rel(24.0.0): update changes [skip ci]

CHANGES.md

@@ -1,23 +1,22 @@
-24.0.0 (TBD)
-============
+24.0.0 (August 29, 2024)
+========================
 This major release includes a substantial refactoring of the pipeline.
 
 One key addition is the addition of the `--level` flag, which can take the arguments minimal, resampling or full. The default is full, which should produce nearly the same results as previous versions. minimal will produce only the minimum necessary to deterministically generate the remaining derivatives. resampling will produce some additional derivatives, intended to simplify resampling with other tools.
 
 The `--derivatives` flag was altered to take arguments in the form `name=/path/to/dir`.
 For each directory provided, if a derivative is found - it will be used instead of computing it from scratch. If a derivative is not found, NiBabies will compute it and proceed as usual.
 
-Taken together, these features can allow a dataset provider to run a minimal NiBabies run, targeting many output spaces, while a user can then run a --derivatives run to generate additional derivatives in only the output spaces they need. Another use case is to provide an precomputed derivative to override the default NiBabies behavior, enabling easier workarounds for bugs or experimentation with alternatives.
+Taken together, these features can allow a dataset provider to run a minimal NiBabies run, targeting many output spaces, while a user can then run a `--derivatives` run to generate additional derivatives in only the output spaces they need. Another use case is to provide an precomputed derivative to override the default NiBabies behavior, enabling easier workarounds for bugs or experimentation with alternatives.
 
-Another new feature is a dynamic anatomical reference, which is set based on surface reconstruction method or through the `--reference-anatomical` flag. Previously, T1w was the default output space.
+Another new feature is a dynamic anatomical reference, which is set based on surface reconstruction method or through the `--reference-anatomical` flag. Previously, T1w was the default output space. Now, the reference anatomical is determined based on the surface reconstruction method.
 
 Additionally, minor adjustments have been made to MCRIBS surface reconstruction to address failure rates. This is still an on-going investigation, but preliminary results look promising.
 
 This release resolves a number of issues with fieldmaps inducing distortions during correction. Phase difference and direct fieldmaps are now masked correctly, preventing the overestimation of distortions outside the brain. Additionally, we now implement Jacobian weighting during unwarping, which corrects for compression and expansion effects on signal intensity. To disable Jacobian weighting, add `fmap-jacobian` to the `--ignore` argument.
 
 Finally, a new resampling method has been added, to better account for susceptibility distortion and motion in a single shot resampling to a volumetric target space. We anticipate extending this to surface targets in the future.
 
-## 24.0.0rc0 (August 01, 2024)
   * RF: Move to fit/apply workflow (#360)
   * FIX: nest pathlib import in fix_multi_source_name (#365)
   * FIX: Avoid retrieving multiple templates from latest TF (#353)
@@ -32,13 +31,12 @@ Finally, a new resampling method has been added, to better account for susceptib
   * FIX: Catch nonexistent derivatives, clean up subworkflow logic (#336)
   * Use fsLR reg sphere for MCRIBS morphometrics resampling (#334)
   * FIX: Multiple T2ws, coerce reference to string (#333)
-
-## 24.0.0a1
   * MAINT: Update to latest migas API (#326)
   * FIX: T2star map MNI scaling (#320)
   * ENH: Alter outputs when MCRIBS reconstruction is used (#329)
   * ENH: Use nireports for Report generation + add reportlet per reconstruction (#328)
 
+
 23.1.0 (November 22, 2023)
 ============
 The next minor release of *NiBabies*, this release includes a number of new goodies, including:

requirements.txt

@@ -34,8 +34,6 @@ botocore==1.34.150
     #   s3transfer
 certifi==2024.7.4
     # via requests
-cffi==1.16.0
-    # via cryptography
 chardet==5.2.0
     # via datalad
 charset-normalizer==3.3.2
@@ -52,8 +50,6 @@ contourpy==1.2.1
     # via
     #   bokeh
     #   matplotlib
-cryptography==43.0.0
-    # via secretstorage
 cycler==0.12.1
     # via matplotlib
 datalad==1.1.2
@@ -81,8 +77,6 @@ formulaic==0.5.2
     # via pybids
 fsspec==2024.6.1
     # via universal-pathlib
-greenlet==3.0.3
-    # via sqlalchemy
 h5py==3.11.0
     # via nitransforms
 humanize==4.10.0
@@ -115,10 +109,6 @@ jaraco-context==5.3.0
     #   keyrings-alt
 jaraco-functools==4.0.1
     # via keyring
-jeepney==0.8.0
-    # via
-    #   keyring
-    #   secretstorage
 jinja2==3.1.4
     # via
     #   bokeh
@@ -305,8 +295,6 @@ pybtex==0.24.0
     # via tedana
 pybtex-apa-style==1.3
     # via tedana
-pycparser==2.22
-    # via cffi
 pydot==3.0.1
     # via nipype
 pyparsing==3.1.2
@@ -379,8 +367,6 @@ seaborn==0.13.2
     # via
     #   nireports
     #   niworkflows
-secretstorage==3.3.3
-    # via keyring
 simplejson==3.19.2
     # via nipype
 six==1.16.0