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BioJulia

Bioinformatics and Computational Biology in Julia
Collective - Host: opensource - https://opencollective.com/biojulia - Website: https://biojulia.net - Code: https://github.com/BioJulia

doctests to @repl due to ansi issues

Separate tests, fix documentation bug

github.com/BioJulia/SubstitutionModels.jl - 881825eb07ccd14cb8323a017551e655d38ba062 authored about 3 years ago by Justin Angevaare <[email protected]>
Constructor safety consistency; fix docs

github.com/BioJulia/SubstitutionModels.jl - fd5380c3a0de91eaf9eb78dd4af7a62150330142 authored about 3 years ago by Justin Angevaare <[email protected]>
Merge pull request #27 from BioJulia/ci-update

Fix package CI/update actions, and update [compat]

github.com/BioJulia/SubstitutionModels.jl - 929ddbe429985c6c3a36c1abcef77c745155441b authored about 3 years ago by Justin Angevaare <[email protected]>
Merge branch 'ci-update' of https://github.com/BioJulia/SubstitutionModels.jl into ci-update

github.com/BioJulia/SubstitutionModels.jl - 3182f118a3730ea0f8efba70c389d730344dd375 authored about 3 years ago by Justin Angevaare <[email protected]>
Update gh actions/use actions for testing

github.com/BioJulia/SubstitutionModels.jl - 87f8716cee9d047e994e4d4ec0c7a5b741a9d1f0 authored about 3 years ago by Justin Angevaare <[email protected]>
Update gh actions/use actions for testing

github.com/BioJulia/SubstitutionModels.jl - 4b9b9836f72792089d1e253332a045925923d9bf authored about 3 years ago by Justin Angevaare <[email protected]>
Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

github.com/BioJulia/PopGen.jl - 8d3566663204e4ddf03f68a1475577793e9f5aa8 authored about 3 years ago by Pavel Dimens <[email protected]>
Update FstPermutations.jl

github.com/BioJulia/PopGen.jl - 196213518e463b0be5758a2381eafd34db89fc26 authored about 3 years ago by Pavel V. Dimens <[email protected]>
CompatHelper: add new compat entry for Meshing at version 0.5, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 8ba4238f04121b170cf60e5bd5171e9740ca0992 authored about 3 years ago by CompatHelper Julia <[email protected]>
Merge remote-tracking branch 'origin/dependabot/github_actions/codecov/codecov-action-2.0.3'

github.com/BioJulia/BioMakie.jl - 61304af50392032df04706e314c45600faaabd08 authored about 3 years ago by Daniel Kool <[email protected]>
Merge remote-tracking branch 'origin/compathelper/new_version/2021-08-23-00-45-49-158-03578038350'

github.com/BioJulia/BioMakie.jl - fb75a7bf52b1071c7257bd0dc7e98b5097c62037 authored about 3 years ago by Daniel Kool <[email protected]>
Bump codecov/codecov-action from 1.5.0 to 2.0.3

Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 1.5.0 to 2.0.3.
-...

github.com/BioJulia/BioMakie.jl - e10d9eb4b064bf75a78b316c1df5613177c9f6dd authored about 3 years ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
docsnmore1

github.com/BioJulia/BioMakie.jl - 0ae58ca772437d944bb886c2a0eb3653be789089 authored about 3 years ago by kool7d <[email protected]>
Full rewrite

github.com/BioJulia/SequenceVariation.jl - 87277268f67564a87580745e5be6efb86a73abe0 authored about 3 years ago by Jakob Nybo Nissen <[email protected]>
CompatHelper: bump compat for MolecularGraph to 0.10, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 917cf9a0d65049757d9b23cf5e703b4f1c3093bf authored about 3 years ago by CompatHelper Julia <[email protected]>
Merge pull request #367 from kool7d/compathelper/new_version/2021-08-18-00-51-32-421-02405385437

CompatHelper: bump compat for Meshes to 0.17, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 46ed2d85aa1329521421637b3155ad99ae6237c5 authored about 3 years ago by Dan Kool <[email protected]>
Merge pull request #366 from kool7d/compathelper/new_version/2021-08-18-00-51-23-261-02555444010

CompatHelper: add new compat entry for ComponentArrays at version 0.11, (keep existing compat)

github.com/BioJulia/BioMakie.jl - ba22d676bed043788b0af6e0109cc59c142a45f3 authored about 3 years ago by Dan Kool <[email protected]>
Merge remote-tracking branch 'origin/compathelper/new_version/2021-08-18-00-51-36-537-02288039854'

github.com/BioJulia/BioMakie.jl - 4ac37354da4740f0e195793972f8b6214a79f1cf authored about 3 years ago by Daniel Kool <[email protected]>
Revert "x2"

This reverts commit 7c0272351545896fdc1cd6d3659238cd7ac23fc5.

github.com/BioJulia/BioMakie.jl - 41fea8851b86e897870c231cd4343260f7cf1d30 authored about 3 years ago by Daniel Kool <[email protected]>
Merge remote-tracking branch 'origin/master'

github.com/BioJulia/BioMakie.jl - 7395bf04e67039b345fe54c6070ce04f3e7ed7c7 authored about 3 years ago by Daniel Kool <[email protected]>
x2

github.com/BioJulia/BioMakie.jl - 7c0272351545896fdc1cd6d3659238cd7ac23fc5 authored about 3 years ago by Daniel Kool <[email protected]>
x1

github.com/BioJulia/BioMakie.jl - 39937508a1a6b091ed09927b3aba2543062ad04d authored about 3 years ago by kool7d <[email protected]>
Merge pull request #85 from jakobnissen/finallookup

Optimize away dict lookup when possible

github.com/BioJulia/Automa.jl - 46d6d336b576fd2dbc25b84e587d797478436631 authored about 3 years ago by Jakob Nybo Nissen <[email protected]>
Optimize away dict lookup when possible

github.com/BioJulia/Automa.jl - 3964b0d1d25ecf31e0fd1bf2be8ab78e297dd03c authored about 3 years ago by Jakob Nybo Nissen <[email protected]>
CompatHelper: add new compat entry for StaticArrays at version 1, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 90b9de0537832f9d53f7c9ccf558c86bb19ec08a authored about 3 years ago by CompatHelper Julia <[email protected]>
CompatHelper: bump compat for Meshes to 0.17, (keep existing compat)

github.com/BioJulia/BioMakie.jl - ac717a78a2adc07de1a6c66fbda5098b94069a24 authored about 3 years ago by CompatHelper Julia <[email protected]>
CompatHelper: add new compat entry for ComponentArrays at version 0.11, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 50245437afee35dce8cb49e81827818c8163982d authored about 3 years ago by CompatHelper Julia <[email protected]>
up1

github.com/BioJulia/BioMakie.jl - 1529c1a4b87244aae1c73ad4c561163aa0ac05de authored about 3 years ago by kool7d <[email protected]>
Update Project.toml

github.com/BioJulia/PopGenCore.jl - 1fa96548bcb6ee6595aecda3ddba567f92914025 authored about 3 years ago by Pavel V. Dimens <[email protected]>
add isbinary conditional

github.com/BioJulia/PopGenCore.jl - 3a2c29ea31344429b38068c53197d6097f7b4c9e authored about 3 years ago by Pavel Dimens <[email protected]>
Merge pull request #365 from kool7d/dev

docc2

github.com/BioJulia/BioMakie.jl - 8a2f0e14ad11a6de4a1800c9cff446dcab0b9d16 authored about 3 years ago by Dan Kool <[email protected]>
docc2

github.com/BioJulia/BioMakie.jl - 33fba98328a6ca0829b265af94149a4dd5c5da1e authored about 3 years ago by kool7d <[email protected]>
Merge pull request #364 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - c928a73c0d6755a991e731f71ba36c66fee90403 authored about 3 years ago by Dan Kool <[email protected]>
Merge branch 'dev' of https://github.com/kool7d/BioMakie.jl into dev

github.com/BioJulia/BioMakie.jl - 770317b5ea8e7f191b5ff7554fa5a3cf93544166 authored about 3 years ago by kool7d <[email protected]>
docc

github.com/BioJulia/BioMakie.jl - 679ff1072e8e50edffc073a42ae42a8191cfb753 authored about 3 years ago by kool7d <[email protected]>
Merge pull request #363 from kool7d/compathelper/new_version/2021-08-15-00-50-23-919-326223036

CompatHelper: add new compat entry for "Pluto" at version "0.15"

github.com/BioJulia/BioMakie.jl - 428cbb07b699cf350ffb2ed54e477711a66e8c96 authored about 3 years ago by Dan Kool <[email protected]>
Merge branch 'master' into compathelper/new_version/2021-08-15-00-50-23-919-326223036

github.com/BioJulia/BioMakie.jl - aa26f50c50eb703a03a3e4618ca5a9c02dbd0d05 authored about 3 years ago by Dan Kool <[email protected]>
Merge pull request #362 from kool7d/compathelper/new_version/2021-08-15-00-50-17-683-2259655754

CompatHelper: add new compat entry for "PlutoUI" at version "0.7"

github.com/BioJulia/BioMakie.jl - f6737d1c63530bff192e0a475f385b846be4f56a authored about 3 years ago by Dan Kool <[email protected]>
Merge pull request #361 from kool7d/compathelper/new_version/2021-08-15-00-50-09-989-3353653923

CompatHelper: add new compat entry for "LiveServer" at version "0.7"

github.com/BioJulia/BioMakie.jl - e9f1e72d2c44c5ebb6769b7c0c6b5fb9cfdc1471 authored about 3 years ago by Dan Kool <[email protected]>
Merge pull request #360 from kool7d/dependabot/github_actions/JuliaRegistries/TagBot-1.14

Bump JuliaRegistries/TagBot from 1.13.1 to 1.14

github.com/BioJulia/BioMakie.jl - 19f938ab8b7c61a22ef34f228683bb82de60ff17 authored about 3 years ago by Dan Kool <[email protected]>
CompatHelper: add new compat entry for "Pluto" at version "0.15"

github.com/BioJulia/BioMakie.jl - a45aaa96ea6319d00177fbc93d8d9767d981409d authored about 3 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: add new compat entry for "PlutoUI" at version "0.7"

github.com/BioJulia/BioMakie.jl - 791f8ac100159c8c4d19b9710dc910f529ab62c5 authored about 3 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: add new compat entry for "LiveServer" at version "0.7"

github.com/BioJulia/BioMakie.jl - 4967b120edfcdce5b69681a638866800f29d9f5f authored about 3 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Bump JuliaRegistries/TagBot from 1.13.1 to 1.14

Bumps [JuliaRegistries/TagBot](https://github.com/JuliaRegistries/TagBot) from 1.13.1 to 1.14.
-...

github.com/BioJulia/BioMakie.jl - f71fad10af4920b636ea50f638c0dd8cb230320c authored about 3 years ago by dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Merge pull request #359 from kool7d/dev

Update README.md

github.com/BioJulia/BioMakie.jl - 6f23b5ac14599718e325e369f32d10e963823273 authored about 3 years ago by Dan Kool <[email protected]>
Update README.md

github.com/BioJulia/BioMakie.jl - 6c2aba4afd3a76edfbd7fabdb95a23df995eefae authored about 3 years ago by Dan Kool <[email protected]>
Merge pull request #358 from kool7d/dev

up2

github.com/BioJulia/BioMakie.jl - 97d8f240ac271512f504dd675a93faeb272f14b5 authored about 3 years ago by Dan Kool <[email protected]>
up2

github.com/BioJulia/BioMakie.jl - 0df71cc713b296449d16e219a86d2670b8536613 authored about 3 years ago by kool7d <[email protected]>
Merge pull request #357 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - c1a1f3edbbccb5a86ac77c9a15245d4ed0c6bb3c authored about 3 years ago by Dan Kool <[email protected]>
up2

github.com/BioJulia/BioMakie.jl - 91a227314c108c2e080e28f4408ed1edde159e35 authored about 3 years ago by kool7d <[email protected]>
ex2

github.com/BioJulia/BioMakie.jl - 35d745097ba3a1e65c37e0016f1d4b5dfe00abcd authored about 3 years ago by kool7d <[email protected]>
ex1

github.com/BioJulia/BioMakie.jl - c658a781d1653a1b20a4f5746b44e0292d6623ef authored about 3 years ago by kool7d <[email protected]>
fix bug: returning noting

github.com/BioJulia/PopGenCore.jl - 368ae25c69425810cc454256f24afd2dee4e3c7c authored about 3 years ago by Pavel Dimens <[email protected]>
purge reshape references

github.com/BioJulia/PopGenCore.jl - 0c9fbdbd760e383faa6f28524baab0b238e5d28c authored about 3 years ago by Pavel Dimens <[email protected]>
workaround for https://github.com/JuliaLang/julia/issues/33143

github.com/BioJulia/PopGenCore.jl - ef21561e452a46bb67e97d89dcd30be1cb235509 authored about 3 years ago by Pavel Dimens <[email protected]>
fix/update keep tests

github.com/BioJulia/PopGenCore.jl - d91982d84340ccf24e9c3c2971e3495ea7082f4e authored about 3 years ago by Pavel Dimens <[email protected]>
update tests

github.com/BioJulia/PopGenCore.jl - b2ab61b0d67d472e79b99e3aebbc0d9522a5365b authored about 3 years ago by Pavel Dimens <[email protected]>
migrate Conditionals.jl

github.com/BioJulia/PopGenCore.jl - 8695452a7bc58a2e3eff1749f3faacc78aad8394 authored about 3 years ago by Pavel Dimens <[email protected]>
update

github.com/BioJulia/PopGenCore.jl - de106a631d4658a53800aaef44c69fe588f97bdc authored about 3 years ago by Pavel Dimens <[email protected]>
add columncheck

github.com/BioJulia/PopGenCore.jl - 601becef5aa6cdc651b942204acee60eaec2a52b authored about 3 years ago by Pavel Dimens <[email protected]>
force strings

github.com/BioJulia/PopGenCore.jl - b5d650c0f3d58b40484e49fce540d23c4bb7534c authored about 3 years ago by Pavel Dimens <[email protected]>
remove text

github.com/BioJulia/PopGenCore.jl - 05010b1c54dd1140d39d6b7153e3d3b218f90737 authored about 3 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/BioJulia/PopGenCore.jl into dev

github.com/BioJulia/PopGenCore.jl - cb5681275947bd42998f8669fead960947ddea49 authored about 3 years ago by Pavel Dimens <[email protected]>
fix if statement

github.com/BioJulia/PopGenCore.jl - b32e9a5fc8229b2d48587cbfc792d9dd1ab80d77 authored about 3 years ago by Pavel Dimens <[email protected]>
fix reader and add precompile

github.com/BioJulia/PopGenCore.jl - b83e7a88b17ba5923f802ef0e3a40461adb64f9a authored about 3 years ago by Pavel Dimens <[email protected]>
rename genotypes to genodata

github.com/BioJulia/PopGenCore.jl - 584e5fdf1736c16c2319531d28b73b58d6c3580e authored about 3 years ago by Pavel Dimens <[email protected]>
Merge pull request #8 from BioJulia/compathelper/new_version/2021-08-08-00-49-42-076-654269997

CompatHelper: add new compat entry for "StaticArrays" at version "1"

github.com/BioJulia/PopGenCore.jl - cd835788d787cb7dfeeb12aef65767bded7d3cf3 authored about 3 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'dev' into compathelper/new_version/2021-08-08-00-49-42-076-654269997

github.com/BioJulia/PopGenCore.jl - 8e82215e9e7d6516ac716b803184e34eb0363952 authored about 3 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #7 from BioJulia/compathelper/new_version/2021-08-08-00-49-38-974-4170492756

CompatHelper: add new compat entry for "StatsBase" at version "0.33"

github.com/BioJulia/PopGenCore.jl - cb6d25e4245719678068b6a3df294a67a09023f8 authored about 3 years ago by Pavel V. Dimens <[email protected]>
rewritten parser

github.com/BioJulia/PopGenCore.jl - 3daffe234504aa9942cacaee0bc1ef5302be7e7e authored about 3 years ago by Pavel Dimens <[email protected]>
added _SNP and _MSat convenience methods

github.com/BioJulia/PopGenCore.jl - 9229282071cfd4521af9b8862779692da269d908 authored about 3 years ago by Pavel Dimens <[email protected]>
Merge pull request #183 from jakobnissen/docwarnings

Fix documenter warnings about broken links

github.com/BioJulia/BioSequences.jl - 14f551b88d95e9c2c3d06ff3cae384ec2982df1b authored about 3 years ago by Jakob Nybo Nissen <[email protected]>
update readers wtith try...catch

github.com/BioJulia/PopGenCore.jl - 6f694d7c7049294ebece5eb562d045d591fc404d authored about 3 years ago by Pavel Dimens <[email protected]>
add SNP and MSat convenience constants

github.com/BioJulia/PopGenCore.jl - 541ecdf62afd016f1b9d2ab267fff2694ba121f9 authored about 3 years ago by Pavel Dimens <[email protected]>
more robust locus phasing

github.com/BioJulia/PopGenCore.jl - 9532de06249f3479258062262f35f5fb3942cea1 authored about 3 years ago by Pavel Dimens <[email protected]>
CompatHelper: add new compat entry for "StaticArrays" at version "1"

github.com/BioJulia/PopGenCore.jl - 066da4aa8970e811639053774f6498d190ff2552 authored about 3 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: add new compat entry for "StatsBase" at version "0.33"

github.com/BioJulia/PopGenCore.jl - a8a6a5438b92c7c26fa72eb00de16cbeb53ccfda authored about 3 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
doc1

github.com/BioJulia/BioMakie.jl - 2f44f5d86db2ecc421939b758845f28d46b184b9 authored about 3 years ago by kool7d <[email protected]>
testfix

github.com/BioJulia/PopGenCore.jl - 1dde094e9d5d64277d6925a56d2b32c1a9935670 authored about 3 years ago by Pavel Dimens <[email protected]>
vcf precompile path (again)

github.com/BioJulia/PopGenCore.jl - f835b87fad21b291612c9a46fff0189757718691 authored about 3 years ago by Pavel Dimens <[email protected]>
fix path

github.com/BioJulia/PopGenCore.jl - 4f22da614cd45054049a37b2dc51851743762669 authored about 3 years ago by Pavel Dimens <[email protected]>
vcf fixes

github.com/BioJulia/PopGenCore.jl - 56f966f6c65ce9cad90030c5ebe967c31c4a6452 authored about 3 years ago by Pavel Dimens <[email protected]>
update stuff

github.com/BioJulia/PopGenCore.jl - d60cfb96de7b98d69c8c0f6baf0a4b57e939567b authored about 3 years ago by Pavel Dimens <[email protected]>
touch up b/vcf

github.com/BioJulia/PopGenCore.jl - 0c00bc7a3877a5f3361ef7e1ae56e31f793dc3ca authored about 3 years ago by Pavel Dimens <[email protected]>
fixes

github.com/BioJulia/PopGenCore.jl - c99dd1c4082e5b93d177534c5e54026e0bd2a680 authored about 3 years ago by Pavel Dimens <[email protected]>
compress all PooledArray constructors

github.com/BioJulia/PopGenCore.jl - 8b4cc539392a98e4bec37a669daf735050c9de3e authored about 3 years ago by Pavel Dimens <[email protected]>
fix structure parser

github.com/BioJulia/PopGenCore.jl - 78212f5d7fa8ade8101ecb22b54858d71aae8b09 authored about 3 years ago by Pavel Dimens <[email protected]>
Merge pull request #356 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - 0abeb5606f42ce065a9982eec003b89935b78075 authored about 3 years ago by Dan Kool <[email protected]>
Update usage.md

github.com/BioJulia/BioMakie.jl - d802f0650e206ee52e17c231cdc098583757f637 authored about 3 years ago by Dan Kool <[email protected]>
Merge pull request #355 from kool7d/master

sw1

github.com/BioJulia/BioMakie.jl - 3ee1ec9e22ce49c2ed36a359f2e7ff91eb039b31 authored about 3 years ago by Dan Kool <[email protected]>
Merge pull request #354 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - 3a027c39208e495052e0c082e0ef428aa098d028 authored about 3 years ago by Dan Kool <[email protected]>
Update usage.md

github.com/BioJulia/BioMakie.jl - febe8e5d54e314fb75709177c6308642ef0dace8 authored about 3 years ago by Dan Kool <[email protected]>
ss1

github.com/BioJulia/BioMakie.jl - c66170a2532fed50826d7ffb425b5f108a176d63 authored about 3 years ago by kool7d <[email protected]>
change precomp and remove loci/samples in utils

github.com/BioJulia/PopGenCore.jl - 44e871d0447f73ec716c64ecacc01381804a3f96 authored about 3 years ago by Pavel Dimens <[email protected]>
add manipulate tests

github.com/BioJulia/PopGenCore.jl - ae6a6f8122ba4754cd7305330e81abecd00bc3d9 authored about 3 years ago by Pavel Dimens <[email protected]>
cp1

github.com/BioJulia/BioMakie.jl - 2f0d62a1aba85b70520d0293d7fc3aa67a64a682 authored about 3 years ago by kool7d <[email protected]>
Fix documenter warnings about broken links

github.com/BioJulia/BioSequences.jl - c58184ddeaf0951c8baf477186f02a54633f37a0 authored about 3 years ago by Jakob Nybo Nissen <[email protected]>
Update Project.toml

github.com/BioJulia/BioMakie.jl - 6db3b33a0b5ae372c19ca3d928b1c5123a756aab authored about 3 years ago by Dan Kool <[email protected]>
Update Project.toml

github.com/BioJulia/BioMakie.jl - 96a114cbfad44da29699783d8b313302db4acb03 authored about 3 years ago by Dan Kool <[email protected]>
Update Project.toml

github.com/BioJulia/BioMakie.jl - 2fc39b067bb4d5ed756e54655e2d112a145dfbb2 authored about 3 years ago by Dan Kool <[email protected]>