From fdfdd5774daa69160cf8291dd7dc1ed1ffd81a07 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Fri, 7 Apr 2023 12:56:35 -0400 Subject: [PATCH] Prepare for 0.3.0 release (#258) * Start preparing for 0.3.0. * Update changelog. * Update CITATION.cff * Update CHANGES.md * Update CHANGES.md --- CHANGES.md | 91 ++++++++++++++++++++++++++++++++++++++++++++++++ CHANGES.rst | 12 ------- CITATION.cff | 4 +-- docs/changes.rst | 2 +- docs/conf.py | 9 +++++ setup.cfg | 2 ++ 6 files changed, 105 insertions(+), 15 deletions(-) create mode 100644 CHANGES.md delete mode 100644 CHANGES.rst diff --git a/CHANGES.md b/CHANGES.md new file mode 100644 index 000000000..a61531cb1 --- /dev/null +++ b/CHANGES.md @@ -0,0 +1,91 @@ +## 0.3.0 + +0.3.0 reflects renewed maintenance for ASLPrep. + +The primary focuses of this release are: +(1) fixing easily-fixable bugs, +(2) disabling broken features with difficult-to-fix bugs, +(3) cleaning up the codebase, +(4) expanding test coverage, +and (5) ensuring that outputs are BIDS-compliant. + +To that end, we have unfortunately had to temporarily drop support for multi-PostLabelingDelay data, +as well as PASL data with the Q2TIPS BolusCutOffTechnique. +We will work on fixing these features for the next release. + +Additionally, this release includes a number of breaking changes. +We have renamed several of the outputs to ensure that they are BIDS-compliant. +These outputs may need to change again in the future, +but that will happen in the next minor release (0.4.0) at the earliest. +See the table below for a list of the changed filenames. + +| Description | <0.3.0 | 0.3.0 | +|---|---|---| +| CBF time series | `_cbf.nii.gz` | `_desc-timeseries_cbf.nii.gz` | +| Mean CBF | `_mean_cbf.nii.gz` | `_cbf.nii.gz` | +| CBF time series after SCORE denoising | `_desc-score_cbf.nii.gz` | `_desc-scoreTimeseries_cbf.nii.gz` | +| Mean CBF after SCORE denoising | `_desc-score_mean_cbf.nii.gz` | `_desc-score_cbf.nii.gz` | +| Bolus arrival time/arterial transit time | `_desc-bat_cbf.nii.gz` | `_att.nii.gz` | + +Additionally, we have changed the atlases that are used for the parcellated CBF files. +We have brought the atlases in line with those used by [XCP-D](https://xcp-d.readthedocs.io/en/latest/). +However, in the near future, we plan to update these atlases _again_, so that they are synchronized across +ASLPrep, XCP-D, and QSIPrep, so please be aware of that upcoming change. + +### 🛠 Breaking Changes +* Rename BIDS-noncompliant derivatives by @tsalo in https://github.com/PennLINC/aslprep/pull/216 +* Use correct bolus values in CBF calculation and temporarily disable Q2TIPS, multi-PLD, and no-BolusCutOff processing by @tsalo in https://github.com/PennLINC/aslprep/pull/235 +* Disable SCORE/SCRUB for GE/short runs and get GE workflow working by @tsalo in https://github.com/PennLINC/aslprep/pull/248 +* Parallelize parcellation and replace atlases by @tsalo in https://github.com/PennLINC/aslprep/pull/254 +* Remove "mean" from mean CBF filenames and add "timeseries" to 4D CBF filenames by @tsalo in https://github.com/PennLINC/aslprep/pull/257 + +### 🎉 Exciting New Features +* Hardcode T1blood for some field strengths and use Zhang 2013 formula for others by @tsalo in https://github.com/PennLINC/aslprep/pull/243 +* Estimate labeling efficiency based on ASL type and number of background suppression pulses by @tsalo in https://github.com/PennLINC/aslprep/pull/244 + +### 🐛 Bug Fixes +* Pin looseversion by @tsalo in https://github.com/PennLINC/aslprep/pull/211 +* Correct ordering of probseg maps by @josephmje in https://github.com/PennLINC/aslprep/pull/192 +* Convert inversion times to a list for compatility with BASIL interface by @tsalo in https://github.com/PennLINC/aslprep/pull/222 +* Pin networkx version by @tsalo in https://github.com/PennLINC/aslprep/pull/227 +* Use LabelingEfficiency as BASIL `--alpha` parameter by @tsalo in https://github.com/PennLINC/aslprep/pull/233 +* Remove BIDS-noncompliant m0z and cbf files by @tsalo in https://github.com/PennLINC/aslprep/pull/236 +* Replace RepetitionTime with RepetitionTimePreparation by @tsalo in https://github.com/PennLINC/aslprep/pull/245 +* Index aslcontext rows with "cbf", not "CBF" by @tsalo in https://github.com/PennLINC/aslprep/pull/252 + +### Other Changes +* Use aslprep_build as base Docker image - attempt 2 by @tsalo in https://github.com/PennLINC/aslprep/pull/204 +* Autoformat with black and isort by @tsalo in https://github.com/PennLINC/aslprep/pull/205 +* Replace relative imports with absolute ones by @tsalo in https://github.com/PennLINC/aslprep/pull/206 +* Remove unused functions and classes by @tsalo in https://github.com/PennLINC/aslprep/pull/207 +* Rename PEP8-noncompliant classes by @tsalo in https://github.com/PennLINC/aslprep/pull/208 +* Consistently use f-strings for string formatting by @tsalo in https://github.com/PennLINC/aslprep/pull/209 +* Work on fixing docstrings and splitting modules by @tsalo in https://github.com/PennLINC/aslprep/pull/210 +* Remove unused arguments throughout package by @tsalo in https://github.com/PennLINC/aslprep/pull/212 +* Replace smriprep calls with dependency calls by @tsalo in https://github.com/PennLINC/aslprep/pull/217 +* Replace pybids calls with dependency calls by @tsalo in https://github.com/PennLINC/aslprep/pull/213 +* Use custom formatting for workflow connections by @tsalo in https://github.com/PennLINC/aslprep/pull/220 +* Improve documentation by @tsalo in https://github.com/PennLINC/aslprep/pull/218 +* Add step to run unit tests by @tsalo in https://github.com/PennLINC/aslprep/pull/221 +* Collect associated files at beginning of workflow by @tsalo in https://github.com/PennLINC/aslprep/pull/246 +* Refactor confounds and QC metrics by @tsalo in https://github.com/PennLINC/aslprep/pull/256 + +## New Contributors +* @tsalo made their first contribution in https://github.com/PennLINC/aslprep/pull/204 +* @josephmje made their first contribution in https://github.com/PennLINC/aslprep/pull/192 + +**Full Changelog**: https://github.com/PennLINC/aslprep/compare/0.2.8...0.3.0 + +## 0.2.7 + +Bids validation + +## 0.2.6 + +11/12/2020 + +ENH - Add GE SCAN processing with deltam or cbf + +ENH - supressed freesurfer processing, FSL FLIRT with BBR for registration + +ENH - basil and scorescrub as options, cbf computation is only default diff --git a/CHANGES.rst b/CHANGES.rst deleted file mode 100644 index 630f91636..000000000 --- a/CHANGES.rst +++ /dev/null @@ -1,12 +0,0 @@ -v0.2.7 -- Bids validation - -v0.2.6 - -11/12/2020 - -ENH - Add GE SCAN processing with deltam or cbf - -ENH - supressed freesurfer processing, FSL FLIRT with BBR for registration - -ENH - basil and scorescrub as options, cbf computation is only default diff --git a/CITATION.cff b/CITATION.cff index 729112d11..a18826e07 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -116,5 +116,5 @@ keywords: - BIDS-App - Neuroimaging license: BSD-3-Clause -version: 0.2.9 -date-released: '2023-02-27' +version: 0.3.0 +date-released: '2023-04-07' diff --git a/docs/changes.rst b/docs/changes.rst index 86b6cd41f..ab149c726 100644 --- a/docs/changes.rst +++ b/docs/changes.rst @@ -4,4 +4,4 @@ What's new ########## -.. include:: ../CHANGES.rst +.. mdinclude:: ../CHANGES.md diff --git a/docs/conf.py b/docs/conf.py index 1d0f4dfe2..264cbd2c7 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -24,6 +24,7 @@ import sys from datetime import datetime +from m2r import MdInclude from packaging import version as pver from sphinx import __version__ as sphinxversion @@ -333,3 +334,11 @@ def setup(app): app.add_css_file("theme_overrides.css") # We need this for the boilerplate script app.add_js_file("https://cdn.rawgit.com/chrisfilo/zenodo.js/v0.1/zenodo.js") + # Fix to https://github.com/sphinx-doc/sphinx/issues/7420 + # from https://github.com/life4/deal/commit/7f33cbc595ed31519cefdfaaf6f415dada5acd94 + # from m2r to make `mdinclude` work + app.add_config_value("no_underscore_emphasis", False, "env") + app.add_config_value("m2r_parse_relative_links", False, "env") + app.add_config_value("m2r_anonymous_references", False, "env") + app.add_config_value("m2r_disable_inline_math", False, "env") + app.add_directive("mdinclude", MdInclude) diff --git a/setup.cfg b/setup.cfg index 90294705c..29fb99769 100644 --- a/setup.cfg +++ b/setup.cfg @@ -54,6 +54,8 @@ packages = find: datalad = datalad doc = doctest-ignore-unicode + m2r + mistune<2 # just temporary until m2r addresses this issue nbsphinx packaging pydot >= 1.2.3