fix: handle non-alphanumeric characters in infer_pattern (#102)

src/filepattern/cpp/pattern.cpp

@@ -644,7 +644,13 @@ std::string Pattern::swSearch(std::string& pattern, std::string& filename, const
                         patternTemplate = "@" + patternTemplate;
                     }
                 } else {
-                    throw std::runtime_error("Non-numeric, non-alphabetic characters found that do not match");
+                    // Handle special characters (non-numeric, non-alphabetic)
+                    // If they match, include them directly in the pattern
+                    if(filename[col-1] == pattern[row-1] && (lastCol != col || lastRow != row)){
+                        patternTemplate = filename[col-1] + patternTemplate;
+                    } else {
+                        throw std::runtime_error("Non-numeric, non-alphabetic characters found that do not match");
+                    }
                 }
 
             } else if(lastCol != col && lastRow != row){ // progrsssion was made so add a placeholder

tests/test_inferpattern_special_chars.py

@@ -0,0 +1,67 @@
+# -*- coding: utf-8 -*-
+"""
+Tests for pattern inference with special (non-alphanumeric) characters in filenames.
+
+Regression tests for GitHub issue #102, which caused RuntimeError when files
+contained special characters like periods, hyphens, or underscores in their names
+(e.g., .ome.tif extension). The error message was "Non-numeric, non-alphabetic
+characters found that do not match" during pattern inference.
+"""
+
+import pytest
+import filepattern as fp
+
+
+class TestInferPatternSpecialChars():
+    """Test cases for pattern inference with special characters in filenames."""
+
+    def test_ome_tif_extension(self):
+        """Test inference with .ome.tif double extension."""
+        files = [
+            "image_001.ome.tif",
+            "image_002.ome.tif",
+            "image_003.ome.tif"
+        ]
+        pattern = fp.infer_pattern(files=files)
+        # Should successfully infer pattern without throwing RuntimeError
+        assert pattern == "image_00{r:d}.ome.tif"
+
+    def test_multiple_periods(self):
+        """Test inference with multiple periods in filename."""
+        files = [
+            "exp.data.v1.001.tif",
+            "exp.data.v1.002.tif",
+            "exp.data.v1.003.tif"
+        ]
+        pattern = fp.infer_pattern(files=files)
+        assert pattern == "exp.data.v1.00{r:d}.tif"
+
+    def test_hyphens_and_underscores(self):
+        """Test inference with hyphens and underscores."""
+        files = [
+            "sample-001_exp_01.tif",
+            "sample-002_exp_02.tif",
+            "sample-003_exp_03.tif"
+        ]
+        pattern = fp.infer_pattern(files=files)
+        assert pattern == "sample-00{r:d}_exp_0{t:d}.tif"
+
+    def test_complex_special_chars(self):
+        """Test inference with multiple types of special characters."""
+        files = [
+            "Week1_22141.ome.001.tif",
+            "Week1_22141.ome.002.tif",
+            "Week1_22141.ome.003.tif"
+        ]
+        pattern = fp.infer_pattern(files=files)
+        assert pattern == "Week1_22141.ome.00{r:d}.tif"
+
+    def test_ome_tif_with_variable_naming(self):
+        """Test .ome.tif files with custom variable names."""
+        files = [
+            "cell_x01_y02_z03.ome.tif",
+            "cell_x04_y05_z06.ome.tif",
+            "cell_x07_y08_z09.ome.tif"
+        ]
+        pattern = fp.infer_pattern(files=files, variables="xyz")
+        assert pattern == "cell_x0{x:d}_y0{y:d}_z0{z:d}.ome.tif"