9

• progress towards pydna-group#261

  manulera

  committed
  03816ec

• WIP

  manulera

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  e065db2

• remove code image from README for pydna-group#261

  manulera

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  474a675

• more README updates + make requirements.txt

  manulera

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  7e2c247

• add requirements file

  manulera

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  ece5d59

• fix configuration

  manulera

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  7464e39

• typing for PrettyTable

  

  Kawin

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  2b010a9

• typing for codon dicts

  

  Kawin

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  982ceb9

• typing for Seq

  

  Kawin

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  490f066

• typing for FakeSeq

  

  Kawin

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  ae04507

• typing for Genbank

  

  Kawin

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  e6e1473

• typing for sequence_picker module

  

  Kawin

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  a591523

• typing for common_sub_strings module

  

  Kawin

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  7f89b8c

• typing for Assembly.__init__ and Assembly.__repr__

  

  Kawin

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  b8dbf7b

• Bump pillow from 10.3.0 to 10.4.0

  Show description for 4b6aa00
  

  dependabot[bot]

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  manulera

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  4b6aa00

• Bump autopep8 from 2.1.0 to 2.3.1

  Show description for d722b93
  

  dependabot[bot]

  authored and

  manulera

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  d722b93

• Bump black from 24.4.2 to 24.8.0

  Show description for ba91fe8
  

  dependabot[bot]

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  ba91fe8

• Bump sphinx-rtd-theme from 2.0.0 to 3.0.0

  Show description for cfd1181
  

  dependabot[bot]

  authored and

  manulera

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  cfd1181

• Bump prettytable from 3.10.0 to 3.11.0

  Show description for 959b5d4
  

  dependabot[bot]

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  manulera

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  959b5d4

• closes pydna-group#261 (pydna-group#297)

  manulera

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  4c2d929

• tests for pydna-group#281 pydna-group#279, add type to pcr (pydna-group#298)

  manulera

  authored
  f063c40

Commits on Oct 9, 2024

• update codecov action for pydna-group#242

  manulera

  committed
  fd8577c

Commits on Oct 10, 2024

• Issue 270 (pydna-group#301)

  Show description for 9e86c43
  manulera

  authored
  9e86c43

• added example.ipynb to tests folder

  BjornFJohansson

  committed
  bd8317c

• removed example.ipynb

  BjornFJohansson

  committed
  4340cee

• deal with Tm = 0

  BjornFJohansson

  committed
  1b142c8

• fix notebook export related to pydna-group#279

  

  manulera

  authored and

  BjornFJohansson

  committed
  9d112d7

Commits on Oct 11, 2024

• New docs (pydna-group#304)

  Show description for 768c6fa
  manulera

  authored
  768c6fa

Commits on Oct 15, 2024

• Fix link in README (pydna-group#310)

  dgruano

  authored
  bca1d08

• Fix action (pydna-group#311)

  Show description for 72cd39b
  manulera

  authored
  72cd39b

• WIP

  dgruano

  committed
  a700da8

• Minimal working example, tests missing

  dgruano

  committed
  71ea805

• WIP, Test implementation with USER cuts in single strands

  Show description for 6aa2736
  dgruano

  committed
  6aa2736

Commits on Oct 16, 2024

• WIP, Add function to extract USER products

  Show description for 0291efa
  dgruano

  committed
  0291efa

Commits on Oct 25, 2024

• USER refactor (#1)

  Show description for 83efa38
  manulera

  authored
  83efa38

• Add tests, passing

  dgruano

  committed
  f4e2d5d

Commits on Oct 30, 2024

• Implement NtBbvCI nickase, add tests (failing)

  Show description for b4fca5f
  dgruano

  committed
  b4fca5f