Merge pull request #4 from bids-standard/more-work

Fix testing suite

.gitattributes

@@ -1 +1 @@
-bids/reports/_version.py export-subst
+bids/ext/reports/_version.py export-subst

.github/dependabot.yml

@@ -0,0 +1,14 @@
+---
+# Documentation
+# https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+version: 2
+updates:
+- package-ecosystem: github-actions
+  directory: /
+  schedule:
+    interval: monthly
+
+- package-ecosystem: gitsubmodule
+  directory: /
+  schedule:
+    interval: monthly

.github/workflows/pypi-publish.yml

@@ -0,0 +1,31 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.7'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*

.github/workflows/testing.yml

@@ -0,0 +1,61 @@
+name: "Run Tests"
+
+on:
+  push:
+    branches:
+      - "main"
+  pull_request:
+    branches:
+      - '*'
+
+concurrency:
+  group: environment-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  # Determine if tests should be run based on commit message.
+  check_skip:
+    runs-on: ubuntu-latest
+    outputs:
+      skip: ${{ steps.result_step.outputs.ci-skip }}
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+      - id: result_step
+        uses: mstachniuk/ci-skip@master
+        with:
+          commit-filter: '[skip ci];[ci skip];[skip github]'
+          commit-filter-separator: ';'
+
+  run_tests:
+    needs: check_skip
+    if: ${{ needs.check_skip.outputs.skip == 'false' }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+        fail-fast: false
+        matrix:
+            os: ["ubuntu-latest", "macos-latest"]
+            python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+    name: ${{ matrix.os }} with Python ${{ matrix.python-version }}
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - uses: actions/checkout@v2
+      - name: 'Set up python'
+        uses: actions/setup-python@v2
+        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 -e .[tests]
+      - name: 'Run tests'
+        shell: bash {0}
+        run: python -m pytest --pyargs bids/ext/reports --cov=bids/ext/reports
+      - name: 'Upload coverage to CodeCov'
+        uses: codecov/codecov-action@v1
+        if: success()

.pre-commit-config.yaml

@@ -0,0 +1,24 @@
+---
+repos:
+
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+  - id: trailing-whitespace
+  - id: end-of-file-fixer
+
+
+- repo: https://github.com/psf/black
+  rev: 22.12.0
+  hooks:
+  - id: black
+
+- repo: https://github.com/pycqa/flake8
+  rev: 6.0.0
+  hooks:
+  - id: flake8
+
+# - repo: https://github.com/pre-commit/mirrors-mypy
+#   rev: v0.991
+#   hooks:
+#   - id: mypy

MANIFEST.in

@@ -1,4 +1,4 @@
 include versioneer.py
-include bids/reports/_version.py
-recursive-include bids/reports/config *.json
-recursive-include bids/reports/tests/data *
+include bids/ext/reports/_version.py
+recursive-include bids/ext/reports/config *.json
+recursive-include bids/ext/reports/tests/data *

bids/ext/__init__.py

@@ -0,0 +1 @@
+__path__ = __import__("pkgutil").extend_path(__path__, __name__)

bids/reports/__init__.py → bids/ext/reports/__init__.py

@@ -1,9 +1,9 @@
 """pybids-reports: A tool for building methods sections for BIDS datasets."""
-from . import _version
+from . import _version, parameters, parsing, report
 from .due import Doi, due
 from .report import BIDSReport
 
-__all__ = ["BIDSReport"]
+__all__ = ["BIDSReport", "parameters", "parsing", "report"]
 
 due.cite(
     Doi("10.1038/sdata.2016.44"),

bids/reports/due.py → bids/ext/reports/due.py

@@ -63,9 +63,7 @@ def _donothing_func(*args, **kwargs):
     if type(e).__name__ not in ("ImportError", "ModuleNotFoundError"):
         import logging
 
-        logging.getLogger("duecredit").error(
-            "Failed to import duecredit due to %s" % str(e)
-        )
+        logging.getLogger("duecredit").error("Failed to import duecredit due to %s" % str(e))
     # Initiate due stub
     due = InactiveDueCreditCollector()
     BibTeX = Doi = Url = Text = _donothing_func

bids/reports/parameters.py → bids/ext/reports/parameters.py

@@ -7,25 +7,22 @@
 import nibabel as nib
 from num2words import num2words
 
-from bids.reports.utils import list_to_str, num_to_str, remove_duplicates
+from .utils import list_to_str, num_to_str, remove_duplicates
 
 logging.basicConfig()
-LOGGER = logging.getLogger("reports.parsing")
+LOGGER = logging.getLogger("pybids-reports.parameters")
 
 
 def describe_slice_timing(img, metadata: dict) -> str:
     """Generate description of slice timing from metadata."""
-
     if "SliceTiming" in metadata:
         slice_order = " in {0} order".format(get_slice_info(metadata["SliceTiming"]))
         n_slices = len(metadata["SliceTiming"])
     else:
         slice_order = ""
         n_slices = img.shape[2]
 
-    return "{n_slices} slices{slice_order}".format(
-        n_slices=n_slices, slice_order=slice_order
-    )
+    return "{n_slices} slices{slice_order}".format(n_slices=n_slices, slice_order=slice_order)
 
 
 def describe_repetition_time(metadata: dict):
@@ -63,9 +60,9 @@ def describe_duration(files) -> str:
         n_vols = n_vols[0]
         dur_str = describe_func_duration(n_vols, tr)
 
-    dur_str = (
-        "Run duration was {0} minutes, during which {1} volumes were acquired."
-    ).format(dur_str, n_vols)
+    dur_str = ("Run duration was {0} minutes, during which {1} volumes were acquired.").format(
+        dur_str, n_vols
+    )
     return dur_str
 
 
@@ -93,7 +90,6 @@ def describe_echo_times(files):
     me_str : str
         Whether the data are multi-echo or single-echo.
     """
-
     echo_times = [f.get_metadata()["EchoTime"] for f in files]
     echo_times = sorted(list(set(echo_times)))
     if len(echo_times) > 1:
@@ -108,7 +104,7 @@ def describe_echo_times(files):
 
 
 def describe_echo_times_fmap(files):
-    """Generate description of echo times from metadata field for fmaps
+    """Generate description of echo times from metadata field for fmaps.
 
     Parameters
     ----------
@@ -160,9 +156,7 @@ def describe_image_size(img):
 def describe_inplane_accel(metadata: dict) -> str:
     """Generate description of in-plane acceleration factor, if any."""
     return (
-        "in-plane acceleration factor={}".format(
-            metadata["ParallelReductionFactorInPlane"]
-        )
+        "in-plane acceleration factor={}".format(metadata["ParallelReductionFactorInPlane"])
         if metadata.get("ParallelReductionFactorInPlane", 1) > 1
         else ""
     )
@@ -184,9 +178,7 @@ def describe_bvals(bval_file) -> str:
     with open(bval_file, "r") as file_object:
         raw_bvals = file_object.read().splitlines()
     # Flatten list of space-separated values
-    bvals = [
-        item for sublist in [line.split(" ") for line in raw_bvals] for item in sublist
-    ]
+    bvals = [item for sublist in [line.split(" ") for line in raw_bvals] for item in sublist]
     bvals = sorted([int(v) for v in set(bvals)])
     bvals = [num_to_str(v) for v in bvals]
     bval_str = list_to_str(bvals)
@@ -210,9 +202,7 @@ def describe_intendedfor_targets(metadata: dict, layout) -> str:
 
         for scan in scans:
             fn = op.basename(scan)
-            if_file = [
-                f for f in layout.get(extension=[".nii", ".nii.gz"]) if fn in f.path
-            ][0]
+            if_file = [f for f in layout.get(extension=[".nii", ".nii.gz"]) if fn in f.path][0]
             run_num = int(if_file.run)
             target_type = if_file.entities["suffix"].upper()
 
@@ -229,9 +219,7 @@ def describe_intendedfor_targets(metadata: dict, layout) -> str:
             run_dict[target_type_str].append(run_num)
 
         for scan in run_dict.keys():
-            run_dict[scan] = [
-                num2words(r, ordinal=True) for r in sorted(run_dict[scan])
-            ]
+            run_dict[scan] = [num2words(r, ordinal=True) for r in sorted(run_dict[scan])]
 
         out_list = []
 
@@ -320,8 +308,7 @@ def describe_sequence(metadata: dict, config: dict):
         seqs += " ({0})".format(os.path.sep.join(seq_abbrs))
 
     variants = [
-        config["seqvar"].get(var, var)
-        for var in metadata.get("SequenceVariant", "").split("_")
+        config["seqvar"].get(var, var) for var in metadata.get("SequenceVariant", "").split("_")
     ]
     variants = list_to_str(variants)