From b7b10d93ac62b6132e95de19b3470ae45121aede Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Wed, 23 Dec 2020 10:09:49 -0500 Subject: [PATCH 1/4] CHANGELOG entry for 0.9.0 --- CHANGELOG.md | 47 +++++++++++++++++++++++++++++++++++------------ 1 file changed, 35 insertions(+), 12 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 32e72bbe..44a18f2b 100644 --- a/CHANGELOG.md +++ b/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-` with `part-` 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 From ca1c5d6b77885b81e74a6a2f72413de8f63e3dbc Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Wed, 23 Dec 2020 10:14:44 -0500 Subject: [PATCH 2/4] [DATALAD RUNCMD] prepare the release === Do not change lines below === { "chain": [], "cmd": "make prep_release", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ --- docs/conf.py | 2 +- docs/installation.rst | 4 ++-- docs/usage.rst | 4 ++-- heudiconv/info.py | 2 +- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index 9cb5fe1f..67a40b92 100644 --- a/docs/conf.py +++ b/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 --------------------------------------------------- diff --git a/docs/installation.rst b/docs/installation.rst index 0bb23800..1ce86db4 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -26,7 +26,7 @@ If `Docker `_ is available on your system, you can visit `our page on Docker Hub `_ 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 `_ 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 diff --git a/docs/usage.rst b/docs/usage.rst index 21b5699a..24ef2f17 100644 --- a/docs/usage.rst +++ b/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" diff --git a/heudiconv/info.py b/heudiconv/info.py index a90c8ccd..fd7b5193 100644 --- a/heudiconv/info.py +++ b/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' From a44204ece488d8ae6fe8272d41711e26b4c6082d Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Wed, 23 Dec 2020 10:19:50 -0500 Subject: [PATCH 3/4] update changelog reference as part of prep release --- utils/prep_release | 2 ++ 1 file changed, 2 insertions(+) diff --git a/utils/prep_release b/utils/prep_release index 6a0823c6..0bf5a544 100755 --- a/utils/prep_release +++ b/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 From 972c1aadeaf57fdbc1150c5f01c822db13e9a032 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Wed, 23 Dec 2020 10:21:27 -0500 Subject: [PATCH 4/4] Add a helper rule to upload to pypi --- Makefile | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/Makefile b/Makefile index e1198a70..e6594df6 100644 --- a/Makefile +++ b/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/* +