BioJulia commits | Ecosyste.ms: OpenCollective

Added ability to read/write feature lines with order(...)

github.com/BioJulia/GenomicAnnotations.jl - 8596eca1f4e09611a3b7dbf4686f253d387f1bbd authored about 6 years ago by Karl Dyrhage <[email protected]>

Fixed Chromosome() bug

github.com/BioJulia/GenomicAnnotations.jl - 103878139e3f66650a4cdf9a2e96ecb8f6b35535 authored about 6 years ago by Karl Dyrhage <[email protected]>

Made sequence(::Gene) consider the strand

github.com/BioJulia/GenomicAnnotations.jl - 89b6a1592ced97b1ef1370f110aefc9eff040a45 authored about 6 years ago by Karl Dyrhage <[email protected]>

Minor changes

github.com/BioJulia/GenomicAnnotations.jl - 5f7839e0d980621e76eafb51d20de9fb0177b6cb authored about 6 years ago by Karl Dyrhage <[email protected]>

Fixed sequence(::Gene) bugs

github.com/BioJulia/GenomicAnnotations.jl - 7a2b53dfc87c549179affbe2e927ed98af14b561 authored about 6 years ago by Karl Dyrhage <[email protected]>

Added more tests

github.com/BioJulia/GenomicAnnotations.jl - 0282fb280da50c84c9f487dafaa98dd4d6523820 authored about 6 years ago by Karl Dyrhage <[email protected]>

Export pushproperty!

github.com/BioJulia/GenomicAnnotations.jl - e285461e71f471ac15ec5ffbf0a747b4bcad4123 authored about 6 years ago by Karl Dyrhage <[email protected]>

Fixed broadcast bug

github.com/BioJulia/GenomicAnnotations.jl - a5e61ed2be64d1c0e7f5ea8a037036fec7a63aa2 authored about 6 years ago by Karl Dyrhage <[email protected]>

Updated @genes to allow symbols in get() expressions

github.com/BioJulia/GenomicAnnotations.jl - a4af6b021777346f9f24709b973682827a0b1303 authored about 6 years ago by Karl Dyrhage <[email protected]>

Fixed delete! bug and added convert method for Locus

github.com/BioJulia/GenomicAnnotations.jl - 93d1505699061f10a3b6d60bc2ebfbc20d884433 authored about 6 years ago by Karl Dyrhage <[email protected]>

Updated README

github.com/BioJulia/GenomicAnnotations.jl - cd8987a99780c7113f2fe13df39d0e3736331233 authored about 6 years ago by Karl Dyrhage <[email protected]>

Renamed genesequence() to sequence()

github.com/BioJulia/GenomicAnnotations.jl - 01e131f240631c01039f2fc6473fe93a30064ec6 authored about 6 years ago by Karl Dyrhage <[email protected]>

setindex!(::GeneDataView) update

github.com/BioJulia/GenomicAnnotations.jl - 32a36864cde31897c9d4f7e823953e3e46d36586 authored about 6 years ago by Karl Dyrhage <[email protected]>

Slight getproperty speedup

github.com/BioJulia/GenomicAnnotations.jl - 691faf959a284bc059ae7b92f49ae90983a649a9 authored about 6 years ago by Karl Dyrhage <[email protected]>

Added support for broadcasted setindex! for GeneDataViews

github.com/BioJulia/GenomicAnnotations.jl - e5dc01311cf9450504b0f64a85f298678bc5cbc3 authored about 6 years ago by Karl Dyrhage <[email protected]>

Fixed setindex!

github.com/BioJulia/GenomicAnnotations.jl - 022359cb33cf18fb37e21d19d3ddaff5be8ed40b authored about 6 years ago by Karl Dyrhage <[email protected]>

Added syntax highlighting

github.com/BioJulia/GenomicAnnotations.jl - e62da08129741a4b2696270dc81794a465cfbc3d authored about 6 years ago by Karl Dyrhage <[email protected]>

update NEWS.md

github.com/BioJulia/BioStructures.jl - 7a1a50925903aa6a6bd50bb11ec2732fdfac828b authored about 6 years ago by Joe Greener <[email protected]>

Visualisation of contact and distance maps (#9)

github.com/BioJulia/BioStructures.jl - 6985e37ecb7fc0186538c280423bd801751774f2 authored about 6 years ago by Joe Greener <[email protected]>

Added BioSequences as dependency

github.com/BioJulia/GenomicAnnotations.jl - 020b6530f14bbf6e35b2aab699bd7c6104e3d0cf authored about 6 years ago by Karl Dyrhage <[email protected]>

Added BioSequences as dependency

github.com/BioJulia/GenomicAnnotations.jl - 54d91448fb2f7df501087a4821bedcf665a487dd authored about 6 years ago by Karl Dyrhage <[email protected]>

Removed setproperty! for AbstractArray{Gene}

github.com/BioJulia/GenomicAnnotations.jl - dc62de93d2430bc0ec83428bb16b699a89975b68 authored about 6 years ago by Karl Dyrhage <[email protected]>

Added examples to README

github.com/BioJulia/GenomicAnnotations.jl - 28aa665940a7269e51a4596f7044a56894733e9d authored about 6 years ago by Karl Dyrhage <[email protected]>

Added examples to README

github.com/BioJulia/GenomicAnnotations.jl - d6618aa355f5e6cda79e3cc61268a1afa2b6ff2a authored about 6 years ago by Karl Dyrhage <[email protected]>

Updated tests

github.com/BioJulia/GenomicAnnotations.jl - 343fe2c36bb0f53435f61b9b9664e1e8d023774c authored about 6 years ago by Karl Dyrhage <[email protected]>

getproperty() speedup + added get() method

github.com/BioJulia/GenomicAnnotations.jl - 6dac0048e4e4232ae0f12bef6e6883e218d0c921 authored about 6 years ago by Karl Dyrhage <[email protected]>

Updates

github.com/BioJulia/GenomicAnnotations.jl - 17a5bea46246a3a5c6b684df102823fd352330f5 authored about 6 years ago by Karl Dyrhage <[email protected]>

Adds support to Julia 1.0 (#7)

github.com/BioJulia/BioTools.jl - bded577dde0a99696e185c15119c409dc0d8d64e authored about 6 years ago by Fernando Gelin <[email protected]>

Ignore .DS_Store files and update docs

github.com/BioJulia/BioAlignments.jl - 54319fd63f964a9d26a8d7a836203b9ab772e9c2 authored about 6 years ago by Ben J. Ward <[email protected]>

Correct a typo in .travis.yml

github.com/BioJulia/BioSequences.jl - 95d64dc58c034cb2a0af54f179478d585e970796 authored about 6 years ago by Ben J. Ward <[email protected]>

Add package sticker

github.com/BioJulia/BioAlignments.jl - a936274c0ef532ebd081492ddd2ffa3354944188 authored about 6 years ago by Ben J. Ward <[email protected]>

Merge pull request #18 from fernandogelin/master

Adds support for Julia 0.7/1.0

github.com/BioJulia/BioServices.jl - cb25daf0c02f8a1b3db8348f877069155fb0439a authored about 6 years ago by Maria Isabel Restrepo <[email protected]>

Julia 1.0 support (#18)

github.com/BioJulia/BioAlignments.jl - 8f1bdca96013b855665458c1d2ddbd9614d46ba6 authored about 6 years ago by Daniel C. Jones <[email protected]>

removed commented lines from travis

github.com/BioJulia/BioServices.jl - 24c74a3ae3c0898ae434957bd0d2edff1dc3d67c authored about 6 years ago by fernandogelin <[email protected]>

addressed pr changes requested

github.com/BioJulia/BioServices.jl - c12a1127e23cceb452853f5d3b23f085c62ae35b authored about 6 years ago by fernandogelin <[email protected]>

Version 1.0 updates (#15)

github.com/BioJulia/GenomicFeatures.jl - 8fc34ff680f5e742e25d2bd3d4722cb33fbe3cd5 authored about 6 years ago by Ben J. Ward <[email protected]>

Merge pull request #10 from jangevaare/docs-fix

Fix LaTeX for P & Q matrix documentation

github.com/BioJulia/SubstitutionModels.jl - 54a8a46bf4ce3d61ec7a58c23bc1b8db54461747 authored about 6 years ago by Justin Angevaare <[email protected]>

Fix LaTeX for P & Q matrix documentation

github.com/BioJulia/SubstitutionModels.jl - 630d880e064d0a546a00f354bfb978250fc56dce authored about 6 years ago by Justin Angevaare <[email protected]>

updates CHANGELOG

github.com/BioJulia/BioServices.jl - e4fd7efc10cc81439837e2e2fb8252a4f7aebf0f authored about 6 years ago by fernandogelin <[email protected]>

changes travis

github.com/BioJulia/BioServices.jl - a59b3c3996c84789dbf9a45df68f0331725cedc1 authored about 6 years ago by fernandogelin <[email protected]>

upgrades packages to julia v1.0

github.com/BioJulia/BioServices.jl - 6e2bb48a1ca2842547f5ea9082b1881c448a4e60 authored about 6 years ago by fernandogelin <[email protected]>

updates julia version on README

github.com/BioJulia/BioServices.jl - 44dc7229cafe5913749795de629893d3a9848cb3 authored about 6 years ago by fernandogelin <[email protected]>

updates julia version on README

github.com/BioJulia/BioServices.jl - de68e2b8b6e51d88ba364b95f69eb52e5647abf4 authored about 6 years ago by fernandogelin <[email protected]>

adds Dates to dependencies

github.com/BioJulia/BioServices.jl - 5fe5c2d466609d035459c2ffc8b0c0559a4b07de authored about 6 years ago by fernandogelin <[email protected]>

fixes missing comma, removes 0.6 from travis

github.com/BioJulia/BioServices.jl - d9ff52f50bd18afd462df1256d03892457b517f1 authored about 6 years ago by fernandogelin <[email protected]>

changes for v0.7 in UMLS module

github.com/BioJulia/BioServices.jl - a7aadad4bc87a32f694f4eb16177d1432d3389a5 authored about 6 years ago by fernandogelin <[email protected]>

updates travis

github.com/BioJulia/BioServices.jl - e4d42475186c34ea8490944c69e5e47b85a2046c authored about 6 years ago by fernandogelin <[email protected]>

changes travis to julia v0.7

github.com/BioJulia/BioServices.jl - bb7fba677e8af163b2c230a0a66da8131f4df67f authored about 6 years ago by fernandogelin <[email protected]>

makes changes for Julia v0.7

github.com/BioJulia/BioServices.jl - 3d834c54788b43addc02d2f959eec5bddab029f2 authored about 6 years ago by fernandogelin <[email protected]>

fix broken plots

github.com/BioJulia/MicrobiomePlots.jl - c319d5b63c47fa467fc58eaef449b16d7c914f0b authored about 6 years ago by Kevin Bonham <[email protected]>

some silly bug fixes

github.com/BioJulia/MicrobiomePlots.jl - 9f3806da918fe9fc3e47856b70868b339723861f authored about 6 years ago by Kevin Bonham <[email protected]>

Update appveyor (#44)

github.com/BioJulia/BioSequences.jl - 75e664fc0a8869f3bca077e1428c249cb7e7355c authored about 6 years ago by Ben J. Ward <[email protected]>

update doc build files

github.com/BioJulia/BioStructures.jl - 323659f365decf416c79fcd4c11c73c434f0a0a3 authored about 6 years ago by Joe Greener <[email protected]>

don't precompile

github.com/BioJulia/BioStructures.jl - 157ab9560a7671dc7a4a44ef0a8ece1128c878a3 authored about 6 years ago by Joe Greener <[email protected]>

Updates to julia v0.7, drop v0.6 (#7)

github.com/BioJulia/BioStructures.jl - 49b4f16e68073c5e875152616f5e19c686cd2f8e authored about 6 years ago by Joe Greener <[email protected]>

Updates for Julia 0.7/1.0 (#8)

github.com/BioJulia/SubstitutionModels.jl - f63583244656b6568b75813cd6f12e1012707694 authored about 6 years ago by Justin Angevaare <[email protected]>

Fixup documentation

github.com/BioJulia/BioSequences.jl - 19a8dfab5875cee937cbb34c94aeaee28e7a8d12 authored about 6 years ago by Ben J. Ward <[email protected]>

Version 1.0 changes (#42)

github.com/BioJulia/BioSequences.jl - f4fcf6368f9157d7393436d3689bc1f11d4054da authored about 6 years ago by Ben J. Ward <[email protected]>

Update README.md

github.com/BioJulia/BioSymbols.jl - 286fe1bc60d9888db6c98d19766b4de6bce812e9 authored about 6 years ago by Ben J. Ward <[email protected]>

Update README.md

github.com/BioJulia/BioSymbols.jl - c4c6982db67e7ccfa01efca8401a081d093cf6c8 authored about 6 years ago by Ben J. Ward <[email protected]>

delete .DS_Store

github.com/BioJulia/IntervalTrees.jl - 2f63a6c73b1bf872ab7bccd859e581f548eba2d2 authored about 6 years ago by Kenta Sato <[email protected]>

run CI on Julia 1.0 as well (#45)

github.com/BioJulia/IntervalTrees.jl - ff24f3622ff7a1c7fa65366193ec2cb34daeb6cd authored about 6 years ago by Kenta Sato <[email protected]>

modernize inbounds style (#44)

github.com/BioJulia/IntervalTrees.jl - a45870b2097f4b53cd94dfe7a8c5dcd36457f0d4 authored about 6 years ago by Kenta Sato <[email protected]>

Add conversion between DNA and RNA symbol types (#31)

github.com/BioJulia/BioSymbols.jl - d9b90db5536b16413229491d3558b1ceb928c0b7 authored about 6 years ago by Ben J. Ward <[email protected]>

Merge pull request #4 from joels94/master

Release v0.1.0

github.com/BioJulia/MMTF.jl - 418c37e30fee67a32aff18baa8cce6e8ae4df3b5 authored about 6 years ago by Joel S <[email protected]>

Release v0.1.0

github.com/BioJulia/MMTF.jl - d8af7e8086de6614d83779b7ec022df1b046c94a authored about 6 years ago by Joel S <[email protected]>

Move functions

github.com/BioJulia/BioCore.jl - 7d90e24e023eb55970067dc1005bf85fee1f87b2 authored about 6 years ago by Ben J. Ward <[email protected]>

Move read, iterate, and tryread to IO.jl

github.com/BioJulia/BioCore.jl - 6a4022071d3394149e790bc220cb5f25e5d823d7 authored about 6 years ago by Ben J. Ward <[email protected]>

use CodecZlib in place of Libz

github.com/BioJulia/BGZFStreams.jl - 37f33e0416ce7c76768854602a2e7e7fecbd4781 authored about 6 years ago by Kenta Sato <[email protected]>

drop Compat.jl

github.com/BioJulia/BGZFStreams.jl - ef4d393454069d7721532cc1abbab084777c4062 authored about 6 years ago by Kenta Sato <[email protected]>

Fix a few more deprecations.

github.com/BioJulia/BGZFStreams.jl - 7c513f206b045201873327d868b0fccef683e508 authored about 6 years ago by Daniel C. Jones <[email protected]>

Fix a deprecation (Void -> Cvoid)

github.com/BioJulia/BGZFStreams.jl - cf334309d4c991f2a3d00e62cca93fcd23048adc authored about 6 years ago by Daniel C. Jones <[email protected]>

Drop julia 0.6 support.

github.com/BioJulia/BGZFStreams.jl - 91e823300f68a270bee38f08ae45a4d9f6eaab45 authored about 6 years ago by Daniel C. Jones <[email protected]>

update CI scripts

github.com/BioJulia/BGZFStreams.jl - d35108caed5f3be2411260749e393ef2722e7718 authored about 6 years ago by Kenta Sato <[email protected]>

Merge pull request #30 from BenJWard/julia1

Julia 1.0 prep

github.com/BioJulia/Codecs.jl - 3d981d5af6ac7983832bd9ad89291a9bec515e99 authored about 6 years ago by Randy Zwitch <[email protected]>

Restore nightly testing

github.com/BioJulia/Codecs.jl - 7465b1dfc618b9008eeb0dd8b49fc531720fbf33 authored about 6 years ago by Ben J. Ward <[email protected]>

Test 1.0 on travis

github.com/BioJulia/Codecs.jl - 7e45025f2f832af5bd074c608142e965130683b0 authored about 6 years ago by Ben J. Ward <[email protected]>

Merge pull request #7 from BioJulia/fbot/deps

Fix deprecations

github.com/BioJulia/IndexableBitVectors.jl - 5f3a69a85bf9db2e274ca0a470341547711fbdc6 authored about 6 years ago by Ben J. Ward <[email protected]>

Merge pull request #5 from BioJulia/rollout-contributing

Contributing files rollout

github.com/BioJulia/IndexableBitVectors.jl - 25d77a14a275f2c579aec0a07c4f1f48259f4039 authored about 6 years ago by Ben J. Ward <[email protected]>

Merge pull request #6 from dcjones/julia1

Julia 1.0 compatibility fixes.

github.com/BioJulia/IndexableBitVectors.jl - c612cd25e280dc1551e89a9f779ed047c0b8f570 authored about 6 years ago by Ben J. Ward <[email protected]>

Update travis and remove compat use

github.com/BioJulia/IndexableBitVectors.jl - d72a67ac0cc320fb62d134f4188beaa503c130b4 authored about 6 years ago by Ben J. Ward <[email protected]>

Comment out some lines of Ragel.jl

With a view to completely removing them later, I don't think they are
used in BioJulia codebases...

github.com/BioJulia/BioCore.jl - e9d6eb7297946dac4b33ffc33df670fb1aab92e0 authored about 6 years ago by Ben J. Ward <[email protected]>

Remove Nullables from REQUIRE

github.com/BioJulia/BioCore.jl - 600fa9a0449974768f3c31af0c471a25f5805e56 authored about 6 years ago by Ben J. Ward <[email protected]>

A few julia 1.0 fixes. (#18)

github.com/BioJulia/BioCore.jl - 139dbeb1fb372fb75856e8ff01d2e6e99f8f4ec7 authored about 6 years ago by Daniel C. Jones <[email protected]>

Fix deprecations

github.com/BioJulia/IndexableBitVectors.jl - 5aff5f5b0cadc4d044282dff251dc7313c14ef07 authored about 6 years ago by femtocleaner[bot] <femtocleaner[bot]@users.noreply.github.com>

Update CHANGELOG

github.com/BioJulia/BioSymbols.jl - cb011e81ac740e169ecfa409ca8c3ac249335629 authored about 6 years ago by Ben J. Ward <[email protected]>

A few more julia 1.0 fixes. (#30)

* Remove testing for julia v0.6

* Remove use of Nullables (#25)

Prior to julia 1.0 (and 0....

github.com/BioJulia/BioSymbols.jl - d5d77db4bdf35f9eda2d656ce4571ded02d3e789 authored about 6 years ago by Daniel C. Jones <[email protected]>

Remove NEWS file

github.com/BioJulia/GeneticVariation.jl - 255572700b3dcf1087c6afc79fb88769dba84183 authored about 6 years ago by Ben J. Ward <[email protected]>

Update doc files

github.com/BioJulia/GeneticVariation.jl - 8997176dcdcec554456a5b2f5f274f0bfa9bbb06 authored about 6 years ago by Ben J. Ward <[email protected]>

Update project files

github.com/BioJulia/GeneticVariation.jl - a709b36570632532f8804a28ad96b65da21b6d66 authored about 6 years ago by Ben J. Ward <[email protected]>

Update CI files

github.com/BioJulia/GeneticVariation.jl - 50bc0d590a831287d99625bb18456b4f74967be4 authored about 6 years ago by Ben J. Ward <[email protected]>

Fix automa version

github.com/BioJulia/BioSymbols.jl - efe94bdc9962b45effb53aa63b07e1a239acb003 authored about 6 years ago by Ben J. Ward <[email protected]>

Changes for Julia v0.7 / v1.0 (#28)

* Replace sticker.svg with optimized version

* Remove testing for julia v0.6

* Require jul...

github.com/BioJulia/BioSymbols.jl - 934421efb91c96d50ee854cf81e52d04b1232817 authored about 6 years ago by Ben J. Ward <[email protected]>

Drop julia 0.4-0.6 support.

github.com/BioJulia/IndexableBitVectors.jl - c13e35cdd3db180d9daedf90a3d63a82e420752c authored about 6 years ago by Daniel C. Jones <[email protected]>

Julia 1.0 compatibility fixes.

github.com/BioJulia/IndexableBitVectors.jl - 2f5b6b970e9574bc5d9fff0d1c1367d1df36c5d4 authored about 6 years ago by Daniel C. Jones <[email protected]>

Version 1.0 changes (#65)

* Adjust .travis.yml and REQUIRE

* Change syntax to latest julia

* Correct travis

* Add...

github.com/BioJulia/Libz.jl - 5b6e825f67bb72b528fa85a78fdd6ba0c1d5c724 authored about 6 years ago by Ben J. Ward <[email protected]>

Merge branch 'master' of github.com:BioJulia/BioCore.jl

github.com/BioJulia/BioCore.jl - 9762d4d4fc34764b92b8cb0028b9b524fe0587d0 authored about 6 years ago by Ben J. Ward <[email protected]>

Update changelog

github.com/BioJulia/BioCore.jl - 8265abe4b2d87f02b21c16c563619674fbf1aff8 authored about 6 years ago by Ben J. Ward <[email protected]>

Julia 0.7/1.0 changes (#17)

github.com/BioJulia/BioCore.jl - 41b2c7b5a33e5e580fc63234a49bba36f726979b authored about 6 years ago by Ben J. Ward <[email protected]>

Start work on module

github.com/BioJulia/MicrobiomePlots.jl - 54524a23211658510cd66bf3b28a893eb748e54e authored about 6 years ago by Kevin Bonham <[email protected]>