github.com/BioJulia/SubstitutionModels.jl commits

Merge pull request #30 from BioJulia/net2dev

Update URLs from biojulia.net to biojulia.dev

90d79eb26371b10a20be5715bf87ed2448cc8b97 authored over 1 year ago by Kevin Bonham <[email protected]>

Update URLs from biojulia.net to biojulia.dev

50f691b3a9fe58252abd3fe68ecd953f4c1b5d15 authored over 1 year ago by Kevin Bonham <[email protected]>

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

ab6116f34e1bfc3c96c8a31f3bc8b5b18f9993b0 authored over 3 years ago by Justin Angevaare <[email protected]>

Doc generation on publishing release

ab09a15a265de582171ffefe8a7dc9756d2eec93 authored over 3 years ago by Justin Angevaare <[email protected]>

Merge pull request #28 from BioJulia/docfixup

Constructor consistency/documentation fix

7b8b3313bbad80fa408c01a7b717820d05f48823 authored over 3 years ago by Justin Angevaare <[email protected]>

doctests to @repl due to ansi issues

Separate tests, fix documentation bug

881825eb07ccd14cb8323a017551e655d38ba062 authored over 3 years ago by Justin Angevaare <[email protected]>

Constructor safety consistency; fix docs

fd5380c3a0de91eaf9eb78dd4af7a62150330142 authored over 3 years ago by Justin Angevaare <[email protected]>

Merge pull request #27 from BioJulia/ci-update

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

929ddbe429985c6c3a36c1abcef77c745155441b authored over 3 years ago by Justin Angevaare <[email protected]>

Merge branch 'ci-update' of https://github.com/BioJulia/SubstitutionModels.jl into ci-update

3182f118a3730ea0f8efba70c389d730344dd375 authored over 3 years ago by Justin Angevaare <[email protected]>

Update gh actions/use actions for testing

87f8716cee9d047e994e4d4ec0c7a5b741a9d1f0 authored over 3 years ago by Justin Angevaare <[email protected]>

Update gh actions/use actions for testing

4b9b9836f72792089d1e253332a045925923d9bf authored over 3 years ago by Justin Angevaare <[email protected]>

Update README.md

dea01e2680b277bdd60694cf745ea04631f14f3c authored over 4 years ago by Justin Angevaare <[email protected]>

Update README.md

757c24e9b3d819568110bc92f3bec30a8aed9e07 authored over 4 years ago by Justin Angevaare <[email protected]>

Update CompatHelper.yml

572266178d8d43236e18d32df1ad5e8f8d30673c authored over 4 years ago by Justin Angevaare <[email protected]>

Update TagBot.yml

201dc901f8f88cf9c25ea76b313cfc374a924676 authored over 4 years ago by Justin Angevaare <[email protected]>

Update Project.toml

2bfe5faa39034c631faa41f183ab0cd36cec1c82 authored over 4 years ago by Justin Angevaare <[email protected]>

Update .zenodo.json

9eac71598d8123569b302a559de33dc914edf616 authored over 4 years ago by Justin Angevaare <[email protected]>

Create .zenodo.json

2497c31e63e042e182ee3f4d737b24afd5958bfc authored over 4 years ago by Justin Angevaare <[email protected]>

Update .travis.yml

da4f71e1ab9390346609dc1d353623676ecc755b authored over 4 years ago by Justin Angevaare <[email protected]>

Remove reference to biojuliaregistry in CI

7222ff50f395109b09e1466e394fa1f55e0d3c56 authored over 4 years ago by Justin Angevaare <[email protected]>

test with julia-1.4, update maintainers in README

9233017509c2885cdd68eb7101e1718199151c20 authored almost 5 years ago by Justin Angevaare <[email protected]>

Update Project.toml

4326e44b204505e47039cd4b08bd76fd94099718 authored almost 5 years ago by Justin Angevaare <[email protected]>

Merge pull request #24 from BioJulia/julia-one

Support BioSymbols 3.x to enable Julia 1.0 to pass

be880220bbc63a9e54d1bc32578ed539a5f8333e authored almost 5 years ago by Justin Angevaare <[email protected]>

Support BioSymbols 3.x to enable Julia 1.0 to pass?

4404eb34f90dd105bc834b01ead6c94cbfbced77 authored almost 5 years ago by Justin Angevaare <[email protected]>

Merge pull request #23 from BioJulia/compathelper/new_version/2020-01-19-01-04-50-082-1406933593

CompatHelper: add new compat entry for "BioSymbols" at version "4.0"

72c41548781e2ca356e9bf58365ecc3e21807fa4 authored almost 5 years ago by Justin Angevaare <[email protected]>

Merge branch 'master' into compathelper/new_version/2020-01-19-01-04-50-082-1406933593

f45775c07e8ec270c91b1aa64ffcca0a7dddc757 authored almost 5 years ago by Justin Angevaare <[email protected]>

Merge pull request #22 from BioJulia/compathelper/new_version/2020-01-19-01-04-44-795-2211115710

CompatHelper: add new compat entry for "StaticArrays" at version "0.12"

ef2b0c4d1e184961528ea662951e108b79cf85f2 authored almost 5 years ago by Justin Angevaare <[email protected]>

Create TagBot.yml

44d0d417442fbb0181f0143a4fe6c1c9c52dc9a3 authored almost 5 years ago by Justin Angevaare <[email protected]>

Create docs.yml

fa5b3395c2ef9cdf64b459ae9c9f2cf44f05aa17 authored almost 5 years ago by Justin Angevaare <[email protected]>

add BioJuliaRegistry, 1.3 testing

ff780913771ebbf70c01bd389f4f5c3fd15362ef authored almost 5 years ago by Justin Angevaare <[email protected]>

CompatHelper: add new compat entry for "BioSymbols" at version "4.0"

237a76ff028db2de3fed5e095b8abdf011efd5f0 authored almost 5 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

CompatHelper: add new compat entry for "StaticArrays" at version "0.12"

2ce7a357a0bbab1dfa2fa1a6a91a2a308f67029a authored almost 5 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

Update CompatHelper.yml

Add BioJulia repository

da1e2794b8c4164980ff188a4662ee3d83d42b18 authored almost 5 years ago by Justin Angevaare <[email protected]>

Create CompatHelper.yml

4f1dbc742281142122846429e134c9c188c4bbc1 authored almost 5 years ago by Justin Angevaare <[email protected]>

Merge pull request #21 from BioJulia/docs_update

Docs update

17ff99b6de9ada0085b65d474982d5dcd5ba602a authored over 5 years ago by Justin Angevaare <[email protected]>

Expand documentation reflecting updates to constructions methods; add a few more tests

ad5a28d4f2a58f88f56f8d8f30a3f98e0b63607c authored over 5 years ago by Justin Angevaare <[email protected]>

Add a few more tests for unsafe construction methods

f428d40844e27bf28fd7a559a38955ed6fbebb4a authored over 5 years ago by Justin Angevaare <[email protected]>

Prepare for v0.4.0

526e5e94c1d0daaf0422b87d1678b3f2c48f8547 authored over 5 years ago by Justin Angevaare <[email protected]>

Merge pull request #18 from BioJulia/constructors

Expansion of constructors methods for Nucleic Acid Substitution Models

9e33bac77c69f094af8cf73fc6e324ce92d5dd53 authored over 5 years ago by Justin Angevaare <[email protected]>

work on unit test coverage

work on unit test coverage

bddaf04b5e83f9ea9ec85d23fadf78551af0b5c3 authored over 5 years ago by Justin Angevaare <[email protected]>

revamp testing, K80 error checking bugfix

d27c5658e744e5f52079e6499f3253b550f9717a authored over 5 years ago by Justin Angevaare <[email protected]>

Add convert methods, they may be useful...

0b3f7cd214401b3bfbada9fd43401caaae5e349a authored over 5 years ago by Justin Angevaare <[email protected]>

reorganize outer constructors, add detection for abs vs rel forms when using parameter/freq vector based constructors

reorganize outer constructors, add detection for abs vs rel forms when using parameter/freq vect...

b072eee46663000cd031f9f402a56dfa3dbd922e authored over 5 years ago by Justin Angevaare <[email protected]>

Update .travis.yml

doc-build environment

Update make.jl

Add LinearAlgebra to deps

Remove non-working badge

0f86165afe1603a3a3a5a5e2a096bedc431bdee2 authored over 5 years ago by Justin Angevaare <[email protected]>

test vector lengths, rather than ignore extra parameters with new outer constructors

3f70e10d9c4360ebf2f6291fe5fca7e36bb2a3f8 authored over 5 years ago by Justin Angevaare <[email protected]>

Allow for construction using parameter vectors

de3d315638eb6a230dde4175701e91c2a1acc27b authored over 5 years ago by Justin Angevaare <[email protected]>

Update Project.toml

ed4348b67f24191d466327bdcc7f8605e8b0d686 authored over 5 years ago by Justin Angevaare <[email protected]>

Merge pull request #17 from BioJulia/project.toml

Transition to Project.toml

f2fa9edd8ffa8614f3d4f93c20120d05bdabe3ca authored over 5 years ago by Justin Angevaare <[email protected]>

add julia 1.1 testing

7e44cd8cb8b90e5a88804944c930d9aad5ca2029 authored over 5 years ago by Justin Angevaare <[email protected]>

generate project.toml

45c5d1a911a6b2a4f862adf35156658a5a91d5cc authored over 5 years ago by Justin Angevaare <[email protected]>

Merge pull request #16 from kgori/scale_q

Methods to scale all Q and P matrices such that a branch length of 1 = 1 expected substitution

b730fed9bbbf6a5762955e3648592e47fe8f0b5f authored over 5 years ago by Justin Angevaare <[email protected]>

Add scaling feature to P and Q matrix calculations

32a1d6aa84268943b5a65e30e75d7295259dfe29 authored over 5 years ago by kgori <[email protected]>

Merge pull request #15 from kgori/tn93_pmatrices

Bugfixes relating to P matrices of TN93 and related models

7e831397c94f93d02206ce97f181adaba44d1557 authored almost 6 years ago by Justin Angevaare <[email protected]>

Tidy up stray ####

5ffa02fd0fda372ce2866c733b4088b30815e178 authored almost 6 years ago by kgori <[email protected]>

Fix typo in P() for TN93 and related models

f12a60e70cfc9cfe6b4cbe626f245bf9eeccca62 authored almost 6 years ago by kgori <[email protected]>

Merge pull request #14 from kgori/fix_eigen

Bugfixes: eig to eigen and JC69 P matrices.

83a979a0205dc42004748967a39c4fcf50923618 authored almost 6 years ago by Justin Angevaare <[email protected]>

Add tests for array form of P_generic

5e551e89973a2f215e702bf4cf166a0ab2a761d2 authored almost 6 years ago by kgori <[email protected]>

Fix typo in Jukes Cantor probabilities

8bdf2f0e4c515933cf7ea190087a899e58546942 authored almost 6 years ago by kgori <[email protected]>

Updated to v1 eigen syntax

c59ab872a1e88723d8191ad8a13bff106fa9e3e2 authored almost 6 years ago by kgori <[email protected]>

Cap Documenter.jl to 0.19 on Travis (#13)

Documenter 0.20 will introduce breaking changes that will invalidate
existing make.jl setups. T...

779db55778abe96aa59f76a06cd3435d4dcc5753 authored about 6 years ago by Morten Piibeleht <[email protected]>

Merge pull request #10 from jangevaare/docs-fix

Fix LaTeX for P & Q matrix documentation

54a8a46bf4ce3d61ec7a58c23bc1b8db54461747 authored over 6 years ago by Justin Angevaare <[email protected]>

Fix LaTeX for P & Q matrix documentation

630d880e064d0a546a00f354bfb978250fc56dce authored over 6 years ago by Justin Angevaare <[email protected]>

Updates for Julia 0.7/1.0 (#8)

f63583244656b6568b75813cd6f12e1012707694 authored over 6 years ago by Justin Angevaare <[email protected]>

Contributing files rollout (#7)

* Rollout file CONTRIBUTING.md

* Rollout file CODE_OF_CONDUCT.md

* Rollout file .github/PU...

ad2c639cb80604b461b6ae1287bb1eb027dfed33 authored over 6 years ago by Ben J. Ward <[email protected]>

Update installation instructions for release ver

9818fdbd6bf2db0311f4df5328e36414ed787756 authored about 7 years ago by Justin Angevaare <[email protected]>

Merge pull request #6 from Ward9250/docs-update

Docs revamp

0ff123395ccd9b297708430eab8050e2d2c1fb18 authored about 7 years ago by Justin Angevaare <[email protected]>

Added index.md as a softlink

8e69ef7f6c1ae8f3f71abd5ecb15288204c3cce2 authored about 7 years ago by Ben J. Ward <[email protected]>

remove index.md

9abb21f9e88ad127f584f31890c61900980d0871 authored about 7 years ago by Ben J. Ward <[email protected]>

Remove mkdocs.yml

062a59d721bfe7c8babf7400909b45312c72e655 authored about 7 years ago by Ben J. Ward <[email protected]>

fixup

c756d2c03313be2364e299581f8558e72b02cda2 authored about 7 years ago by Ben J. Ward <[email protected]>

Fix PR suggestions

97fc1a12e68f0ebfbaedf6afe541baa479c026f7 authored about 7 years ago by Ben J. Ward <[email protected]>

Docs revamp

71dcca938cf2df8dfbc08bbe6b9c9c4249bc0053 authored about 7 years ago by Ben J. Ward <[email protected]>

Merge pull request #5 from Ward9250/pre-release-review

Some minor review edits.

602596cc3c45bfc3da8cc9b05afd3639076d69f4 authored about 7 years ago by Justin Angevaare <[email protected]>

Update nucleic_acid.jl

f1698277aef4a1e6c0d406f218e444c6238c2e3b authored about 7 years ago by Ben J. Ward <[email protected]>

Update core.jl

9b72318762efd5eca732e28f57f19611f2a8f044 authored about 7 years ago by Ben J. Ward <[email protected]>

Some minor review edits.

ae0d8c36b620aab91eb10976d5d1483a90b14d7b authored about 7 years ago by Ben J. Ward <[email protected]>

fix docstrings so LaTeX will render with makedocs

97b8c7b1617fbca8e55c223a7485ebf291aa7811 authored about 7 years ago by Justin Angevaare <[email protected]>

Merge pull request #3 from Ward9250/indexing

Inline the Base.getindex method

1356f06ad69e353f0861001e95a6af3acf007d26 authored over 7 years ago by Justin Angevaare <[email protected]>

Merge pull request #4 from Ward9250/format-edits

Edits to CI infrastructure

5e7f6cf02edd93b1cfb2868c3e34d21a105caedb authored over 7 years ago by Justin Angevaare <[email protected]>

Edits to CI infrastructure

28e3914ff0355f68e698a2ebc349d30724daf63a authored over 7 years ago by Ben J. Ward <[email protected]>

inline getindex method

ab18db358d87c5a9449d507dce416f40b731a566 authored over 7 years ago by Ben J. Ward <[email protected]>

Merge pull request #2 from Ward9250/indexing

Eliminate the need for an indexing lookup table

b19fcc2c58446392942ff6f6c9456e6a83781d3e authored over 7 years ago by Justin Angevaare <[email protected]>

Eliminate the need for an indexing lookup table

773cf6cb959d247f66f76fe38f5674faedfdae99 authored over 7 years ago by Ben J. Ward <[email protected]>

Attempt to set up documentation pages with documenter.jl

Add mkdocs.yml file

Further work on documentation

Further documentation work

add makelocal.jl...

68bb8592a0df468142225bbe9438b878c8a3f5d1 authored over 7 years ago by Justin Angevaare <[email protected]>

define Q matrices directly for most substitution models

fix require

5897b93674f95788ce2a877c067545c58678608f authored over 7 years ago by Justin Angevaare <[email protected]>

Add efficient P matrix method to TN93, add error checks to P()

32a9beaa82380e09a4abbe690d3c28a0b7130ee7 authored over 7 years ago by Justin Angevaare <[email protected]>

Add efficient P matrix method to HKY85

1a75106442437b66929845a5648247a5a2cac08d authored over 7 years ago by Justin Angevaare <[email protected]>

Add efficient P matrix method to F84, fix matrix orientations

b530ee4e0c01d1f6db686dc240bef75e4d9f522e authored over 7 years ago by Justin Angevaare <[email protected]>

Add faster P method for F81 models

1b0027bf70492fcae629df83d30579a70e3d51cd authored over 7 years ago by Justin Angevaare <[email protected]>

Add more efficient P method to K80 models, add more tests

40defc74a7841b9331f15dec08d70e1a964df60f authored over 7 years ago by Justin Angevaare <[email protected]>

Small readme changes

3b8e63575c8b4e437c7a53660bfcc474037dcfc5 authored over 7 years ago by Justin Angevaare <[email protected]>

Prepare documentation for repo transfer to BioJulia

rename SubstitutionModels2 to SubstitutionModels throughout package

rename SubstitutionModels2 ...

f6f1fdfb2c7f29857ce275cad694e4d18889a76d authored over 7 years ago by Justin Angevaare <[email protected]>

Add show methods for all substitution models

ccc9b57e7836a942f5515c3ef7cc5d47fd84941a authored over 7 years ago by Justin Angevaare <[email protected]>

Faster P method for JC69 models

71705a1c7093c256b7fd3879c62fbb08aa82e850 authored over 7 years ago by Justin Angevaare <[email protected]>

code cleanup

6924e8dfacd1f882689917fc47fc95e062cb5378 authored over 7 years ago by Justin Angevaare <[email protected]>

Add GTR

b174ad2fce717d1bb0b4188d03f04aced2330543 authored over 7 years ago by Justin Angevaare <[email protected]>

Add TN93

780cad211487c991950dcf5c0169bde4fdfb98fc authored over 7 years ago by Justin Angevaare <[email protected]>

Add HKY85, correct F84

b1119764249a7fe04153254beaaab73ac358cd81 authored over 7 years ago by Justin Angevaare <[email protected]>

Add F84 model

7f576e1800b88602e5256f68c8d50a64174ffe1b authored over 7 years ago by Justin Angevaare <[email protected]>

Add f81 model, fix Q matrix calculation

eb7a3233108f83891368a612d9f05953a376ec33 authored over 7 years ago by Justin Angevaare <[email protected]>

Ecosyste.ms: OpenCollective

github.com/BioJulia/SubstitutionModels.jl