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Rustify #5

Merged
merged 158 commits into from
Nov 22, 2023
Merged

Rustify #5

merged 158 commits into from
Nov 22, 2023

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ktmeaton
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Katherine Eaton and others added 30 commits November 21, 2023 22:14
@ktmeaton
repo: remove old files for rust rewrite
7308b60
@ktmeaton
rustify: add rust init files
7e0ab98
@ktmeaton
ci: cleanup old workflows
2ef13c3
@ktmeaton
lint: add rust tools to pre-commit
2143f06
@ktmeaton
lint: toml
2e4e884
@ktmeaton
chore(cliff): add cliff toml
df9b513
@ktmeaton
chore(toolchain): set rust to 1.69.0
e563860
@ktmeaton
chore(fmt): add rustfmt toml
841aa75
@ktmeaton
feat(trait): add to_yaml
e026866
@ktmeaton
chore(dependencies): remove unused dependencies
ad746c0
@ktmeaton
feature(dataset): add enums DatasetName and DatasetVersion
76c44b2
@ktmeaton
feature(dataset): start new func download_sequences
bbcddcc
@ktmeaton
feature(cli): add new cli arg parser
6a1dff8 
temporarily disable pre-commit fmt
@ktmeaton
docs(readme): add readme
b7b2307
@ktmeaton
feat(dataset): add func download_reference
47020e1
@ktmeaton
feat(dataset): add new fun decompress_file
9e4bc33
@ktmeaton
feat(dataset): add more download error handling
8028fa6
@ktmeaton
feat(dataset): simplify dataset download
61bba01
@ktmeaton
fix(dataset): zstd decompression
c17c8bc
@ktmeaton
feat(dataset): add load function
e956756
@ktmeaton
chore(dataset): break structs into submodules
052647c
@ktmeaton
feat(sequence): add seq parsing to from_record
ebfc438
@ktmeaton
feat(sequence): add seq parsing to from_record
7a103e5
@ktmeaton
feat(dataset): add name, tag, summary
b13be84
@ktmeaton
chore(git): don't ignore src dataaset
cd2f063
@ktmeaton
chore(cargo): add fast compilation config
49332fc
@ktmeaton
feat(dataset): fix constants url
5c4a084
@ktmeaton
feat(dataset): continue find_best_match, clippy skip
dd1371b
@ktmeaton
feat(phylogeny): add phylogeny module to dataset
9a322a8
@ktmeaton
feat(phylogeny): add import and export functions
eaa7e95
@ktmeaton
ci: specify workflow_run branch dependency
30bda5a
@ktmeaton
ci: test specify branch in download-artifact
5e12d18
@ktmeaton
ci: test manually specify rustify branch
4f4e52a
@ktmeaton
ci: test try reusable workflow
b7c74d9
@ktmeaton
ci: test try no spaces
06e3836
@ktmeaton
ci: use local path for build include
e85108e
@ktmeaton
ci: use very specific ./ prefix
f661892
@ktmeaton
ci: test don't specify build file sha
d14d1b0
@ktmeaton
ci: build add workflow_call for reusable
1633d0e
@ktmeaton
ci: test add needs
b4e570b
@ktmeaton
ci: add build reusable to latest
e07f885
@ktmeaton
ci: force latest to fail
195030a
@ktmeaton
ci: latest fix grep path, still force fail
2c8074c
@ktmeaton
ci: latest fail check complete
cc57ae2
@ktmeaton
ci: release test artifact download
0317bb3
@ktmeaton
ci: check release binary upload
ccfea18
@ktmeaton
ci: artifacts as csv
45868f4
@ktmeaton
ci: release add test tag
9e4a4c4
@ktmeaton
recombination: shuffle around novel recombination classification
b632a82
@ktmeaton
edge_case: add sars-cov-2 XCM
585d007
@ktmeaton
ci: release finish test
2585ba7
@ktmeaton
edge_case: add sars-cov-2 XCQ
2342853
@ktmeaton
dataset: add toy1
47a2f9f
@ktmeaton
docs: update readme
77f7be5
@ktmeaton ktmeaton mentioned this pull request Nov 22, 2023
Closed
@ktmeaton ktmeaton merged commit 8484a3e into main Nov 22, 2023
12 checks passed
@ktmeaton ktmeaton mentioned this pull request Nov 22, 2023
Open
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@ktmeaton