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Dev (v0.2) rewrite #3

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merged 11 commits into from
Jan 21, 2024
Merged

Dev (v0.2) rewrite #3

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5c6ca2e
Rewrite of regNJ and code organization
BenjaminDoran Jan 20, 2024
4b46366
Update Testing
BenjaminDoran Jan 20, 2024
84f0a36
add gitignore to docs folder
BenjaminDoran Jan 20, 2024
ba8279b
update gitignores
BenjaminDoran Jan 20, 2024
be969c1
update tests
BenjaminDoran Jan 21, 2024
66f0e14
add benchmark
BenjaminDoran Jan 21, 2024
0ed209e
Merge branch 'main' into dev
BenjaminDoran Jan 21, 2024
b603fba
Try workflow update
BenjaminDoran Jan 21, 2024
b611059
update julia compat to 1.8 to use allequal function
BenjaminDoran Jan 21, 2024
e970090
Update docs and doctests
BenjaminDoran Jan 21, 2024
62f9700
add benchmark project file
BenjaminDoran Jan 21, 2024
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27 changes: 27 additions & 0 deletions .github/workflows/Benchmark.yml
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@@ -0,0 +1,27 @@
name: Run benchmarks

on:
pull_request:

jobs:
Benchmark:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: julia-actions/setup-julia@latest
with:
version: 1
- uses: julia-actions/julia-buildpkg@latest
- name: Install dependencies
run: julia -e 'using Pkg; pkg"add PkgBenchmark [email protected]"'
- name: Run benchmarks
run: julia -e 'using BenchmarkCI; BenchmarkCI.judge(; baseline = "origin/main")'
- name: Post results
run: julia -e 'using BenchmarkCI; BenchmarkCI.postjudge()'
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- name: Push results
run: julia -e "using BenchmarkCI; BenchmarkCI.pushresult()"
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
SSH_KEY: ${{ secrets.DOCUMENTER_KEY }}
2 changes: 1 addition & 1 deletion .github/workflows/CI.yml
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Expand Up @@ -18,7 +18,7 @@ jobs:
fail-fast: false
matrix:
version:
- '1.5'
- '1.8'
- '1'
- 'nightly'
os:
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5 changes: 4 additions & 1 deletion .gitignore
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@@ -1,5 +1,8 @@
*.jl.*.cov
*.jl.cov
*.jl.mem
/Manifest.toml
**/Manifest.toml
/docs/build/
/.benchmarkci
/benchmark/*.json
# /benchmark/benchmarkdata/dist_mtx*
15 changes: 5 additions & 10 deletions Project.toml
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@@ -1,18 +1,13 @@
name = "NeighborJoining"
uuid = "3f465f53-8c2e-426b-b4f1-431dfde0fdf8"
authors = ["Benjamin Doran and collaborators"]
version = "0.1.2"
version = "0.2.0"

[deps]
ArgCheck = "dce04be8-c92d-5529-be00-80e4d2c0e197"
Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"

[compat]
julia = "^1.5"

[extras]
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
NewickTree = "b0a14db8-6308-4ebc-8917-f72cd81f5094"
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

[targets]
test = ["Test", "NewickTree", "LinearAlgebra"]
ArgCheck = "2.3"
Printf = "^1.8"
julia = "^1.8"
5 changes: 5 additions & 0 deletions benchmark/Project.toml
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[deps]
BenchmarkCI = "20533458-34a3-403d-a444-e18f38190b5b"
BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
NeighborJoining = "3f465f53-8c2e-426b-b4f1-431dfde0fdf8"
PkgBenchmark = "32113eaa-f34f-5b0d-bd6c-c81e245fc73d"
1,025 changes: 1,025 additions & 0 deletions benchmark/benchmarkdata/dist_mtx_1024.txt
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129 changes: 129 additions & 0 deletions benchmark/benchmarkdata/dist_mtx_128.txt
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17 changes: 17 additions & 0 deletions benchmark/benchmarkdata/dist_mtx_16.txt
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Original file line number Diff line number Diff line change
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16
Tip0 0.000000000000 0.963081734110 0.624313848059 0.925815786052 0.572697533597 0.258379974053 0.606970292080 1.439715678301 0.912013899378 1.177409200000 0.968317514541 1.658330445478 1.473440805554 0.866029913638 1.612330561438 0.816788625130
Tip1 0.963081734110 0.000000000000 1.064738817651 0.234632262248 0.461021881522 0.861571428330 0.495294640005 0.781408160938 0.588904352163 0.519101682637 0.310009997179 1.000022928116 0.815133288192 0.754354261563 0.954023044075 0.493679077914
Tip10 0.624313848059 1.064738817651 0.000000000000 1.027472869593 0.674354617137 0.522803542279 0.708627375620 1.541372761842 1.013670982919 1.279066283540 1.069974598082 1.759987529019 1.575097889095 0.967686997179 1.713987644978 0.918445708671
Tip11 0.925815786052 0.234632262248 1.027472869593 0.000000000000 0.423755933464 0.824305480272 0.458028691947 0.744142212880 0.551638404104 0.481835734579 0.272744049120 0.962756980058 0.777867340134 0.717088313505 0.916757096017 0.456413129856
Tip12 0.572697533597 0.461021881522 0.674354617137 0.423755933464 0.000000000000 0.471187227817 0.045978027584 0.937655825712 0.409954046790 0.675349347411 0.466257661953 1.156270592890 0.971380952966 0.305037649142 1.110270708849 0.314728772542
Tip13 0.258379974053 0.861571428330 0.522803542279 0.824305480272 0.471187227817 0.000000000000 0.505459986300 1.338205372521 0.810503593599 1.075898894220 0.866807208761 1.556820139699 1.371930499774 0.764519607858 1.510820255658 0.715278319350
Tip14 0.606970292080 0.495294640005 0.708627375620 0.458028691947 0.045978027584 0.505459986300 0.000000000000 0.971928584195 0.444226805273 0.709622105894 0.500530420436 1.190543351373 1.005653711449 0.297921778232 1.144543467332 0.349001531025
Tip15 1.439715678301 0.781408160938 1.541372761842 0.744142212880 0.937655825712 1.338205372521 0.971928584195 0.000000000000 1.065538296353 0.511519674511 0.520563329442 0.424109007886 0.087011070210 1.230988205754 0.378109123846 0.970313022105
Tip2 0.912013899378 0.588904352163 1.013670982919 0.551638404104 0.409954046790 0.810503593599 0.444226805273 1.065538296353 0.000000000000 0.803231818052 0.594140132593 1.284153063531 1.099263423607 0.703286426832 1.238153179490 0.351045148765
Tip3 1.177409200000 0.519101682637 1.279066283540 0.481835734579 0.675349347411 1.075898894220 0.709622105894 0.511519674511 0.803231818052 0.000000000000 0.258256851140 0.730134441689 0.545244801765 0.968681727453 0.684134557648 0.708006543804
Tip4 0.968317514541 0.310009997179 1.069974598082 0.272744049120 0.466257661953 0.866807208761 0.500530420436 0.520563329442 0.594140132593 0.258256851140 0.000000000000 0.739178096619 0.554288456695 0.759590041994 0.693178212579 0.498914858345
Tip5 1.658330445478 1.000022928116 1.759987529019 0.962756980058 1.156270592890 1.556820139699 1.190543351373 0.424109007886 1.284153063531 0.730134441689 0.739178096619 0.000000000000 0.457834135140 1.449602972932 0.073843524556 1.188927789283
Tip6 1.473440805554 0.815133288192 1.575097889095 0.777867340134 0.971380952966 1.371930499774 1.005653711449 0.087011070210 1.099263423607 0.545244801765 0.554288456695 0.457834135140 0.000000000000 1.264713333007 0.411834251099 1.004038149358
Tip7 0.866029913638 0.754354261563 0.967686997179 0.717088313505 0.305037649142 0.764519607858 0.297921778232 1.230988205754 0.703286426832 0.968681727453 0.759590041994 1.449602972932 1.264713333007 0.000000000000 1.403603088891 0.608061152583
Tip8 1.612330561438 0.954023044075 1.713987644978 0.916757096017 1.110270708849 1.510820255658 1.144543467332 0.378109123846 1.238153179490 0.684134557648 0.693178212579 0.073843524556 0.411834251099 1.403603088891 0.000000000000 1.142927905242
Tip9 0.816788625130 0.493679077914 0.918445708671 0.456413129856 0.314728772542 0.715278319350 0.349001531025 0.970313022105 0.351045148765 0.708006543804 0.498914858345 1.188927789283 1.004038149358 0.608061152583 1.142927905242 0.000000000000
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