Merge tag '1.5.10' into rel/20.0.6

1.5.10 (April 16, 2020) Bug-fix release in the 1.5.x series. This release fixes a bug for **phase-difference fieldmaps that are not in RAS+ orientation**. The bug presented as an error if the orientation was reordered relative to RAS+ (for example, AIL+) and the swapped dimensions were not of the same size. Otherwise, the bug introduced a poor masking of the phase difference map, and could be quite subtle if the original orientation was LAS+. Runs of fMRIPrep that used other susceptibility distortion correction (SDC) methods are not currently considered problematic. This bug affects all previous versions of fMRIPrep, as well as versions 20.0.0-20.0.5. * FIX: Do not reorient magnitude images (nipreps/sdcflows#98)
nipreps · Apr 16, 2020 · 770d641 · 770d641
2 parents 2602ccc + b529274
commit 770d641
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diff --git a/.versions.json b/.versions.json
@@ -1,16 +1,85 @@
 {
 	"flagged": {
 		"1.0.0": "Deprecated / too old",
-		"1.5.0rc1": "Nipype unstable",
-		"1.5.0rc2": "Nipype unstable",
-		"1.5.0": "Nipype unstable",
-		"1.5.1rc1": "Nipype unstable",
-		"1.5.1rc2": "Nipype unstable",
-		"20.0.0rc1": "fsLR resampling error (problematic only when using the --cifti-output flag)",
-		"20.0.0rc2": "fsLR resampling error (problematic only when using the --cifti-output flag)",
-		"20.0.0rc3": "fsLR resampling error (problematic only when using the --cifti-output flag)",
-		"20.0.0": "fsLR resampling error (problematic only when using the --cifti-output flag)",
-		"20.0.1": "fsLR resampling error (problematic only when using the --cifti-output flag)",
-		"20.0.2": "fsLR resampling error (problematic only when using the --cifti-output flag)"
+		"1.0.1": "Phase-difference fieldmap bug",
+		"1.0.2": "Phase-difference fieldmap bug",
+		"1.0.3": "Phase-difference fieldmap bug",
+		"1.0.4": "Phase-difference fieldmap bug",
+		"1.0.5": "Phase-difference fieldmap bug",
+		"1.0.6": "Phase-difference fieldmap bug",
+		"1.0.6-1": "Phase-difference fieldmap bug",
+		"1.0.6-2": "Phase-difference fieldmap bug",
+		"1.0.7": "Phase-difference fieldmap bug",
+		"1.0.8": "Phase-difference fieldmap bug",
+		"1.0.9": "Phase-difference fieldmap bug",
+		"1.0.10": "Phase-difference fieldmap bug",
+		"1.0.11": "Phase-difference fieldmap bug",
+		"1.0.12": "Phase-difference fieldmap bug",
+		"1.0.13": "Phase-difference fieldmap bug",
+		"1.0.14": "Phase-difference fieldmap bug",
+		"1.0.15": "Phase-difference fieldmap bug",
+		"1.1.0": "Phase-difference fieldmap bug",
+		"1.1.1": "Phase-difference fieldmap bug",
+		"1.1.2": "Phase-difference fieldmap bug",
+		"1.1.3": "Phase-difference fieldmap bug",
+		"1.1.4": "Phase-difference fieldmap bug",
+		"1.1.5": "Phase-difference fieldmap bug",
+		"1.1.6": "Phase-difference fieldmap bug",
+		"1.1.7": "Phase-difference fieldmap bug",
+		"1.1.8": "Phase-difference fieldmap bug",
+		"1.2.0": "Phase-difference fieldmap bug",
+		"1.2.1": "Phase-difference fieldmap bug",
+		"1.2.2": "Phase-difference fieldmap bug",
+		"1.2.3": "Phase-difference fieldmap bug",
+		"1.2.4": "Phase-difference fieldmap bug",
+		"1.2.5": "Phase-difference fieldmap bug",
+		"1.2.6": "Phase-difference fieldmap bug",
+		"1.2.6-1": "Phase-difference fieldmap bug",
+		"1.3.0": "Phase-difference fieldmap bug",
+		"1.3.0.post1": "Phase-difference fieldmap bug",
+		"1.3.0.post2": "Phase-difference fieldmap bug",
+		"1.3.0.post3": "Phase-difference fieldmap bug",
+		"1.3.1": "Phase-difference fieldmap bug",
+		"1.3.1.post1": "Phase-difference fieldmap bug",
+		"1.3.1.post2": "Phase-difference fieldmap bug",
+		"1.3.1.post3": "Phase-difference fieldmap bug",
+		"1.3.1.post4": "Phase-difference fieldmap bug",
+		"1.3.2": "Phase-difference fieldmap bug",
+		"1.4.0a0": "Phase-difference fieldmap bug",
+		"1.4.0a1": "Phase-difference fieldmap bug",
+		"1.4.0": "Phase-difference fieldmap bug",
+		"1.4.1rc1": "Phase-difference fieldmap bug",
+		"1.4.1rc2": "Phase-difference fieldmap bug",
+		"1.4.1rc3": "Phase-difference fieldmap bug",
+		"1.4.1rc4": "Phase-difference fieldmap bug",
+		"1.4.1rc5": "Phase-difference fieldmap bug",
+		"1.4.1": "Phase-difference fieldmap bug",
+		"1.5.0rc1": "Nipype unstable; Phase-difference fieldmap bug",
+		"1.5.0rc2": "Nipype unstable; Phase-difference fieldmap bug",
+		"1.5.0": "Nipype unstable; Phase-difference fieldmap bug",
+		"1.5.1rc1": "Nipype unstable; Phase-difference fieldmap bug",
+		"1.5.1rc2": "Nipype unstable; Phase-difference fieldmap bug",
+		"1.5.1": "Phase-difference fieldmap bug",
+		"1.5.2": "Phase-difference fieldmap bug",
+		"1.5.3rc1": "Phase-difference fieldmap bug",
+		"1.5.3rc2": "Phase-difference fieldmap bug",
+		"1.5.3": "Phase-difference fieldmap bug",
+		"1.5.4": "Phase-difference fieldmap bug",
+		"1.5.5": "Phase-difference fieldmap bug",
+		"1.5.6": "Phase-difference fieldmap bug",
+		"1.5.7": "Phase-difference fieldmap bug",
+		"1.5.8": "Phase-difference fieldmap bug",
+		"1.5.9": "Phase-difference fieldmap bug",
+		"20.0.0rc1": "fsLR resampling error (problematic only when using the --cifti-output flag); Phase-difference fieldmap bug",
+		"20.0.0rc2": "fsLR resampling error (problematic only when using the --cifti-output flag); Phase-difference fieldmap bug",
+		"20.0.0rc3": "fsLR resampling error (problematic only when using the --cifti-output flag); Phase-difference fieldmap bug",
+		"20.0.0": "fsLR resampling error (problematic only when using the --cifti-output flag); Phase-difference fieldmap bug",
+		"20.0.1": "fsLR resampling error (problematic only when using the --cifti-output flag); Phase-difference fieldmap bug",
+		"20.0.2": "fsLR resampling error (problematic only when using the --cifti-output flag); Phase-difference fieldmap bug",
+		"20.0.3": "Phase-difference fieldmap bug",
+		"20.0.4": "Phase-difference fieldmap bug",
+		"20.0.5": "Phase-difference fieldmap bug",
+		"20.1.0rc1": "Phase-difference fieldmap bug",
+		"20.1.0rc2": "Phase-difference fieldmap bug"
 	}
 }
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,3 +1,21 @@
+1.5.10 (April 16, 2020)
+=======================
+Bug-fix release in the 1.5.x series.
+
+This release fixes a bug for **phase-difference fieldmaps that are not in RAS+ orientation**.
+The bug presented as an error if the orientation was reordered relative to RAS+ (for example,
+AIL+) and the swapped dimensions were not of the same size.
+Otherwise, the bug introduced a poor masking of the phase difference map, and could be quite subtle
+if the original orientation was LAS+.
+Runs of fMRIPrep that used other susceptibility distortion correction (SDC) methods are not
+currently considered problematic.
+
+This bug affects all previous versions of fMRIPrep, as well as versions 20.0.0-20.0.5.
+
+  * FIX: Do not reorient magnitude images (`nipreps/sdcflows#98`_)
+
+.. _`nipreps/sdcflows#98`: https://github.com/nipreps/sdcflows/pull/98
+
 20.0.5 (March 19, 2020)
 =======================
 Bug-fix release in 20.0.x series.

diff --git a/setup.cfg b/setup.cfg
@@ -30,7 +30,7 @@ install_requires =
     psutil >= 5.4
     pybids >= 0.9.4
     pyyaml
-    sdcflows ~= 1.2.0
+    sdcflows ~= 1.2.2
     smriprep ~= 0.5.2
     tedana >= 0.0.5
     templateflow >= 0.5.1rc1
@@ -50,7 +50,7 @@ doc =
     packaging
     pydot >=1.2.3
     pydotplus
-    sphinx >=1.5.3
+    sphinx >=1.5.3, <3
     sphinx-argparse
     sphinx_rtd_theme
     sphinxcontrib-napoleon