Merge pull request #3 from BenjaminDoran/dev

Dev (v0.2) rewrite

*Revise regNJ function:*

It now only uses the memory space of a single distance matrix, and overwrites new nodes into one of the merged nodes. This does change the ordering of merges in the algorithm (i.e. the pseudoroot may change) but the unrooted tree is confirmed to be the same (i.e. patristic distances don't change).

*Update testing framework:*

followed SciML organization with safetestsets and made each testset a regular script

*Update Docs:*

added doctests, and new docstrings for `heights` and `merges` functions

*Add benchmark suite:*

I am now testing on matrices up to size 1024, with the revision regNJ seems much faster than before, but some of that seems to be testing on yuletree matrices rather than uniformly random matrices

.github/workflows/Benchmark.yml

@@ -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 }}

.github/workflows/CI.yml

@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.5'
+          - '1.8'
           - '1'
           - 'nightly'
         os:

.gitignore

@@ -1,5 +1,8 @@
 *.jl.*.cov
 *.jl.cov
 *.jl.mem
-/Manifest.toml
+**/Manifest.toml
 /docs/build/
+/.benchmarkci
+/benchmark/*.json
+# /benchmark/benchmarkdata/dist_mtx*

Project.toml

@@ -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"

benchmark/Project.toml

@@ -0,0 +1,5 @@
+[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"

benchmark/benchmarkdata/dist_mtx_16.txt

@@ -0,0 +1,17 @@
+16
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+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