ENH: Set-up testing framework

Close nipreps#1.

Opening the way for nipreps#6.

.circleci/config.yml

@@ -65,6 +65,100 @@ jobs:
          paths:
             - /tmp/cache/docker.tar.gz
 
+  cache_test_data:
+    machine:
+      image: circleci/classic:201711-01
+    working_directory: /tmp/data
+    steps:
+      - restore_cache:
+          keys:
+            - data-v0-{{ .Branch }}-
+            - data-v0-master-
+            - data-v0-
+      - run:
+          name: Setup git-annex
+          command: |
+            mkdir -p /tmp/cache
+            if [[ ! -e "/tmp/cache/git-annex-standalone.tar.gz" ]]; then
+              wget -O- http://neuro.debian.net/lists/trusty.us-ca.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
+              sudo apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9
+              sudo apt update && sudo apt-get install -y --no-install-recommends git-annex-standalone
+              mkdir -p /tmp/cache
+              tar czvf /tmp/cache/git-annex-standalone.tar.gz /usr/bin/git-annex /usr/bin/git-annex-shell /usr/lib/git-annex.linux
+            else
+              sudo tar xzfv /tmp/cache/git-annex-standalone.tar.gz -C /
+            fi
+            git config --global user.name 'CRN'
+            git config --global user.email '[email protected]'
+
+      - run:
+          name: Setup DataLad
+          command: |
+            pyenv global 3.5.2
+            virtualenv venv
+            pip install --no-cache-dir -U pip
+            pip install --no-cache-dir -U datalad
+      - run:
+          name: Install ds001600
+          command: |
+            datalad install -r https://github.com/OpenNeuroDatasets/ds001600.git
+            datalad update ds001600/
+            datalad get -r ds001600/sub-1/fmap/*
+      - run:
+          name: Get testdata
+          command: |
+            if [[ ! -d /tmp/data/testdata ]]; then
+              wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
+                  -O testdata.zip "https://files.osf.io/v1/resources/9sy2a/providers/osfstorage/5d44b940bcd6d900198ed6be/?zip="
+              unzip testdata.zip -d /tmp/data/testdata
+            fi
+
+      - save_cache:
+         key: data-v0-{{ .Branch }}-{{ .BuildNum }}
+         paths:
+            - "/opt/circleci/.pyenv/versions/3.5.2"
+            - /tmp/data
+            - /tmp/cache
+
+      - persist_to_workspace:
+          root: /tmp
+          paths:
+            - data
+
+  test_sdcflows:
+    machine:
+      image: circleci/classic:201711-01
+    working_directory: /tmp/tests
+    steps:
+      - attach_workspace:
+          at: /tmp
+      - checkout:
+          path: /tmp/src/sdcflows
+      - run:
+          name: Load Docker image layer cache
+          no_output_timeout: 30m
+          command: |
+            docker info
+            set +o pipefail
+            if [ -f /tmp/cache/docker.tar.gz ]; then
+              sudo apt update && sudo apt -y install pigz
+              pigz -d --stdout /tmp/cache/docker.tar.gz | docker load
+              docker images
+            fi
+      - run:
+          name: Run tests
+          command: |
+            docker run -it --rm=false -e TEST_DATA_HOME=/data/ -e TEST_OUTPUT_DIR=/out \
+                   -v /tmp/data:/data:ro -v /tmp/src:/src -v /tmp/tests:/out -w /src/sdcflows \
+                   poldracklab/sdcflows:latest \
+                   pytest -n auto --junit-xml=/out/pytest.xml sdcflows
+
+      - store_artifacts:
+          path: /tmp/tests
+
+      - store_test_results:
+          path: /tmp/tests
+
   deploy_docker:
     machine:
       image: circleci/classic:201711-01
@@ -207,6 +301,20 @@ workflows:
           filters:
             tags:
               only: /.*/
+      - cache_test_data:
+          filters:
+            tags:
+              only: /.*/
+
+      - test_sdcflows:
+          requires:
+            - build
+            - cache_test_data
+          filters:
+            tags:
+              only: /.*/
+
+
       - test_package:
           filters:
             tags:

Dockerfile

@@ -117,7 +117,6 @@ ENV IS_DOCKER_8395080871=1
 
 RUN ldconfig
 WORKDIR /tmp/
-ENTRYPOINT ["/usr/local/miniconda/bin/sdcflows"]
 
 ARG BUILD_DATE
 ARG VCS_REF

sdcflows/cli/run.py

@@ -31,11 +31,17 @@ def get_parser():
     # Options that affect how pyBIDS is configured
     g_bids = parser.add_argument_group('Options for filtering BIDS queries')
     g_bids.add_argument('--participant-label', action='store', type=str,
-                        nargs='*', help='process only particular subjects')
+                        nargs='*', dest='subject', help='process only particular subjects')
     g_bids.add_argument('--task', action='store', type=str, nargs='*',
                         help='select a specific task to be processed')
+    g_bids.add_argument('--dir', action='store', type=str, nargs='*',
+                        help='select a specific direction entity to be processed')
+    g_bids.add_argument('--acq', action='store', type=str, nargs='*', dest='acquisition',
+                        help='select a specific acquisition entity to be processed')
     g_bids.add_argument('--run', action='store', type=int, nargs='*',
                         help='select a specific run identifier to be processed')
+    g_bids.add_argument('--suffix', action='store', type=str, nargs='*', default='bold',
+                        help='select a specific run identifier to be processed')
 
     g_perfm = parser.add_argument_group('Options to handle performance')
     g_perfm.add_argument("-v", "--verbose", dest="verbose_count", action="count", default=0,
@@ -58,6 +64,7 @@ def main():
     from multiprocessing import set_start_method
     from bids.layout import BIDSLayout
     from nipype import logging as nlogging
+    from ..workflows.base import init_sdc_wf
     set_start_method('forkserver')
 
     opts = get_parser().parse_args()
@@ -88,21 +95,18 @@ def main():
     if not nthreads or nthreads < 1:
         nthreads = cpu_count()
 
-    derivatives_dir = opts.derivatives_dir.resolve()
-    bids_dir = opts.bids_dir or derivatives_dir.parent
+    output_dir = opts.output_dir.resolve()
+    bids_dir = opts.bids_dir or output_dir.parent
 
     # Get absolute path to BIDS directory
     bids_dir = opts.bids_dir.resolve()
-    layout = BIDSLayout(str(bids_dir), validate=False, derivatives=str(derivatives_dir))
-    query = {'domains': 'derivatives', 'desc': 'preproc',
-             'suffix': 'bold', 'extensions': ['.nii', '.nii.gz']}
-
-    if opts.participant_label:
-        query['subject'] = '|'.join(opts.participant_label)
-    if opts.run:
-        query['run'] = '|'.join(opts.run)
-    if opts.task:
-        query['task'] = '|'.join(opts.task)
+    layout = BIDSLayout(str(bids_dir), validate=False, derivatives=str(output_dir))
+    query = {'suffix': opts.suffix, 'extension': ['.nii', '.nii.gz']}
+
+    for entity in ('subject', 'task', 'dir', 'acquisition', 'run'):
+        arg = getattr(opts, entity, None)
+        if arg is not None:
+            query[entity] = arg
 
 
 if __name__ == '__main__':

sdcflows/conftest.py

@@ -0,0 +1,38 @@
+"""py.test configuration"""
+import os
+from pathlib import Path
+import numpy
+import pytest
+from bids.layout import BIDSLayout
+
+test_data_env = os.getenv('TEST_DATA_HOME', str(Path.home() / 'sdcflows-tests'))
+test_output_dir = os.getenv('TEST_OUTPUT_DIR')
+
+layouts = {p.name: BIDSLayout(str(p), validate=False)
+           for p in Path(test_data_env).glob('*') if p.is_dir()}
+
+
+def pytest_report_header(config):
+    msg = "Datasets found: %s" % ', '.join([v.root for v in layouts.values()])
+    if test_output_dir is not None:
+        msg += '\nOutput folder: %s' % Path(test_output_dir).resolve()
+    return msg
+
+
+@pytest.fixture(autouse=True)
+def add_np(doctest_namespace):
+    doctest_namespace['np'] = numpy
+    doctest_namespace['os'] = os
+    doctest_namespace['Path'] = Path
+    for key, val in list(layouts.items()):
+        doctest_namespace[key] = Path(val.root)
+
+
+@pytest.fixture
+def output_path():
+    return None if test_output_dir is None else Path(test_output_dir)
+
+
+@pytest.fixture
+def bids_layouts():
+    return layouts