github.com/BioJulia/PopGen.jl_archive commits

Merge pull request #13 from pdimens/release

merge release branch upstream

bfff98ff7b093902523f2170edf9e7d16a02249c authored over 3 years ago by Pavel V. Dimens <[email protected]>

Merge pull request #57 from pdimens/dev

merge 0.4.4 into release

9e01294057e6512d57da3993f89e1f7f939fe6b4 authored over 3 years ago by Pavel V. Dimens <[email protected]>

bump version for the fixes

97abb5d0891e96e569ff131bbce4d91c5b91ffc7 authored over 3 years ago by Pavel Dimens <[email protected]>

swap docstrings to avoid scary warning

0f7c5e90e6321ad8472726f699a0523d92c7e1d4 authored over 3 years ago by Pavel Dimens <[email protected]>

fix using call

3bba045f0ba537f43c4bcc287faf5169cc3abcc1 authored over 3 years ago by Pavel Dimens <[email protected]>

possibly fix the .@requires calls

8b76a18010cd82d7d0dc577253a3caff8dab6b8f authored over 3 years ago by Pavel Dimens <[email protected]>

attempt varcall fix

ceb16ee4290f6336d7fbf5d7f9611376a78163af authored over 3 years ago by Pavel Dimens <[email protected]>

update readme

77a29d6a87b8205bd66a0d867984be09e73fec3e authored over 3 years ago by Pavel Dimens <[email protected]>

rm text

01a6fb6fc4f8f47cf075d9e0a949907f4749411c authored over 3 years ago by Pavel Dimens <[email protected]>

update variantcall

7de3a61680ee1cd81ceef17dbc321ff9adee0f2c authored over 3 years ago by Pavel Dimens <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

5f7b547d18fe614668793cd78ed79c494143c1ee authored over 3 years ago by Pavel Dimens <[email protected]>

Update Project.toml

@JuliaRegistrator register branch=release

95d64531fe776a2abad938c280aae016b8753dbd authored over 3 years ago by Pavel V. Dimens <[email protected]>

Merge pull request #56 from pdimens/dev

bugfixes for 0.4.3

93d9a553f58bc5c31ad023006c97615f25e719bb authored over 3 years ago by Pavel V. Dimens <[email protected]>

split out GZip @requires block

94b828fb932e049ab6a8be53e1e53d28f03ddf21 authored over 3 years ago by Pavel Dimens <[email protected]>

Merge pull request #55 from pdimens/compathelper/new_version/2021-02-04-00-44-40-082-3447285803

CompatHelper: bump compat for "PooledArrays" to "1.1"

5249bb36c527719ae7fd91cd6921ce3fc09f8918 authored over 3 years ago by Pavel V. Dimens <[email protected]>

CompatHelper: bump compat for "PooledArrays" to "1.1"

838583699da16029ff10b07974f6255f5bbf37a5 authored over 3 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

update geno_count and geno_freq types and tests

ad0bdddacc0f1950467ca5adc56c5ce6efd370be authored over 3 years ago by Pavel Dimens <[email protected]>

fix output types and tests for geno_count_xxx

e18323a95e2b51b60b2abad7317fa1d2f25bf847 authored over 3 years ago by Pavel Dimens <[email protected]>

ok fix summary tests for real

6077733b5e1960680a7aae1855f6256adecc8a9b authored over 3 years ago by Pavel Dimens <[email protected]>

fix summary test

0b6e1e1e734828aeeae94d4fdf4b18d27d6b98e8 authored over 3 years ago by Pavel Dimens <[email protected]>

fix summary

1efe24a98db376dbadef2f61ebcf5a5456cbc022 authored over 3 years ago by Pavel Dimens <[email protected]>

simplify allele_freq after alleles splitting

77442cdf5005633a3d2bbf6e2ed7a280151f94d3 authored over 3 years ago by Pavel Dimens <[email protected]>

separate alleles methods

9a883eab31e2d2825801f5b6da5821aa9a32b3b7 authored over 3 years ago by Pavel Dimens <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

428081e2080368afc3f674500b12dad0936204d0 authored over 3 years ago by Pavel Dimens <[email protected]>

fix allele_avg type signature

c9aa3086a493c6441cbbb8a9bc7738e991db75f6 authored almost 4 years ago by Pavel Dimens <[email protected]>

fix allele_freq tests

67acb6451231a5340b8d14f5a3271ad9323b1556 authored almost 4 years ago by Pavel Dimens <[email protected]>

fix missings and update tests

126840da6183b92c5b67672938f650b1921f9da3 authored almost 4 years ago by Pavel Dimens <[email protected]>

(hopefully) fix the alleles(x) type bug in allele_freq

b2e287cf1e758aec7c1a920db064063bcea6ea87 authored almost 4 years ago by Pavel Dimens <[email protected]>

wishful thinking port added to scratch

19979a6ce0c5f12ccd26a3651f27d2025795ceda authored almost 4 years ago by Pavel Dimens <[email protected]>

optimize geno/allele freq methods using StatsBase

36fcce224a8ccb806148f3b784f40b7a7aae175a authored almost 4 years ago by Pavel Dimens <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

aa555a44718b42c517397acad1b7de00e063ab6d authored almost 4 years ago by Pavel Dimens <[email protected]>

fix typo bug in function definition

eda4a4b07c96f900ed6ea9b63eb5119ff90cfedd authored almost 4 years ago by Pavel Dimens <[email protected]>

clean up fstats code/bugs

10deac8981f5ab0e7786d253edc6edb01eb1bf87 authored almost 4 years ago by Pavel Dimens <[email protected]>

simplify perm code

8ad2dc929d6620ce7df1ebf31d9f28281d20c0b4 authored almost 4 years ago by Pavel Dimens <[email protected]>

Base.show flexibility

0500b48a9c41eec1487cef2f5c3834e8ebb64ff5 authored almost 4 years ago by Pavel Dimens <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

f424bd823734b7f9b423d5e1565fcfcf60238434 authored almost 4 years ago by Pavel Dimens <[email protected]>

fix rename

0fb45cd789aff612379e84642d9443e1295c0f38 authored almost 4 years ago by Pavel Dimens <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

d6ae516f9a6cf3f37ce0ca8858199edebaf46d0b authored almost 4 years ago by Pavel Dimens <[email protected]>

replace popdata2____ as methods

ba11037197f14b713a6694620ebd379fb687c34e authored almost 4 years ago by Pavel Dimens <[email protected]>

Add Base.show flexibility

96d6f1089887167c05ab833941dca233a2e2367b authored almost 4 years ago by Pavel Dimens <[email protected]>

add PooledArrays to test deps

03adc111a076f317617754d2b33813520e749da8 authored almost 4 years ago by Pavel Dimens <[email protected]>

revert meta creation

a305a9bee633f2d3ab5b200704743a68dd6c106c authored almost 4 years ago by Pavel Dimens <[email protected]>

actually add Test to project.toml

5d84856b88d8aa62ea02b438453ba216cc5a7f21 authored almost 4 years ago by Pavel Dimens <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

f1fba544a4c897c0b816a34bba3450356e62fde6 authored almost 4 years ago by Pavel Dimens <[email protected]>

add geneticvariation/gzip test deps

ba15bf02f364a4949a29a0fdd95c0f9dff7d2235 authored almost 4 years ago by Pavel Dimens <[email protected]>

Merge pull request #51 from pdimens/compathelper/new_version/2020-12-12-00-52-16-869-2184825279

CompatHelper: add new compat entry for "RandomNumbers" at version "1.4"

624afb8ee4490223b6d9ecae45d721c11dc4ecc8 authored almost 4 years ago by Pavel V. Dimens <[email protected]>

add more tests

c16d5db7cd3486cbaa50af3c3332bfd058640b19 authored almost 4 years ago by Pavel Dimens <[email protected]>

replace manual creation with generate_meta

e470c48cc96ddeb3ed0efeac86a0985601882724 authored almost 4 years ago by Pavel Dimens <[email protected]>

rename missing to missing_data

11f8611a59dce1a87fdc231085ceee0e2f3bdc4f authored almost 4 years ago by Pavel Dimens <[email protected]>

add generate_meta

4067dc988fb7b70aa18c7ffe537bbf3d322db969 authored almost 4 years ago by Pavel Dimens <[email protected]>

make robust against missings

f16db7e0baba167bdeb839743f676d3cd7f5c546 authored almost 4 years ago by Pavel Dimens <[email protected]>

fixed DataFrames v0.22 syntax deprecation bug

2d3b98ce290dd2879f467fdc24fdc4450f733e8e authored almost 4 years ago by Pavel Dimens <[email protected]>

update tests for get_genotypes api change

b1b0da0d76ed9f5e80a725da06969e05f5cf7a12 authored almost 4 years ago by Pavel Dimens <[email protected]>

fix occurences of deprecated sharks/cats datasets

b17dac1e37130cf924330e92159bd3da7ab02a16 authored almost 4 years ago by Pavel Dimens <[email protected]>

CompatHelper: add new compat entry for "RandomNumbers" at version "1.4"

b42d593582e7bdc023616a225bcc849482d1b846 authored almost 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

clean completed todos, bugfix

69c9abff378b424478b15ad9bb037dcd7d9e563e authored almost 4 years ago by Pavel Dimens <[email protected]>

make richness() kwarg consistent

879e0bbb058a87f2d4e4c040cfd2731b66454e97 authored almost 4 years ago by Pavel Dimens <[email protected]>

add X_freqtable functions

855db6dbfa1ce4784fe8e05818c1113da2de022f authored almost 4 years ago by Pavel Dimens <[email protected]>

posthoc MT => Xorshift

a6775b729b94755005412f150659f4e4b091c808 authored almost 4 years ago by Pavel Dimens <[email protected]>

add RandomNumbers.jl and replace MT w/ Xorshift

a9970f761303dffe1241503e1fa59f0c2fc90e8a authored almost 4 years ago by Pavel Dimens <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

25ab16a4ad6dbde99cf077fa98c2293d355b8a6e authored almost 4 years ago by Pavel Dimens <[email protected]>

fix dataset macros

116e631166ed2e690fe3b2f8586f8faaeedc0710 authored almost 4 years ago by Pavel Dimens <[email protected]>

Merge pull request #50 from pdimens/compathelper/new_version/2020-11-28-00-43-49-199-1751520

CompatHelper: bump compat for "StaticArrays" to "1.0"

5edc10f7a7b6f13446452d2573b1155f1210398b authored almost 4 years ago by Pavel V. Dimens <[email protected]>

add relatedness_posthoc

de6f598678d87efe547ecb335ba7009e0f62151f authored almost 4 years ago by Pavel Dimens <[email protected]>

CompatHelper: bump compat for "StaticArrays" to "1.0"

ceacd79d6843784db876073fb78e4e5957901ba2 authored almost 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

Merge pull request #48 from pdimens/dev

bump to 0.4.2

b5cb5e5e4cebc0ea2574a59ce9fbafa479346dca authored almost 4 years ago by Pavel V. Dimens <[email protected]>

directory restructuring for scratch

616d4d53c607a6c47d4d8e9141a7bcd4db580ec9 authored almost 4 years ago by Pavel Dimens <[email protected]>

bump vers and update tests for macro sharks/cats

0e59ebf118b6451d01b1ed8a95e7bcfbca472fa5 authored almost 4 years ago by Pavel Dimens <[email protected]>

add @nancycats @gulfsharks, depwarns on old

5466ef8fc79fec8d9e40ad6625adb764bf892be2 authored almost 4 years ago by Pavel Dimens <[email protected]>

remove graphs deps

complete accident that they were included

d91fd8a6276f8507e17eab327091d0fb4fae61a3 authored almost 4 years ago by Pavel V. Dimens <[email protected]>

fixed population!()

e3fa407122c4fbac960cdb8732fbae4a5f110014 authored almost 4 years ago by Pavel Dimens <[email protected]>

bump vers

72c2db31838d648d00207811fd8b68b62d5cd705 authored almost 4 years ago by Pavel Dimens <[email protected]>

bump version number, correctly

3cf0fd84d9fac480d739abda5f365d5586cf3d6c authored almost 4 years ago by Pavel Dimens <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

e7eac853d036bd04940b13755dd4cd0d4ccf77bf authored almost 4 years ago by Pavel Dimens <[email protected]>

Merge pull request #42 from pdimens/compathelper/new_version/2020-11-15-00-39-45-225-947094218

CompatHelper: bump compat for "CSV" to "0.8" and fix version number

dd4080a3d7e8ef9b1dd7359580759c2b319b8c65 authored almost 4 years ago by Pavel V. Dimens <[email protected]>

Merge branch 'dev' into compathelper/new_version/2020-11-15-00-39-45-225-947094218

e99e5db119d0e832eb5d298e921007df36817b21 authored almost 4 years ago by Pavel V. Dimens <[email protected]>

Merge pull request #43 from pdimens/compathelper/new_version/2020-11-16-00-39-29-445-2465782919

CompatHelper: bump compat for "DataFrames" to "0.22"

00ece5b7d6914e73942a0584bd6947c4f40ea46e authored almost 4 years ago by Pavel V. Dimens <[email protected]>

Merge pull request #44 from pdimens/compathelper/new_version/2020-11-16-00-39-43-936-4263952489

CompatHelper: bump compat for "JLD2" to "0.3"

b56e23d92dc2529840b5671b18af0adf2d8fd5bc authored almost 4 years ago by Pavel V. Dimens <[email protected]>

CompatHelper: bump compat for "JLD2" to "0.3"

9939806ba94c5afeecfc44d6ea19eacc86ec82af authored almost 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

CompatHelper: bump compat for "DataFrames" to "0.22"

c31f1550bcf515355819a1c27003de92fba19e53 authored almost 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

CompatHelper: bump compat for "CSV" to "0.8"

cf85482d902f409f89e7ec69b4941e2d320867ec authored almost 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

remove references to wang/dyadML

ae808599e7f1f2c07686ed0842a1aa34e923d342 authored almost 4 years ago by Pavel Dimens <[email protected]>

Update TagBot.yml

bd539518b71d157c74ea4b36b4d858c406fa77f7 authored almost 4 years ago by Pavel V. Dimens <[email protected]>

Merge pull request #39 from pdimens/dev

stage 0.1.0 release

a218bf41ab249199099e2a411ff62b9c1b4b5303 authored almost 4 years ago by Pavel V. Dimens <[email protected]>

Merge branch 'release' into dev

36e1dfc7c3477555659472d052c30b536bd702d3 authored almost 4 years ago by Pavel V. Dimens <[email protected]>

change to v0.1.0

change version number to reflect breaking changes.

2ba045707d20a9b76b03bdeedd3287dd4309b7a1 authored almost 4 years ago by Pavel V. Dimens <[email protected]>

fix alleles miss=true and type stability

109b7105115254bf1aeb82ccbe6c78035219c937 authored almost 4 years ago by Pavel Dimens <[email protected]>

Update Utils.jl

acf122fb6e6582ad5f022d7139b48aa6f36d1006 authored almost 4 years ago by Pavel V. Dimens <[email protected]>

add relatedness posthocs

48b67e5af2238ca74f781e30879f79f6ddd045ee authored almost 4 years ago by Pavel Dimens <[email protected]>

add manipulate tests

5467d3c7155afd43d14ddc2f8af2ed9919cf45e3 authored almost 4 years ago by Pavel Dimens <[email protected]>

mroe test fixes

808155cfa992cff467e7cf1c9df0daf48d762541 authored almost 4 years ago by Pavel Dimens <[email protected]>

fix tests

2d011b40076f7506b052ad3aad08910142a64ef0 authored almost 4 years ago by Pavel Dimens <[email protected]>

fix and add tests

1d5f685a304fb1524b3868f4221f918fddc26642 authored almost 4 years ago by Pavel Dimens <[email protected]>

add missing, missing method

30cdacb4f58abb176aa384cf17e2d50cbd36b733 authored almost 4 years ago by Pavel Dimens <[email protected]>

add more tests

a13759618c0740f3ea29b7ad34c107548cfd2b76 authored almost 4 years ago by Pavel Dimens <[email protected]>

hopefully fix CI

0b02f6475f2b751b87c97d494e9d8603eddde193 authored almost 4 years ago by Pavel Dimens <[email protected]>

add first tests

1519e6d28fccca657b72f31aa0f8d37b5fbf466f authored almost 4 years ago by Pavel Dimens <[email protected]>

fix hetero_e for locus missing in pop

709be89a928f96d688f30aff07013d6d001c2a19 authored almost 4 years ago by Pavel Dimens <[email protected]>

add julia 1.5 build test

1c8f9c7ccde3b03df6955a5b81c32a103eed6c8b authored almost 4 years ago by Pavel V. Dimens <[email protected]>

Update Project.toml

76a392fff4ae3dc87e4c02fb8499e5d6bc17e8de authored almost 4 years ago by Pavel V. Dimens <[email protected]>

Ecosyste.ms: OpenCollective

github.com/BioJulia/PopGen.jl_archive