Merge pull request #894 from effigies/doc/update_config

DOC: Attempt to find versioneer version when building docs

Author: effigies

.travis.yml

@@ -121,8 +121,7 @@ script:
           flake8 nibabel
       elif [ "${CHECK_TYPE}" == "doc" ]; then
           cd doc
-          make html;
-          make doctest;
+          make html && make doctest
       elif [ "${CHECK_TYPE}" == "test" ]; then
           # Change into an innocuous directory and find tests from installation
           mkdir for_testing

Changelog

@@ -79,7 +79,7 @@ Enhancements
 
 Bug fixes
 ---------
-* Sliced ``Tractogram``s no longer ``apply_affine`` to the original
+* Sliced ``Tractogram``\s no longer ``apply_affine`` to the original
   ``Tractogram``'s streamlines. (pr/811) (MC, reviewed by Serge Koudoro,
   Philippe Poulin, CM, MB)
 * Change strings with invalid escapes to raw strings (pr/827) (EL, reviewed
@@ -98,7 +98,7 @@ Maintenance
 API changes and deprecations
 ----------------------------
 * Fully remove deprecated ``checkwarns`` and ``minc`` modules. (pr/852) (CM)
-* The ``keep_file_open`` argument to file load operations and ``ArrayProxy``s
+* The ``keep_file_open`` argument to file load operations and ``ArrayProxy``\s
   no longer acccepts the value ``"auto"``, raising a ``ValueError``. (pr/852)
   (CM)
 * Deprecate ``ArraySequence.data`` in favor of ``ArraySequence.get_data()``,
@@ -420,7 +420,7 @@ New features
 * Support for MRtrix TCK streamlines file format (pr/486) (MC, reviewed by
   MB, Arnaud Bore, J-Donald Tournier, Jean-Christophe Houde)
 * Added ``get_fdata()`` as default method to retrieve scaled floating point
-  data from ``DataobjImage``s (pr/551) (MB, reviewed by CM, SG)
+  data from ``DataobjImage``\s (pr/551) (MB, reviewed by CM, SG)
 
 Enhancements
 ------------

doc/source/conf.py

@@ -21,10 +21,8 @@
 
 import sys
 import os
-try:
-    from configparser import ConfigParser
-except ImportError:
-    from ConfigParser import ConfigParser  # PY2
+from runpy import run_path
+from configparser import ConfigParser
 
 # Check for external Sphinx extensions we depend on
 try:
@@ -51,9 +49,7 @@
 # -- General configuration ----------------------------------------------------
 
 # We load the nibabel release info into a dict by explicit execution
-rel = {}
-with open(os.path.join('..', '..', 'nibabel', 'info.py'), 'r') as fobj:
-    exec(fobj.read(), rel)
+rel = run_path(os.path.join('..', '..', 'nibabel', 'info.py'))
 
 # Write long description from info
 with open('_long_description.inc', 'wt') as fobj:
@@ -62,10 +58,7 @@
 # Load metadata from setup.cfg
 config = ConfigParser()
 config.read(os.path.join('..', '..', 'setup.cfg'))
-try:
-    metadata = config['metadata']
-except AttributeError:
-    metadata = dict(config.items('metadata'))  # PY2
+metadata = config['metadata']
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.

doc/tools/build_modref_templates.py

@@ -5,6 +5,7 @@
 # stdlib imports
 import sys
 import re
+import os
 from os.path import join as pjoin
 
 # local imports
@@ -48,12 +49,25 @@ def abort(error):
 
     installed_version = V(module.__version__)
 
-    info_file = pjoin('..', package, 'info.py')
-    info_lines = open(info_file).readlines()
-    source_version = '.'.join([v.split('=')[1].strip(" '\n.")
-                               for v in info_lines if re.match(
-                                       '^_version_(major|minor|micro|extra)', v
-                                       )])
+    version_file = pjoin('..', package, '_version.py')
+    source_version = None
+    if os.path.exists(version_file):
+        # Versioneer
+        from runpy import run_path
+        try:
+            source_version = run_path(version_file)['get_versions']()['version']
+        except (FileNotFoundError, KeyError):
+            pass
+        if source_version == '0+unknown':
+            source_version = None
+    if source_version is None:
+        # Legacy fall-back
+        info_file = pjoin('..', package, 'info.py')
+        info_lines = open(info_file).readlines()
+        source_version = '.'.join([v.split('=')[1].strip(" '\n.")
+                                   for v in info_lines if re.match(
+                                           '^_version_(major|minor|micro|extra)', v
+                                           )])
     print('***', source_version)
 
     if source_version != installed_version:
@@ -68,6 +82,7 @@ def abort(error):
                                         r'.*test.*$',
                                         r'\.info.*$',
                                         r'\.pkg_info.*$',
+                                        r'\.py3k.*$',
                                         ]
     docwriter.write_api_docs(outdir)
     docwriter.write_index(outdir, 'index', relative_to=outdir)

nibabel/affines.py

@@ -306,7 +306,7 @@ def obliquity(affine):
     This implementation is inspired by `AFNI's implementation
     <https://github.com/afni/afni/blob/b6a9f7a21c1f3231ff09efbd861f8975ad48e525/src/thd_coords.c#L660-L698>`_.
     For further details about *obliquity*, check `AFNI's documentation
-    <https://sscc.nimh.nih.gov/sscc/dglen/Obliquity>_.
+    <https://sscc.nimh.nih.gov/sscc/dglen/Obliquity>`_.
 
     Parameters
     ----------

nibabel/brikhead.py

@@ -250,7 +250,7 @@ def __init__(self, file_like, header, mmap=True, keep_file_open=None):
             a new file handle is created every time the image is accessed.
             If ``file_like`` refers to an open file handle, this setting has no
             effect. The default value (``None``) will result in the value of
-            ``nibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT` being used.
+            ``nibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT`` being used.
         """
         super(AFNIArrayProxy, self).__init__(file_like,
                                              header,
@@ -533,7 +533,7 @@ def from_file_map(klass, file_map, mmap=True, keep_file_open=None):
             a new file handle is created every time the image is accessed.
             If ``file_like`` refers to an open file handle, this setting has no
             effect. The default value (``None``) will result in the value of
-            ``nibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT` being used.
+            ``nibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT`` being used.
         """
         with file_map['header'].get_prepare_fileobj('rt') as hdr_fobj:
             hdr = klass.header_class.from_fileobj(hdr_fobj)
@@ -553,6 +553,7 @@ def filespec_to_file_map(klass, filespec):
         afni.nimh.nih.gov/pub/dist/doc/program_help/README.compression.html.
         Thus, if you have AFNI files my_image.HEAD and my_image.BRIK.gz and you
         want to load the AFNI BRIK / HEAD pair, you can specify:
+
             * The HEAD filename - e.g., my_image.HEAD
             * The BRIK filename w/o compressed extension - e.g., my_image.BRIK
             * The full BRIK filename - e.g., my_image.BRIK.gz

nibabel/cifti2/__init__.py

@@ -26,4 +26,4 @@
                      Cifti2TransformationMatrixVoxelIndicesIJKtoXYZ,
                      Cifti2Vertices, Cifti2Volume, CIFTI_BRAIN_STRUCTURES,
                      Cifti2HeaderError, CIFTI_MODEL_TYPES, load, save)
-from .cifti2_axes import (Axis, BrainModelAxis, ParcelsAxis, SeriesAxis, LabelAxis, ScalarAxis)
+from .cifti2_axes import (Axis, BrainModelAxis, ParcelsAxis, SeriesAxis, LabelAxis, ScalarAxis)

nibabel/cifti2/cifti2.py

@@ -172,7 +172,7 @@ def _to_xml_element(self):
 
 
 class Cifti2LabelTable(xml.XmlSerializable, MutableMapping):
-    """ CIFTI-2 label table: a sequence of ``Cifti2Label``s
+    """ CIFTI-2 label table: a sequence of ``Cifti2Label``\s
 
     * Description - Used by NamedMap when IndicesMapToDataType is
       "CIFTI_INDEX_TYPE_LABELS" in order to associate names and display colors
@@ -927,8 +927,8 @@ class Cifti2MatrixIndicesMap(xml.XmlSerializable, MutableSequence):
     * Text Content: [NA]
     * Parent Element - Matrix
 
-    Attribute
-    ---------
+    Attributes
+    ----------
     applies_to_matrix_dimension : list of ints
         Dimensions of this matrix that follow this mapping
     indices_map_to_data_type : str one of CIFTI_MAP_TYPES

nibabel/cifti2/cifti2_axes.py

@@ -23,7 +23,7 @@
 (except for SeriesAxis objects, which have to remain monotonically increasing or decreasing).
 
 Creating new CIFTI-2 axes
------------------------
+-------------------------
 New Axis objects can be constructed by providing a description for what is contained
 in each row/column of the described tensor. For each Axis sub-class this descriptor is:
 
@@ -250,7 +250,7 @@ def __init__(self, name, voxel=None, vertex=None, affine=None,
         factory methods:
 
         - :py:meth:`~BrainModelAxis.from_mask`: creates surface or volumetric BrainModelAxis axis
-        from respectively 1D or 3D masks
+          from respectively 1D or 3D masks
         - :py:meth:`~BrainModelAxis.from_surface`: creates a surface BrainModelAxis axis
 
         The resulting BrainModelAxis axes can be concatenated by adding them together.

nibabel/gifti/gifti.py

@@ -207,18 +207,21 @@ class GiftiCoordSystem(xml.XmlSerializable):
     Attributes
     ----------
     dataspace : int
-        From the spec: "Contains the stereotaxic space of a DataArray's data
+        From the spec: Contains the stereotaxic space of a DataArray's data
         prior to application of the transformation matrix. The stereotaxic
         space should be one of:
-            NIFTI_XFORM_UNKNOWN
-            NIFTI_XFORM_SCANNER_ANAT
-            NIFTI_XFORM_ALIGNED_ANAT
-            NIFTI_XFORM_TALAIRACH
-            NIFTI_XFORM_MNI_152"
+
+          - NIFTI_XFORM_UNKNOWN
+          - NIFTI_XFORM_SCANNER_ANAT
+          - NIFTI_XFORM_ALIGNED_ANAT
+          - NIFTI_XFORM_TALAIRACH
+          - NIFTI_XFORM_MNI_152
+
     xformspace : int
         Spec: "Contains the stereotaxic space of a DataArray's data after
         application of the transformation matrix. See the DataSpace element for
         a list of stereotaxic spaces."
+
     xform : array-like shape (4, 4)
         Affine transformation matrix
     """