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

@@ -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

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'

docs/changes.rst

@@ -4,4 +4,4 @@
 What's new
 ##########
 
-.. include:: ../CHANGES.rst
+.. mdinclude:: ../CHANGES.md

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)

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