From 2042b734c7c18bf5b53b08222eab9e8d80480691 Mon Sep 17 00:00:00 2001 From: mathiasg Date: Tue, 21 Nov 2023 11:43:37 -0500 Subject: [PATCH 1/5] chore: bump niprep deps --- pyproject.toml | 10 +++++----- requirements.txt | 12 ++++++++---- 2 files changed, 13 insertions(+), 9 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index f40ba9ec..c80997d2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,8 +23,8 @@ dependencies = [ "nibabel >= 5.0.0", "nipype >= 1.8.5", "nitime", - "nitransforms >= 21.0.0", - "niworkflows >= 1.8.1", + "nitransforms >= 23.0.1", + "niworkflows >= 1.9.0", # "niworkflows @ git+https://github.com/nipreps/niworkflows.git@master", "numpy >= 1.21.0", "packaging", @@ -32,11 +32,11 @@ dependencies = [ "psutil >= 5.4", "pybids >= 0.15.0", "requests", - "sdcflows >= 2.5.1", + "sdcflows >= 2.6.0", # "sdcflows @ git+https://github.com/nipreps/sdcflows.git@master", - "smriprep >= 0.12.1", + "smriprep >= 0.13.0", # "smriprep @ git+https://github.com/nipreps/smriprep.git@master", - "tedana ~= 0.0.12", + "tedana >= 0.0.12", "templateflow >= 0.6", "toml", ] diff --git a/requirements.txt b/requirements.txt index f191cd94..6573b659 100644 --- a/requirements.txt +++ b/requirements.txt @@ -50,6 +50,10 @@ idna==3.4 # via requests imageio==2.31.1 # via scikit-image +importlib-resources==6.1.1 + # via + # niworkflows + # sdcflows indexed-gzip==1.7.1 # via smriprep interface-meta==1.3.0 @@ -126,12 +130,12 @@ nipype==1.8.6 # smriprep nitime==0.10.1 # via nibabies (pyproject.toml) -nitransforms==23.0.0 +nitransforms==23.0.1 # via # nibabies (pyproject.toml) # niworkflows # sdcflows -niworkflows==1.8.1 +niworkflows==1.9.0 # via # nibabies (pyproject.toml) # sdcflows @@ -258,7 +262,7 @@ scipy==1.11.1 # scikit-learn # sdcflows # tedana -sdcflows==2.5.1 +sdcflows==2.6.0 # via nibabies (pyproject.toml) seaborn==0.12.2 # via niworkflows @@ -268,7 +272,7 @@ six==1.16.0 # via # isodate # python-dateutil -smriprep==0.12.1 +smriprep==0.13.0 # via nibabies (pyproject.toml) sqlalchemy==2.0.17 # via pybids From fff9f48b37b93f747f8239b2ca143221861ab9a1 Mon Sep 17 00:00:00 2001 From: mathiasg Date: Tue, 21 Nov 2023 11:43:50 -0500 Subject: [PATCH 2/5] chore: update changes --- CHANGES.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/CHANGES.md b/CHANGES.md index da6e4928..c834c489 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -1,4 +1,4 @@ -23.1.0 (TBD) +23.1.0 (November 21, 2023) ============ The next minor release of *NiBabies*, this release includes a number of new goodies, including: @@ -17,6 +17,9 @@ An option to determine and exclude high-variance voxels from being projected to ### Single anatomical processing Running *NiBabies* is now less restrictive, and will still process data missing either a T1w / T2w image. However, for best results, it is recommended to collect and include both for processing. +### Anat-specific derivatives inputs +Previous, *NiBabies* expected input from the `--derivatives` flag to be in T1w space, using the entity `space-orig`. This has now been changed to support derivatives in either T1w or T2w space. For more information, please see https://nibabies.readthedocs.io/en/23.1.0/faqs.html#leveraging-precomputed-results + ## Full Changelog * CI: Purge codecov python package (#282) @@ -35,6 +38,7 @@ Running *NiBabies* is now less restrictive, and will still process data missing * FIX: Ensure age is extracted from sessions file (#291) * FIX: Restore CIFTI medial wall masking, subcortical volume LAS reorientation (#298) * FIX: Recify "goodvoxels" surface projection (#301) + * FIX: Connect derivatives mask to mcribs recon (#323) * MAINT: Drop TemplateFlowSelect patches (#290) 23.0.0 (January 23, 2023) From 99da586924d507d4184fc4ec962b8ffc65308378 Mon Sep 17 00:00:00 2001 From: mathiasg Date: Tue, 21 Nov 2023 16:27:06 -0500 Subject: [PATCH 3/5] maint: drop py38 support, update niprep deps Co-authored-by: Chris Markiewicz --- .github/workflows/pytest.yml | 2 +- .github/workflows/style.yml | 2 +- pyproject.toml | 7 +++---- requirements.txt | 2 +- 4 files changed, 6 insertions(+), 7 deletions(-) diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 65fdd4f0..3477a60d 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -24,7 +24,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.8', '3.9', '3.10'] + python-version: ['3.9', '3.10', '3.11'] steps: - name: Set up Python ${{ matrix.python-version }} diff --git a/.github/workflows/style.yml b/.github/workflows/style.yml index f34b48f7..8cd82acf 100644 --- a/.github/workflows/style.yml +++ b/.github/workflows/style.yml @@ -20,7 +20,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ['3.9'] + python-version: ['3.10'] steps: - uses: actions/checkout@v3 diff --git a/pyproject.toml b/pyproject.toml index c80997d2..a1946d43 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -12,12 +12,12 @@ classifiers = [ "Intended Audience :: Science/Research", "Topic :: Scientific/Engineering :: Image Recognition", "License :: OSI Approved :: Apache Software License", - "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", ] license = {file = "LICENSE"} -requires-python = ">=3.8" +requires-python = ">=3.9" dependencies = [ 'importlib_resources; python_version < "3.9"', "nibabel >= 5.0.0", @@ -34,7 +34,7 @@ dependencies = [ "requests", "sdcflows >= 2.6.0", # "sdcflows @ git+https://github.com/nipreps/sdcflows.git@master", - "smriprep >= 0.13.0", + "smriprep ~= 0.12.1", # "smriprep @ git+https://github.com/nipreps/smriprep.git@master", "tedana >= 0.0.12", "templateflow >= 0.6", @@ -100,7 +100,6 @@ version-file = "nibabies/_version.py" [tool.black] line-length = 99 -target-version = ['py39'] skip-string-normalization = true [tool.isort] diff --git a/requirements.txt b/requirements.txt index 6573b659..06796dea 100644 --- a/requirements.txt +++ b/requirements.txt @@ -272,7 +272,7 @@ six==1.16.0 # via # isodate # python-dateutil -smriprep==0.13.0 +smriprep==0.12.2 # via nibabies (pyproject.toml) sqlalchemy==2.0.17 # via pybids From 5b3ce9e03817d7b4391203885c0a8a8029aaeb43 Mon Sep 17 00:00:00 2001 From: mathiasg Date: Wed, 22 Nov 2023 10:31:02 -0500 Subject: [PATCH 4/5] MAINT: Push back new fit/apply sdcflows to next minor --- pyproject.toml | 2 +- requirements.txt | 6 ++---- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index a1946d43..d60da58a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,7 +32,7 @@ dependencies = [ "psutil >= 5.4", "pybids >= 0.15.0", "requests", - "sdcflows >= 2.6.0", + "sdcflows ~= 2.5.2", # "sdcflows @ git+https://github.com/nipreps/sdcflows.git@master", "smriprep ~= 0.12.1", # "smriprep @ git+https://github.com/nipreps/smriprep.git@master", diff --git a/requirements.txt b/requirements.txt index 06796dea..e5405c70 100644 --- a/requirements.txt +++ b/requirements.txt @@ -51,9 +51,7 @@ idna==3.4 imageio==2.31.1 # via scikit-image importlib-resources==6.1.1 - # via - # niworkflows - # sdcflows + # via niworkflows indexed-gzip==1.7.1 # via smriprep interface-meta==1.3.0 @@ -262,7 +260,7 @@ scipy==1.11.1 # scikit-learn # sdcflows # tedana -sdcflows==2.6.0 +sdcflows==2.5.2 # via nibabies (pyproject.toml) seaborn==0.12.2 # via niworkflows From 862a60f27fedeaad522fde1e55f42e3530d47bcd Mon Sep 17 00:00:00 2001 From: Mathias Goncalves Date: Wed, 22 Nov 2023 14:50:36 -0500 Subject: [PATCH 5/5] Update CHANGES.md --- CHANGES.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGES.md b/CHANGES.md index c834c489..f64f0dc6 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -1,4 +1,4 @@ -23.1.0 (November 21, 2023) +23.1.0 (November 22, 2023) ============ The next minor release of *NiBabies*, this release includes a number of new goodies, including: