Update datalad commands

.github/workflows/pytest.yml

@@ -26,4 +26,4 @@ jobs:
         run: uv pip install --editable ./
 
       - name: Run tests with uv
-        run: uv run pytest
+        run: uv run pytest tests

.gitignore

@@ -9,6 +9,7 @@ empty_log_process_temp.py
 
 tests/**/bids/
 tests/test_main_functionality/data/projects/test-project/sub-100
+tests/pytest-autobids_config.yaml
 tests/data
 # Byte-compiled / optimized / DLL files
 __pycache__/

lslautobids/datalad_create.py

@@ -7,7 +7,7 @@ def create_and_add_files_to_datalad_dataset(dataset_path,logger):
     #if flag==0:
 
     try:
-        dl.Dataset(dataset_path)
+        dl.Dataset(dataset_path).status()
     except:
         message ="LSL Auto BIDS: new datalad dataset created"
         # Create a new dataset
@@ -30,5 +30,6 @@ def create_and_add_files_to_datalad_dataset(dataset_path,logger):
 
     # commit current files
     logger.info('Committing current changes........')
+    os.chdir(dataset_path) # bug in datalad that requires to be in the same folder to save the datalad thingy
     dl.save(path = dataset_path, message=message)
 

tests/conftest.py

@@ -35,8 +35,8 @@ def setup_project(monkeypatch):
 
     from lslautobids.gen_project_config import main as gen_project_config_main
 
-    # Create dummy user config for the test
-    config_file_test = ("tests/pytest-autobids_config.yaml")
+    # Create dummy user config for the test using absolute path
+    config_file_test = os.path.join(PROJECT_ROOT, "pytest-autobids_config.yaml")
 
     #os.makedirs(os.path.dirname(config_file_test), exist_ok=True)
     config_data = {

tests/test_main_functionality/test_main_functionality.py

@@ -64,8 +64,10 @@ def test_process_main_functionality(setup_project, monkeypatch):
     fixture_path = os.path.join(paths["bids_root"],project_name,"sub-100","ses-001","eeg","sub-100_ses-001_task-freeviewing_run-2_eeg.set")
     assert os.path.exists(fixture_path)
 
-    # cleanup
+    # cleanup 
     shutil.rmtree(os.path.join(paths["project_root"], project_name,"sub-100"))
+
+    # # does not work for some reason with git-annex, needs sudo
     #shutil.rmtree(paths["bids_root"])
 
 

tests/test_old_suffix/test_old_suffix.py

@@ -33,6 +33,7 @@ def test_process_new_files_with_old_suffix(setup_project, monkeypatch):
     logger = get_logger(project_name)
     logger.debug(f" Starting test_process_new_files_with_old_suffix in {project_name} ")
 
+
     # Reset sys.argv to something that lslautobids.main.main() expects
     sys.argv = [
         "lslautobids.main",

tests/test_otherfiles-renaming/test_otherfiles-renaming.py

@@ -44,7 +44,7 @@ def test_process_otherfiles_renaming(setup_project, monkeypatch):
     import lslautobids.main
     lslautobids.main.main()
 
-    # cleanup
-    shutil.rmtree(paths["bids_root"])
+    # cleanup # does not work for some reason with git-annex, needs sudo
+    #shutil.rmtree(paths["bids_root"])