[med-svn] [Git][med-team/nitime][upstream] New upstream version 0.9
Nilesh Patra
gitlab at salsa.debian.org
Sun Dec 20 15:06:01 GMT 2020
Nilesh Patra pushed to branch upstream at Debian Med / nitime
Commits:
eafe9579 by Nilesh Patra at 2020-12-20T20:16:34+05:30
New upstream version 0.9
- - - - -
14 changed files:
- + .github/workflows/test.yml
- − .travis.yml
- doc/sphinxext/github.py
- doc/sphinxext/only_directives.py
- nitime/__init__.py
- nitime/algorithms/event_related.py
- nitime/analysis/base.py
- − nitime/six.py
- nitime/timeseries.py
- nitime/version.py
- nitime/viz.py
- requirements-dev.txt
- setup.py
- tools/apigen.py
Changes:
=====================================
.github/workflows/test.yml
=====================================
@@ -0,0 +1,32 @@
+name: Test suite
+
+on: [push, pull_request]
+
+jobs:
+ build:
+
+ runs-on: ubuntu-latest
+ strategy:
+ max-parallel: 4
+ matrix:
+ python-version: [3.7, 3.8]
+
+ steps:
+ - name: Checkout repo
+ uses: actions/checkout at v1
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python at v1
+ with:
+ python-version: ${{ matrix.python-version }}
+ - name: Install
+ run: |
+ python -m pip install --upgrade pip
+ python -m pip install -r requirements.txt
+ python -m pip install -r requirements-dev.txt
+ python -m pip install .
+ - name: Lint
+ run: |
+ flake8 --ignore N802,N806,W504 --select W503 `find . -name \*.py | grep -v setup.py | grep -v version.py | grep -v __init__.py | grep -v /docs/`
+ - name: Test
+ run: |
+ cd && mkdir for_test && cd for_test && pytest --pyargs nitime --cov-report term-missing --cov=AFQ
=====================================
.travis.yml deleted
=====================================
@@ -1,18 +0,0 @@
-language: python
-sudo: false
-
-python:
-- 3.6
-- 3.4
-- 2.7
-
-install:
-- travis_retry pip install -r requirements-dev.txt
-- travis_retry pip install -r requirements.txt
-- travis_retry pip install -e .
-
-script:
- - py.test --pyargs nitime --cov-report term-missing --cov=nitime --verbose
-
-after_success:
-- coveralls
=====================================
doc/sphinxext/github.py
=====================================
@@ -19,6 +19,7 @@ Authors
from docutils import nodes, utils
from docutils.parsers.rst.roles import set_classes
+from sphinx.util import logging
def make_link_node(rawtext, app, type, slug, options):
"""Create a link to a github resource.
@@ -146,7 +147,8 @@ def setup(app):
:param app: Sphinx application context.
"""
- app.info('Initializing GitHub plugin')
+ LOG = logging.getLogger(__name__)
+ LOG.info('Initializing GitHub plugin')
app.add_role('ghissue', ghissue_role)
app.add_role('ghpull', ghissue_role)
app.add_role('ghuser', ghuser_role)
=====================================
doc/sphinxext/only_directives.py
=====================================
@@ -37,8 +37,8 @@ def builder_inited(app):
html_only.traverse = only_base.dont_traverse
def setup(app):
- app.add_directive('htmlonly', html_only_directive, True, (0, 0, 0))
- app.add_directive('latexonly', latex_only_directive, True, (0, 0, 0))
+ app.add_directive('htmlonly', html_only_directive, True)
+ app.add_directive('latexonly', latex_only_directive, True)
app.add_node(html_only)
app.add_node(latex_only)
=====================================
nitime/__init__.py
=====================================
@@ -26,6 +26,5 @@ from .version import __version__
from . import algorithms
from . import timeseries
from . import analysis
-from . import six
from .timeseries import *
=====================================
nitime/algorithms/event_related.py
=====================================
@@ -55,10 +55,7 @@ def fir(timeseries, design):
and Unbiased Approach. Human Brain Mapping, 11:249-260
"""
- h = np.array(np.dot(np.dot(linalg.pinv(np.dot(design.T, design)),
- design.T),
- timeseries.T))
- return h
+ return linalg.pinv(design.T @design) @ design.T @ timeseries.T
def freq_domain_xcorr(tseries, events, t_before, t_after, Fs=1):
=====================================
nitime/analysis/base.py
=====================================
@@ -1,8 +1,5 @@
-try:
- from inspect import getfullargspec
-except ImportError: # PY2
- from inspect import getargspec as getfullargspec
+from inspect import getfullargspec
from nitime import descriptors as desc
=====================================
nitime/six.py deleted
=====================================
@@ -1,585 +0,0 @@
-"""Utilities for writing code that runs on Python 2 and 3"""
-
-# Copyright (c) 2010-2013 Benjamin Peterson
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in all
-# copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-# SOFTWARE.
-
-import operator
-import sys
-import types
-
-__author__ = "Benjamin Peterson <benjamin at python.org>"
-__version__ = "1.4.1"
-
-
-# Useful for very coarse version differentiation.
-PY2 = sys.version_info[0] == 2
-PY3 = sys.version_info[0] == 3
-
-if PY3:
- string_types = str,
- integer_types = int,
- class_types = type,
- text_type = str
- binary_type = bytes
-
- MAXSIZE = sys.maxsize
-else:
- string_types = basestring,
- integer_types = (int, long)
- class_types = (type, types.ClassType)
- text_type = unicode
- binary_type = str
-
- if sys.platform.startswith("java"):
- # Jython always uses 32 bits.
- MAXSIZE = int((1 << 31) - 1)
- else:
- # It's possible to have sizeof(long) != sizeof(Py_ssize_t).
- class X(object):
- def __len__(self):
- return 1 << 31
- try:
- len(X())
- except OverflowError:
- # 32-bit
- MAXSIZE = int((1 << 31) - 1)
- else:
- # 64-bit
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- del X
-
-
-def _add_doc(func, doc):
- """Add documentation to a function."""
- func.__doc__ = doc
-
-
-def _import_module(name):
- """Import module, returning the module after the last dot."""
- __import__(name)
- return sys.modules[name]
-
-
-class _LazyDescr(object):
-
- def __init__(self, name):
- self.name = name
-
- def __get__(self, obj, tp):
- result = self._resolve()
- setattr(obj, self.name, result)
- # This is a bit ugly, but it avoids running this again.
- delattr(tp, self.name)
- return result
-
-
-class MovedModule(_LazyDescr):
-
- def __init__(self, name, old, new=None):
- super(MovedModule, self).__init__(name)
- if PY3:
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- self.mod = old
-
- def _resolve(self):
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-
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- else:
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- self.attr = new_attr
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- self.mod = old_mod
- if old_attr is None:
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-
- def _resolve(self):
- module = _import_module(self.mod)
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-
-
-
-class _MovedItems(types.ModuleType):
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-
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-
-
-
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-
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-
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-
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- import io
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-else:
- def b(s):
- return s
- def u(s):
- return unicode(s, "unicode_escape")
- unichr = unichr
- int2byte = chr
- def byte2int(bs):
- return ord(bs[0])
- def indexbytes(buf, i):
- return ord(buf[i])
- def iterbytes(buf):
- return (ord(byte) for byte in buf)
- import StringIO
- StringIO = BytesIO = StringIO.StringIO
-_add_doc(b, """Byte literal""")
-_add_doc(u, """Text literal""")
-
-
-if PY3:
- exec_ = getattr(moves.builtins, "exec")
-
-
- def reraise(tp, value, tb=None):
- if value.__traceback__ is not tb:
- raise value.with_traceback(tb)
- raise value
-
-else:
- def exec_(_code_, _globs_=None, _locs_=None):
- """Execute code in a namespace."""
- if _globs_ is None:
- frame = sys._getframe(1)
- _globs_ = frame.f_globals
- if _locs_ is None:
- _locs_ = frame.f_locals
- del frame
- elif _locs_ is None:
- _locs_ = _globs_
- exec("""exec _code_ in _globs_, _locs_""")
-
-
- exec_("""def reraise(tp, value, tb=None):
- raise tp, value, tb
-""")
-
-
-print_ = getattr(moves.builtins, "print", None)
-if print_ is None:
- def print_(*args, **kwargs):
- """The new-style print function for Python 2.4 and 2.5."""
- fp = kwargs.pop("file", sys.stdout)
- if fp is None:
- return
- def write(data):
- if not isinstance(data, basestring):
- data = str(data)
- # If the file has an encoding, encode unicode with it.
- if (isinstance(fp, file) and
- isinstance(data, unicode) and
- fp.encoding is not None):
- errors = getattr(fp, "errors", None)
- if errors is None:
- errors = "strict"
- data = data.encode(fp.encoding, errors)
- fp.write(data)
- want_unicode = False
- sep = kwargs.pop("sep", None)
- if sep is not None:
- if isinstance(sep, unicode):
- want_unicode = True
- elif not isinstance(sep, str):
- raise TypeError("sep must be None or a string")
- end = kwargs.pop("end", None)
- if end is not None:
- if isinstance(end, unicode):
- want_unicode = True
- elif not isinstance(end, str):
- raise TypeError("end must be None or a string")
- if kwargs:
- raise TypeError("invalid keyword arguments to print()")
- if not want_unicode:
- for arg in args:
- if isinstance(arg, unicode):
- want_unicode = True
- break
- if want_unicode:
- newline = unicode("\n")
- space = unicode(" ")
- else:
- newline = "\n"
- space = " "
- if sep is None:
- sep = space
- if end is None:
- end = newline
- for i, arg in enumerate(args):
- if i:
- write(sep)
- write(arg)
- write(end)
-
-_add_doc(reraise, """Reraise an exception.""")
-
-
-def with_metaclass(meta, *bases):
- """Create a base class with a metaclass."""
- return meta("NewBase", bases, {})
-
-def add_metaclass(metaclass):
- """Class decorator for creating a class with a metaclass."""
- def wrapper(cls):
- orig_vars = cls.__dict__.copy()
- orig_vars.pop('__dict__', None)
- orig_vars.pop('__weakref__', None)
- for slots_var in orig_vars.get('__slots__', ()):
- orig_vars.pop(slots_var)
- return metaclass(cls.__name__, cls.__bases__, orig_vars)
- return wrapper
=====================================
nitime/timeseries.py
=====================================
@@ -32,7 +32,6 @@ import numpy as np
# Our own
from nitime import descriptors as desc
-import nitime.six as six
#-----------------------------------------------------------------------------
# Module globals
@@ -95,7 +94,7 @@ def get_time_unit(obj):
except TypeError:
return None
else:
- return get_time_unit(six.advance_iterator(it))
+ return get_time_unit(next(it))
class TimeArray(np.ndarray, TimeInterface):
@@ -903,7 +902,8 @@ class Frequency(float):
def __repr__(self):
- return str(self) + ' Hz'
+ return str(float(self)) + ' Hz'
+
def to_period(self, time_unit=base_unit):
"""Convert the value of a frequency to the corresponding period
@@ -1517,7 +1517,7 @@ class Events(TimeInterface):
# Ensure that the dict of data values has a known, uniform structure:
# all values must be arrays, with at least one dimension.
new_data = {}
- for k, v in six.iteritems(data):
+ for k, v in data.items():
if np.iterable(v):
v = np.asanyarray(v)
else:
=====================================
nitime/version.py
=====================================
@@ -2,9 +2,9 @@
# Format expected by setup.py and doc/source/conf.py: string of form "X.Y.Z"
_version_major = 0
-_version_minor = 8
-_version_micro = 1 # use '' for first of series, number for 1 and above
-# _version_extra = 'dev'
+_version_minor = 9
+_version_micro = '' # use '' for first of series, number for 1 and above
+# _version_extra = 'dev'
_version_extra = '' # Uncomment this for full releases
# Construct full version string from these.
@@ -75,20 +75,20 @@ for usage, and a DISCLAIMER OF ALL WARRANTIES.
All trademarks referenced herein are property of their respective holders.
-Copyright (c) 2006-2016, NIPY Developers
+Copyright (c) 2006-2020, NIPY Developers
All rights reserved.
"""
NAME = "nitime"
MAINTAINER = "Nipy Developers"
-MAINTAINER_EMAIL = "nipy-devel at neuroimaging.scipy.org"
+MAINTAINER_EMAIL = "neuroimaging at python.org"
DESCRIPTION = description
LONG_DESCRIPTION = long_description
URL = "http://nipy.org/nitime"
DOWNLOAD_URL = "http://github.com/nipy/nitime/downloads"
LICENSE = "Simplified BSD"
AUTHOR = "Nitime developers"
-AUTHOR_EMAIL = "nipy-devel at neuroimaging.scipy.org"
+AUTHOR_EMAIL = "neuroimaging at python.org"
PLATFORMS = "OS Independent"
MAJOR = _version_major
MINOR = _version_minor
@@ -96,3 +96,4 @@ MICRO = _version_micro
VERSION = __version__
PACKAGE_DATA = {"nitime": ["LICENSE", "tests/*.txt", "tests/*.npy",
"data/*.nii.gz", "data/*.txt", "data/*.csv"]}
+PYTHON_REQUIRES = ">=3.5"
=====================================
nitime/viz.py
=====================================
@@ -7,8 +7,6 @@ from __future__ import print_function
# If you are running nosetests right now, you might want to use 'agg' as a backend:
import sys
-from nitime.six.moves import map
-from nitime.six.moves import zip
# Then do all the rest of it:
import numpy as np
=====================================
requirements-dev.txt
=====================================
@@ -1,5 +1,6 @@
sphinx
-pytest==3.6.1
+pytest
pytest-cov
nibabel
-networkx
\ No newline at end of file
+networkx
+flake8
=====================================
setup.py
=====================================
@@ -45,6 +45,7 @@ opts = dict(name=NAME,
package_data=PACKAGE_DATA,
install_requires=REQUIRES,
requires=REQUIRES,
+ python_requires=PYTHON_REQUIRES,
)
try:
=====================================
tools/apigen.py
=====================================
@@ -216,8 +216,8 @@ class ApiDocWriter(object):
ad = '.. AUTO-GENERATED FILE -- DO NOT EDIT!\n\n'
chap_title = uri_short
- ad += (chap_title+'\n'+ self.rst_section_levels[1] * len(chap_title)
- + '\n\n')
+ ad += (chap_title+'\n' + self.rst_section_levels[1] *
+ len(chap_title) + '\n\n')
# Set the chapter title to read 'module' for all modules except for the
# main packages
View it on GitLab: https://salsa.debian.org/med-team/nitime/-/commit/eafe95796f1206d92a58ca94235972979cbe9b16
--
View it on GitLab: https://salsa.debian.org/med-team/nitime/-/commit/eafe95796f1206d92a58ca94235972979cbe9b16
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