Merge pull request #52 from nipreps/tst/cleanup

TEST: Cleanup and start running GitHub actions

Author: effigies

Diff for: .github/workflows/pytest.yml

@@ -0,0 +1,40 @@
+name: Pytest
+
+on:
+  push:
+    branches: [ '*' ]
+    tags: [ '*' ]
+  pull_request:
+    branches: [ master, 'maint/*' ]
+
+jobs:
+  build:
+    if: "!contains(github.event.head_commit.message, '[skip ci]')"
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7, 3.8, 3.9]
+
+    steps:
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+    - name: Install nibabies
+      run: |
+        python -m venv /tmp/venv
+        source /tmp/venv/bin/activate
+        python -m pip install -U pip
+        python -m pip install --use-feature=in-tree-build ".[test]"
+    - name: Run Pytest
+      run: |
+        source /tmp/venv/bin/activate
+        pytest -sv --doctest-modules --cov nibabies --cov-report xml nibabies
+    - name: Submit coverage
+      run: |
+        # Pin codecov version to reduce scope for malicious updates
+        python -m pip install "codecov==2.1.11"
+        python -m codecov --file coverage.xml

Diff for: nibabies/__init__.py

@@ -1,4 +1,13 @@
-
 from ._version import get_versions
 __version__ = get_versions()['version']
 del get_versions
+
+# Silence PyBIDS warning for extension entity behavior
+# Can be removed once minimum PyBIDS dependency hits 0.14
+try:
+    import bids
+    bids.config.set_option('extension_initial_dot', True)
+except (ImportError, ValueError):
+    pass
+else:
+    del bids

Diff for: nibabies/interfaces/conftest.py

@@ -0,0 +1,30 @@
+"""py.test configuration"""
+from pathlib import Path
+import pytest
+from tempfile import TemporaryDirectory
+
+
+FILES = (
+    'functional.nii',
+    'anatomical.nii',
+    'epi.nii',
+    'T1w.nii',
+    'func_to_struct.mat',
+    'sub-01_run-01_echo-1_bold.nii.gz',
+    'sub-01_run-01_echo-2_bold.nii.gz',
+    'sub-01_run-01_echo-3_bold.nii.gz',
+)
+
+
+@pytest.fixture(scope="package")
+def data_dir():
+    with TemporaryDirectory() as tmpdir:
+        tmp_path = Path(tmpdir)
+        for fname in FILES:
+            Path.touch(tmp_path / fname)
+        yield tmp_path
+
+
+@pytest.fixture(autouse=True)
+def set_namespace(doctest_namespace, data_dir):
+    doctest_namespace["data_dir"] = data_dir

Diff for: nibabies/interfaces/multiecho.py

@@ -63,15 +63,17 @@ class T2SMap(CommandLine):
 
     Example
     =======
-    >>> from fmriprep.interfaces import multiecho
+    >>> from nibabies.interfaces import multiecho
     >>> t2smap = multiecho.T2SMap()
-    >>> t2smap.inputs.in_files = ['sub-01_run-01_echo-1_bold.nii.gz', \
-                                  'sub-01_run-01_echo-2_bold.nii.gz', \
-                                  'sub-01_run-01_echo-3_bold.nii.gz']
+    >>> t2smap.inputs.in_files = [
+    ...     data_dir / 'sub-01_run-01_echo-1_bold.nii.gz',
+    ...     data_dir / 'sub-01_run-01_echo-2_bold.nii.gz',
+    ...     data_dir / 'sub-01_run-01_echo-3_bold.nii.gz']
     >>> t2smap.inputs.echo_times = [0.013, 0.027, 0.043]
-    >>> t2smap.cmdline  # doctest: +ELLIPSIS
-    't2smap -d sub-01_run-01_echo-1_bold.nii.gz sub-01_run-01_echo-2_bold.nii.gz \
-sub-01_run-01_echo-3_bold.nii.gz -e 13.0 27.0 43.0 --fittype curvefit'
+    >>> t2smap.cmdline  # doctest: +ELLIPSIS +NORMALIZE_WHITESPACE
+    't2smap -d .../sub-01_run-01_echo-1_bold.nii.gz \
+    .../sub-01_run-01_echo-2_bold.nii.gz \
+    .../sub-01_run-01_echo-3_bold.nii.gz -e 13.0 27.0 43.0 --fittype curvefit'
     """
     _cmd = 't2smap'
     input_spec = T2SMapInputSpec

Diff for: nibabies/reports/core.py

@@ -36,29 +36,6 @@ def run_reports(
 ):
     """
     Run the reports.
-
-    .. testsetup::
-
-    >>> cwd = os.getcwd()
-    >>> os.chdir(tmpdir)
-
-    >>> from pkg_resources import resource_filename
-    >>> from shutil import copytree
-    >>> test_data_path = resource_filename('fmriprep', 'data/tests/work')
-    >>> testdir = Path(tmpdir)
-    >>> data_dir = copytree(test_data_path, str(testdir / 'work'))
-    >>> (testdir / 'fmriprep').mkdir(parents=True, exist_ok=True)
-
-    .. doctest::
-
-    >>> run_reports(testdir / 'out', '01', 'madeoutuuid', packagename='fmriprep',
-    ...             reportlets_dir=testdir / 'work' / 'reportlets' / 'fmriprep')
-    0
-
-    .. testcleanup::
-
-    >>> os.chdir(cwd)
-
     """
     return Report(
         out_dir,

Diff for: nibabies/utils/bids.py

@@ -83,8 +83,7 @@ def extract_entities(file_list):
     {'subject': '01', 'suffix': 'T1w', 'datatype': 'anat', 'extension': '.nii.gz'}
     >>> extract_entities(['sub-01/anat/sub-01_run-1_T1w.nii.gz',
     ...                   'sub-01/anat/sub-01_run-2_T1w.nii.gz'])
-    {'subject': '01', 'run': [1, 2], 'suffix': 'T1w', 'datatype': 'anat',
-     'extension': '.nii.gz'}
+    {'subject': '01', 'run': [1, 2], 'suffix': 'T1w', 'datatype': 'anat', 'extension': '.nii.gz'}
     """
     from collections import defaultdict
     from bids.layout import parse_file_entities

Diff for: nibabies/workflows/base.py

@@ -382,7 +382,6 @@ def init_single_subject_wf(subject_id):
     fmap_estimators = None
     if "fieldmap" not in config.workflow.ignore:
         from sdcflows.utils.wrangler import find_estimators
-        from sdcflows.workflows.base import init_fmap_preproc_wf
 
         # SDC Step 1: Run basic heuristics to identify available data for fieldmap estimation
         # For now, no fmapless

Diff for: nibabies/workflows/bold/base.py

@@ -449,7 +449,6 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
         # for meepi, iterate over all meepi echos to boldbuffer
         boldbuffer.iterables = ('bold_file', bold_file)
 
-
     # MULTI-ECHO EPI DATA #############################################
     if multiecho:  # instantiate relevant interfaces, imports
         from niworkflows.func.util import init_skullstrip_bold_wf