Merge pull request #829 from nipy/rel/3.0.0rc1

REL: 3.0.0rc1

Author: effigies

.mailmap

@@ -14,6 +14,7 @@ Basile Pinsard <[email protected]> bpinsard <[email protected]>
 Basile Pinsard <[email protected]> bpinsard <[email protected]>
 Ben Cipollini <[email protected]> Ben Cipollini <[email protected]>
 Bertrand Thirion <[email protected]> bthirion <[email protected]>
+Cameron Riddell <[email protected]> <[email protected]>
 Christian Haselgrove <[email protected]> Christian Haselgrove <[email protected]>
 Christopher J. Markiewicz <[email protected]> Chris Johnson <[email protected]>
 Christopher J. Markiewicz <[email protected]> Chris Markiewicz <[email protected]>
@@ -40,6 +41,8 @@ Kesshi Jordan <[email protected]> kesshijordan <[email protected]>
 Kevin S. Hahn <[email protected]> Kevin S. Hahn <[email protected]>
 Konstantinos Raktivan <[email protected]> constracti <[email protected]>
 Krish Subramaniam <[email protected]> Krish Subramaniam <[email protected]>
+Krzysztof J. Gorgolewski <[email protected]>
+Krzysztof J. Gorgolewski <[email protected]> <[email protected]>
 Marc-Alexandre Côté <[email protected]> Marc-Alexandre Cote <[email protected]>
 Mathias Goncalves <[email protected]> mathiasg <[email protected]>
 Matthew Cieslak <[email protected]> Matt Cieslak <[email protected]>
@@ -48,6 +51,7 @@ Michael Hanke <[email protected]> <[email protected]>
 Michiel Cottaar <[email protected]> Michiel Cottaar <[email protected]>
 Ly Nguyen <[email protected]> lxn2 <[email protected]>
 Oliver P. Hinds <[email protected]> ohinds <[email protected]>
+Oscar Esteban <[email protected]>
 Paul McCarthy <[email protected]> Paul McCarthy <[email protected]>
 Satrajit Ghosh <[email protected]> Satrajit Ghosh <[email protected]>
 Serge Koudoro <[email protected]> skoudoro <[email protected]>

.zenodo.json

@@ -68,6 +68,10 @@
       "name": "Lee, Gregory R.",
       "orcid": "0000-0001-8895-2740"
     },
+    {
+      "name": "Wang, Hao-Ting",
+      "orcid": "0000-0003-4078-2038"
+    },
     {
       "affiliation": "Harvard University - Psychology",
       "name": "Kastman, Erik",
@@ -92,6 +96,11 @@
       "name": "Goncalves, Mathias",
       "orcid": "0000-0002-7252-7771"
     },
+    {
+      "affiliation": "Department of Psychology, University of California Davis, CA, USA",
+      "name": "Riddell, Cameron",
+      "orcid": "0000-0001-8950-0375"
+    },
     {
       "name": "Burns, Christopher"
     },
@@ -119,9 +128,24 @@
     {
       "name": "Vincent, Robert D."
     },
+    {
+      "affiliation": "Center for Magnetic Resonance Research, University of Minnesota",
+      "name": "Braun, Henry",
+      "orcid": "0000-0001-7003-9822"
+    },
     {
       "name": "Subramaniam, Krish"
     },
+    {
+      "affiliation": "MIT",
+      "name": "Jarecka, Dorota",
+      "orcid": "0000-0003-1857-8129"
+    },
+    {
+      "affiliation": "Google",
+      "name": "Gorgolewski, Krzysztof J.",
+      "orcid": "0000-0003-3321-7583"
+    },
     {
       "affiliation": "Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada",
       "name": "Raamana, Pradeep Reddy",
@@ -147,6 +171,11 @@
     {
       "name": "Hymers, Mark"
     },
+    {
+      "affiliation": "Department of Psychology, Stanford University, CA, USA",
+      "name": "Esteban, Oscar",
+      "orcid": "0000-0001-8435-6191"
+    },
     {
       "name": "Koudoro, Serge"
     },
@@ -170,6 +199,10 @@
     {
       "name": "St-Jean, Samuel"
     },
+    {
+      "name": "Panfilov, Egor",
+      "orcid": "0000-0002-2500-6375"
+    },
     {
       "name": "Garyfallidis, Eleftherios"
     },
@@ -197,9 +230,6 @@
     {
       "name": "Fauber, Bennet"
     },
-    {
-      "name": "Panfilov, Egor"
-    },
     {
       "affiliation": "McGill University",
       "name": "Poline, Jean-Baptiste",
@@ -244,11 +274,6 @@
       "name": "P\u00e9rez-Garc\u00eda, Fernando",
       "orcid": "0000-0001-9090-3024"
     },
-    {
-      "affiliation": "Center for Magnetic Resonance Research, University of Minnesota",
-      "name": "Braun, Henry",
-      "orcid": "0000-0001-7003-9822"
-    },
     {
       "name": "Solovey, Igor"
     },

Changelog

@@ -25,6 +25,59 @@ Eric Larson (EL), Demian Wassermann, and Stephan Gerhard.
 
 References like "pr/298" refer to github pull request numbers.
 
+3.0.0 (To Be Determined)
+========================
+
+New features
+------------
+* ArrayProxy method ``get_scaled()`` scales data with a dtype of a
+  specified precision, promoting as necessary to avoid overflow. This
+  is to used in ``img.get_fdata()`` to control memory usage. (pr/833)
+  (CM, reviewed by Ross Markello)
+* GiftiImage method ``agg_data()`` to return usable data arrays (pr/793)
+  (Hao-Ting Wang, reviewed by CM)
+* Accept ``os.PathLike`` objects in place of filenames (pr/610) (Cameron
+  Riddell, reviewed by MB, CM)
+* Function to calculate obliquity of affines (pr/815) (Oscar Esteban,
+  reviewed by MB)
+
+Enhancements
+------------
+* ``get_fdata(dtype=np.float32)`` will attempt to avoid casting data to
+  ``np.float64`` when scaling parameters would otherwise promote the data
+  type unnecessarily. (pr/833) (CM, reviewed by Ross Markello)
+* ``ArraySequence`` now supports a large set of Python operators to combine
+  or update in-place. (pr/811) (MC, reviewed by Serge Koudoro, Philippe Poulin,
+  CM, MB)
+* Warn, rather than fail, on DICOMs with unreadable Siemens CSA tags (pr/818)
+  (Henry Braun, reviewed by CM)
+* Improve clarity of coordinate system tutorial (pr/823) (Egor Panfilov,
+  reviewed by MB)
+
+Bug fixes
+---------
+* Sliced ``Tractogram``s no longer ``apply_affine`` to the original
+  ``Tractogram``'s streamlines. (pr/811) (MC, reviewed by Serge Koudoro,
+  Philippe Poulin, CM, MB)
+* Re-import externals/netcdf.py from scipy to resolve numpy deprecation
+  (pr/821) (CM)
+
+Maintenance
+-----------
+* Support Python >=3.5.1, including Python 3.8.0 (pr/787) (CM)
+* Manage versioning with slightly customized Versioneer (pr/786) (CM)
+* Reference Nipy Community Code and Nibabel Developer Guidelines in
+  GitHub community documents (pr/778) (CM, reviewed by MB)
+
+API changes and deprecations
+----------------------------
+* Deprecate ``ArraySequence.data`` in favor of ``ArraySequence.get_data()``,
+  which will return a copy. ``ArraySequence.data`` now returns a read-only
+  view. (pr/811) (MC, reviewed by Serge Koudoro, Philippe Poulin, CM, MB)
+* Deprecate ``DataobjImage.get_data()`` API, to be removed in nibabel 5.0
+  (pr/794, pr/809) (CM, reviewed by MB)
+
+
 2.5.1 (Monday 23 September 2019)
 ================================
 

doc/source/index.rst

@@ -96,9 +96,14 @@ contributed code and discussion (in rough order of appearance):
 * Samir Reddigari
 * Konstantinos Raktivan
 * Matt Cieslak
-* Egor Pafilov
+* Egor Panfilov
 * Jath Palasubramaniam
 * Henry Braun
+* Oscar Esteban
+* Cameron Riddell
+* Hao-Ting Wang
+* Dorota Jarecka
+* Chris Gorgolewski
 
 License reprise
 ===============

nibabel/_version.py

@@ -208,6 +208,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         # sorting will prefer e.g. "2.0" over "2.0rc1"
         if ref.startswith(tag_prefix):
             r = ref[len(tag_prefix):]
+            # CJM: Nibabel fix to filter out refs that exactly match prefix
+            # or that don't start with a number once the prefix is stripped
+            # (Mostly a concern when prefix is '')
+            if not re.match(r'\d', r):
+                continue
             if verbose:
                 print("picking %s" % r)
             return {"version": r,

nibabel/info.py

@@ -13,7 +13,7 @@
 _version_major = 3
 _version_minor = 0
 _version_micro = 0
-_version_extra = 'dev'
+_version_extra = 'rc1'
 # _version_extra = ''
 
 # Format expected by setup.py and doc/source/conf.py: string of form "X.Y.Z"

versioneer.py

@@ -629,6 +629,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         # sorting will prefer e.g. "2.0" over "2.0rc1"
         if ref.startswith(tag_prefix):
             r = ref[len(tag_prefix):]
+            # CJM: Nibabel fix to filter out refs that exactly match prefix
+            # or that don't start with a number once the prefix is stripped
+            # (Mostly a concern when prefix is '')
+            if not re.match(r'\d', r):
+                continue
             if verbose:
                 print("picking %%s" %% r)
             return {"version": r,
@@ -1029,6 +1034,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         # sorting will prefer e.g. "2.0" over "2.0rc1"
         if ref.startswith(tag_prefix):
             r = ref[len(tag_prefix):]
+            # CJM: Nibabel fix to filter out refs that exactly match prefix
+            # or that don't start with a number once the prefix is stripped
+            # (Mostly a concern when prefix is '')
+            if not re.match(r'\d', r):
+                continue
             if verbose:
                 print("picking %s" % r)
             return {"version": r,