Rust tests

.github/workflows/pypi.yml

@@ -1,4 +1,4 @@
-name: pypi
+name: pypi upload
 
 on:
   create:

.github/workflows/planemo.yml → .github/workflows/test_planemo.yml

@@ -1,4 +1,4 @@
-name: Planemo
+name: tests_planemo
 on: [push, pull_request, workflow_dispatch]
 
 env:

.github/workflows/test.yml → .github/workflows/test_pytest.yml

@@ -1,4 +1,4 @@
-name: Test
+name: tests_pytest
 on: [push, pull_request, workflow_dispatch]
 
 defaults:
@@ -41,7 +41,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9','3.10', '3.11', '3.12']
+        python-version: ['3.9','3.10', '3.11', '3.12', '3.13']
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
@@ -73,7 +73,7 @@ jobs:
     runs-on: macOS-latest
     strategy:
       matrix:
-        python-version: ['3.9','3.10', '3.11', '3.12']
+        python-version: ['3.9','3.10', '3.11', '3.12', '3.13']
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5

.github/workflows/cargo_test.yml → .github/workflows/test_rust.yml

@@ -1,4 +1,4 @@
-name: Cargo
+name: tests_rust
 on: [push, pull_request, workflow_dispatch]
 
 jobs:

.github/workflows/maturin.yml → .github/workflows/wheels.yml

@@ -1,11 +1,10 @@
-name: Wheels
+name: build wheels
 # maturin generate-ci github > .github/workflows/maturin.yml
 # Also, see: https://github.com/jackh726/bigtools/blob/master/.github/workflows/release-python.yml
 
 on:
   push:
   pull_request:
-  workflow_dispatch:
 
 permissions:
   contents: read

src/lib.rs

@@ -10,7 +10,7 @@ mod filtering;
 mod multibamsummary;
 mod normalization;
 #[cfg(test)]
-mod test;
+mod tests;
 
 #[pymodule]
 fn hp(m: &Bound<'_, PyModule>) -> PyResult<()> {

src/tests/mod.rs

@@ -0,0 +1,2 @@
+pub mod test_calc;
+pub mod test_normalization;

src/tests/test_calc.rs

@@ -0,0 +1,115 @@
+use crate::calc::*;
+use ndarray::{Array1, Array2};
+
+mod vector_calculations_tests{
+    use super::*;
+
+    #[test]
+    fn test_median() {
+        let v: Vec<u32> = vec![1,2,3,4,5];
+        assert_eq!(median(v), 3.0);
+    }
+
+    #[test]
+    fn test_mean_float() {
+        let v: Vec<f32> = vec![1.0, 2.0, 3.0, 4.0, 5.0];
+        assert_eq!(mean_float(v.iter().collect()), 3.0);
+    }
+
+    #[test]
+    fn test_median_float() {
+        let v: Vec<f32> = vec![1.0, 2.0, 3.0, 4.0, 5.0];
+        assert_eq!(median_float(v.iter().collect()), 3.0);
+    }
+
+
+    #[test]
+    fn test_min_float() {
+        let v: Vec<f32> = vec![1.0, 2.0, 3.0, 4.0, 5.0];
+        assert_eq!(min_float(v.iter().collect()), 1.0);
+    }
+
+    #[test]
+    fn test_max_float() {
+        let v: Vec<f32> = vec![1.0, 2.0, 3.0, 4.0, 5.0];
+        assert_eq!(max_float(v.iter().collect()), 5.0);
+    }
+
+    #[test]
+    fn test_sum_float() {
+        let v: Vec<f32> = vec![1.0, 2.0, 3.0, 4.0, 5.0];
+        assert_eq!(sum_float(v.iter().collect()), 15.0);
+    }
+
+    #[test]
+    fn test_std_float() {
+        let v: Vec<f32> = vec![1.0, 2.0, 3.0, 4.0, 5.0];
+        assert_eq!(std_float(v.iter().collect()), 1.5811388);
+
+        let v: Vec<f32> = vec![1.0, 1.0, 1.0];
+        assert_eq!(std_float(v.iter().collect()), 0.0);
+
+        assert_eq!(std_float(vec![]), 0.0);
+    }
+}
+
+mod scalefactor_calculations_tests{
+    use super::*;
+    #[test]
+    fn test_calc_ratio() {
+        let cov1: f32 = 5.0;
+        let cov2: f32 = 10.0;
+
+        let sf1: f32 = 1.0;
+        let sf2: f32 = 2.0;
+
+        let pc1: f32 = 1.0;
+        let pc2: f32 = 2.0;
+
+        let log2 = "log2";
+        let ratio = "ratio";
+        let reciprocal_ratio = "reciprocal_ratio";
+        let subtract = "subtract";
+
+        let r1 = calc_ratio(
+            cov1, cov2,
+            &sf1, &sf2,
+            &pc1, &pc2,
+            log2
+        );
+        let r2 = calc_ratio(
+            cov1, cov2,
+            &sf1, &sf2,
+            &pc1, &pc2,
+            ratio
+        );
+        let r3 = calc_ratio(
+            cov1, cov2,
+            &sf1, &sf2,
+            &pc1, &pc2,
+            reciprocal_ratio
+        );
+        let r4 = calc_ratio(
+            cov1, cov2,
+            &sf1, &sf2,
+            &pc1, &pc2,
+            subtract
+        );
+        assert_eq!(r1, -1.87);
+        assert_eq!(r2, 0.27);
+        assert_eq!(r3, -0.27);
+        assert_eq!(r4, -16.0);
+    }
+
+    #[test]
+    fn test_deseq_scalefactors() {
+        let counts = Array2::from_shape_vec((3, 3), vec![
+            1.0, 2.0, 3.0,
+            4.0, 5.0, 6.0,
+            7.0, 8.0, 9.0
+        ]).unwrap();
+        let sf = deseq_scalefactors(&counts);
+        let expected_sf = Array1::from_vec(vec![1.233106, 0.9864848, 0.82207066]);
+        assert_eq!(sf, expected_sf);
+    }
+}

src/tests/test_normalization.rs

@@ -0,0 +1,84 @@
+use crate::normalization::*;
+
+mod scale_factor_tests {
+    use super::*;
+
+    #[test]
+    fn test_scale_factor_rpkm() {
+        let nm = "RPKM";
+        let sf = scale_factor(
+            nm,
+            1000, 10, 10000,
+            20.0, 20.0,
+            1.0, &false
+        );
+        assert_eq!(sf, 99999.99);
+    }
+
+    #[test]
+    fn test_scale_factor_cpm() {
+        let nm = "CPM";
+        let sf = scale_factor(
+            nm,
+            1000, 10, 10000,
+            20.0, 20.0,
+            1.0, &false
+        );
+        assert_eq!(sf, 999.99994);
+    }
+
+    #[test]
+    fn test_scale_factor_bpm() {
+        let nm = "BPM";
+        let sf = scale_factor(
+            nm,
+            1000, 10, 10000,
+            20.0, 20.0,
+            1.0, &false
+        );
+        assert_eq!(sf, 999.99994);
+    }
+
+    #[test]
+    fn test_scale_factor_rpgc() {
+        let nm = "RPGC";
+        let sf = scale_factor(
+            nm,
+            1000, 10, 10000,
+            20.0, 20.0,
+            1.0, &false
+        );
+        assert_eq!(sf, 0.5);
+    }
+
+    #[test]
+    fn test_preset_scalefactor() {
+        let nm = "RPKM";
+        let sf = scale_factor(
+            nm,
+            1000, 10, 10000,
+            20.0, 20.0,
+            5.5, &false
+        );
+        assert_eq!(sf, 5.5);
+    }
+}
+
+mod bamcompare_scale_factor_tests{
+    use super::*;
+
+    #[test]
+    fn test_bamcompare_readcount() {
+        let nm = "readCount";
+        let (sf1, sf2) = scale_factor_bamcompare(
+            nm,
+            1000, 2000,
+            10, 10000,
+            "RPKM", 
+            20.0, 20.0,
+            1.0, 1.0
+        );
+        assert_eq!(sf1, 1.0);
+        assert_eq!(sf2, 0.5);
+    }
+}