Merge branch 'main' into switch-to-skani-cli

Author: AroneyS

.github/workflows/test-galah.yml

@@ -12,13 +12,12 @@ jobs:
         matrix:
             os: ["ubuntu-latest"]
     steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: test
           environment-file: galah.yml
           auto-activate-base: false
-          mamba-version: "*"
           channels: conda-forge,defaults,bioconda
       - run: |
           conda info

src/skani.rs

@@ -212,3 +212,45 @@ pub fn calculate_skani(fasta1: &str, fasta2: &str, min_aligned_threshold: f32) -
     finish_command_safely(process, "skani");
     to_return
 }
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    fn init() {
+        let _ = env_logger::builder().is_test(true).try_init();
+    }
+
+    #[test]
+    #[should_panic(
+        expected = "Error: skani produces inaccurate results with ANI less than 85%. Provided: 80"
+    )]
+    fn test_precluster_skani_with_low_ani() {
+        init();
+        precluster_skani(
+            &[
+                "tests/data/abisko4/73.20120800_S1X.13.fna",
+                "tests/data/abisko4/73.20120600_S2D.19.fna",
+                "tests/data/abisko4/73.20120700_S3X.12.fna",
+                "tests/data/abisko4/73.20110800_S2D.13.fna",
+            ],
+            80.0,
+            0.2,
+        );
+    }
+
+    #[test]
+    fn test_precluster_skani_with_valid_ani() {
+        init();
+        precluster_skani(
+            &[
+                "tests/data/abisko4/73.20120800_S1X.13.fna",
+                "tests/data/abisko4/73.20120600_S2D.19.fna",
+                "tests/data/abisko4/73.20120700_S3X.12.fna",
+                "tests/data/abisko4/73.20110800_S2D.13.fna",
+            ],
+            95.0,
+            0.2,
+        );
+    }
+}

tests/test_cmdline.rs

@@ -312,6 +312,37 @@ mod tests {
                 .unwrap();
     }
 
+    #[test]
+    fn test_skani_with_low_ani() {
+        Assert::main_binary()
+            .with_args(&[
+                "cluster",
+                "--genome-fasta-files",
+                "tests/data/abisko4/73.20120800_S1X.13.fna",
+                "tests/data/abisko4/73.20120600_S2D.19.fna",
+                "tests/data/abisko4/73.20120700_S3X.12.fna",
+                "tests/data/abisko4/73.20110800_S2D.13.fna",
+                "--precluster-method",
+                "skani",
+                "--cluster-method",
+                "skani",
+                "--precluster-ani",
+                "80",
+                "--ani",
+                "80",
+                "--output-cluster-definition",
+                "/dev/stdout",
+                "--checkm-tab-table",
+                "tests/data/abisko4/abisko4.csv",
+            ])
+            .fails()
+            .stderr()
+            .contains(
+                "Error: skani produces inaccurate results with ANI less than 85%. Provided: 80",
+            )
+            .unwrap();
+    }
+
     #[test]
     fn test_github7() {
         Assert::main_binary()