Merge remote-tracking branch 'upstream/maint/20.2.x'

.circleci/config.yml

@@ -17,7 +17,10 @@ jobs:
       - run:
           name: Check whether build should be skipped
           command: |
-            if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
+            set -x +e
+            COMMIT_MSG="$(git log --format='format:%s' -n 1 $CIRCLE_SHA1)"
+            DOCBUILD="$(echo ${COMMIT_MSG} | grep -i -E '^docs?(\(\w+\))?:')"
+            if [ -z "$CIRCLE_TAG" -a -n "$DOCBUILD" ]; then
               echo "Only docs build"
               circleci step halt
             fi
@@ -277,11 +280,15 @@ jobs:
           name: Check whether build should be skipped
           command: |
             cd /home/circleci/src/fmriprep
-            if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
+            set -x +e
+            COMMIT_MSG="$(git log --format='format:%s' -n 1 $CIRCLE_SHA1)"
+            DOCBUILD="$(echo ${COMMIT_MSG} | grep -i -E '^docs?(\(\w+\))?:')"
+            SKIP_PYTEST="$(echo ${COMMIT_MSG} | grep -i -E '\[skip[ _]?tests\]')"
+            if [ -z "$CIRCLE_TAG" -a -n "$DOCBUILD" ]; then
               echo "Only docs build"
               circleci step halt
             fi
-            if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[skip[ _]?tests\]' )" != "" ]]; then
+            if [ -z "$CIRCLE_TAG" -a -n "$SKIP_PYTEST" ]; then
               echo "Skipping pytest job"
               circleci step halt
             fi
@@ -370,18 +377,23 @@ jobs:
       - checkout:
           path: /home/circleci/src/fmriprep
       - run:
-          name: Check whether build should be skipped
+          name: Check whether build should be skipped or fast-tracked
           command: |
             cd /home/circleci/src/fmriprep
-            if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
+            set -x +e
+            COMMIT_MSG="$(git log --format='format:%s' -n 1 $CIRCLE_SHA1)"
+            DOCBUILD="$(echo ${COMMIT_MSG} | grep -i -E '^docs?(\(\w+\))?:' )"
+            SKIP_DS005="$(echo ${COMMIT_MSG} | grep -i -E '\[skip[ _]?ds005\]' )"
+            NO_FASTTRACK="$(echo ${COMMIT_MSG} | grep -i -E '\[no[ _-]?fasttrack\]' )"
+            if [ -z "$CIRCLE_TAG" -a -n "$DOCBUILD" ]; then
               echo "Only docs build"
               circleci step halt
             fi
-            if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[skip[ _]?ds005\]' )" != "" ]]; then
+            if [ -z "$CIRCLE_TAG" -a -n "$SKIP_DS005" ]; then
               echo "Skipping ds000005 build"
               circleci step halt
             fi
-            if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[no[ _-]?fasttrack\]' )" != "" ]]; then
+            if [[ -n "$NO_FASTTRACK" ]]; then
               touch /tmp/.nofasttrack
               echo "Anatomical fasttrack reusing sMRIPrep's derivatives will not be used."
             fi
@@ -608,11 +620,15 @@ jobs:
           name: Check whether build should be skipped
           command: |
             cd /home/circleci/src/fmriprep
-            if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
+            set -x +e
+            COMMIT_MSG="$(git log --format='format:%s' -n 1 $CIRCLE_SHA1)"
+            DOCBUILD="$(echo ${COMMIT_MSG} | grep -i -E '^docs?(\(\w+\))?:')"
+            SKIP_DS054="$(echo ${COMMIT_MSG} | grep -i -E '\[skip[ _]?ds054\]' )"
+            if [ -z "$CIRCLE_TAG" -a -n "$DOCBUILD" ]; then
               echo "Only docs build"
               circleci step halt
             fi
-            if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[skip[ _]?ds054\]' )" != "" ]]; then
+            if [ -z "$CIRCLE_TAG" -a -n "$SKIP_DS054" ]; then
               echo "Skipping ds000054 build"
               circleci step halt
             fi
@@ -773,11 +789,15 @@ jobs:
           name: Check whether build should be skipped
           command: |
             cd /home/circleci/src/fmriprep
-            if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
+            set -x +e
+            COMMIT_MSG="$(git log --format='format:%s' -n 1 $CIRCLE_SHA1)"
+            DOCBUILD="$(echo ${COMMIT_MSG} | grep -i -E '^docs?(\(\w+\))?:')"
+            SKIP_DS210="$(echo ${COMMIT_MSG} | grep -i -E '\[skip[ _]?ds054\]' )"
+            if [ -z "$CIRCLE_TAG" -a -n "$DOCBUILD" ]; then
               echo "Only docs build"
               circleci step halt
             fi
-            if [[ "$( git log --format=oneline -n 1 $CIRCLE_SHA1 | grep -i -E '\[skip[ _]?ds210\]' )" != "" ]]; then
+            if [ -z "$CIRCLE_TAG" -a -n "$SKIP_DS210" ]; then
               echo "Skipping ds000210 build"
               circleci step halt
             fi
@@ -919,14 +939,6 @@ jobs:
             fi
       - checkout:
           path: /home/circleci/src/fmriprep
-      - run:
-          name: Check whether build should be skipped
-          command: |
-            cd /home/circleci/src/fmriprep
-            if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
-              echo "Only docs build"
-              circleci step halt
-            fi
       - restore_cache:
           keys:
             - build-v4-{{ .Branch }}-{{ .Revision }}
@@ -975,7 +987,10 @@ jobs:
           name: Check whether build should be skipped
           command: |
             cd /home/circleci/src/fmriprep
-            if [[ "$( git log --format='format:%s' -n 1 $CIRCLE_SHA1 | grep -i -E '^docs?(\(\w+\))?:' )" != "" ]]; then
+            set -x +e
+            COMMIT_MSG="$(git log --format='format:%s' -n 1 $CIRCLE_SHA1)"
+            DOCBUILD="$(echo ${COMMIT_MSG} | grep -i -E '^docs?(\(\w+\))?:')"
+            if [ -z "$CIRCLE_TAG" -a -n "$DOCBUILD" ]; then
               echo "Only docs build"
               circleci step halt
             fi

.github/workflows/contrib.yml

@@ -0,0 +1,41 @@
+name: Contribution checks
+
+on:
+  push:
+    branches:
+      - master
+      - maint/*
+  pull_request:
+    branches:
+      - master
+      - maint/*
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  stable:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ['ubuntu-latest']
+        python-version: [3.9]
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+      - name: Install flake8
+        run: python -m pip install flake8
+      - name: Check fMRIPrep
+        run: python -m flake8 fmriprep
+      - name: Check wrapper
+        run: python -m flake8 wrapper

CHANGES.rst

@@ -54,6 +54,18 @@ A new major version of fMRIPrep is finally here!
   * MAINT: Migrate from poldracklab to nipreps orgs (#2290)
   * MAINT: Ease CI packaging tests (#2472)
 
+20.2.5 (October 12, 2021)
+=========================
+Bug-fix release in the 20.2.x LTS series.
+
+This release includes a fix to `--slice-time-ref` parsing. Also, some
+issues in anatomical processing are resolved, including poorly-interpolated
+labels in aseg segmentations, and probabilistic segmentations have reverted
+to FAST.
+
+  * FIX: --slice-time-ref option parsing (#2573)
+  * CI: Add style checks (missing since Travis got throttled) (#2570)
+
 20.2.4 (October 04, 2021)
 =========================
 Bug-fix release in the 20.2.x LTS series.

fmriprep/cli/parser.py

@@ -25,8 +25,11 @@
 from .. import config
 
 
-def _build_parser():
-    """Build parser object."""
+def _build_parser(**kwargs):
+    """Build parser object.
+
+    ``kwargs`` are passed to ``argparse.ArgumentParser`` (mainly useful for debugging).
+    """
     from functools import partial
     from pathlib import Path
     from argparse import (
@@ -112,11 +115,13 @@ def _slice_time_ref(value, parser):
             config.environment.version
         ),
         formatter_class=ArgumentDefaultsHelpFormatter,
+        **kwargs,
     )
     PathExists = partial(_path_exists, parser=parser)
     IsFile = partial(_is_file, parser=parser)
     PositiveInt = partial(_min_one, parser=parser)
     BIDSFilter = partial(_bids_filter, parser=parser)
+    SliceTimeRef = partial(_slice_time_ref, parser=parser)
 
     # Arguments as specified by BIDS-Apps
     # required, positional arguments
@@ -355,7 +360,7 @@ def _slice_time_ref(value, parser):
         required=False,
         action="store",
         default=None,
-        type=_slice_time_ref,
+        type=SliceTimeRef,
         help="The time of the reference slice to correct BOLD values to, as a fraction "
              "acquisition time. 0 indicates the start, 0.5 the midpoint, and 1 the end "
              "of acquisition. The alias `start` corresponds to 0, and `middle` to 0.5. "
@@ -655,9 +660,8 @@ def parse_args(args=None, namespace=None):
     config.from_dict(vars(opts))
 
     if not config.execution.notrack:
-        try:
-            import sentry_sdk
-        except ImportError:
+        import pkgutil
+        if pkgutil.find_loader("sentry_sdk") is None:
             config.execution.notrack = True
             config.loggers.cli.warning("Telemetry disabled because sentry_sdk is not installed.")
         else:

fmriprep/cli/tests/test_parser.py

@@ -177,3 +177,19 @@ def test_bids_filter_file(tmp_path, capsys):
 
     err = capsys.readouterr().err
     assert "JSON syntax error in:" in err
+    _reset_config()
+
+
+@pytest.mark.parametrize("st_ref", (None, "0", "1", "0.5", "start", "middle"))
+def test_slice_time_ref(tmp_path, st_ref):
+    bids_path = tmp_path / "data"
+    out_path = tmp_path / "out"
+    args = [str(bids_path), str(out_path), "participant"]
+    if st_ref:
+        args.extend(["--slice-time-ref", st_ref])
+    bids_path.mkdir()
+
+    parser = _build_parser()
+
+    parser.parse_args(args)
+    _reset_config()