Fix test scripts to work on any machine

.circleci/config.yml

@@ -18,26 +18,23 @@ jobs:
           name: pytest of BABS
           no_output_timeout: 1h
           command: |
-            docker build \
-            -t pennlinc/slurm-docker-ci:unstable \
-            -f Dockerfile_testing .
-
-            # Make a directory that will hold the test artifacts
             mkdir -p ${HOME}/e2e-testing
             docker run -it \
-                -v ${PWD}:/tests \
+                -v ${PWD}:/babs \
                 -v ${HOME}/e2e-testing:/test-temp:rw \
+                -w /babs \
                 -h slurmctl --cap-add sys_admin \
                 --privileged \
-                pennlinc/slurm-docker-ci:unstable \
+                pennlinc/slurm-docker-ci:0.14 \
+                bash -c "pip install -e .[tests] && \
                 pytest -n 4 -sv \
                     --durations=0 \
                     --timeout=300 \
                     --junitxml=/test-temp/junit.xml \
                     --cov-report term-missing \
                     --cov-report xml:/test-temp/coverage.xml \
                     --cov=babs \
-                    /babs
+                    /babs/tests/"
 
       - store_test_results:
           path: /home/circleci/e2e-testing/junit.xml
@@ -54,22 +51,10 @@ jobs:
       - checkout:
           path: /home/circleci/src/babs
       - run:
-          name: pytest of BABS
+          name: e2e SLURM tests
           no_output_timeout: 1h
           command: |
-            docker build \
-            -t pennlinc/slurm-docker-ci:unstable \
-            -f Dockerfile_testing .
-
-            # Make a directory that will hold the test artifacts
-            mkdir -p ${HOME}/e2e-testing
-            docker run -it \
-                -v ${PWD}:/tests \
-                -v ${HOME}/e2e-testing:/test-temp:rw \
-                -h slurmctl --cap-add sys_admin \
-                --privileged \
-                pennlinc/slurm-docker-ci:unstable \
-                /tests/tests/e2e-slurm/container/walkthrough-tests.sh
+            E2E_DIR=${HOME}/e2e-testing bash tests/e2e_in_docker.sh
 
       - run:
           name: clean up test artifacts

docs/developer_how_to_test.rst

@@ -25,8 +25,25 @@ Manually run pytest
 
 The easiest way to run pytest is to run the ``tests/pytest_in_docker.sh`` script
 from the root directory of BABS.
-This will build a docker container that has a running SLURM job scheduler system.
-It will also install the local copy of BABS and run the pytests in the container.
+This runs the tests inside a Docker container that has a running SLURM job scheduler system,
+and installs the local copy of BABS at runtime via volume mount.
+
+.. code-block:: bash
+
+   bash tests/pytest_in_docker.sh
+
+To run the end-to-end walkthrough tests (``babs init`` → ``submit`` → ``merge``):
+
+.. code-block:: bash
+
+   bash tests/e2e_in_docker.sh
+
+By default, e2e test artifacts go to a temporary directory under ``/tmp``.
+To specify a location (e.g., for inspection after the run):
+
+.. code-block:: bash
+
+   E2E_DIR=/path/to/output bash tests/e2e_in_docker.sh
 
 -----------------------------
 Automatic pytest via CircleCI

tests/e2e_in_docker.sh

@@ -1,17 +1,12 @@
 #!/bin/bash
-mkdir -p "${HOME}"/projects/e2e-testing
-docker build --platform linux/amd64 \
-    -t pennlinc/slurm-docker-ci:unstable \
-    -f Dockerfile_testing .
+E2E_DIR="${E2E_DIR:-$(mktemp -d /tmp/babs-e2e-XXXXXX)}"
+mkdir -p "${E2E_DIR}"
+echo "E2E_DIR=${E2E_DIR}"
 docker run -it \
     --platform linux/amd64 \
-    -v "${HOME}"/projects/babs:/tests \
-    -v "${HOME}"/projects/e2e-testing:/test-temp:rw \
+    -v "$(pwd)":/tests \
+    -v "${E2E_DIR}":/test-temp:rw \
     -h slurmctl --cap-add sys_admin \
     --privileged \
-    pennlinc/slurm-docker-ci:unstable #\
-        #/babs/tests/e2e-slurm/container/walkthrough-tests.sh
-
-
-    #pytest -svx --pdb \
-    #/babs/tests
+    pennlinc/slurm-docker-ci:0.14 \
+        /tests/tests/e2e-slurm/container/walkthrough-tests.sh

tests/pytest_in_docker.sh

@@ -1,15 +1,14 @@
 #!/bin/bash
-docker build --platform linux/amd64 -t pennlinc/slurm-docker-ci:unstable -f Dockerfile_testing .
 docker run -it \
     --platform linux/amd64 \
     -h slurmctl --cap-add sys_admin \
     --privileged \
-    -v "${HOME}"/projects/babs:/babs \
-    pennlinc/slurm-docker-ci:unstable \
-        pytest -svx \
+    -v "$(pwd)":/babs \
+    -w /babs \
+    pennlinc/slurm-docker-ci:0.14 \
+        bash -c "pip install -e .[tests] && pytest -svx \
         --cov-report=term-missing \
-        --cov-report=xml \
+        --cov-report=xml:/tmp/coverage.xml \
         --cov=babs \
         --pdb \
-        /babs/tests/
-
+        /babs/tests/"

tests/test_generate_bidsapp_runscript.py

@@ -112,7 +112,7 @@ def test_get_input_unipping_cmds():
 
 
 @pytest.mark.parametrize(('input_datasets', 'config_file', 'processing_level'), testing_pairs)
-def test_generate_bidsapp_runscript(input_datasets, config_file, processing_level):
+def test_generate_bidsapp_runscript(input_datasets, config_file, processing_level, tmp_path):
     """Test that the bidsapp runscript is generated correctly."""
     config_path = NOTEBOOKS_DIR / config_file
     container_name = config_file.split('_')[1]
@@ -130,7 +130,7 @@ def test_generate_bidsapp_runscript(input_datasets, config_file, processing_leve
         templateflow_home='/path/to/templateflow_home',
     )
 
-    out_fn = Path('.') / f'{config_path.name}_{processing_level}.sh'
+    out_fn = tmp_path / f'{config_path.name}_{processing_level}.sh'
     with open(out_fn, 'w') as f:
         f.write(script_content)
     passed, status = run_shellcheck(str(out_fn))
@@ -164,7 +164,7 @@ def run_shellcheck(script_path):
         return False, str(e)
 
 
-def test_generate_pipeline_runscript():
+def test_generate_pipeline_runscript(tmp_path):
     """Test that the pipeline runscript is generated correctly."""
     config_path = NOTEBOOKS_DIR / 'eg_nordic-fmriprep_pipeline.yaml'
     config = read_yaml(config_path)
@@ -180,7 +180,7 @@ def test_generate_pipeline_runscript():
         final_zip_foldernames=config.get('zip_foldernames', {}),
     )
 
-    out_fn = Path('.') / f'{config_path.name}_pipeline.sh'
+    out_fn = tmp_path / f'{config_path.name}_pipeline.sh'
     with open(out_fn, 'w') as f:
         f.write(script_content)
     passed, status = run_shellcheck(str(out_fn))

tests/test_generate_submit_script.py

@@ -91,7 +91,7 @@
 
 
 @pytest.mark.parametrize(('input_datasets', 'config_file', 'processing_level'), testing_pairs)
-def test_generate_submit_script(input_datasets, config_file, processing_level):
+def test_generate_submit_script(input_datasets, config_file, processing_level, tmp_path):
     """Test that the bidsapp runscript is generated correctly."""
     config_path = NOTEBOOKS_DIR / config_file
     container_name = config_file.split('_')[1]
@@ -107,7 +107,7 @@ def test_generate_submit_script(input_datasets, config_file, processing_level):
         zip_foldernames=config['zip_foldernames'],
     )
 
-    out_fn = Path('.') / f'participant_job_{config_path.name}_{processing_level}.sh'
+    out_fn = tmp_path / f'participant_job_{config_path.name}_{processing_level}.sh'
     with open(out_fn, 'w') as f:
         f.write(script_content)
     passed, status = run_shellcheck(str(out_fn))