Moving Fastsurfer and Pytest environment setup to local_runner image,…

… thus simplifying, and streamlining the workflow and improving execution time significantly.

Adding Labelled output directories for each run

Removing unnecessary import statements from pytest files

Cleaning up code:

- migrating from os.path.join to pathlib Path

- changing str to Path

- cleaning up comments and docstrings

.github/workflows/quicktest_runner.yaml

@@ -62,76 +62,26 @@ jobs:
           echo "Error: FreeSurfer installation directory does not exist at $FREESURFER_HOME"
           exit 1
         fi
-      # Set up Python using setup-python@v3 action
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v3
-      with:
-        python-version: "3.10"
-      # Check if FastSurfer environment already exists
-    - name: Check Environment
-      run: |
-        if [ ! -f "$MAMBAPATH" ]; then
-          echo "FastSurfer environment does not exist. Creating FastSurfer Environment..."
-          echo "HAS_MAMBA=true" >> $GITHUB_OUTPUT
-        else
-          echo "FastSurfer environment exists. Skipping FastSurfer Environment creation..."
-          echo "HAS_MAMBA=false" >> $GITHUB_OUTPUT
-        fi
-      id: check-environment
-      # Create FastSurfer environment if it does not exist
-    - name: Create FastSurfer Environment
-      uses: mamba-org/setup-micromamba@v1
-      with:
-        environment-file: env/fastsurfer.yml
-        micromamba-root-path: $MAMBAROOT
-        micromamba-binary-path: $MAMBAPATH
-        cache-downloads: true
-        cache-environment: true
-        init-shell: none
-      if: steps.check-environment.outputs.HAS_MAMBA == 'true'
-      # Set up cache for python packages
-    - name: Cache Python packages
-      uses: actions/cache@v3
-      with:
-        path: /home/.cache/pip
-        key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-
-      # Install required python packages
-    - name: Install package
-      run: |
-        python -m pip install --progress-bar off --upgrade pip \
-        setuptools wheel
-        python -m pip install --progress-bar off .[test]
-      # Run fastsurfer on list of subjects
+    # Run FastSurfer on test subjects
     - name: Run FastSurfer
       run: |
         echo "Running FastSurfer..."
-        export FREESURFER_HOME=/freesurfer
-        source $FREESURFER_HOME/SetUpFreeSurfer.sh
+        echo "Output will be saved in data/${GITHUB_SHA:0:7}"
         export FASTSURFER_HOME=$(pwd)
         export THIS_RUN_OUTDIR=${GITHUB_SHA:0:7}
         mkdir -p $SUBJECTS_DIR/$THIS_RUN_OUTDIR
         ./brun_fastsurfer.sh --subject_list $RUNNER_FS_MRI_DATA/subjects_list.txt \
-                             --sd $SUBJECTS_DIR/$THIS_RUN_OUTDIR \
+                             --sd $SUBJECTS_DIR/$THIS_RUN_OUTDIR --license $FS_LICENSE\
                              --parallel --threads 4 --3T --parallel_subjects surf
         export TEST_DIR=$THIS_RUN_OUTDIR
 
   # Test fastsurfer output
   run-pytest:
     runs-on: self-hosted
+    if: always()
     needs: run-fastsurfer
     steps:
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v3
-      with:
-        python-version: "3.10"
-    - name: Cache Python packages
-      uses: actions/cache@v3
-      with:
-        path: /home/.cache/pip
-        key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-
     - name: Run pytest
-      run: python -m pytest test/quick_test
+      run: |
+        source /venv-pytest/bin/activate
+        python -m pytest test/quick_test

test/quick_test/conftest.py

@@ -20,4 +20,4 @@ def reference_dir():
 
 @pytest.fixture
 def subjects_list():
-    return os.environ["SUBJECTS_LIST"]
+    return Path(os.environ["SUBJECTS_LIST"])

test/quick_test/test_errors_in_logfiles.py

@@ -1,4 +1,3 @@
-import os
 import pytest
 import yaml
 from pathlib import Path
@@ -24,7 +23,7 @@ def load_errors():
 
     # Open the error_file_path and read the errors and whitelist into arrays
 
-    error_file_path = os.path.join(Path(__file__).parent, "data/logfile.errors.yaml")
+    error_file_path = Path(__file__).parent / "data" / "logfile.errors.yaml"
 
     with open(error_file_path, 'r') as file:
         data = yaml.safe_load(file)
@@ -34,13 +33,13 @@ def load_errors():
     return errors, whitelist
 
 
-def load_log_files(test_subject: str):
+def load_log_files(test_subject: Path):
     """
     Retrieve the log files in the given log directory.
 
     Parameters
     ----------
-    test_subject : str
+    test_subject : Path
         Subject directory to test.
 
     Returns
@@ -51,24 +50,24 @@ def load_log_files(test_subject: str):
 
     # Retrieve the log files in given log directory
 
-    log_directory = os.path.join(test_subject, "scripts")
+    log_directory = test_subject / "scripts"
     log_files = [file for file in Path(log_directory).iterdir() if file.suffix == '.log']
 
     return log_files
 
 
 @pytest.mark.parametrize("test_subject", load_test_subjects())
-def test_errors(subjects_dir, test_dir, test_subject):
+def test_errors(subjects_dir: Path, test_dir: Path, test_subject: Path):
     """
     Test if there are any errors in the log files.
 
     Parameters
     ----------
-    subjects_dir : str
+    subjects_dir : Path
         Subjects directory.
-    test_dir : str
+    test_dir : Path
         Tests directory.
-    test_subject : str
+    test_subject : Path
         Subject to test.
 
     Raises
@@ -77,7 +76,7 @@ def test_errors(subjects_dir, test_dir, test_subject):
         If any of the keywords are in the log files.
     """
 
-    test_subject = os.path.join(subjects_dir, test_dir, test_subject)
+    test_subject = subjects_dir / test_dir / test_subject
     log_files = load_log_files(test_subject)
 
     error_flag = False

test/quick_test/test_file_existence.py

@@ -1,44 +1,21 @@
-import os
 import pytest
-import yaml
 
 from .common import *
 
 from logging import getLogger
 
+from pathlib import Path
+
 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_folder(folder_path: str):
+def get_files_from_folder(folder_path: Path):
     """
     Get the list of files in the directory relative to the folder path.
 
     Parameters
     ----------
-    folder_path : str
+    folder_path : Path
         Path to the folder.
 
     Returns
@@ -49,27 +26,26 @@ def get_files_from_folder(folder_path: str):
 
     # Get a list of all files in the folder recursively
     filenames = []
-    for root, _, files in os.walk(folder_path):
-        for file in files:
-            filenames.append(os.path.relpath(os.path.join(root, file), folder_path))
+    for file in Path(folder_path).rglob('*'):
+        filenames.append(str(file.relative_to(folder_path)))
 
     return filenames
 
 
 @pytest.mark.parametrize("test_subject", load_test_subjects())
-def test_file_existence(subjects_dir, test_dir, reference_dir, test_subject):
+def test_file_existence(subjects_dir: Path, test_dir: Path, reference_dir: Path, test_subject: Path):
     """
     Test the existence of files in the folder.
 
     Parameters
     ----------
-    subjects_dir : str
+    subjects_dir : Path
         Path to the subjects directory.
-    test_dir : str
+    test_dir : Path
         Name of the test directory.
-    reference_dir : str
+    reference_dir : Path
         Name of the reference directory.
-    test_subject : str
+    test_subject : Path
         Name of the test subject.
 
     Raises
@@ -81,11 +57,11 @@ def test_file_existence(subjects_dir, test_dir, reference_dir, test_subject):
     print(test_subject)
 
     # Get reference files from the reference subject directory
-    reference_subject = os.path.join(subjects_dir, reference_dir, test_subject)
+    reference_subject = subjects_dir / reference_dir / test_subject
     reference_files = get_files_from_folder(reference_subject)
 
     # Get test list of files in the test subject directory
-    test_subject = os.path.join(subjects_dir, test_dir, test_subject)
+    test_subject = subjects_dir / test_dir / test_subject
     test_files = get_files_from_folder(test_subject)
 
     # Check if each file in the reference list exists in the test list