Merge tag 'v0.9.0' into debian

Various improvements and compatibility/support (dcm2niix, datalad,
duecredit) changes.  Major change is placement of output files to the
target output directory during conversion.

- #454 zenodo referencing in README.rst and support for ducredit for
  heudiconv and reproin heuristic
- #445 more tutorial references in README.md

- [#485][] placed files during conversion right away into the target
  directory (with a `_heudiconv???` suffix, renamed into ultimate target
  name later on), which avoids hitting file size limits of /tmp ([#481][]) and
  helped to avoid a regression in dcm2nixx 1.0.20201102
- #477 replaced `rec-<magnitude|phase>` with `part-<mag|phase>` now
  that BIDS supports the part entity
- #473 made default for CogAtlasID to be a TODO URL
- #459 made AcquisitionTime used for acq_time scans file field
- #451 retained sub-second resolution in scans files
- #442 refactored code so there is now heudiconv.main.workflow for
  more convenient use as a Python module

- minimal version of nipype set to 1.2.3 to guarantee correct handling
  of DWI files ([#480][])
- `heudiconvDCM*` temporary directories are removed now ([#462][])
- compatibility with DataLad 0.13 ([#464][])

- #443 pathlib as a dependency (we are Python3 only now)

* tag 'v0.9.0':
  Add a helper rule to upload to pypi
  update changelog reference as part of prep release
  [DATALAD RUNCMD] prepare the release
  CHANGELOG entry for 0.9.0

Author: yarikoptic

CHANGELOG.md

@@ -4,16 +4,42 @@ 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).
 
-## [0.8.1] - Date
+## [0.9.0] - 2020-12-23
 
-TODO Summary
+Various improvements and compatibility/support (dcm2niix, datalad,
+duecredit) changes.  Major change is placement of output files to the
+target output directory during conversion.
 
 ### Added
+
+- #454 zenodo referencing in README.rst and support for ducredit for
+  heudiconv and reproin heuristic
+- #445 more tutorial references in README.md
+
 ### Changed
-### Deprecated
+
+- [#485][] placed files during conversion right away into the target
+  directory (with a `_heudiconv???` suffix, renamed into ultimate target
+  name later on), which avoids hitting file size limits of /tmp ([#481][]) and
+  helped to avoid a regression in dcm2nixx 1.0.20201102
+- #477 replaced `rec-<magnitude|phase>` with `part-<mag|phase>` now
+  that BIDS supports the part entity
+- #473 made default for CogAtlasID to be a TODO URL
+- #459 made AcquisitionTime used for acq_time scans file field
+- #451 retained sub-second resolution in scans files
+- #442 refactored code so there is now heudiconv.main.workflow for
+  more convenient use as a Python module
+
 ### Fixed
+
+- minimal version of nipype set to 1.2.3 to guarantee correct handling
+  of DWI files ([#480][])
+- `heudiconvDCM*` temporary directories are removed now ([#462][])
+- compatibility with DataLad 0.13 ([#464][])
+
 ### Removed
-### Security
+
+- #443 pathlib as a dependency (we are Python3 only now)
 
 
 ## [0.8.0] - 2020-04-15
@@ -323,6 +349,7 @@ TODO Summary
 [#366]: https://github.com/nipy/heudiconv/issues/366
 [#368]: https://github.com/nipy/heudiconv/issues/368
 [#373]: https://github.com/nipy/heudiconv/issues/373
+[#485]: https://github.com/nipy/heudiconv/issues/485
 [#293]: https://github.com/nipy/heudiconv/issues/293
 [#304]: https://github.com/nipy/heudiconv/issues/304
 [#306]: https://github.com/nipy/heudiconv/issues/306
@@ -360,11 +387,7 @@ TODO Summary
 [#434]: https://github.com/nipy/heudiconv/issues/434
 [#436]: https://github.com/nipy/heudiconv/issues/436
 [#437]: https://github.com/nipy/heudiconv/issues/437
-[#425]: https://github.com/nipy/heudiconv/issues/425
-[#420]: https://github.com/nipy/heudiconv/issues/420
-[#425]: https://github.com/nipy/heudiconv/issues/425
-[#430]: https://github.com/nipy/heudiconv/issues/430
-[#432]: https://github.com/nipy/heudiconv/issues/432
-[#434]: https://github.com/nipy/heudiconv/issues/434
-[#436]: https://github.com/nipy/heudiconv/issues/436
-[#437]: https://github.com/nipy/heudiconv/issues/437
+[#462]: https://github.com/nipy/heudiconv/issues/462
+[#464]: https://github.com/nipy/heudiconv/issues/464
+[#480]: https://github.com/nipy/heudiconv/issues/480
+[#481]: https://github.com/nipy/heudiconv/issues/481

Makefile

@@ -1,6 +1,18 @@
+PYTHON ?= python3
+
 all:
 	echo 'nothing by default'
 
 prep_release:
 	# take previous one, and replace with the next one
 	utils/prep_release
+
+release-pypi: prep_release
+	# avoid upload of stale builds
+	test ! -e dist
+	# make sure all is still clean/committed
+	! bash -c 'git diff | grep -q .'
+	$(PYTHON) setup.py sdist
+	$(PYTHON) setup.py bdist_wheel
+	twine upload dist/*
+

docs/conf.py

@@ -26,7 +26,7 @@
 # The short X.Y version
 version = ''
 # The full version, including alpha/beta/rc tags
-release = '0.8.0'
+release = '0.9.0'
 
 
 # -- General configuration ---------------------------------------------------

docs/installation.rst

@@ -26,7 +26,7 @@ If `Docker <https://docs.docker.com/install/>`_ is available on your system, you
 can visit `our page on Docker Hub <https://hub.docker.com/r/nipy/heudiconv/tags>`_
 to view available releases. To pull the latest release, run::
 
-    $ docker pull nipy/heudiconv:0.8.0
+    $ docker pull nipy/heudiconv:0.9.0
 
 
 Singularity
@@ -35,4 +35,4 @@ If `Singularity <https://www.sylabs.io/singularity/>`_ is available on your syst
 you can use it to pull and convert our Docker images! For example, to pull and
 build the latest release, you can run::
 
-    $ singularity pull docker://nipy/heudiconv:0.8.0
+    $ singularity pull docker://nipy/heudiconv:0.9.0

docs/usage.rst

@@ -82,7 +82,7 @@ The second script processes a DICOM directory with ``heudiconv`` using the built
     DCMDIR=${DCMDIRS[${SLURM_ARRAY_TASK_ID}]}
     echo Submitted directory: ${DCMDIR}
 
-    IMG="/singularity-images/heudiconv-0.8.0-dev.sif"
+    IMG="/singularity-images/heudiconv-0.9.0-dev.sif"
     CMD="singularity run -B ${DCMDIR}:/dicoms:ro -B ${OUTDIR}:/output -e ${IMG} --files /dicoms/ -o /output -f reproin -c dcm2niix -b notop --minmeta -l ."
 
     printf "Command:\n${CMD}\n"
@@ -97,7 +97,7 @@ This script creates the top-level bids files (e.g.,
     set -eu
 
     OUTDIR=${1}
-    IMG="/singularity-images/heudiconv-0.8.0-dev.sif"
+    IMG="/singularity-images/heudiconv-0.9.0-dev.sif"
     CMD="singularity run -B ${OUTDIR}:/output -e ${IMG} --files /output -f reproin --command populate-templates"
 
     printf "Command:\n${CMD}\n"

heudiconv/info.py

@@ -1,4 +1,4 @@
-__version__ = "0.8.0"
+__version__ = "0.9.0"
 __author__ = "HeuDiConv team and contributors"
 __url__ = "https://github.com/nipy/heudiconv"
 __packagename__ = 'heudiconv'

utils/prep_release

@@ -9,6 +9,8 @@ curver=$(python -c 'import heudiconv; print(heudiconv.__version__)')
 # check
 test "$oldver" = "$curver"
 
+utils/link_issues_CHANGELOG
+
 sed -i -e "s,${oldver//./\\.},$newver,g" \
     docs/conf.py docs/installation.rst docs/usage.rst heudiconv/info.py