BioJulia commits | Ecosyste.ms: OpenCollective

Merge pull request #8 from BioJulia/dev

Finish biopython/bioconductor sections, add initial 'installing julia/biojulia' sections

github.com/BioJulia/BioJuliaDocs - bb3686348977c80d36136391f72999fbe3e37e1f authored over 1 year ago

finish biopython/bioconductor sections, add initial 'installing julia/biojulia' section

github.com/BioJulia/BioJuliaDocs - ecc13ab04bb42be1e4660d39db7336b995845600 authored over 1 year ago

changes from code review

github.com/BioJulia/Contributing - b62ed3bbcf234260c40565b2bce2f77e0a6fff11 authored over 1 year ago

update changelog

github.com/BioJulia/Contributing - a2fb208b97cadcc6906999641b186c5911a2aea4 authored over 1 year ago

update issue and PR templates

github.com/BioJulia/Contributing - aacc38a88caa066097fc68860a5994fa835b0279 authored over 1 year ago

update Humans

github.com/BioJulia/Contributing - de1face48da9d57e333d63b61668b59241de3101 authored over 1 year ago

prepare demos for next version

github.com/BioJulia/BioMakie.jl - f54a4f3ddda3acc8f8a31ee122e4d2d938569a2f authored over 1 year ago

remove prefix?

github.com/BioJulia/biojulia.github.io - 23957a3da445915e8d023e2a9890defcbc12940d authored over 1 year ago

work on build

github.com/BioJulia/biojulia.github.io - e6fd6f054676f5d14c8f4dae0ae59fde7eb2f4c1 authored over 1 year ago

fix build?

github.com/BioJulia/biojulia.github.io - f4e32966769cc9104e363e3d0e2b7d92a168e61d authored over 1 year ago

Update README.md

github.com/BioJulia/biojulia.github.io - 7a5925430a89616078b299a47ce23bc63a0ba444 authored over 1 year ago

Merge pull request #16 from BioJulia/franklin

Remake website with Xranklin

github.com/BioJulia/biojulia.github.io - f7572a9428bef30579abfbcdfd77de65c1256d17 authored over 1 year ago

Merge pull request #7 from BioJulia/biojulia-update

Biojulia update

github.com/BioJulia/BioJuliaDocs - 867967982b24de29b5db9e66a7dabf5e36c69296 authored over 1 year ago

ignore cache

github.com/BioJulia/biojulia.github.io - bdf9b687a357932d830921b5ba03b02b5d7153ac authored over 1 year ago

recreate getting started

github.com/BioJulia/biojulia.github.io - 0257f24fc543117fec043d5c68c784dfe548fe5e authored over 1 year ago

markdown styles (esp sembr)

github.com/BioJulia/BioJuliaDocs - 91b0816092dd11dfb32e11033e14ce504dbde785 authored over 1 year ago

update links

github.com/BioJulia/BioJuliaDocs - 240272fb138fc2e3538fd852a9ceab41a663d81b authored over 1 year ago

Update README.md (#8)

github.com/BioJulia/SingleCellProjections.jl - 27ed5541d551dae23057845b7e25c24f44d486c2 authored over 1 year ago

Add old post with Markdown

github.com/BioJulia/biojulia.github.io - e607fce8ee14262325dae8146ca91dc5e181b1d2 authored over 1 year ago

add Literate example

github.com/BioJulia/biojulia.github.io - 9fced9aad0cc50be2b4ffd4d752c79103725ba52 authored over 1 year ago

ignore build

github.com/BioJulia/biojulia.github.io - 6add37ec6ebba6fcfb0651e9d42bc14af292c336 authored over 1 year ago

bare bones

github.com/BioJulia/biojulia.github.io - 00cc96050b4a2cc009e598359b455bf4ea3a92b9 authored over 1 year ago

remove latex fun

github.com/BioJulia/biojulia.github.io - 435322764b168dc98bff6f4ee548f866e90b5f29 authored over 1 year ago

initial template

github.com/BioJulia/biojulia.github.io - 83ee71a79941ff8ea43b3de227b822a93962c6e9 authored over 1 year ago

Merge pull request #15 from BioJulia/rewrite-prep

Rewrite prep

github.com/BioJulia/biojulia.github.io - 65f44bc83d6b91863fb85afacb4c2b20e409ac0d authored over 1 year ago

remove retro from kevin

github.com/BioJulia/biojulia.github.io - 40e6229837aca98ca1d342f01c39d2fa544f6c89 authored over 1 year ago

update images

github.com/BioJulia/biojulia.github.io - 693be2deb988ee3381d59ded9165ba0012ba0db3 authored over 1 year ago

rename

github.com/BioJulia/biojulia.github.io - c5a30b08c81f5d82eccbd5550d1e61f3929dd6b7 authored over 1 year ago

Merge pull request #19 from M-PERSIC/master

Enable documenter-dark theme, add minimum compat entries for docs dependencies

github.com/BioJulia/ReadDatastores.jl - 52741ee57dfc456fffee97de36153fb1a53c4679 authored over 1 year ago

msa inspect bugfix, protosyn deps

github.com/BioJulia/BioMakie.jl - 24e96404ba2d34b5f29fc513264f21c3025a3ad6 authored over 1 year ago

Merge pull request #548 from kool7d/master

workflows or something?

github.com/BioJulia/BioMakie.jl - e539bdd397fda715be459e86e148da3909b6fc06 authored over 1 year ago

Merge pull request #29 from CiaranOMara/hotfix/ensure_buffered_data

Correct `ensure_buffered_data`

github.com/BioJulia/BGZFStreams.jl - bf71956a81a7d4affdcb422bd2686f119a900e1b authored over 1 year ago

Merge pull request #547 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - c9a1ea77dcace7c28b17200f52d69edb903e4410 authored over 1 year ago

msa selection

github.com/BioJulia/BioMakie.jl - e1b3ee309160a3c7d3fbaf4523739fc7ddece919 authored over 1 year ago

Merge branch 'release/v0.2.3'

github.com/BioJulia/GFF3.jl - e3e92aacacf1da187fc1b0d42cf464c44bded7ae authored over 1 year ago

Merge branch 'master' into develop

github.com/BioJulia/GFF3.jl - a8fa0dd932783a634b89263bfe749d03c179fe23 authored over 1 year ago

structure selection and fixes

github.com/BioJulia/BioMakie.jl - 0da714ab8929e77df23a108194534f5ad01583dd authored over 1 year ago

fix headers, Biopython lowercase

github.com/BioJulia/BioJuliaDocs - f1340a905b077898b6e3e0f917e9817a79e8eb19 authored over 1 year ago

more fixes to the Comparisons section

github.com/BioJulia/BioJuliaDocs - 68c158ca2febdc3ccfcccf8c57217c1fb1a2d5dd authored over 1 year ago

Flesh out Python package equivalents

github.com/BioJulia/BioJuliaDocs - 55b7dceee94d1e25833e2d5cbc0adf22b9bd8939 authored over 1 year ago

Flesh out R comparison, some README additions

github.com/BioJulia/BioJuliaDocs - 34f272f36b7d117f7c4b9e2057634b7fa0ca40d0 authored over 1 year ago

More BioPython fixes

github.com/BioJulia/BioJuliaDocs - 93a69acf8e0cbf9e4f79c85eadcfa43ec2605d7f authored over 1 year ago

BioPython section fixes

github.com/BioJulia/BioJuliaDocs - 7cf2e63ffc933d3e8d8af4eece30f1e13fb7e6fc authored over 1 year ago

Begin comparisons section, add BioPython entry

github.com/BioJulia/BioJuliaDocs - 708e2d2954af1f8d70c21da346c47545b4df1554 authored over 1 year ago

Merge pull request #546 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - 206eed7d0816b1fdcd9b4f931d5c7554027b023b authored over 1 year ago

docs2

github.com/BioJulia/BioMakie.jl - 5a67abd3f0f6c8faa896bc9123d8fdd4d1c9caa3 authored over 1 year ago

docs1

github.com/BioJulia/BioMakie.jl - 1ac170fe4219efe5feb40b7b4ae302f376105495 authored over 1 year ago

Update and rename ci.yml to CI.yml

github.com/BioJulia/BioMakie.jl - f7d3406fc9ebdd253187e4485308315d3db0e996 authored over 1 year ago

Merge pull request #545 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - a07d81cb95f22336bf9b9ac712eafbfcf91a572f authored over 1 year ago

imagecore compat

github.com/BioJulia/BioMakie.jl - 70f024289e7e5999405a8f9ad1923ce2ce5419dd authored over 1 year ago

imageshow compat

github.com/BioJulia/BioMakie.jl - 946a865308edefc2c80302b0cff275acdc7560aa authored over 1 year ago

Merge pull request #542 from kool7d/dev

fix project

github.com/BioJulia/BioMakie.jl - c6a9c818e8faf3a9c626886ab49030192fb3e277 authored over 1 year ago

fix project

github.com/BioJulia/BioMakie.jl - d23921eb6a520381b47b0b000b670bfa69750a4e authored over 1 year ago

Merge pull request #541 from kool7d/dev

tweak kwargs

github.com/BioJulia/BioMakie.jl - 9e0149adea8083fd50c1827f89cbada286bf4848 authored over 1 year ago

tweak kwargs

github.com/BioJulia/BioMakie.jl - 265cc7f1dd2add15495dbaa085e0ac0cdffdf5bb authored over 1 year ago

Merge pull request #540 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - cacfe72fc72e082437ba43020e25d527e861be98 authored over 1 year ago

add docs back in

github.com/BioJulia/BioMakie.jl - 427a8f00e02b239fd7753336b9ecd15cf02cf0ce authored over 1 year ago

testfix

github.com/BioJulia/BioMakie.jl - 17fe75f3407344260896a6cd5e03ef1da2131859 authored over 1 year ago

Merge pull request #539 from kool7d/dev

docs again 2

github.com/BioJulia/BioMakie.jl - 06899818b810518c7dd551900b314cb446618ef5 authored over 1 year ago

docs again 2

github.com/BioJulia/BioMakie.jl - dc394286c852e3ce4a0fa94887f4b3580a8f2e7a authored over 1 year ago

Merge pull request #538 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - 10ddeb8f2c4a5fe66e31b8a69437f0d52ffb40db authored over 1 year ago

docs again

github.com/BioJulia/BioMakie.jl - 05b3bc24ab3d9cea83a54577cd8283a055e4dff3 authored over 1 year ago

remake docs

github.com/BioJulia/BioMakie.jl - 354bed52e6e59b048b22c8ed8a703e0e792a786e authored over 1 year ago

Update make.jl

github.com/BioJulia/BioMakie.jl - ed74f44961a4a48add57389a7e70fc8312bc380f authored over 1 year ago

documenter pls

github.com/BioJulia/BioMakie.jl - 7851d6dc30d30ca5b5c519de24ff68edaf7294a5 authored over 1 year ago

try fix docs 1

github.com/BioJulia/BioMakie.jl - 87bf6300ca1503111cd1f958915c2a800e15845f authored over 1 year ago

compilation problem test

github.com/BioJulia/BioMakie.jl - a1140dbf884b98f5c7b741359279071dfec1235e authored over 1 year ago

misplaced `$`

github.com/BioJulia/BioMakie.jl - 9980a25f7490ce90d6d53778ff678e665ac05c64 authored over 1 year ago

bond fixes, no Observable inspect label

github.com/BioJulia/BioMakie.jl - ee6311332f0d0d8e17d49eb6d89f90519a813cbf authored over 1 year ago

Migrate to Automa v1

github.com/BioJulia/FASTX.jl - 45854a40c6f6e8bcadd3b16ac5ed080c5fd809c9 authored over 1 year ago

Add validator convenience function

github.com/BioJulia/Automa.jl - 64abea8d6aa6f0a476bfe56908007c1d79fbdf55 authored over 1 year ago

Add default error in generated reader function

github.com/BioJulia/Automa.jl - 074d6af4de925fa19caea5fe96c3c521447f55db authored over 1 year ago

Disable SIMD capability

I've come to the conclusion that Julia does not make it possible to robustly
check what CPU inst...

github.com/BioJulia/Automa.jl - 887ebb5cb4bf38b52a6df6103bbb029ccc392e8a authored over 1 year ago

Comment generate_reader better

github.com/BioJulia/Automa.jl - fce5489e3d2584ac78fb00a71b3f180f448444fe authored over 1 year ago

Saner default for p_eof and p_end

github.com/BioJulia/Automa.jl - 49004a6368d8f3806dc79067cbc461b12d1b5e8d authored over 1 year ago

Fix warnings when running tests

github.com/BioJulia/Automa.jl - 666c8b4f8afd11ad9b0f16a6db30ec38ad7922e6 authored over 1 year ago

Add check for invalid RE.action keys

nfa2dfa now errors if any RE object has a .actions field with an unsupported
key. This prevents ...

github.com/BioJulia/Automa.jl - 74ef3d9b83ac8e0c001ca4c4caa1741978f32b8e authored over 1 year ago

Add todo to gitignore

github.com/BioJulia/Automa.jl - d759de2d91141476b89328c010e9c6cb50858027 authored over 1 year ago

Export user-facing names

One of the issues with using Automa is that its lack of exports makes it unclear
what is interna...

github.com/BioJulia/Automa.jl - e1bfb7566a25f721c25130086fdb52e0d5f26eef authored over 1 year ago

Remove SIMD and inline generator

Honestly, four generators and a tokenizer was excessive.
Inline generator was probably not reall...

github.com/BioJulia/Automa.jl - 563c7dfd5650775d4fe4d864d584cb293deef610 authored over 1 year ago

Check preconditions before declaring NFA ambiguous

If two edges in equivalent paths have distinct preconditions, these could be
used to distinguish...

github.com/BioJulia/Automa.jl - c2b23fe7842d3a9e160b0954bcbd9abd0bbd1a5d authored over 1 year ago

Update FASTA example

github.com/BioJulia/Automa.jl - ddcf22f58d16492b84fdd996934eb9f65f2199f6 authored over 1 year ago

Tweak: Allow | and & ops b/w chars/str and RE

github.com/BioJulia/Automa.jl - 4a1ee2deb76717f1f3d3dbbc7bce208bd411405f authored over 1 year ago

Add input error code to generate_code function

The user probably wants to use the input error code in most use cases, except
when running a mac...

github.com/BioJulia/Automa.jl - 5af00fec323c36f52376faf1432c68bc7a566712 authored over 1 year ago

Migrate from SnoopPrecompile to PrecompileTools

github.com/BioJulia/Automa.jl - cc9fb668f79ee13f14d53a2892790a5c26f45ed2 authored over 1 year ago

Do not make TranscodingStreams an extension

Since Automa doesn't just extend an existing function but adds a new function
based on Transcodi...

github.com/BioJulia/Automa.jl - cbd1568d2736e595e7f321cae53475bc983b38b6 authored over 1 year ago

Rename generate_validator_function

github.com/BioJulia/Automa.jl - 88ec2946b3096785df5e8fc986221edd60ced67a authored over 1 year ago

Remove Stream module

This module doesn't make any sense in v1 for two reasons:
First, we can not longer consider the ...

github.com/BioJulia/Automa.jl - 83796edc14ed46a0067d2f28c85a19dc66ed2dcf authored over 1 year ago

Also check ambiguities for final and all actions

An oversight in the ambiguity check meant that actions placed on non-epsilon
edges were accident...

github.com/BioJulia/Automa.jl - 6a4da4876640fe17f70d262d6f8084ec69f86ed4 authored over 1 year ago

Remove last Stream non-pseudomacros

The existence of these as real macros does not actually work with arbitrary
`CodeGenContext`s.
T...

github.com/BioJulia/Automa.jl - eb2b2610ac5ee50084587034d2c871275b25417b authored over 1 year ago

Remove loop unrolling

github.com/BioJulia/Automa.jl - 6f1f6f9c29cc901758a21e831222cd26e00fcf39 authored over 1 year ago

Update README.md

github.com/BioJulia/Automa.jl - efd3344d22e8ed9d571a6b7e6dd61cf2080dd257 authored over 1 year ago

Remove report_col kwarg

Instead of buffering an entire line, simply keep track of the number of columns
cleared from the...

github.com/BioJulia/Automa.jl - 09a124b6557a438a38a422a8144d63182ecd9d25 authored over 1 year ago

Add generate_io_validator

github.com/BioJulia/Automa.jl - b7ef8ce13b76ebd5e1d5f49f3c8e58530c833658 authored over 1 year ago

Allow CodeGenContext to be elided

github.com/BioJulia/Automa.jl - e66a282646495166c9931945773abc5f2145dc4a authored over 1 year ago

Export machine2dot

github.com/BioJulia/Automa.jl - 9d2222e2d478361218d3e97a9ae34fae844b33d8 authored over 1 year ago

Make generate_buffer_validator goto into kwarg

github.com/BioJulia/Automa.jl - 36fcaa50d340a531c347a4a587d300cc6f22b00e authored over 1 year ago

Fix bug in execute_debug

github.com/BioJulia/Automa.jl - 7d2cf2d4896ee2d9db424484d3acbeae0ab29be4 authored over 1 year ago

Add tests for regex set operations

github.com/BioJulia/Automa.jl - cb5054eaeb4479a2df8914b7e94b070d24318c2b authored over 1 year ago

Fix Project

github.com/BioJulia/Automa.jl - d032b16538e19e420295aea1dfeb20d8d8544dc5 authored over 1 year ago