Merge pull request #226 from mgxd/rel/0.5.1

rel: 0.5.1

Author: mgxd

CHANGELOG.md

@@ -4,20 +4,32 @@ All notable changes to this project will be documented (for humans) in this file
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-## [UNRELEASED] - 2018-??-??
-TODO Summary
-### Added
+## [0.5.1] - 2018-07-05
+Bugfix release
 
+### Added
+- Video tutorial / updated slides
+- Helper to set metadata restrictions correctly
+- Usage is now shown when run without arguments
+- New fields to Seqinfo
+  - series_uid
+- Reproin heuristic support for xnat
 ### Changed
-
-### Deprecated
-
+- Dockerfile updated to use `dcm2niix v1.0.20180622`
+- Conversion table will be regenerated if heurisic has changed
+- Do not touch existing BIDS files
+  - events.tsv
+  - task JSON
 ### Fixed
-
-### Removed
-
-### Security
-
+- Python 2.7.8 and older installation
+- Support for updated packages
+  - `Datalad` 0.10
+  - `pydicom` 1.0.2
+- Later versions of `pydicom` are prioritized first
+- JSON pretty print should not remove spaces
+- Phasediff fieldmaps behavior
+  - ensure phasediff exists
+  - support for single magnitude acquisitions
 
 ## [0.5] - 2018-03-01
 The first release after major refactoring:

Dockerfile

@@ -5,7 +5,7 @@
 # pull request on our GitHub repository:
 #     https://github.com/kaczmarj/neurodocker
 #
-# Timestamp: 2018-05-14 16:30:58
+# Timestamp: 2018-06-29 18:14:08
 
 FROM debian:stretch
 
@@ -33,15 +33,15 @@ RUN apt-get update -qq && apt-get install -yq --no-install-recommends  \
 ENTRYPOINT ["/neurodocker/startup.sh"]
 
 #------------------------
-# Install dcm2niix v1.0.20180328
+# Install dcm2niix v1.0.20180622
 #------------------------
 WORKDIR /tmp
 RUN deps='cmake g++ gcc git make pigz zlib1g-dev' \
     && apt-get update -qq && apt-get install -yq --no-install-recommends $deps \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
     && mkdir dcm2niix \
-    && curl -sSL https://github.com/rordenlab/dcm2niix/tarball/v1.0.20180328 | tar xz -C dcm2niix --strip-components 1 \
+    && curl -sSL https://github.com/rordenlab/dcm2niix/tarball/v1.0.20180622 | tar xz -C dcm2niix --strip-components 1 \
     && mkdir dcm2niix/build && cd dcm2niix/build \
     && cmake .. && make \
     && make install \
@@ -120,7 +120,7 @@ RUN echo '{ \
     \n    [ \
     \n      "dcm2niix", \
     \n      { \
-    \n        "version": "v1.0.20180328" \
+    \n        "version": "v1.0.20180622" \
     \n      } \
     \n    ], \
     \n    [ \
@@ -160,6 +160,6 @@ RUN echo '{ \
     \n      "/neurodocker/startup.sh heudiconv" \
     \n    ] \
     \n  ], \
-    \n  "generation_timestamp": "2018-05-14 16:30:58", \
+    \n  "generation_timestamp": "2018-06-29 18:14:08", \
     \n  "neurodocker_version": "0.3.2" \
     \n}' > /neurodocker/neurodocker_specs.json

heudiconv/info.py

@@ -1,4 +1,4 @@
-__version__ = "0.5.dev1"
+__version__ = "0.5.1"
 __author__ = "HeuDiConv team and contributors"
 __url__ = "https://github.com/nipy/heudiconv"
 __packagename__ = 'heudiconv'

utils/gen-docker-image.sh

@@ -5,7 +5,7 @@ set -eu
 VER=$(grep -Po '(?<=^__version__ = ).*' ../heudiconv/info.py | sed 's/"//g')
 
 docker run --rm kaczmarj/neurodocker:v0.3.2 generate -b debian:stretch -p apt \
-    --dcm2niix version=v1.0.20180328 \
+    --dcm2niix version=v1.0.20180622 \
     --neurodebian os_codename=stretch download_server=usa-nh pkgs=git-annex-standalone \
     --install git gcc pigz \
     --copy . /src/heudiconv \

utils/update_changes.sh

@@ -0,0 +1,55 @@
+#!/bin/bash
+#
+# Adapted from https://github.com/nipy/nipype/blob/master/tools/update_changes.sh
+#
+# This is a script to be run before releasing a new version.
+#
+# Usage /bin/bash update_changes.sh 0.5.1
+#
+
+# Setting      # $ help set
+set -u         # Treat unset variables as an error when substituting.
+set -x         # Print command traces before executing command.
+
+CHANGES=../CHANGELOG.md
+
+
+# Add changelog documentation
+cat > newchanges <<'_EOF'
+# Changelog
+All notable changes to this project will be documented (for humans) in this file.
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+
+_EOF
+
+# List all merged PRs
+curl -s https://api.github.com/repos/nipy/heudiconv/pulls?state=closed+milestone=$1 | jq -r \
+'.[] | "\(.title) #\(.number) milestone:\(.milestone.title) \(.merged_at)"' | sed '/null/d' | sed '/milestone:0.5 /d' >> newchanges
+echo "" >> newchanges
+echo "" >> newchanges
+
+
+# Elaborate today's release header
+HEADER="## [$1] - $(date '+%Y-%m-%d')"
+echo $HEADER >> newchanges
+echo "TODO Summary" >> newchanges
+echo "### Added" >> newchanges
+echo "" >> newchanges
+echo "### Changed" >> newchanges
+echo "" >> newchanges
+echo "### Deprecated" >> newchanges
+echo "" >> newchanges
+echo "### Fixed" >> newchanges
+echo "" >> newchanges
+echo "### Removed" >> newchanges
+echo "" >> newchanges
+echo "### Security" >> newchanges
+echo "" >> newchanges
+
+# Append old CHANGES
+tail -n+7 $CHANGES >> newchanges
+
+# Replace old CHANGES with new file
+mv newchanges $CHANGES