Ecosyste.ms: OpenCollective

An open API service for software projects hosted on Open Collective.

BioJulia

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

Update TagBot workflow

github.com/BioJulia/GFF3.jl - ef5577d7daa00ec217aa66ed2df8526a8c4eec56 authored about 2 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/GFF3.jl - 1a7f99797c1557d4a46785e8ebeeb8edbf305655 authored about 2 years ago by Ciarán O'Mara <[email protected]>
Merge pull request #13 from BioJulia/hotfix/biosequences

Remove BioSequences dependency.

github.com/BioJulia/GFF3.jl - 6ba310e8167203426cbfe1686486dc3a6fc23ed6 authored about 2 years ago by Ciarán O'Mara <[email protected]>
Increment version

github.com/BioJulia/GFF3.jl - 84aa4cc6a58ab6538709f5e308ddce1a8b0a6833 authored about 2 years ago by Ciarán O'Mara <[email protected]>
Remove BioSequences dependency

github.com/BioJulia/GFF3.jl - be9aa29ba25e8ea0449a39a881ad629b09d37651 authored about 2 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'hotfix/2.2.0'

# Conflicts:
# CHANGELOG.md
# Project.toml
# src/submat.jl

github.com/BioJulia/BioAlignments.jl - 782063c0fa02531dfdb62762455eeee93e7f79e2 authored about 2 years ago by Ciarán O’Mara <[email protected]>
Merge pull request #236 from CiaranOMara/feature/findall-doc

Documentation for `findall` method.

github.com/BioJulia/BioSequences.jl - 5542811a412695b5a1cda163c41aabff0e037250 authored about 2 years ago by Ciarán O'Mara <[email protected]>
Suppress output

github.com/BioJulia/BioSequences.jl - 871bba9b669e97bb3ed3ad22da88570ca1daf154 authored about 2 years ago by Ciarán O'Mara <[email protected]>
Tweak nomenclature

github.com/BioJulia/BioSequences.jl - b7223a1c6313c9ee4a717f68d4c11c49b22726ef authored about 2 years ago by Ciarán O'Mara <[email protected]>
Add `findall` to examples

github.com/BioJulia/BioSequences.jl - 5292edb4c7dd34da596cd7a391bb84f0452cfaa1 authored about 2 years ago by Ciarán O'Mara <[email protected]>
Documentation for `findall` method

github.com/BioJulia/BioSequences.jl - fd25505b8e4e390bfd1d097b7f0747322a4cef8c authored about 2 years ago by Ciarán O’Mara <[email protected]>
Merge pull request #237 from CiaranOMara/feature/doctests

- Add doctests to unit tests.
- Include minor doctest corrections.
- Enable checkdocs for buil...

github.com/BioJulia/BioSequences.jl - 1a0abc7743cf38d67aaf76eeeba3aff9b21441e0 authored about 2 years ago by Ciarán O'Mara <[email protected]>
Improve robustness of rand tests (#255)

github.com/BioJulia/BioSequences.jl - 6251d756e3a5c35e6e030a32a69aaf20ace2745f authored about 2 years ago by Jakob Nybo Nissen <[email protected]>
Bump version to 3.1.0

github.com/BioJulia/BioSequences.jl - 16fe17810a3bbf8f0b01398cadf1bd6c9cf03188 authored about 2 years ago by Jakob Nybo Nissen <[email protected]>
Various small doc fixes (#253)

github.com/BioJulia/BioSequences.jl - c3d7b750e8365417cdce52822b63055e0c423398 authored about 2 years ago by Jakob Nybo Nissen <[email protected]>
Bump version (#13)

github.com/BioJulia/BioGenerics.jl - 3c20b77668aacd9a4b47f814cc7992a4d1077e3b authored about 2 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #12 from jakobnissen/dokw

Add varargs and kwargs to T(open(f, ::IO)) methods

github.com/BioJulia/BioGenerics.jl - b99d19cc338fdea07c5bdf40405b9fd4b6be851f authored about 2 years ago by Jakob Nybo Nissen <[email protected]>
start adding rf

github.com/BioJulia/PopGen.jl - a2beea79737ee994d69e60bd4581849feea8afa4 authored about 2 years ago by Pavel Dimens <[email protected]>
add uinquebialleles()

github.com/BioJulia/PopGenCore.jl - 574f94614b3d0c56015a59d43617daed6679d393 authored about 2 years ago by Pavel Dimens <[email protected]>
Update Project.toml

github.com/BioJulia/PopGenCore.jl - d3e954801430f4b4f68199e7e72567ca7fb14605 authored about 2 years ago by Pavel V. Dimens <[email protected]>
Add varargs and kwargs to T(open(f, ::IO)) methods

This allows users to do Reader(GzipDecompressorStream(open(path)), kw=true),
thus making the use...

github.com/BioJulia/BioGenerics.jl - 97d6bcbf79febe93ab18f56cc223dc2e6de3e16b authored about 2 years ago by Jakob Nybo Nissen <[email protected]>
Add getter function entry to CHANGELOG

github.com/BioJulia/BioAlignments.jl - 797c5663749cb5ef3534b35820e68d606ab73848 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Clarify the docstring for alignment(::PairwiseAlignmentResult)

alignment(::AlignedSequence) and alignment(::PairwiseAlignmentResult)
both return an Alignment, ...

github.com/BioJulia/BioAlignments.jl - 54aaab02c98f71cd99c2320d3ca1e6ca221e9b75 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add doctest for sequence(::PairwiseAlignmentResult)

github.com/BioJulia/BioAlignments.jl - 2e3e16d5b93ace0c6e2eb66156f301713b4ced6f authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add sequence getter function for PairwiseAlignment

github.com/BioJulia/BioAlignments.jl - aaa5ecf3b21826bbaf2b657330e394aa5af409ef authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add getter function docs for `AlignedSequence`

github.com/BioJulia/BioAlignments.jl - d7a35a25a730ce4d1ee13625bbb969823613f0e1 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add sequence getter function for PairwiseAlignmentResult

github.com/BioJulia/BioAlignments.jl - 99d6c0dd3c2c02a982c59578f4d1d0a6a3590d28 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add alignment getter function for PairwiseAlignment

github.com/BioJulia/BioAlignments.jl - cb02c85147002f6f9d00896a35510404c2f294d6 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add sequence getter function for AlignedSequence

github.com/BioJulia/BioAlignments.jl - 514541ec7068fa7b45188ddda0a71c59039ce5b6 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add alignment getter function for AlignedSequence

github.com/BioJulia/BioAlignments.jl - 09042be1d737c3fa48d6abbfb3d99c1bd1677111 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
reexport plink

github.com/BioJulia/PopGen.jl - 5bb24c93e02f7c10abf6e8eeef20b2ea8039e69e authored over 2 years ago by Pavel Dimens <[email protected]>
integrate plink

github.com/BioJulia/PopGenCore.jl - 98f6d8b2c2f62d3dd62aca4f717f3f31fb7b8918 authored over 2 years ago by Pavel Dimens <[email protected]>
fix docstring

github.com/BioJulia/PopGen.jl - f4fdf0f2008a3d29e4b95778998e614b04fa66e1 authored over 2 years ago by Pavel Dimens <[email protected]>
replace kinship with new methods

github.com/BioJulia/PopGen.jl - 9de533f42e46d8cf78aa71ad02136dc6ea596061 authored over 2 years ago by Pavel Dimens <[email protected]>
Update downstream.yml

github.com/BioJulia/PopGenCore.jl - 033ba7f3113369291019d2ccc5f2f6d9f0b02b8c authored over 2 years ago by Pavel V. Dimens <[email protected]>
bump to next minor version

github.com/BioJulia/PopGen.jl - bb52f7a087bde10918361569530ec75235e1d649 authored over 2 years ago by Pavel Dimens <[email protected]>
bump to next minor version

github.com/BioJulia/PopGen.jl - c8514c8881c7868332d35db5912b59f58f9c6be3 authored over 2 years ago by Pavel Dimens <[email protected]>
bump to next minor version

github.com/BioJulia/PopGenCore.jl - 6787f72564b9baf5b3ce042dfa7bd265169dfd0c authored over 2 years ago by Pavel Dimens <[email protected]>
error handling to catch incorrect missings

github.com/BioJulia/PopGenCore.jl - 503728404b13403fa9335a40567b2848e1f3971a authored over 2 years ago by Pavel Dimens <[email protected]>
rm deprecated function exports

github.com/BioJulia/PopGenCore.jl - 623348558a975c3050fe82cacae2100b6062383a authored over 2 years ago by Pavel Dimens <[email protected]>
remove deprecated countmatrix calls

github.com/BioJulia/PopGenCore.jl - 364221a701edc8306b02bfcdbb86d938fb761e7f authored over 2 years ago by Pavel Dimens <[email protected]>
Fix variables in generate_reader

The code in generate_reader did not respect the Vars or CodeGenContext.

github.com/BioJulia/Automa.jl - 69d16f5cad2edadef5b9715a32afcebaa480ad09 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
update test

github.com/BioJulia/PopGen.jl - 9ac6cd6ea789cad7e5a4db22de9744e05cbae1b0 authored over 2 years ago by Pavel Dimens <[email protected]>
dispatch on Val() methods

github.com/BioJulia/PopGen.jl - 70eb159a5a7a810dab189b156b3fb6849d6be996 authored over 2 years ago by Pavel Dimens <[email protected]>
nicer dispatch

github.com/BioJulia/PopGen.jl - 115dbf21c68028ef78c98abdf520b73d643466cb authored over 2 years ago by Pavel Dimens <[email protected]>
leverage Val{} dispatch

github.com/BioJulia/PopGenCore.jl - 48d0052eef27f6332d9ac369c4ec8a84d0fff9e4 authored over 2 years ago by Pavel Dimens <[email protected]>
cleanup junk code from yaml

github.com/BioJulia/PopGen.jl - 567dfd24f89740c6897ef058fc97e664d2847700 authored over 2 years ago by Pavel Dimens <[email protected]>
add back all testing deps

github.com/BioJulia/PopGen.jl - 1c85f405ce4f702fe824d7675069cedcb8feac56 authored over 2 years ago by Pavel Dimens <[email protected]>
rm name and such

github.com/BioJulia/PopGen.jl - 89e77938c435ec808ceaf8973f0cedae3825201b authored over 2 years ago by Pavel Dimens <[email protected]>
fix toml

github.com/BioJulia/PopGen.jl - aac551fd6088ae3100a3caed9bd1ed74a1f16807 authored over 2 years ago by Pavel Dimens <[email protected]>
hail mary

github.com/BioJulia/PopGen.jl - 11bddd6239ef9c94ff443109fd8f0c2f6bb42226 authored over 2 years ago by Pavel Dimens <[email protected]>
add testing project.toml back

github.com/BioJulia/PopGen.jl - ecb9c5db22429c98e9bbde6bece75cef06b2f4e2 authored over 2 years ago by Pavel Dimens <[email protected]>
nother try

github.com/BioJulia/PopGen.jl - 52020c36c128aa20205a59b9f4a2646d09c13d23 authored over 2 years ago by Pavel Dimens <[email protected]>
fix uuid

github.com/BioJulia/PopGen.jl - 1b0ac329c6731800aaf7c96a30c3862a38bc7b3b authored over 2 years ago by Pavel Dimens <[email protected]>
set project folder

github.com/BioJulia/PopGen.jl - 256a58ecbc72f62e49b5a400873a9e04adc85d35 authored over 2 years ago by Pavel Dimens <[email protected]>
fix shell call

github.com/BioJulia/PopGen.jl - 1a7ba8482105733d9688b319e1b5b22966a4b47c authored over 2 years ago by Pavel Dimens <[email protected]>
try another method

github.com/BioJulia/PopGen.jl - 9bbc3e6ff7c883c74a1a91de46dcd98af2077c01 authored over 2 years ago by Pavel Dimens <[email protected]>
clean up names

github.com/BioJulia/PopGen.jl - eea4a9308c8342c25bc88906d59f7497da196208 authored over 2 years ago by Pavel Dimens <[email protected]>
update workflows

github.com/BioJulia/PopGen.jl - 76164a15197bd07a231ffc29d255c95b555802e6 authored over 2 years ago by Pavel Dimens <[email protected]>
remove testing project.toml

github.com/BioJulia/PopGen.jl - cb0955cded99835771d9bcdac0ebf8927f29e561 authored over 2 years ago by Pavel Dimens <[email protected]>
try again

github.com/BioJulia/PopGen.jl - 5ed3f2b6e0a55af08381804183ebf1434ca63e59 authored over 2 years ago by Pavel Dimens <[email protected]>
another attempt

github.com/BioJulia/PopGen.jl - a1efd6e04ad9ae798c6210d3eada4fc9065518d6 authored over 2 years ago by Pavel Dimens <[email protected]>
fix action

github.com/BioJulia/PopGen.jl - 656dd21eafca283096419a8f2ac48deb77767f35 authored over 2 years ago by Pavel Dimens <[email protected]>
try again

github.com/BioJulia/PopGen.jl - 5379cda5cc014e1c3905c1dcbbaed2cf33ce4823 authored over 2 years ago by Pavel Dimens <[email protected]>
fix path

github.com/BioJulia/PopGen.jl - 7b41a7646c0621a932b46d89fadaff2ac971d8c5 authored over 2 years ago by Pavel Dimens <[email protected]>
change pkg add syntax

github.com/BioJulia/PopGen.jl - b624fdf9dfb9f94d2d4ae24032d6a5b6b0ffa394 authored over 2 years ago by Pavel Dimens <[email protected]>
fix Pkg.add() call

github.com/BioJulia/PopGen.jl - 216744188aa1fcd88e16aaabc4ee5c5cc26db6d5 authored over 2 years ago by Pavel Dimens <[email protected]>
attempt to add upstream testing

github.com/BioJulia/PopGen.jl - 4a57317c5e938baf41571fffd62ee7385a41dbc4 authored over 2 years ago by Pavel Dimens <[email protected]>
rm progressbar here

github.com/BioJulia/PopGen.jl - a3079afc62b3be576aa40abc299a98c397fae268 authored over 2 years ago by Pavel Dimens <[email protected]>
update Term.progress => Term.Progress

github.com/BioJulia/PopGen.jl - 94480cfcea8a4710e06033888a70d79b8761d812 authored over 2 years ago by Pavel Dimens <[email protected]>
fix another critical typo

github.com/BioJulia/PopGenCore.jl - a78a89dd5d86e61c35acec7659500e4b19809a34 authored over 2 years ago by Pavel Dimens <[email protected]>
allelematrix => matrix

github.com/BioJulia/PopGen.jl - 13d8334fb60898dfa1f607cae93154c7fefb4ad4 authored over 2 years ago by Pavel Dimens <[email protected]>
fix critical typo

github.com/BioJulia/PopGenCore.jl - 752376dd52954c31737fe78f790492118602281e authored over 2 years ago by Pavel Dimens <[email protected]>
allelematrix => matrix

github.com/BioJulia/PopGenCore.jl - 9e12c5a8bff7d86bf18e8c4ee707c4cbae35dc5d authored over 2 years ago by Pavel Dimens <[email protected]>
Add generate_input_error_code to improve error messages

A current limitation of Automa is that it can be difficult to understand why
a certain string do...

github.com/BioJulia/Automa.jl - 7647e9f95b6cf600990a420d776b69d279452969 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Improve error message on ambiguous NFA

Now prints the minimal possible input to trigger the ambiguity.

github.com/BioJulia/Automa.jl - d4bd3eca1ad8d9181f09a1d8831ba133926c7228 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Add debug_execute

github.com/BioJulia/Automa.jl - 241c16ea9303c876886f57463cec59b8ce26fc47 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Improve debugging

github.com/BioJulia/Automa.jl - 8537d8aa1b0e3304f4f5fca18ae880659cf03d62 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Release v0.1.1 (#19)

github.com/BioJulia/SequenceVariation.jl - c945dc63ddabdbcc7b0953afd8033d2b70d7fe1c authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Disable unambiguity check again (#98)

I want to release one more non-breaking release before v1, which requires us
to remove the break...

github.com/BioJulia/Automa.jl - 1e645f4f2f0771456da72c5712a0acd5c0a9fbf5 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Add constructor for Variant based on Variations

A Variant is a collection of Variations, right? Unfortunately there was no
way to convert a coll...

github.com/BioJulia/SequenceVariation.jl - 1bbb85153c176ff1fb4c909136b0e8ea8369de9e authored over 2 years ago by Thomas A. Christensen II <[email protected]>
add featurematrix

github.com/BioJulia/PopGenCore.jl - e4b48cbd17921f59b8e1cfebb282f6c2f410bc44 authored over 2 years ago by Pavel Dimens <[email protected]>
migrate from popgen (still testing)

github.com/BioJulia/PopGenCore.jl - 78ea85ca484f924d91ce0308a25285e99a392cc8 authored over 2 years ago by Pavel Dimens <[email protected]>
housekeeping

github.com/BioJulia/PopGen.jl - 748a2f4589bd959f81e791fa658d439edd80387b authored over 2 years ago by Pavel Dimens <[email protected]>
Merge pull request #106 from BioJulia/compathelper/new_version/2022-06-21-02-01-06-924-00475557151

CompatHelper: bump compat for Term to 1, (keep existing compat)

github.com/BioJulia/PopGen.jl - 2156dd0d3c97a05fc01a2c0a6032446123be6c17 authored over 2 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'dev' into compathelper/new_version/2022-06-21-02-01-06-924-00475557151

github.com/BioJulia/PopGen.jl - 0842cc67de023564fd78f13b43e528d4f030794c authored over 2 years ago by Pavel V. Dimens <[email protected]>
fix for real

github.com/BioJulia/PopGenCore.jl - 68a65b69a133d5bdb2723cdb93d9ba6b16c88e5c authored over 2 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/BioJulia/PopGenCore.jl into dev

github.com/BioJulia/PopGenCore.jl - 13ef1228dbf5c5ed25eaac91430afc350ed0c704 authored over 2 years ago by Pavel Dimens <[email protected]>
fix truncatepath text parsing. Make it more generic

github.com/BioJulia/PopGenCore.jl - 0ca0a8e06dc9f76763444652555783224529a13f authored over 2 years ago by Pavel Dimens <[email protected]>
fix typo

github.com/BioJulia/PopGenCore.jl - 7d9439f9a70b28f1371a6bb763072f3a0e7bd09b authored over 2 years ago by Pavel V. Dimens <[email protected]>
fix truncatedpath

github.com/BioJulia/PopGenCore.jl - 03c3fb277d0f6f7c3bf270b38832cb9d680f481d authored over 2 years ago by Pavel V. Dimens <[email protected]>
group by population first to avoid conflicts

github.com/BioJulia/PopGenCore.jl - 98afcc169cf0eb87f157dd3ae5d65e7790fb5497 authored over 2 years ago by Pavel Dimens <[email protected]>
add method for tuple

github.com/BioJulia/PopGenCore.jl - 87ae8893810ceefcd0faa8a93edf8c203d95f655 authored over 2 years ago by Pavel Dimens <[email protected]>
Use smaller integer width for table generator (#97)

Most generators have < 128 states, basically all have < 32,000. This suggests
we should be able...

github.com/BioJulia/Automa.jl - 39b4c3c352e64de3d1a26a18ca642941b1c16ed5 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Remove ByteSet (#96)

Automa's dependency ScanByte implements a ByteSet. Use it instead.

github.com/BioJulia/Automa.jl - 3f4e69070f37eb5e5a1af9c71d9e53770e6dd64f authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Fixup parse_class (#94)

* Disallow unicode in parse_class
* Allow byte ranges in class

github.com/BioJulia/Automa.jl - c7f06e35b16041b0572c6a5b0889e6d954e88624 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Add rand!([::AbstractRNG], ::LongSequence, [::Sampler]) methods (#250)

* Add rand!([::AbstractRNG], ::LongSequence, [::Sampler]) methods

I had apparently forgotten ...

github.com/BioJulia/BioSequences.jl - f2536a6c4426269427f1fb365e9a34be30f05cc5 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #16 from MillironX/feature/getbases

github.com/BioJulia/SequenceVariation.jl - 6a77d6d58928c69083bc7f1c3d07dcbd40c874c0 authored over 2 years ago by Thomas A. Christensen II <[email protected]>