[ENH] Update to NiPreps-style config file (#745)

.circleci/get_data.sh

@@ -402,10 +402,10 @@ get_bids_data() {
     # Get Multi Shell outputs
     if [[ ${DS} = multishell_output ]]; then
       ${WGET} \
-        -O multishell_output.tar.gz \
-        "https://upenn.box.com/shared/static/nwxdn4ale8dkebvpjmxbx99dqjzwvlmh.gz"
-      tar xvfz multishell_output.tar.gz -C ${WORKDIR}/data/
-      rm multishell_output.tar.gz
+        -O multishell_output.tar.xz \
+        "https://upenn.box.com/shared/static/hr7xnxicbx9iqndv1yl35bhtd61fpalp.xz"
+      tar xvfJ multishell_output.tar.xz -C ${WORKDIR}/data/
+      rm multishell_output.tar.xz
     fi
 
     # Get Single Shell outputs

qsiprep/__init__.py

@@ -1,15 +1,34 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""
+#
+# Copyright The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""Top-module metadata."""
 
-"""
+try:
+    from ._version import __version__
+except ImportError:
+    __version__ = "0+unknown"
 
 import warnings
 
-from .__about__ import __copyright__, __credits__, __packagename__, __version__  # noqa
-
 # cmp is not used by qsiprep, so ignore nipype-generated warnings
 warnings.simplefilter("ignore")
 warnings.filterwarnings("ignore", r"cmp not installed")

qsiprep/_warnings.py

@@ -0,0 +1,48 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copied without change from fMRIPrep
+#
+# Copyright The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""Manipulate Python warnings."""
+
+import logging
+import warnings
+
+_wlog = logging.getLogger("py.warnings")
+_wlog.addHandler(logging.NullHandler())
+
+
+def _warn(message, category=None, stacklevel=1, source=None):
+    """Redefine the warning function."""
+    if category is not None:
+        category = type(category).__name__
+        category = category.replace("type", "WARNING")
+
+    logging.getLogger("py.warnings").warning(f"{category or 'WARNING'}: {message}")
+
+
+def _showwarning(message, category, filename, lineno, file=None, line=None):
+    _warn(message, category=category)
+
+
+warnings.warn = _warn
+warnings.showwarning = _showwarning