Merge pull request #20 from jeffersonfparil/dev

Close issue #19

.github/workflows/rust.yml

@@ -0,0 +1,61 @@
+name: 🚀
+on:
+  push:
+    branches:
+      - main
+      - dev
+jobs:
+  compile:
+    name: Compile
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup | Checkout
+        uses: actions/checkout@v3
+      - name: Setup | Rust
+        uses: ATiltedTree/setup-rust@v1
+        with:
+          rust-version: stable
+      - name: Build | Compile
+        run: cargo check
+  test:
+    name: Test
+    strategy:
+      matrix:
+        os:
+          - ubuntu-latest
+          - windows-latest
+          # - macOS-latest
+        rust:
+          - stable
+          # - beta
+          # - nightly
+    runs-on: ${{ matrix.os }}
+    needs: [compile]
+    steps:
+      - name: Setup | Checkout
+        uses: actions/checkout@v3
+      - name: Setup | Rust
+        uses: ATiltedTree/setup-rust@v1
+        with:
+          rust-version: ${{ matrix.rust }}
+      - name: Tests | Rust
+        run: cargo test
+      - name: Build | Compile | Test on test data
+        run: | 
+          cargo run -- -h
+
+          cargo run -- -f tests/test_2.csv -m mean
+          cargo run -- -f tests/test_2.sync -m mean
+          cargo run -- -f tests/test_2.vcf -m mean
+
+          cargo run -- -f tests/test_2.csv -m mean --pool-sizes=11,12,13,14,15,16,17,18,19,20
+          cargo run -- -f tests/test_2.sync -m mean --pool-sizes=11,12,13,14,15,16,17,18,19,20
+          cargo run -- -f tests/test_2.vcf -m mean --pool-sizes=11,12,13,14,15,16,17,18,19,20
+
+          cargo run -- -f tests/test_2.csv
+          cargo run -- -f tests/test_2.sync
+          cargo run -- -f tests/test_2.vcf
+
+          cargo run -- -f tests/test_2.csv --min-loci-corr=-1.0 --max-pool-dist=-1.0 --min-l-loci=1 --min-k-neighbours=1
+          cargo run -- -f tests/test_2.sync --min-loci-corr=-1.0 --max-pool-dist=-1.0 --min-l-loci=1 --min-k-neighbours=1
+          cargo run -- -f tests/test_2.vcf --min-loci-corr=-1.0 --max-pool-dist=-1.0 --min-l-loci=1 --min-k-neighbours=1

.gitignore

@@ -1,7 +1,9 @@
-/src/rust/Cargo.lock
-/src/rust/target/
-/src/rust/tests/test-*
-/tests/test.vcf-*
+/Cargo.lock
+/target/
+/tests/test*-*
+/tests/test*.vcf-*
+/tests/test*.sync-*
+/tests/test*.csv-*
 /tests/perf.slurm
 /tests/slurm-*
 /tests/apple.vcf

src/rust/Cargo.toml → Cargo.toml

@@ -3,15 +3,12 @@ name = 'imputef'
 version = '0.1.0'
 edition = '2021'
 
-[lib]
-crate-type = [ 'staticlib' ]
-name = 'imputef'
-
 [dependencies]
-extendr-api = '*'
+clap = { version="3.2.23", features=["derive"]}
 ndarray = { version = "0.15.6", features = ["rayon"]}
+ndarray-linalg = "0.16"
+# ndarray-linalg = { version = "0.16.0", features = ["intel-mkl-static"] } 
 # ndarray-linalg = { version = "0.16.0", features = ["openblas"] }
-ndarray-linalg = { version = "0.16.0", features = ["intel-mkl-static"] }
 statrs = "0.16.0"
 rand = "0.8.5"
 rayon = "1.7.0"