Merge branch 'master' of github.com:nipy/nibabel

* 'master' of github.com:nipy/nibabel:
  ChangeLog ready for release
  DOC - updated and expanded README
  NF - makefile target to make sdist, install, test
  MRG - updated from nisext upstream; adding zip tests

Author: jarrodmillman

Changelog

@@ -6,11 +6,8 @@
 NiBabel Development Changelog
 -----------------------------
 
-Modifications are done by Michael Hanke, if not indicated otherwise. 'Closes'
-statement IDs refer to the Debian bug tracking system and can be queried by
-visiting the URL::
-
-  http://bugs.debian.org/<bug id>
+NiBabel is the successor to the much-loved PyNifti package. Here we list the
+releases for both packages.
 
 'Close gh-' statements refer to GitHub issues that are available at::
 
@@ -20,20 +17,49 @@ The full VCS changelog is available here:
 
   http://github.com/hanke/nibabel/commits/master
 
+Releases
+~~~~~~~~
 
-Unreleased changes
-  Changes described here are not yet released, but available from VCS
-  repository.
-
-  * This is a complete rewrite of a pure-Python module to access various
-    neuroimaging data formats. It replaces the now obsolete PyNIfTI.
-  * Support for SPM-style ANALYZE images.
-  * MINC format support.
-  * Comprehensive unittest suite.
+NiBabel
++++++++
+
+Most work on NiBabel so far has been by Matthew Brettt (MB) and Michael Hanke
+(MH).
+
+* 1.0.0 (Thursday, 13, Oct 2010)
+
+  * This is the first public release of the NiBabel package.
+  * NiBabel is a complete rewrite of the PyNifti package in pure python.  It was
+    designed to make the code simpler and easier to work with. Like PyNifti,
+    NiBabel has fairly comprehensive NIfTI read and write support.
+  * Extended support for SPM Analyze images, including orientation affines from
+    matlab ``.mat`` files.
+  * Basic support for simple MINC 1.0 files (MB).  Please let us know if you
+    have MINC files that we don't support well.
+  * Support for reading and writing PAR/REC images (MH)
+  * Very preliminary, limited and highly experimental DICOM reading support (MB,
+    Ian Nimmo Smith).
+  * Some functions (`nibabel.funcs`) for basic image shape changes, including
+    the ability to transform to the image with data closest to the cononical
+    image orientation (first axis left-to-right, second back-to-front, third
+    down-to-up) (MB, Jonathan Taylor)
+  * Gifti format read and write support (preliminary) (Stephen Gerhard) 
+  * Added utilities to use nipy-style data packages, by rip then edit of nipy
+    data package code (MB)
+  * Some improvements to release support (Jarrod Millman, MB, Fernando Perez)
+  * Huge downward step in the quality and coverage by the docs, caused by MB,
+    mostly fixed by a lot of good work by MH.
+  * NiBabel will not work with Python < 2.5, and we haven't even tested it with
+    Python 3.  We will get to it soon...
+
+PyNifti
++++++++
 
+Modifications are done by Michael Hanke, if not indicated otherwise. 'Closes'
+statement IDs refer to the Debian bug tracking system and can be queried by
+visiting the URL::
 
-Releases
-~~~~~~~~
+  http://bugs.debian.org/<bug id>
 
 * 0.20090303.1 (Tue, 3 Mar 2009)
 

Makefile

@@ -239,6 +239,10 @@ check-version-info:
 installed-tests:
 	$(PYTHON) -c 'from nisext.testers import tests_installed; tests_installed("nibabel")'
 
+# Run tests from installed code
+sdist-tests:
+	$(PYTHON) -c 'from nisext.testers import sdist_tests; sdist_tests("nibabel")'
+
 # Update nisext subtree from remote
 update-nisext:
 	git fetch nisext

README.txt

@@ -1,7 +1,6 @@
 .. -*- rest -*-
 .. vim:syntax=rest
 
-
 =======
 NiBabel
 =======
@@ -20,6 +19,20 @@ PyNIfTI_.
 The various image format classes give full or selective access to header (meta)
 information and access to the image data is made available via NumPy arrays.
 
+Website
+=======
+
+Current information can always be found at the NIPY nibabel website::
+
+    http://nipy.org/nibabel
+
+Mailing Lists
+=============
+
+Please see the developer's list here::
+
+    http://mail.scipy.org/mailman/listinfo/nipy-devel
+
 Code
 ====
 
@@ -34,3 +47,11 @@ You can find our sources and single-click downloads:
 .. _Documentation: http://nipy.org/nibabel
 .. _current trunk: http://github.com/nipy/nibabel/archives/master
 .. _available releases: http://github.com/nipy/nibabel/downloads
+
+License
+=======
+
+Nibabel is licensed under the terms of the MIT license. Some code included with
+nibabel is licensed under the BSD license.  Please the COPYING file in the
+nibabel distribution.
+

nisext/testers.py

@@ -13,6 +13,7 @@
 
 import os
 from os.path import join as pjoin
+from glob import glob
 import shutil
 import tempfile
 import zipfile
@@ -188,25 +189,58 @@ def info_from_here(mod_name):
         shutil.rmtree(install_path)
 
 
-def tests_installed(mod_name, repo_path=None):
-    """ Install from `repo_path` into temporary directory; run tests
+def tests_installed(mod_name, source_path=None):
+    """ Install from `source_path` into temporary directory; run tests
 
     Parameters
     ----------
     mod_name : str
         name of module - e.g. 'nibabel'
-    repo_path : None or str
+    source_path : None or str
         Path from which to install.  If None, defaults to working directory
     """
-    if repo_path is None:
-        repo_path = os.path.abspath(os.getcwd())
+    if source_path is None:
+        source_path = os.path.abspath(os.getcwd())
     install_path = tempfile.mkdtemp()
     try:
-        site_pkgs_path = install_from_to(repo_path,
+        site_pkgs_path = install_from_to(source_path,
                                          install_path,
                                          PY_LIB_SDIR)
         run_mod_cmd(mod_name, site_pkgs_path, mod_name + '.test()')
     finally:
         shutil.rmtree(install_path)
 
 
+def tests_from_zip(mod_name, zip_fname):
+    """ Runs test from sdist zip source archive """
+    install_path = tempfile.mkdtemp()
+    try:
+        zip_extract_all(zip_fname, install_path)
+        pkg_dirs = glob(pjoin(install_path, mod_name + "*"))
+        if len(pkg_dirs) != 1:
+            raise OSError('There must be one and only one package dir')
+        pkg_contents = pjoin(install_path, pkg_dirs[0])
+        tests_installed(mod_name, pkg_contents)
+    finally:
+        shutil.rmtree(install_path)
+
+
+def sdist_tests(mod_name, repo_path=None):
+    """ Make sdist zip, install from it, and run tests """
+    pwd = os.path.abspath(os.getcwd())
+    if repo_path is None:
+        repo_path = pwd
+    install_path = tempfile.mkdtemp()
+    try:
+        os.chdir(repo_path)
+        my_call('python setup.py sdist --formats=zip --dist-dir='
+                + install_path)
+        zip_fnames = glob(pjoin(install_path, mod_name + "*.zip"))
+        if len(zip_fnames) != 1:
+            raise OSError('There must be one and only one zip file, '
+                          'but I found "%s"' % ': '.join(zip_fnames))
+        tests_from_zip(mod_name, zip_fnames[0])
+    finally:
+        os.chdir(pwd)
+        shutil.rmtree(install_path)
+