From 2b62af3bdbe2466420b3c0b39f9810704a123d60 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Mon, 10 Jun 2024 11:33:42 -0400
Subject: [PATCH] Add last test (not working).

---
 .circleci/config.yml                     | 18 ++++++++++--
 pyproject.toml                           |  1 +
 qsiprep/tests/data/multi_t1w_outputs.txt |  0
 qsiprep/tests/test_cli.py                | 36 ++++++++++++++++++++++++
 4 files changed, 52 insertions(+), 3 deletions(-)
 create mode 100644 qsiprep/tests/data/multi_t1w_outputs.txt

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 7ec08b1b..946eab81 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -380,13 +380,25 @@ jobs:
       CIRCLE_CPUS: 4
     steps:
       - checkout
+      - restore_cache:
+          key: twoses-01
       - run: *runinstall
       - run:
           name: Test the mri robust template for T1w images
           no_output_timeout: 1h
           command: |
-            cd .circleci
-            bash MultiT1w.sh
+            pytest -rP -o log_cli=true -m "multi_t1w" --cov-config=/src/qsiprep/pyproject.toml --cov-append --cov-report term-missing --cov=qsiprep --data_dir=/src/qsiprep/.circleci/data --output_dir=/src/qsiprep/.circleci/out --working_dir=/src/qsiprep/.circleci/work qsiprep
+            mkdir /src/coverage
+            mv /src/qsiprep/.coverage /src/coverage/.coverage.multi_t1w
+            # remove nifti files before uploading artifacts
+            find /src/qsiprep/.circleci/out/ -name "*.nii.gz" -type f -delete
+            find /src/qsiprep/.circleci/out/ -name "*.fib.gz" -type f -delete
+      - persist_to_workspace:
+          root: /src/coverage/
+          paths:
+            - .coverage.multi_t1w
+      - store_artifacts:
+          path: /src/qsiprep/.circleci/out/multi_t1w/
 
   Recon_3Tissue_Singleshell_ACT:
     <<: *dockersetup
@@ -857,7 +869,7 @@ workflows:
 
       - MultiT1w:
           requires:
-            - build
+            - download_twoses
           filters:
             branches:
               ignore:
diff --git a/pyproject.toml b/pyproject.toml
index 1a361de1..2bb03bfd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -190,6 +190,7 @@ markers = [
     "pyafq_recon_full: test 19",
     "mrtrix3_recon: test 20",
     "tortoise_recon: test 21",
+    "multi_t1w: test 22",
 ]
 env = [
     "RUNNING_PYTEST = 1",
diff --git a/qsiprep/tests/data/multi_t1w_outputs.txt b/qsiprep/tests/data/multi_t1w_outputs.txt
new file mode 100644
index 00000000..e69de29b
diff --git a/qsiprep/tests/test_cli.py b/qsiprep/tests/test_cli.py
index dbf4d6ed..02d9b783 100644
--- a/qsiprep/tests/test_cli.py
+++ b/qsiprep/tests/test_cli.py
@@ -743,6 +743,42 @@ def test_intramodal_template(data_dir, output_dir, working_dir):
     _run_and_generate(TEST_NAME, parameters, test_main=True)
 
 
+@pytest.mark.integration
+@pytest.mark.multi_t1w
+def test_multi_t1w(data_dir, output_dir, working_dir):
+    """MultiT1w test
+
+    This tests the following features:
+    - freesurfer's robust template
+
+    Inputs
+    ------
+    - DSDTI BIDS data (data/DSDTI)
+    """
+    TEST_NAME = "multi_t1w"
+
+    dataset_dir = download_test_data("twoses", data_dir)
+    # XXX: Having to modify dataset_dirs is suboptimal.
+    dataset_dir = os.path.join(dataset_dir, "DSDTI")
+    out_dir = os.path.join(output_dir, TEST_NAME)
+    work_dir = os.path.join(working_dir, TEST_NAME)
+
+    parameters = [
+        dataset_dir,
+        out_dir,
+        "participant",
+        f"-w={work_dir}",
+        "--b1-biascorrect-stage=none",
+        "--hmc_model=none",
+        "--b0-motion-corr-to=first",
+        "--output-resolution=5",
+        "--intramodal-template-transform=BSplineSyN",
+        "--intramodal-template-iters=2",
+    ]
+
+    _run_and_generate(TEST_NAME, parameters, test_main=True)
+
+
 @pytest.mark.integration
 @pytest.mark.scalar_mapper
 def test_scalar_mapper(data_dir, output_dir, working_dir):