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‎README.rst

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.. image:: https://codecov.io/gh/nipy/nipy/branch/main/graph/badge.svg
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:target: https://app.codecov.io/gh/nipy/nipy/branch/main
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.. Following contents should be from LONG_DESCRIPTION in nipy/info.py
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====
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NIPY
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====

‎doc/devel/guidelines/make_release.rst

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A guide for developers who are doing a nipy release
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.. _release-tools:
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Release tools
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=============
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Run::
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make check-version-info
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This installs the code from a git archive, from the repository, and for
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in-place use, and runs the ``get_info()`` function to confirm that
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installation is working and information parameters are set correctly. Look for the output at the end, which should look something like::
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########
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Versions
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########
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nipy - zip: 0.5.0
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nipy - install: 0.5.0
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nipy - editable: 0.5.0
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where the `0.5.0` should be the version in `nipy/info.py`.
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.. _release-checklist:
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Release checklist
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* Check the copyright years in ``doc/conf.py`` and ``LICENSE``
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* Refresh the ``README.rst`` text from the ``LONG_DESCRIPTION`` in ``info.py``
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by running ``make refresh-readme``.
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Check the output of::
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* Check the output of::
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rst2html.py README.rst > ~/tmp/readme.html
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because this will be the output used by PyPI_
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* Check the dependencies listed in ``nipy/info.py`` (e.g.
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``NUMPY_MIN_VERSION``) and in ``requirements.txt`` and in
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``doc/users/installation.rst``. They should at least match. Do they still
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hold? Make sure ``.travis.yml`` is testing these minimum dependencies
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specifically.
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* Check the dependencies listed in ``pyproject.toml`` and in
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``requirements.txt`` and in ``doc/users/installation.rst``. They should at
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least match. Do they still hold? Make sure ``.travis.yml`` is testing these
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minimum dependencies specifically.
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* Check the examples in python 2 and python 3, by
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running something like::
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* The release should now be ready.
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* Edit :file:`nipy/info.py` to set ``_version_extra`` to ``''``; commit.
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* Edit :file:`nipy/__init__.py` to set ``version`` to e.g. ``0.5.2``; commit.
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Then::
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make source-release
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* For the wheel build / upload, follow the `wheel builder README`_
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instructions again. Edit the ``.travis.yml`` and ``appveyor.yml`` files (if
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present) to give the release tag to build. Check the build has passed on
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the Travis-CI interface at https://travis-ci.org/MacPython/nipy-wheels. Now
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follow the instructions in the page above to download the built wheels to a
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local machine and upload to PyPI.
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instructions again. Push. Check the build has passed on the Github
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interface. Now follow the instructions in the page above to download the
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built wheels to a local machine and upload to PyPI.
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* Once everything looks good, you are ready to upload the source release to
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PyPI. See `setuptools intro`_. Make sure you have a file ``\$HOME/.pypirc``,
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further substantial development (often called 'trunk') and another for
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maintenance releases.
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* Branch to maintenance::
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git co -b maint/0.5.x
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Set ``_version_extra`` back to ``.dev1`` and bump ``_version_micro`` by
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1. Thus the maintenance series will have version numbers like - say
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- '0.5.1.dev1' until the next maintenance release - say '0.5.1'.
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Commit. Don't forget to push upstream with something like::
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git push upstream maint/0.2.x --set-upstream
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* Start next development series::
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git co main-master
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then restore ``.dev`` to ``_version_extra``, and bump
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``_version_minor`` by 1. Thus the development series ('trunk') will
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then restore ``.dev`` to ``__version__``, and bump
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the minor version by 1. Thus the development series ('trunk') will
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have a version number here of '0.3.0.dev' and the next full release
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will be '0.3.0'.
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‎nipy/__init__.py

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""" Nipy
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Nipy is a library for neuroimaging analysis.
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"""
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import os
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from .info import LONG_DESCRIPTION as __doc__
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from .info import STATUS as __status__
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from .info import URL as __url__
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from .info import __version__
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__version__ = "0.5.1.dev1"
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def _test_local_install():
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# Cleanup namespace
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del _test_local_install
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# If this file is exec after being imported, the following lines will
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# fail
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try:
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del version
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del Tester
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except:
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pass

‎nipy/algorithms/statistics/formula/formulae.py

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def terms(names, **kwargs):
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''' Return list of terms with names given by `names`
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r''' Return list of terms with names given by `names`
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This is just a convenience in defining a set of terms, and is the
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equivalent of ``sympy.symbols`` for defining symbols in sympy.
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names : str or sequence of str
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If a single str, can specify multiple ``Term``s with string
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containing space or ',' as separator.
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\\**kwargs : keyword arguments
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\*\*kwargs : keyword arguments
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keyword arguments as for ``sympy.symbols``
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Returns

‎nipy/core/reference/coordinate_map.py

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inv_xform)
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def __call__(self, *args, **kwargs):
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""" Create affine or non-affine coordinate map
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r""" Create affine or non-affine coordinate map
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Parameters
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----------
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\\*args :
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\*args :
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Arguments to ``make_affine`` or ``make_cmap`` methods. We check the
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first argument to see if it is a scalar or an affine, and pass the
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\\*args, \\*\\*kwargs to ``make_cmap`` or ``make_affine``
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\*args, \*\*kwargs to ``make_cmap`` or ``make_affine``
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respectively
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\\*\\*kwargs:
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\*\*kwargs:
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See above
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Returns
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-------
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cmap : ``CoordinateMap`` or ``AffineTransform``
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Affine if the first \\*arg was an affine array, otherwise a
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Affine if the first \*arg was an affine array, otherwise a
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Coordinate Map.
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"""
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arg0 = np.asarray(args[0])

‎nipy/info.py

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""" This file contains defines parameters for nipy that we use to fill
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settings in setup.py, the nipy top-level docstring, and for building the
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docs. In setup.py in particular, we exec this file, so it cannot import nipy
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""" Data package information
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"""
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# nipy version information. An empty _version_extra corresponds to a
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# full release. '.devN' as a _version_extra string means this is a development
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# version
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# See: https://www.python.org/dev/peps/pep-0440
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_version_major = 0
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_version_minor = 5
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_version_micro = 1
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_version_extra = '.dev1' # For development
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# _version_extra = 'rc1' # For release candidate
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# _version_extra = '' # For release
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# Format expected by setup.py and doc/source/conf.py: string of form "X.Y.Z"
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__version__ = f"{_version_major}.{_version_minor}.{_version_micro}{_version_extra}"
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CLASSIFIERS = ["Development Status :: 3 - Alpha",
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"Environment :: Console",
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"Intended Audience :: Science/Research",
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"License :: OSI Approved :: BSD License",
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"Operating System :: OS Independent",
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"Programming Language :: Python",
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"Topic :: Scientific/Engineering"]
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description = 'A python package for analysis of neuroimaging data'
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# Note: this long_description is the canonical place to edit this text.
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# It also appears in README.rst, but it should get there by running
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# ``tools/refresh_readme.py`` which pulls in this version.
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long_description = \
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"""
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====
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NIPY
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====
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Neuroimaging tools for Python.
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The aim of NIPY is to produce a platform-independent Python environment for
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the analysis of functional brain imaging data using an open development model.
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In NIPY we aim to:
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1. Provide an open source, mixed language scientific programming environment
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suitable for rapid development.
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2. Create software components in this environment to make it easy to develop
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tools for MRI, EEG, PET and other modalities.
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3. Create and maintain a wide base of developers to contribute to this
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platform.
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4. To maintain and develop this framework as a single, easily installable
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bundle.
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NIPY is the work of many people. We list the main authors in the file
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``AUTHOR`` in the NIPY distribution, and other contributions in ``THANKS``.
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Website
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=======
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Current information can always be found at the `NIPY project website
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<http://nipy.org/nipy>`_.
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Mailing Lists
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=============
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For questions on how to use nipy or on making code contributions, please see
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the ``neuroimaging`` mailing list:
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https://mail.python.org/mailman/listinfo/neuroimaging
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Please report bugs at github issues:
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https://github.com/nipy/nipy/issues
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You can see the list of current proposed changes at:
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https://github.com/nipy/nipy/pulls
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Code
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====
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You can find our sources and single-click downloads:
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* `Main repository`_ on Github;
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* Documentation_ for all releases and current development tree;
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* Download the `current development version`_ as a tar/zip file;
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* Downloads of all `available releases`_.
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.. _main repository: https://github.com/nipy/nipy
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.. _Documentation: http://nipy.org/nipy
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.. _current development version: https://github.com/nipy/nipy/archive/main.zip
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.. _available releases: http://pypi.python.org/pypi/nipy
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Tests
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=====
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To run nipy's tests, you will need to install the pytest_ Python testing
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package::
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pip install pytest
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Then::
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pytest nipy
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You can run the doctests along with the other tests with::
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pip install pytest-doctestplus
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Then::
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pytest --doctest-plus nipy
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Installation
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============
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See the latest `installation instructions`_.
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License
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=======
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We use the 3-clause BSD license; the full license is in the file ``LICENSE`` in
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the nipy distribution.
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.. links:
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.. _python: http://python.org
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.. _numpy: http://numpy.org
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.. _scipy: http://scipy.org
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.. _sympy: http://sympy.org
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.. _nibabel: http://nipy.org/nibabel
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.. _ipython: http://ipython.org
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.. _matplotlib: http://matplotlib.org
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.. _pytest: http://pytest.org
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.. _installation instructions: http://nipy.org/nipy/users/installation.html
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"""
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# minimum versions
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# Update in readme text above
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# Update in requirements.txt
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NUMPY_MIN_VERSION='1.22'
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SCIPY_MIN_VERSION = '1.8'
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NIBABEL_MIN_VERSION = '4.0'
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SYMPY_MIN_VERSION = '1.9'
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MAYAVI_MIN_VERSION = '4.7'
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CYTHON_MIN_VERSION = '0.12.1'
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NAME = 'nipy'
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MAINTAINER = "nipy developers"
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MAINTAINER_EMAIL = "neuroimaging@python.org"
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DESCRIPTION = description
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LONG_DESCRIPTION = long_description
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URL = "http://nipy.org/nipy"
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DOWNLOAD_URL = "http://github.com/nipy/nipy/archives/main"
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LICENSE = "BSD license"
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CLASSIFIERS = CLASSIFIERS
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AUTHOR = "nipy developmers"
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AUTHOR_EMAIL = "neuroimaging@python.org"
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PLATFORMS = "OS Independent"
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MAJOR = _version_major
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MINOR = _version_minor
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MICRO = _version_micro
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ISRELEASE = _version_extra == ''
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VERSION = __version__
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REQUIRES = ["numpy", "scipy", "sympy", "nibabel"]
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STATUS = 'beta'
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# For compatibility
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from . import __version__
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# Versions and locations of optional data packages
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NIPY_DATA_URL= 'http://nipy.org/data-packages/'

‎nipy/modalities/fmri/design.py

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r""" Stack a sequence of design / contrast dictionary pairs
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Uses multiple calls to :func:`stack2designs`
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