From 0dc05b32b5c475608c58ab0c532dd4bb181d9b5d Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 15 May 2024 14:34:00 -0400
Subject: [PATCH] TEST: Get tests working

---
 src/fmripost_aroma/tests/conftest.py  | 49 ++++++---------------------
 src/fmripost_aroma/tests/test_base.py |  5 ++-
 tox.ini                               |  2 +-
 3 files changed, 15 insertions(+), 41 deletions(-)

diff --git a/src/fmripost_aroma/tests/conftest.py b/src/fmripost_aroma/tests/conftest.py
index 16ee568..98738fe 100644
--- a/src/fmripost_aroma/tests/conftest.py
+++ b/src/fmripost_aroma/tests/conftest.py
@@ -1,64 +1,35 @@
 """Fixtures for the CircleCI tests."""
 
 import base64
+import importlib.resources
 import os
 
 import pytest
 
 
-def pytest_addoption(parser):
-    """Collect pytest parameters for running tests."""
-    parser.addoption(
-        '--data_dir',
-        action='store',
-        default='/home/runner/work/fmripost-aroma/fmripost-aroma/src/fmripost_aroma/tests/data',
-    )
-    parser.addoption(
-        '--output_dir',
-        action='store',
-        default='/home/runner/work/pytests/out',
-    )
-    parser.addoption(
-        '--working_dir',
-        action='store',
-        default='/home/runner/work/pytests/work',
-    )
-
-
 # Set up the commandline options as fixtures
 @pytest.fixture(scope='session')
-def data_dir(request):
+def data_dir():
     """Grab data directory."""
-    return request.config.getoption('--data_dir')
-
-
-@pytest.fixture(scope='session')
-def working_dir(request):
-    """Grab working directory."""
-    workdir = request.config.getoption('--working_dir')
-    os.makedirs(workdir, exist_ok=True)
-    return workdir
-
-
-@pytest.fixture(scope='session')
-def output_dir(request):
-    """Grab output directory."""
-    outdir = request.config.getoption('--output_dir')
-    os.makedirs(outdir, exist_ok=True)
-    return outdir
+    test_data = importlib.resources.files('fmripost_aroma.tests') / 'data'
+    with importlib.resources.as_file(test_data) as data:
+        yield data
 
 
 @pytest.fixture(scope='session', autouse=True)
-def _fslicense(working_dir):
+def _fslicense(tmp_path_factory):
     """Set the FreeSurfer license as an environment variable."""
+    working_dir = tmp_path_factory.mktemp('fslicense')
     FS_LICENSE = os.path.join(working_dir, 'license.txt')
-    os.environ['FS_LICENSE'] = FS_LICENSE
     LICENSE_CODE = (
         'bWF0dGhldy5jaWVzbGFrQHBzeWNoLnVjc2IuZWR1CjIwNzA2CipDZmVWZEg1VVQ4clkKRlNCWVouVWtlVElDdwo='
     )
     with open(FS_LICENSE, 'w') as f:
         f.write(base64.b64decode(LICENSE_CODE).decode())
 
+    os.putenv('FS_LICENSE', FS_LICENSE)
+    return
+
 
 @pytest.fixture(scope='session')
 def base_config():
diff --git a/src/fmripost_aroma/tests/test_base.py b/src/fmripost_aroma/tests/test_base.py
index 84f56cc..9dc8e64 100644
--- a/src/fmripost_aroma/tests/test_base.py
+++ b/src/fmripost_aroma/tests/test_base.py
@@ -1,7 +1,7 @@
 """Tests for fmripost_aroma.workflows."""
 
 from fmripost_aroma import config
-from fmripost_aroma.tests.tests import mock_config
+from fmriprep.workflows.tests import mock_config
 
 
 def test_init_ica_aroma_wf(tmp_path_factory):
@@ -12,6 +12,9 @@ def test_init_ica_aroma_wf(tmp_path_factory):
     with mock_config():
         config.workflow.fmripost_aroma_dir = tempdir / 'out'
         config.workflow.work_dir = tempdir / 'work'
+        config.workflow.denoise_method = ['nonaggr', 'orthaggr']
+        config.workflow.melodic_dim = -200
+        config.workflow.err_on_warn = False
 
         wf = init_ica_aroma_wf(
             bold_file='sub-01_task-rest_bold.nii.gz',
diff --git a/tox.ini b/tox.ini
index 945869d..2e8c1cc 100644
--- a/tox.ini
+++ b/tox.ini
@@ -42,7 +42,7 @@ deps =
   min: pybids ==0.15.6
 commands =
   pytest --doctest-modules --cov fmripost_aroma --cov-report xml \
-  --junitxml=test-results.xml -v src/fmripost_aroma
+  --junitxml=test-results.xml -v src/fmripost_aroma {posargs}
 
 [testenv:docs]
 description = Build documentation site