Use existing function to call photon mosaic

tests/conftest.py

@@ -6,6 +6,7 @@
 """
 
 import argparse
+import subprocess
 from datetime import datetime
 from pathlib import Path
 
@@ -16,6 +17,37 @@
 from tests.tree_helpers import tree as tree_lines
 
 
+@pytest.fixture
+def run_photon_mosaic():
+    def inner_run_photon_mosaic(workdir, configfile, timeout=None):
+        """Helper function to run photon-mosaic CLI with dry-run.
+
+        timeout: seconds to wait for the subprocess to complete. If None,
+        wait indefinitely (no timeout).
+        """
+        cmd = [
+            "photon-mosaic",
+            "--config",
+            str(configfile),
+            "--log-level",
+            "DEBUG",
+        ]
+
+        result = subprocess.run(
+            cmd,
+            cwd=workdir,
+            capture_output=True,
+            text=True,
+            timeout=timeout,
+            encoding="utf-8",
+            errors="replace",
+        )
+
+        return result
+
+    return inner_run_photon_mosaic
+
+
 @pytest.fixture
 def test_data_root():
     """Return the path to test data directory."""
@@ -62,24 +94,6 @@ def metadata_base_config():
     return config
 
 
-@pytest.fixture
-def map_of_tiffs():
-    """
-    Create a map of tiffs in test data using rglob -
-    for backward compatibility with unit tests that use static data.
-    For integration tests, use the map_of_tiffs from snake_test_env instead.
-    """
-
-    photon_mosaic_path = Path(__file__).parent / "data"
-    map_of_tiffs = {}
-    for dataset in photon_mosaic_path.glob("*"):
-        if dataset.is_dir():
-            # Get just the filenames, not the full paths
-            tiff_files = [f.name for f in dataset.rglob("*.tif")]
-            map_of_tiffs[dataset.name] = tiff_files
-    return map_of_tiffs
-
-
 @pytest.fixture
 def cli_args(snake_test_env):
     """

tests/test_integration/test_whole_workflow.py

@@ -244,21 +244,11 @@ def test_snakemake_with_contrast(snake_test_env, test_config_with_contrast):
     )
 
 
-def test_photon_mosaic_cli_dry_run(snake_test_env):
+def test_photon_mosaic_cli_dry_run(snake_test_env, run_photon_mosaic):
     """Test that photon-mosaic can do a dry run."""
-    cmd = [
-        "photon-mosaic",
-        "--config",
-        str(snake_test_env["configfile"]),
-    ]
-
-    result = subprocess.run(
-        cmd,
-        cwd=snake_test_env["workdir"],
-        capture_output=True,
-        text=True,
-        encoding="utf-8",
-        errors="replace",
+    result = run_photon_mosaic(
+        snake_test_env["workdir"],
+        snake_test_env["configfile"],
     )
 
     assert result.returncode == 0, (
@@ -267,21 +257,11 @@ def test_photon_mosaic_cli_dry_run(snake_test_env):
     )
 
 
-def test_photon_mosaic_cli(snake_test_env):
+def test_photon_mosaic_cli(snake_test_env, run_photon_mosaic):
     """Test photon-mosaic pipeline."""
-    cmd = [
-        "photon-mosaic",
-        "--config",
-        str(snake_test_env["configfile"]),
-    ]
-
-    result = subprocess.run(
-        cmd,
-        cwd=snake_test_env["workdir"],
-        capture_output=True,
-        text=True,
-        encoding="utf-8",
-        errors="replace",
+    result = run_photon_mosaic(
+        snake_test_env["workdir"],
+        snake_test_env["configfile"],
     )
 
     assert result.returncode == 0, (

tests/test_unit/test_metadata.py

@@ -7,35 +7,13 @@
 
 import re
 import shutil
-import subprocess
 from pathlib import Path
 
 import yaml
 
 from photon_mosaic.dataset_discovery import DatasetDiscoverer
 
 
-def run_photon_mosaic(workdir, configfile, timeout=None):
-    """Helper function to run photon-mosaic CLI with dry-run.
-
-    timeout: seconds to wait for the subprocess to complete. If None,
-    wait indefinitely (no timeout).
-    """
-    cmd = [
-        "photon-mosaic",
-        "--config",
-        str(configfile),
-        "--log-level",
-        "DEBUG",
-    ]
-
-    result = subprocess.run(
-        cmd, cwd=workdir, capture_output=True, text=True, timeout=timeout
-    )
-
-    return result
-
-
 class TestMetadataFunctionality:
     """Test class for metadata extraction functionality."""
 
@@ -206,7 +184,9 @@ def test_neuroblueprint_format_validation(self):
                 name, "sub"
             ), f"{name} should be invalid"
 
-    def test_photon_mosaic_cli_custom_metadata(self, custom_metadata_env):
+    def test_photon_mosaic_cli_custom_metadata(
+        self, custom_metadata_env, run_photon_mosaic
+    ):
         """Test photon-mosaic CLI with custom metadata format."""
         # Run photon-mosaic with dry-run to test metadata processing
         result = run_photon_mosaic(
@@ -229,7 +209,7 @@ def test_photon_mosaic_cli_custom_metadata(self, custom_metadata_env):
         ), "Pipeline should complete successfully"
 
     def test_photon_mosaic_cli_neuroblueprint_metadata(
-        self, neuroblueprint_env
+        self, neuroblueprint_env, run_photon_mosaic
     ):
         """Test photon-mosaic CLI with NeuroBlueprint metadata format."""
         # Run photon-mosaic with dry-run to test metadata processing
@@ -253,7 +233,7 @@ def test_photon_mosaic_cli_neuroblueprint_metadata(
         ), "Pipeline should complete successfully with NeuroBlueprint format"
 
     def test_noncontinuous_ids_preservation(
-        self, neuroblueprint_noncontinuous_env
+        self, neuroblueprint_noncontinuous_env, run_photon_mosaic
     ):
         """Test that non-continuous subject and session IDs are preserved."""
         # local variables use module-level imports: re, Path
@@ -343,7 +323,7 @@ def test_noncontinuous_ids_preservation(
                 )
 
     def test_alphanumeric_subject_and_session_ids(
-        self, tmp_path, metadata_base_config
+        self, tmp_path, metadata_base_config, run_photon_mosaic
     ):
         """Test that alphanumeric folder names are preserved in transformed
         names.