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github.com/BioJulia/BioSymbols.jl

Nucleic and amino acid primitive types
https://github.com/BioJulia/BioSymbols.jl

Expand on documentation for `compatbits` (#63)

Make it more clear exactly what this function promises.

a35961c42bd91d784ae39f6630c3ede64f1910aa authored 11 months ago by Jakob Nybo Nissen <[email protected]>
Optimise complementation of nucleotides (#62)

While BioSequences complement nucleotides in bulk, making this necessity not
important, the upc...

2f4b82cde5e67c20f23c694e6786f040d29e59cb authored 12 months ago by Jakob Nybo Nissen <[email protected]>
Update issue and PR template to match BioJulia guidelines (#61)

In BioJulia discussion 11, and BioJulia/Contributing, we've decided to make the
template less v...

41070d2c449bd08d721b7e33b755ae7887a26414 authored about 1 year ago by Jakob Nybo Nissen <[email protected]>
Bump Documenter to 1.0 (#60)

85c62c9c921062016a9f60bc4a6f735e6b266799 authored about 1 year ago by Jakob Nybo Nissen <[email protected]>
Bump version to v5.1.3 (#59)

efb84c88f3c83bf190923ca3e7c94480c97667dc authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Migrate from SnoopPrecompile to PrecompileTools (#58)

c0a6a265ade02fc912185d28afd28513c4bb2948 authored over 1 year ago by Tim Holy <[email protected]>
Improve error on predefined convert(::BioSymbol, ::Char) (#57)

Now properly render invalid Char, e.g. display ' ' with ticks instead of an
actual empty space ...

e34e56fca5c9360312519c86f99e5fd861c9b2ec authored almost 2 years ago by Jakob Nybo Nissen <[email protected]>
Add `gap(::Type{Char})` to prevent piracy from BioSequences. (#56)

e026408ff8ed1fbe32c3ae0051d09f7bd411862b authored about 2 years ago by Jakob Nybo Nissen <[email protected]>
Add SnoopPrecompile (#54)

Add SnoopPrecompile

2ea9143a9605e0a249efd9a6299cc57b5233f37b authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #52 from jakobnissen/v511

Bump version

3311b5b6dc67a9cb71e552e41944c058196719f9 authored over 2 years ago by Kevin Bonham <[email protected]>
Bump version

37bbae4f9c486eb96f29923e8711489d337012fb authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Optimise hashing (#51)

Default implementation of Base.hash uses objectid, which is slow.
Use a new implementation whic...

040a11f27f480974da73203140dcbb880172196a authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Add workflow for downstream tests (#49)

9228385bf9ed51fbcf2611315d8ed49daf1f71b1 authored about 3 years ago by Ciarán O'Mara <[email protected]>
Add stringbyte function (#48)

Add stringbyte function

c8e893b3577763a0e65cf0807ca4fc3f0c2e85f2 authored about 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #47 from jamiecm17/docstring_JM

Add docstring to describe functionality

f07b9d70ba24bfdfa55087075c38c88372c41ff8 authored about 3 years ago by Kevin Bonham <[email protected]>
Functions in unordered list

94aecb27fbdd267e7e9ddeafafe74b93cc38c1a0 authored about 3 years ago by jamiecm17 <[email protected]>
Shortened BioSymbols docstring

60d47c7c97d729c76ecd011e9b6cf80c834e8b3b authored about 3 years ago by jamiecm17 <[email protected]>
Add docstring to describe functionality

faf14092a6853d5431916fbb8dbc998e447d15e7 authored about 3 years ago by jamiecm17 <[email protected]>
Update TagBot.yml

3d796d12a6504a3a9d4495a42c87f239fd848250 authored over 3 years ago by Ben J. Ward <[email protected]>
Update TagBot.yml

970189a986f4ddd544496eedbd531085c56857b7 authored over 3 years ago by Ben J. Ward <[email protected]>
Update Project.toml

Bump version number a major increment

8e6966acfabf0c0b1fe51016b67e820cfb598b31 authored over 3 years ago by Ben J. Ward <[email protected]>
Merge pull request #44 from jakobnissen/noautoma

Removed Automa parsing

54bff1aba4799cb7b96f23090c92a7f6ed470284 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Removed Automa parsing

460ad173a376e172619be9f6ca5af83115eb7239 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #43 from jakobnissen/removeiter

Remove iteration of BioSymbol

6f0180fa1bb839b87e9828ed190865e198251ce6 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>
Add broadcasting

698855b0374d1f38b2ca7a3ba2fa1f6bcc43fb51 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>
Remove iteration of BioSymbol

Also removed `length(::BioSymbol)`

63c1d325b8384a40e5f6db9ee1d0fdaf7669cb85 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #38 from jakobnissen/intconvert

Remove integer conversion and arithmetic

4d11c1eac43c3fd48e1ad85f68b1529c08d32be8 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #39 from jakobnissen/master

Change small lookup tables to Tuple

5ab12d7e2a1c01eed6d02690a7f2ecdc131a7135 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #40 from jakobnissen/fixinfer

Improve inferrability

1092429f2381483274cd823adcd7eafb86907083 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>
Improve inferrability

18c5881d3f07b07b7a028abe48b05062368e3425 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>
Re-add logical ops

ae96f92cfea5fca3b2127ef55dcbdac613800018 authored over 4 years ago by Jakob Nybo Nissen <[email protected]>
Move from reinterpret to encode

7e6404e0f42cdf21fcd7f23ddf468679542397cd authored over 4 years ago by Jakob Nybo Nissen <[email protected]>
Remove biosymbol integer conversion

f9cac2f59ccf270e824d106ac715d2370567cba5 authored over 4 years ago by Jakob Nybo Nissen <[email protected]>
Update Project.toml

04ee588e51c65dd0beb5c56900569c9e829f6731 authored over 4 years ago by Ben J. Ward <[email protected]>
LTS support (#37)

* Support LTS

* Update .gitignore

* Update CI

e19b13cc609c1e5a040103d269448453aa25ce7b authored over 4 years ago by Ciarán O'Mara <[email protected]>
Remove old installation instructions

824104c7a35ac52197affd9d0f4f4f19093b88c4 authored over 4 years ago by Ben J. Ward <[email protected]>
Install tagbot

3a228158f105393b80b21650d69ad2243fa36268 authored over 4 years ago by Ben J. Ward <[email protected]>
Update Project.toml

1a394fa15a73e62a75230a1853acbe87d081dad4 authored almost 5 years ago by Ben J. Ward <[email protected]>
Update Project.toml

0bfe6ce9e1717f12f3744417e006b197a54e9b69 authored almost 5 years ago by Ben J. Ward <[email protected]>
Bump version number

67d8c0a9a2ced0e333e4a20385399da9839708c8 authored almost 5 years ago by Ben J. Ward <[email protected]>
Change small lookup tables to Tuple (#36)

8f6d212e6691374dfae4717b662fda80c6fe13bb authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>
Change small lookup tables to Tuple

9c68815c2dcc31d2241fc63facc27e516eb77edb authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>
Fixed missing iterate and length methods

ec7427d794c1952f29cb80f4dfe81eabb13d2520 authored over 5 years ago by Ben J. Ward <[email protected]>
Project update (#33)

This removes testing for julia v0.6 and removes the use of Nullables.

Prior to julia 1.0 (and 0...

ea6f595a4f14211b9cbba98ef01e4699b223a5cc authored over 5 years ago by Ben J. Ward <[email protected]>
Cap Documenter.jl to 0.19 on Travis (#32)

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

bddc09c4675e196baa60e68b319a0486cee81b0b authored about 6 years ago by Morten Piibeleht <[email protected]>
Update README.md

286fe1bc60d9888db6c98d19766b4de6bce812e9 authored over 6 years ago by Ben J. Ward <[email protected]>
Update README.md

c4c6982db67e7ccfa01efca8401a081d093cf6c8 authored over 6 years ago by Ben J. Ward <[email protected]>
Add conversion between DNA and RNA symbol types (#31)

d9b90db5536b16413229491d3558b1ceb928c0b7 authored over 6 years ago by Ben J. Ward <[email protected]>
Update CHANGELOG

cb011e81ac740e169ecfa409ca8c3ac249335629 authored over 6 years ago by Ben J. Ward <[email protected]>
A few more julia 1.0 fixes. (#30)

* Remove testing for julia v0.6

* Remove use of Nullables (#25)

Prior to julia 1.0 (and 0....

d5d77db4bdf35f9eda2d656ce4571ded02d3e789 authored over 6 years ago by Daniel C. Jones <[email protected]>
Fix automa version

efe94bdc9962b45effb53aa63b07e1a239acb003 authored over 6 years ago by Ben J. Ward <[email protected]>
Changes for Julia v0.7 / v1.0 (#28)

* Replace sticker.svg with optimized version

* Remove testing for julia v0.6

* Require jul...

934421efb91c96d50ee854cf81e52d04b1232817 authored over 6 years ago by Ben J. Ward <[email protected]>
Merge pull request #22 from BioJulia/pmapfix

This PR fixed some errors when using the pmap method.
The error was caused by the NucleicAcid a...

42c33533e2aa999fde5fe13d940ce1906886333f authored over 6 years ago by Ben J. Ward <[email protected]>
Update project files and add package sticker

2585cd62a8ef88b7bd75902bd16636099c6f62a6 authored over 6 years ago by Ben J. Ward <[email protected]>
Update the changelog

30434db22d4773f376b3d7a95e440412b9bb4c3f authored over 6 years ago by Ben J. Ward <[email protected]>
Add tests for read and write

6f070f39573f546a018e69e3f05c30a0300d791c authored over 6 years ago by Ben J. Ward <[email protected]>
Add write and print methods

0c77e938e7430487591308f7157046353f0854df authored over 6 years ago by Ben J. Ward <[email protected]>
Merge branch 'master' of github.com:BioJulia/BioSymbols.jl

73b1034e04b82ea3fbce3c1121a2fc15fd73d719 authored over 6 years ago by Ben J. Ward <[email protected]>
Add CHANGELOG and update REQUIRE

048ff9eb0e8d467032c00377d022f499cdf60c4b authored over 6 years ago by Ben J. Ward <[email protected]>
Contributing files rollout (#20)

* Rollout file CONTRIBUTING.md

* Rollout file CODE_OF_CONDUCT.md

* Rollout file .github/PU...

d51fcd1305c9cc5ce266dca5d33ee1dc553858e9 authored over 6 years ago by Ben J. Ward <[email protected]>
Rollout file .github/ISSUE_TEMPLATE.md

5153bfa9f38d51a043e65f0b2485e32f8f7fd8ef authored over 6 years ago by Ben J. Ward <[email protected]>
Rollout file .github/PULL_REQUEST_TEMPLATE.md

1158860c5cdb0960bb0eaaa66d8a97e2ab818615 authored over 6 years ago by Ben J. Ward <[email protected]>
Rollout file CODE_OF_CONDUCT.md

eda8f2f82af6a6b1a19ab7d65dd23928ee5a6f2a authored over 6 years ago by Ben J. Ward <[email protected]>
Rollout file CONTRIBUTING.md

96560de4ecd804d741dd18477d56338b1290f917 authored over 6 years ago by Ben J. Ward <[email protected]>
Add lower bound requirement for Compat

1e7b4e9fccd5f55897c5f2b0d19c59f8b3a17aa4 authored almost 7 years ago by Ben J. Ward <[email protected]>
Update readme and appveyor

85db2208f54464aa01515d47e76e8505b75cbb3d authored almost 7 years ago by Ben J. Ward <[email protected]>
Prep syntax for julia 0.7, drop julia 0.5 (#17)

* Updated parametric syntax

* Using Nullables and Test from Compat

* Use convert to Char r...

1a7495fc4bf9375dac2aa3ea017dc7a1e0665429 authored almost 7 years ago by Ben J. Ward <[email protected]>
improve test coverage (#16)

* add more tests on amino acids

* add more tests on DNA/RNA

9680751fabdb26ddc7a841c2115c149ec78e7617 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add a description on (try)parse (#15)

0540e11417a34e90bcdbba4b9b1a0fba7081956d authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
generate amino acid parser with Automa.jl (#13)

900875371caa194c650d6cc1d2db0af2fe37038e authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Restructure docs (#12)

* use material

* fix index.md

* decompose docs

* references

* rename index page

*...

d57f19253b7c5bc9e3f3f9152d26905fbf218161 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Method generalisations (#10)

* Generalised UInt8 -> NucleicAcid conversion

Nessecery for the current design of BioBridgeR'...

c614cffa8c20ac54584aa34822d771b3fa5ad3dc authored over 7 years ago by Ben J. Ward <[email protected]>
fix docstrings (#11)

9443faf071a10e44b223b1c631c947d17d8c53bc authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Updated Readme.md

08368ecd3edd25b353b8f389bdf4e7838b06f37b authored over 7 years ago by Ben J. Ward <[email protected]>
Update CI URLs to point to new caching infrastructure (#9)

035316a637365709bbae1207524d1ca37f538b4e authored over 7 years ago by Elliot Saba <[email protected]>
update docs (#8)

da0fb8f37acf6776e6b77a406dc46281b772797d authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix package name in docs (#7)

9dc6576df1e84a549fbd59e1734f8515201cbcbf authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Fix to make.jl in docs

f70c1ca7824173b69f073c0b3f2fc6e25f4803d0 authored over 7 years ago by Ben J. Ward <[email protected]>
export ACGTN and ACGUN (#6)

0dbbf631fa67904446e5c341fda2a5a033163227 authored over 7 years ago by Ben J. Ward <[email protected]>
Minor changes to mkdocs and types.md (#5)

71cc62f1f3b670d5c2fd2c8af5719e66d7031d93 authored over 7 years ago by Ben J. Ward <[email protected]>
restructure files in type-centric way (#4)

ba23a9ad2b4a9d9e01b0556e5ae633d319352c65 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
improve test coverage (#3)

e6b9fdac756529f52212d082b3a79184faf7142d authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add a converage badge to README.md (#2)

7b3e8b241e7ed04b1fb556059c3c49a9aa0aa9e8 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
remove takebuf_string from tests (#1)

07306d673924abae16e327e289358fa2b20600c0 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Added compat minimum version

Rename of package

Minor test fixes

Rename

Minor change to file header

c87580388b10088e044a899a98038b24e65717e5 authored almost 8 years ago by Ben J. Ward <[email protected]>
Corrected readme typo

dfe07e28ff3304b6e33bbac121f97aa456a82d9d authored almost 8 years ago by Ben J. Ward <[email protected]>
Revert "Corrected readme typo"

This reverts commit f192cf0e59a1b8fff76b4bc62d62cc2659984bc3.

2cbfb1d22b126be6694a3a73f8e49486d51f0728 authored almost 8 years ago by Ben J. Ward <[email protected]>
Added nucleic acids, amino acids, and setup integrations & docs

Edited docbuilding

Corrected some docs

Corrected make.jl

Corrected doctests

Added docs ...

7e236aaefcf0cc3d998b8db77fa5f7cfe7cfde9f authored almost 8 years ago by Ben J. Ward <[email protected]>
Initial commit

5c788968f011edfaa408d9b02cf14cabdc8d441f authored almost 8 years ago by Ben J. Ward <[email protected]>