[FIX] extract tests (#107)

* extract tests

* run on proper folder

* clean

* rm scope fixture

.github/workflows/testing.yml

@@ -20,12 +20,9 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
     runs-on: ${{ matrix.os }}
     name: ${{ matrix.os }} with Python ${{ matrix.python-version }}
-    defaults:
-      run:
-        shell: bash
     steps:
     - uses: actions/checkout@v4
       with:
@@ -35,14 +32,11 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Display Python version
-      shell: bash {0}
       run: python -c "import sys; print(sys.version)"
     - name: Install pybids-reports
-      shell: bash {0}
-      run: pip install .[tests]
+      run: pip install tox
     - name: Run tests
-      shell: bash {0}
-      run: pytest --pyargs bids.ext.reports --doctest-modules --cov=bids.ext.reports
+      run: tox run -e test -- tests
     - name: Upload coverage to CodeCov
       uses: codecov/codecov-action@v5
       if: success()

.github/workflows/testing_cli.yml

@@ -20,7 +20,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.12']
+        python-version: ['3.13']
     runs-on: ${{ matrix.os }}
     name: ${{ matrix.os }} with Python ${{ matrix.python-version }}
     defaults:
@@ -35,19 +35,12 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Display Python version
-      shell: bash {0}
       run: python -c "import sys; print(sys.version)"
-    - name: Install bids examples
-      run: git clone https://github.com/bids-standard/bids-examples.git
     - name: Install pybids-reports
-      shell: bash {0}
       run: pip install .
     - name: Info CLI
-      shell: bash {0}
       run: |
         pybids_reports --version
         pybids_reports --help
     - name: Run test for CLI
-      shell: bash {0}
-      run: |
-        bash tools/run_on_examples.sh
+      run: bash tools/run_on_examples.sh

bids/ext/reports/report.py

@@ -3,8 +3,8 @@
 from __future__ import annotations
 
 import json
-import os.path as op
 from collections import Counter
+from pathlib import Path
 from typing import Any
 
 from bids.layout import BIDSFile, BIDSLayout
@@ -48,17 +48,17 @@ class BIDSReport:
     supported.
     """
 
-    def __init__(self, layout: BIDSLayout, config: None | str | dict[str, dict[str, str]] = None):
+    def __init__(
+        self, layout: BIDSLayout, config: None | str | Path | dict[str, dict[str, str]] = None
+    ):
         self.layout = layout
         if config is None:
-            config = op.join(
-                op.dirname(op.abspath(__file__)),
-                "config",
-                "converters.json",
-            )
+            config = Path(__file__).absolute().parent / "templates" / "config" / "converters.json"
 
         if isinstance(config, str):
-            with open(config) as fobj:
+            config = Path(config)
+        if isinstance(config, Path):
+            with config.open() as fobj:
                 config = json.load(fobj)
 
         if not isinstance(config, dict):
@@ -85,22 +85,6 @@ def generate_from_files(self, files: list[BIDSFile]) -> Counter[str]:
             pattern is most likely the most complete. In cases where the
             file list contains multiple protocols, each pattern will need to be
             inspected manually.
-
-        Examples
-        --------
-        >>> from os.path import join
-        >>> from bids.layout import BIDSLayout
-        >>> from bids.reports import BIDSReport
-        >>> from bids.tests import get_test_data_path
-        >>> layout = BIDSLayout(join(get_test_data_path(), 'synthetic'))
-        >>> report = BIDSReport(layout)
-        >>> files = layout.get(session='01', extension=['.nii.gz', '.nii'])
-        >>> counter = report.generate_from_files(files)
-        Number of patterns detected: 1
-        Remember to double-check everything and to replace <deg> with a degree symbol.
-
-        >>> counter.most_common()[0][0]  # doctest: +ELLIPSIS
-        'In session 01, MR data were...'
         """
         descriptions = []
 
@@ -155,21 +139,6 @@ def generate(self, **kwargs: Any) -> Counter[str]:
             pattern is most likely the most complete. In cases where the
             dataset contains multiple protocols, each pattern will need to be
             inspected manually.
-
-        Examples
-        --------
-        >>> from os.path import join
-        >>> from bids.layout import BIDSLayout
-        >>> from bids.reports import BIDSReport
-        >>> from bids.tests import get_test_data_path
-        >>> layout = BIDSLayout(join(get_test_data_path(), 'synthetic'))
-        >>> report = BIDSReport(layout)
-        >>> counter = report.generate(session='01')
-        Number of patterns detected: 1
-        Remember to double-check everything and to replace <deg> with a degree symbol.
-
-        >>> counter.most_common()[0][0]  # doctest: +ELLIPSIS
-        'In session 01, MR data were...'
         """
         descriptions = []
 

pyproject.toml

@@ -17,7 +17,7 @@ classifiers = [
 ]
 dependencies = [
     "chevron",
-    "pybids>=0.15",
+    "pybids>=0.18",
     "nibabel",
     "num2words",
     "rich"
@@ -91,7 +91,7 @@ target-version = ['py39']
 
 [tool.codespell]
 ignore-words-list = "te"
-skip = "./.git,bids/ext/reports/tests/data/*"
+skip = "./.git,tests/data/*"
 
 [tool.coverage.paths]
 source = [
@@ -101,6 +101,10 @@ source = [
 
 [tool.coverage.report]
 include_namespace_packages = true
+# Regexes for lines to exclude from consideration
+omit = [
+    "*/templates/*"
+]
 
 [tool.hatch.build.hooks.vcs]
 version-file = "bids/ext/reports/_version.py"
@@ -137,7 +141,7 @@ module = [
 ]
 
 [tool.pytest.ini_options]
-addopts = "-ra --strict-config --strict-markers --doctest-modules --showlocals -s -vv --durations=0"
+addopts = "-ra --strict-config --strict-markers --showlocals -s -vv --durations=0"
 doctest_optionflags = "NORMALIZE_WHITESPACE ELLIPSIS"
 junit_family = "xunit2"
 minversion = "6.0"

bids/ext/reports/tests/conftest.py → tests/conftest.py

@@ -3,28 +3,32 @@
 from __future__ import annotations
 
 import json
-from os.path import abspath, join
+from pathlib import Path
 
 import nibabel as nib
 import pytest
 from bids.layout import BIDSLayout
-from bids.tests import get_test_data_path
 
 
-@pytest.fixture(scope="module")
-def testdataset():
+@pytest.fixture
+def data_path():
+    return Path(__file__).parent / "data"
+
+
+@pytest.fixture
+def testdataset(data_path):
     """Path to a BIDS dataset for testing."""
-    data_dir = join(get_test_data_path(), "synthetic")
+    data_dir = data_path / "synthetic"
     return data_dir
 
 
-@pytest.fixture(scope="module")
+@pytest.fixture
 def testlayout(testdataset):
     """A BIDSLayout for testing."""
     return BIDSLayout(testdataset)
 
 
-@pytest.fixture(scope="module")
+@pytest.fixture
 def testimg(testlayout):
     """A Nifti1Image for testing."""
     func_files = testlayout.get(
@@ -37,7 +41,7 @@ def testimg(testlayout):
     return nib.load(func_files[0].path)
 
 
-@pytest.fixture(scope="module")
+@pytest.fixture
 def testdiffimg(testlayout):
     """A Nifti1Image for testing."""
     dwi_files = testlayout.get(
@@ -49,10 +53,10 @@ def testdiffimg(testlayout):
     return nib.load(dwi_files[0].path)
 
 
-@pytest.fixture(scope="module")
+@pytest.fixture
 def testconfig():
     """The standard config file for testing."""
-    config_file = abspath(join(get_test_data_path(), "../../reports/config/converters.json"))
+    config_file = Path(__file__).parent / "config" / "converters.json"
     with open(config_file) as fobj:
         config = json.load(fobj)
     return config

tests/data/ds000117/.bidsignore

@@ -0,0 +1,2 @@
+run-*_echo-*_FLASH.json
+**/sub-*_ses-mri_run-*_echo-*_FLASH.nii.gz

tests/data/ds000117/CHANGES

@@ -0,0 +1,14 @@
+Revision history for OpenfMRI dataset ds000117
+
+1.0.0 2017-11-08
+
+  - Converted to BIDS format
+  - Changed subject order (see README)
+
+0.1.1 2016-09-17
+
+  - Replaced ds117_R0.1.0/sub004/MEG/run_02_sss.fif and ds117_R0.1.0/sub006/MEG/run_03_sss.fif since the original versions were corrupted
+
+0.1.0 2014-11-03
+
+  - Initial Release

tests/data/ds000117/README

@@ -0,0 +1,89 @@
+This dataset was obtained from the OpenfMRI project (http://www.openfmri.org).
+Accession #: ds000117
+Description:  Multi-subject, multi-modal (sMRI+fMRI+MEG+EEG) neuroimaging dataset on face recognition
+
+Please cite the following references if you use these data:
+
+A multi-subject, multi-modal human neuroimaging dataset
+
+Wakeman, D.G. & Henson, R.N. (2015). A multi-subject, multi-modal human neuroimaging dataset. Sci. Data 2:150001 doi: 10.1038/sdata.2015.1
+
+
+  Multi-subject, multi-modal (sMRI+fMRI+MEG+EEG) neuroimaging dataset on face recognition
+    ==================================================================================
+
+Please note that the subject ordering has changed since version 0.1.x (non-BIDS) of this
+dataset. Additionally, three subjects have been left out. The mapping is as follows:
+0.1.x:   02 03 05 14 08 09 10 11 12 15 16 17 18 23 24 25
+current: 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16
+
+func/
+-----
+The experiment began at the third nifti volume (corresponding to 5 ignored scans: 3 forced siemens dummies (no files) and 2 included in the data).
+
+meg/
+----
+Three anatomical fiducials were digitized for aligning the MEG with the MRI: the nasion
+(lowest depression between the eyes) and the left and right ears (lowest depression
+between the tragus and the helix, above the tragus). This procedure is illustrated here:
+http://neuroimage.usc.edu/brainstorm/CoordinateSystems#Subject_Coordinate_System_.28SCS_.2F_CTF.29
+and in task-facerecognition_fidinfo.pdf
+
+The following triggers are included in the .fif files and are also used in the “trigger” column of the meg and bold events files:
+
+Trigger            Label               Simplified Label
+
+5         Initial Famous Face               FAMOUS
+6         Immediate Repeat Famous Face      FAMOUS
+7         Delayed Repeat Famous Face        FAMOUS
+13        Initial Unfamiliar Face           UNFAMILIAR
+14        Immediate Repeat Unfamiliar Face  UNFAMILIAR
+15        Delayed Repeat Unfamiliar Face    UNFAMILIAR
+17        Initial Scrambled Face            SCRAMBLED
+18        Immediate Repeat Scrambled Face   SCRAMBLED
+19        Delayed Repeat Scrambled Face     SCRAMBLED
+
+stimuli/meg/
+------------
+The .bmp files correspond to those described in the text. There are 6 additional images in this directory, which were used in the practice experiment to familiarize participants with the task.
+
+stimuli/mri/
+------------
+The .bmp files correspond to those described in the text.
+
+
+If you wish to publish any of these data, please acknowledge Daniel Wakeman and Richard Henson. The data has been published so far in:
+
+    Wakeman, D.G. & Henson, R.N. (2015). A multi-subject, multi-modal human neuroimaging dataset. Sci. Data 2:150001 doi: 10.1038/sdata.2015.1
+
+    Henson, R.N., Wakeman, D.G., Litvak, V. & Friston, K.J. (2011). A Parametric Empirical Bayesian framework for the EEG/MEG inverse problem: generative models for multisubject and multimodal integration. Frontiers in Human Neuroscience, 5, 76, 1-16.
+
+    Henson, R.N., Wakeman, D.G., Phillips, C. & Rowe, J. (2012). Effective Connectivity between OFA and FFA during face perception: DCM of evoked MEG, EEG and fMRI responses. HBM2012 Abstract.
+
+
+### Comments added by Openfmri Curators ###
+===========================================
+
+General Comments
+----------------
+
+
+Defacing
+--------
+Defacing was performed by the submitter
+
+Quality Control
+---------------
+Mriqc was run on the dataset. Results are located in derivatives/mriqc. Learn more about it here: https://mriqc.readthedocs.io/en/latest/
+
+Where to discuss the dataset
+----------------------------
+1) www.openfmri.org/dataset/ds000117/ See the comments section at the bottom of the dataset
+page.
+2) www.neurostars.org Please tag any discussion topics with the tags openfmri and ds000117.
+3) Send an email to [email protected]. Please include the accession number in
+your email.
+
+Known Issues
+------------
+N/A

tests/data/ds000117/acq-epi_T1w.json

@@ -0,0 +1,9 @@
+{
+  "RepetitionTime": 2,
+  "EchoTime": 0.095,
+  "FlipAngle": 90,
+  "Manufacturer": "Siemens",
+  "ManufacturersModelName": "TIM TRIO",
+  "MagneticFieldStrength": 3,
+  "PulseSequenceType": "EPI"
+}

tests/data/ds000117/acq-mprage_T1w.json

@@ -0,0 +1,10 @@
+{
+  "RepetitionTime": 2.25,
+  "EchoTime": 0.00298,
+  "InversionTime": 0.9,
+  "FlipAngle": 9,
+  "Manufacturer": "Siemens",
+  "ManufacturersModelName": "TIM TRIO",
+  "MagneticFieldStrength": 3,
+  "PulseSequenceType": "MPRAGE"
+}

tests/data/ds000117/dataset_description.json

@@ -0,0 +1,10 @@
+{
+	"BIDSVersion": "1.0.2",
+	"License": "CC0",
+	"Name": "A multi-subject, multi-modal human neuroimaging dataset",
+	"Authors": ["Wakeman, DG", "Henson, RN"],
+	"Acknowledgements": "This work was supported by the UK Medical Research Council (MC_A060_5PR10) and Elekta Ltd. We would also like to acknowledge the contribution of Andre van der Kouwe and the A.A. Martinos Center for Biomedical Imaging (MGH) for providing the Multi-Echo FLASH sequences used in this work.",
+	"HowToAcknowledge": "Cite this paper: https://www.ncbi.nlm.nih.gov/pubmed/25977808 and consider including the following message: 'This data was obtained from the OpenfMRI database. Its accession number is ds000117'",
+	"ReferencesAndLinks": ["https://www.ncbi.nlm.nih.gov/pubmed/25977808", "https://openfmri.org/dataset/ds000117/"],
+	"Funding": ["UK Medical Research Council (MC_A060_5PR10)","Elekta Ltd."]
+}

tests/data/ds000117/participants.tsv

@@ -0,0 +1,18 @@
+participant_id	age	sex	first_ses
+sub-01	31	M	meg
+sub-02	25	M	meg
+sub-03	30	M	meg
+sub-04	26	F	meg
+sub-05	23	F	meg
+sub-06	26	M	meg
+sub-07	31	F	meg
+sub-08	26	M	meg
+sub-09	29	M	meg
+sub-10	23	M	meg
+sub-11	24	F	meg
+sub-12	24	F	meg
+sub-13	25	F	meg
+sub-14	24	F	mri
+sub-15	30	M	mri
+sub-16	25	M	mri
+sub-emptyroom	n/a	n/a	n/a