Previous PR review changes

- documentation fixes in quicktest.yaml

- docstring fixes in test_errors_in_logfiles.py

- removed loop over assert in test_file_existence.py

.github/workflows/quicktest.yaml

@@ -6,8 +6,7 @@ name: quicktest
 # Functionality: This workflow runs some quick integration tests on FastSurfer commits. It checks out the new
 #                FastSurfer repo, sets up Python, builds a Singularity image, runs FastSurfer on sample MRI data, and
 #                runs pytest to check if the results are acceptable
-# Usage: This workflow is triggered on a push or pull-request to the dev and main branch of DeepMI/FastSurfer.
-#        It can also be triggered manually with workflow-dispatch
+# Usage: This workflow is exclusively triggered manually with workflow-dispatch in DeepMI/FastSurfer.
 
 
 on:
@@ -57,7 +56,6 @@ jobs:
           echo "SIF File does not exist. Building file."
           cd $FASTSURFER_HOME
           python3 Docker/build.py --device cuda --tag fastsurfer_gpu:cuda
-          cd $RUNNER_FASTSURFER_IMGS
           apptainer build --force fastsurfer-gpu.sif docker-daemon://fastsurfer_gpu:cuda
         else
           echo "File already exists"
@@ -85,7 +83,7 @@ jobs:
                       --env FASTSURFER_HOME=/fastsurfer-dev \
                       -B $RUNNER_FS_MRI_DATA:/data \
                       -B $RUNNER_FS_OUTPUT:/output \
-                      -B $RUNNER_FS_LICENSE:/fs_license \
+                      -B $RUNNER_FS_LICENSE:/fs_license/.license \
                       $RUNNER_FASTSURFER_IMGS/fastsurfer-gpu.sif \
                       /fastsurfer/brun_fastsurfer.sh \
                       --fs_license /fs_license/.license \

test/quick_test/test_errors_in_logfiles.py

@@ -12,13 +12,13 @@
 
 def load_errors():
     """
-    Load the errors and whitelist from the given file path.
+    Load the errors and whitelist strings from ./data/logfile.errors.yaml.
 
     Returns
     -------
-    errors : list
+    errors : list[str]
         List of errors.
-    whitelist : list
+    whitelist : list[str]
         List of whitelisted errors.
     """
 
@@ -45,7 +45,7 @@ def load_log_files(test_subject: str):
 
     Returns
     -------
-    log_files : list
+    log_files : list[Path]
         List of log files in the given log directory.
     """
 
@@ -88,7 +88,7 @@ def test_errors(subjects_dir, test_dir, test_subject):
 
     # Check if any of the keywords are in the log files
     for log_file in log_files:
-        rel_path = log_file.relative_to(os.environ["SUBJECTS_DIR"])
+        rel_path = log_file.relative_to(subjects_dir)
         logger.debug(f"Checking file: {rel_path}")
         try:
             with log_file.open('r') as file:

test/quick_test/test_file_existence.py

@@ -9,27 +9,27 @@
 logger = getLogger(__name__)
 
 
-def get_files_from_yaml(file_path: str):
-    """
-    Get the list of files from the YAML file.
-
-    Parameters
-    ----------
-    file_path : str
-        Path to the YAML file.
-
-    Returns
-    -------
-    list
-        List of files specified in the YAML file.
-    """
-
-    # Open the file_path and read the files into an array
-    with open(file_path, 'r') as file:
-        data = yaml.safe_load(file)
-        files = data.get('files', [])
-
-    return files
+# def get_files_from_yaml(file_path: str):
+#     """
+#     Get the list of files from the YAML file.
+#
+#     Parameters
+#     ----------
+#     file_path : str
+#         Path to the YAML file.
+#
+#     Returns
+#     -------
+#     list
+#         List of files specified in the YAML file.
+#     """
+#
+#     # Open the file_path and read the files into an array
+#     with open(file_path, 'r') as file:
+#         data = yaml.safe_load(file)
+#         files = data.get('files', [])
+#
+#     return files
 
 
 def get_files_from_folder(folder_path: str):
@@ -89,7 +89,7 @@ def test_file_existence(subjects_dir, test_dir, reference_dir, test_subject):
     test_files = get_files_from_folder(test_subject)
 
     # Check if each file in the reference list exists in the test list
-    for file in reference_files:
-        assert file in test_files, f"File '{file}' does not exist."
+    missing_files = [file for file in reference_files if file not in test_files]
+    assert not missing_files, f"Files '{missing_files}' do not exist in test subject."
 
     logger.debug("\nAll files present.")