test and formatting

Author: brentp

somalier.nimble

@@ -18,4 +18,5 @@ bin = @["somalier"]
 
 task test, "run the tests":
   exec "nim c  -d:useSysAssert -d:useGcAssert --lineDir:on --debuginfo -r tests/test_groups"
+  exec "nim c  -d:useSysAssert -d:useGcAssert --lineDir:on --debuginfo -r tests/test_format_float_clean"
   exec "bash tests/functional-tests.sh"

src/somalierpkg/pedrel.nim

@@ -2,13 +2,35 @@ import strutils
 import strformat
 import argparse
 import pedfile
-import sequtils
-import algorithm
+
+proc formatFloatClean*(f: float32): string =
+  ## Format a float32 as string, removing trailing zeros after decimal point
+  ## but keeping at least one zero if the number is whole (e.g., "1.0" not "1.")
+  # Use precision=6 to avoid floating-point precision artifacts
+  let formatted = formatFloat(f, ffDecimal, precision=6)
+
+  # Find the decimal point
+  let decimalPos = formatted.find('.')
+  if decimalPos == -1:
+    return formatted  # No decimal point, return as is
+
+  # Remove trailing zeros from the decimal part
+  var cleaned = formatted
+  while cleaned.len > decimalPos + 1 and cleaned[^1] == '0':
+    cleaned = cleaned[0..^2]  # Remove last character
+
+  # If we removed all decimal digits, add one back to keep "1.0" format
+  if cleaned[^1] == '.':
+    cleaned &= "0"
+
+  return cleaned
 
 proc pedrel_main*() =
   var argv = commandLineParams()
   if argv[0] == "pedrel":
     argv = argv[1..argv.high]
+  if len(argv) == 0:
+    argv = @["-h"]
 
   var p = newParser("somalier pedrel"):
     help("report pairwise relationships from pedigree file")
@@ -47,13 +69,14 @@ proc pedrel_main*() =
       let sampleB = samples[j]
       let rel = sampleA.relatedness(sampleB)
 
-      if rel > min_rel:
+      if rel >= min_rel:
         # Ensure consistent ordering (alphabetical by sample ID)
         let (sample1, sample2) = if sampleA.id < sampleB.id:
                                   (sampleA.id, sampleB.id)
                                 else:
                                   (sampleB.id, sampleA.id)
-        output_file.write_line(&"{sample1}\t{sample2}\t{rel:.6f}")
+        let relf = formatFloatClean(rel)
+        output_file.write_line(&"{sample1}\t{sample2}\t{relf}")
 
   if opts.output != "stdout":
     output_file.close()

src/somalierpkg/version.nim

@@ -1 +1 @@
-let somalierVersion* = "0.3.0"
+let somalierVersion* = "0.3.1"

tests/test_format_float_clean.nim

@@ -0,0 +1,35 @@
+import unittest
+
+# Import the function from pedrel module
+import ../src/somalierpkg/pedrel
+
+suite "formatFloatClean function":
+  test "handles decimal numbers correctly":
+    check formatFloatClean(1.234'f32) == "1.234"
+    check formatFloatClean(1.2'f32) == "1.2"
+    check formatFloatClean(1.1'f32) == "1.1"
+    check formatFloatClean(1.0'f32) == "1.0"
+    check formatFloatClean(0.5'f32) == "0.5"
+
+  test "handles whole numbers correctly":
+    check formatFloatClean(5.0'f32) == "5.0"
+    check formatFloatClean(0.0'f32) == "0.0"
+    check formatFloatClean(100.0'f32) == "100.0"
+
+  test "handles small decimal values":
+    check formatFloatClean(0.1'f32) == "0.1"
+    check formatFloatClean(0.01'f32) == "0.01"
+    check formatFloatClean(0.001'f32) == "0.001"
+
+  test "handles negative numbers":
+    check formatFloatClean(-1.234'f32) == "-1.234"
+    check formatFloatClean(-1.2'f32) == "-1.2"
+    check formatFloatClean(-1.0'f32) == "-1.0"
+
+  test "handles edge cases with precision":
+    check formatFloatClean(1.000001'f32) == "1.000001"
+    check formatFloatClean(1.0001'f32) == "1.0001"
+    check formatFloatClean(1.000000'f32) == "1.0"
+
+  test "handles very small differences":
+    check formatFloatClean(1.0000001'f32) == "1.0"