Ecosyste.ms: Issues

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GitHub / jvrana/DASi-DNA-Design issues and pull requests

#63 - Bump certifi from 2020.6.20 to 2022.12.7

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#62 - Bump pillow from 7.2.0 to 9.3.0

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#61 - Add CodeQL workflow for GitHub code scanning

Pull Request - State: open - Opened by lgtm-com[bot] about 2 years ago

#60 - Bump arrow from 0.14.7 to 0.15.1

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#59 - Bump pillow from 8.1.0 to 8.3.2

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#58 - fixed documentation; built docs

Pull Request - State: closed - Opened by jvrana almost 4 years ago

#57 - Release 0.2

Pull Request - State: closed - Opened by jvrana about 4 years ago - 3 comments

#56 - V0.1 release

Pull Request - State: closed - Opened by jvrana over 4 years ago

#55 - better parallelization

Issue - State: open - Opened by jvrana over 4 years ago - 1 comment
Labels: enhancement

#53 - expand_synthesized fragments during library compilation

Pull Request - State: closed - Opened by jvrana over 4 years ago

#52 - Long Gibson Assembly Parameters should be different than short gibson assemblies

Issue - State: open - Opened by jvrana over 4 years ago
Labels: enhancement

#51 - Designs should keep record of errors (instead of raising Exception)

Issue - State: open - Opened by jvrana over 4 years ago
Labels: enhancement

#50 - Annotations on SeqRecords are not being carried through to output.

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: bug

#49 - Users should be able to control thresholds for valid primer pairs

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: enhancement

#48 - Add examples module users can pull from to test out DASi

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: enhancement

#47 - Information about input sequences should be present in

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: enhancement

#46 - Bug: `Sequence is cyclic but there are no precessors` error

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: bug

#45 - Attach notes to edges when efficiency is adjusted in Graph post processing

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: enhancement

#44 - Find invalid assemblies

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: bug, enhancement

#43 - JSON Schema display in Sphinx should be more condensed

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: documentation

#42 - *more* tests are fixed

Pull Request - State: closed - Opened by jvrana almost 5 years ago

#40 - Better Integration between Aquarium <> Terrarium <> DASi <> {Benchling, SynBioHub}

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: Epic

#39 - Clean up integration IO for DASi

Issue - State: open - Opened by jvrana almost 5 years ago

#38 - Understand why some designs fail to assemble

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: bug, enhancement

#37 - Preferrably tests short tests in automated CI

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: enhancement

#36 - DNA complexity tests sometimes fail

Issue - State: open - Opened by jvrana almost 5 years ago

#35 - Randomized tests occasionally fails

Issue - State: open - Opened by jvrana almost 5 years ago

#34 - Randomized tests occassionally fail

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: bug, Epic

#33 - SBOL Output

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: enhancement

#32 - Improve Documentation

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: documentation

#31 - Top level reaction

Pull Request - State: closed - Opened by jvrana almost 5 years ago

#30 - Shared sequence cost often does not match final cost

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: bug

#29 - Better explaination for DASi design failures

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: bug, enhancement

#28 - JSON output schema

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: enhancement

#27 - Testing Utilities: More control over random library generation

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: enhancement

#26 - Invalid fragment PCR products are produced.

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: bug

#25 - Input parameters should be exposed

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: enhancement

#24 - Add library design

Pull Request - State: closed - Opened by jvrana almost 5 years ago

#23 - Vendor Configurations (e.g. IDT, Twist)

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: enhancement

#22 - speed improvements

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: enhancement

#21 - Better Logger

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: enhancement

#20 - Add gap partition

Pull Request - State: closed - Opened by jvrana almost 5 years ago

#19 - Add gap partition

Pull Request - State: closed - Opened by jvrana almost 5 years ago

#18 - PDF Assembly Reports

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: enhancement

#17 - Implement sharing of primer and PCR product design

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: enhancement

#16 - Implement DNA Synthesis Sharing

Issue - State: open - Opened by jvrana almost 5 years ago
Labels: enhancement

#15 - RuntimeWarning: invalid value encountered in true_divide

Issue - State: open - Opened by jvrana about 5 years ago
Labels: bug

#14 - Implement DNA complexity to efficiency for graphs

Issue - State: closed - Opened by jvrana about 5 years ago
Labels: enhancement

#13 - Optimal Partitioning Schema

Issue - State: open - Opened by jvrana about 5 years ago
Labels: enhancement

#12 - Develop

Pull Request - State: closed - Opened by jvrana about 5 years ago

#11 - Develop include time in cost calc

Pull Request - State: closed - Opened by jvrana about 5 years ago

#10 - Linear DNA Design

Issue - State: open - Opened by jvrana about 5 years ago
Labels: enhancement

#9 - Degenerate designs

Issue - State: open - Opened by jvrana about 5 years ago
Labels: enhancement

#8 - Implement tblastn for CDS searches

Issue - State: open - Opened by jvrana about 5 years ago
Labels: enhancement

#7 - Gap Synthesis Complexity Span Cost

Issue - State: closed - Opened by jvrana about 5 years ago
Labels: enhancement

#6 - Develop

Pull Request - State: closed - Opened by jvrana about 5 years ago

#5 - Refactoring and docs

Pull Request - State: closed - Opened by jvrana about 5 years ago

#4 - Refactor optimization try2

Pull Request - State: closed - Opened by jvrana about 5 years ago

#3 - Create LICENSE

Pull Request - State: closed - Opened by jvrana about 5 years ago

#2 - Speed improvements

Pull Request - State: closed - Opened by jvrana over 5 years ago

#1 - Merging library design into development branch

Pull Request - State: closed - Opened by jvrana over 5 years ago