warpkit 1.2.1__tar.gz → 1.2.2__tar.gz

{warpkit-1.2.1 → warpkit-1.2.2}/.github/workflows/build.yml

@@ -41,7 +41,8 @@ jobs:
           {version: '3.11', glob: cp311*},
           {version: '3.12', glob: cp312*},
           {version: '3.13', glob: cp313*},
-          {version: '3.14', glob: cp314*}
+          {version: '3.14', glob: cp314-*},
+          {version: '3.14t', glob: cp314t*}
           ]
     name: Python ${{ matrix.python-versions.version }} wheel on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}

{warpkit-1.2.1 → warpkit-1.2.2}/CLAUDE.md

@@ -10,7 +10,7 @@ DIstortion Correction). Phase unwrapping uses a self-contained C++17 port of
 **no Julia runtime is involved**; do not reintroduce one (no `julia.py`, no
 conda recipe, no `FindJulia.cmake`).
 
-Pre-print: <https://www.biorxiv.org/content/10.1101/2023.11.28.568744v1>.
+Paper (Imaging Neuroscience): <https://doi.org/10.1162/IMAG.a.1262>.
 
 ## Layout
 
@@ -131,12 +131,15 @@ and call out anything CI-relevant (wheel matrix, pybind11 ABI, ITK).
 
 ## CI specifics
 
-GitHub Actions builds wheels for Python 3.11–3.14 on `ubuntu-latest`,
+GitHub Actions builds wheels for Python 3.11–3.14 (both standard and free-threaded) on `ubuntu-latest`,
 `ubuntu-24.04-arm`, and `macos-latest` via cibuildwheel.
-`pyproject.toml`'s `[tool.cibuildwheel]` skips `*musllinux*` and the
-`cp314t-*` free-threaded build; re-enabling free-threaded support requires
-auditing the pybind11 + ITK code paths for the no-GIL ABI. The sdist job
-also runs `uv run coverage run` then `coverage report -m` — keep coverage
-healthy when adding code (the `[tool.coverage.report]` config in
+`pyproject.toml`'s `[tool.cibuildwheel]` skips only `*musllinux*` builds.
+Free-threaded support is enabled via `py::mod_gil_not_used()` in
+`src/warpkit.cpp`. `PyErr_CheckSignals()` calls in `include/warps.h` are
+wrapped in a `WARPKIT_CHECK_SIGNALS()` macro that compiles to a no-op under
+`Py_GIL_DISABLED`, so GIL builds keep Ctrl+C interruptibility during long ITK
+operations and the free-threaded build skips the GIL-requiring check. The
+sdist job also runs `uv run coverage run` then `coverage report -m` — keep
+coverage healthy when adding code (the `[tool.coverage.report]` config in
 `pyproject.toml` omits the test files). PyPI publish and the GHCR Docker
 image only run on a published GitHub release.

{warpkit-1.2.1 → warpkit-1.2.2}/LICENSE

@@ -1,7 +1,10 @@
 Copyright (c) 2022 Washington University.
 Authored by: Andrew Van							
 
-Please cite https://www.biorxiv.org/content/10.1101/2023.11.28.568744v1	
+Please cite:
+Van AN, Montez DF, Laumann TO, Cho PN, Suljic V, Madison T, et al.
+Frame-wise multi-echo distortion correction for superior functional MRI.
+Imaging Neuroscience 2026; 4 IMAG.a.1262. doi: https://doi.org/10.1162/IMAG.a.1262
 
 warpkit is free for non-commercial use by academic, government,
 and non-profit/not-for-profit institutions. A commercial version of the software is

{warpkit-1.2.1 → warpkit-1.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: warpkit
-Version: 1.2.1
+Version: 1.2.2
 Summary: A python library for neuroimaging transformations
 Keywords: neuroimaging
 Author-Email: Andrew Van <vanandrew77@gmail.com>
@@ -8,6 +8,7 @@ License-File: LICENSE
 License-File: include/romeo/LICENSE
 Classifier: Programming Language :: Python :: 3
 Project-URL: github, https://github.com/vanandrew/warpkit
+Project-URL: paper, https://doi.org/10.1162/IMAG.a.1262
 Requires-Python: >=3.11
 Requires-Dist: nibabel>=4.0.2
 Requires-Dist: numpy>=1.23.3
@@ -21,10 +22,9 @@ Description-Content-Type: text/markdown
 
 [![Build](https://github.com/vanandrew/warpkit/actions/workflows/build.yml/badge.svg)](https://github.com/vanandrew/warpkit/actions)
 [![PyPI](https://img.shields.io/pypi/v/warpkit)](https://pypi.org/project/warpkit/)
-[![docker](https://ghcr-badge.egpl.dev/vanandrew/warpkit/latest_tag?trim=major&label=ghcr&nbsp;latest)](https://github.com/vanandrew/warpkit/pkgs/container/warpkit)
 [![codecov](https://codecov.io/gh/vanandrew/warpkit/graph/badge.svg?token=S6ZZKOAF8V)](https://codecov.io/gh/vanandrew/warpkit)
 
-A Python library for neuroimaging transforms, focused on the Multi-Echo DIstortion Correction (MEDIC) algorithm. The pre-print is available at <https://www.biorxiv.org/content/10.1101/2023.11.28.568744v1>.
+A Python library for neuroimaging transforms, focused on the Multi-Echo DIstortion Correction (MEDIC) algorithm. The paper is published in *Imaging Neuroscience* at <https://doi.org/10.1162/IMAG.a.1262>.
 
 The phase-unwrapping core is a self-contained C++17 port of [ROMEO](https://github.com/korbinian90/ROMEO) — there is no Julia runtime to install, and binary wheels ship with the ITK pieces statically linked. If you used an older release of warpkit that required `julia` on `PATH`, that step is gone.
 
@@ -213,6 +213,15 @@ wk-convert-fieldmap \
   --output sub-01_run-01_fieldmap.nii
 ```
 
+## Citation
+
+If you use warpkit, please cite:
+
+> Van AN, Montez DF, Laumann TO, Cho PN, Suljic V, Madison T, et al.
+> Frame-wise multi-echo distortion correction for superior functional MRI.
+> *Imaging Neuroscience* 2026; 4 IMAG.a.1262.
+> doi: <https://doi.org/10.1162/IMAG.a.1262>
+
 ## Authors
 
 Vahdeta Suljic &lt;suljic@wustl.edu&gt;, Andrew Van &lt;vanandrew77@gmail.com&gt;

{warpkit-1.2.1 → warpkit-1.2.2}/README.md

@@ -2,10 +2,9 @@
 
 [![Build](https://github.com/vanandrew/warpkit/actions/workflows/build.yml/badge.svg)](https://github.com/vanandrew/warpkit/actions)
 [![PyPI](https://img.shields.io/pypi/v/warpkit)](https://pypi.org/project/warpkit/)
-[![docker](https://ghcr-badge.egpl.dev/vanandrew/warpkit/latest_tag?trim=major&label=ghcr latest)](https://github.com/vanandrew/warpkit/pkgs/container/warpkit)
 [![codecov](https://codecov.io/gh/vanandrew/warpkit/graph/badge.svg?token=S6ZZKOAF8V)](https://codecov.io/gh/vanandrew/warpkit)
 
-A Python library for neuroimaging transforms, focused on the Multi-Echo DIstortion Correction (MEDIC) algorithm. The pre-print is available at <https://www.biorxiv.org/content/10.1101/2023.11.28.568744v1>.
+A Python library for neuroimaging transforms, focused on the Multi-Echo DIstortion Correction (MEDIC) algorithm. The paper is published in *Imaging Neuroscience* at <https://doi.org/10.1162/IMAG.a.1262>.
 
 The phase-unwrapping core is a self-contained C++17 port of [ROMEO](https://github.com/korbinian90/ROMEO) — there is no Julia runtime to install, and binary wheels ship with the ITK pieces statically linked. If you used an older release of warpkit that required `julia` on `PATH`, that step is gone.
 
@@ -194,6 +193,15 @@ wk-convert-fieldmap \
   --output sub-01_run-01_fieldmap.nii
 ```
 
+## Citation
+
+If you use warpkit, please cite:
+
+> Van AN, Montez DF, Laumann TO, Cho PN, Suljic V, Madison T, et al.
+> Frame-wise multi-echo distortion correction for superior functional MRI.
+> *Imaging Neuroscience* 2026; 4 IMAG.a.1262.
+> doi: <https://doi.org/10.1162/IMAG.a.1262>
+
 ## Authors
 
 Vahdeta Suljic &lt;suljic@wustl.edu&gt;, Andrew Van &lt;vanandrew77@gmail.com&gt;

{warpkit-1.2.1 → warpkit-1.2.2}/include/warps.h

@@ -19,6 +19,18 @@
 
 namespace py = pybind11;
 
+// PyErr_CheckSignals() needs the GIL; free-threaded builds (Py_GIL_DISABLED)
+// declare `py::mod_gil_not_used()` and skip the check, trading Ctrl+C
+// interruptibility during long ITK operations for no-GIL execution.
+#ifdef Py_GIL_DISABLED
+#define WARPKIT_CHECK_SIGNALS() ((void)0)
+#else
+#define WARPKIT_CHECK_SIGNALS()                                  \
+    do {                                                         \
+        if (PyErr_CheckSignals() != 0) throw py::error_already_set(); \
+    } while (0)
+#endif
+
 /**
  * @brief Invert a displacement map
  *
@@ -139,9 +151,9 @@ py::array_t<T, py::array::f_style> invert_displacement_map(py::array_t<T, py::ar
 
     // Get output
     typename DisplacementMapType::Pointer inv_map = identity_filter->GetOutput();
-    if (PyErr_CheckSignals() != 0) throw py::error_already_set();
+    WARPKIT_CHECK_SIGNALS();
     inv_map->Update();
-    if (PyErr_CheckSignals() != 0) throw py::error_already_set();
+    WARPKIT_CHECK_SIGNALS();
     itk::ImageRegionConstIteratorWithIndex<DisplacementMapType> inv_map_it(inv_map,
                                                                            inv_map->GetLargestPossibleRegion());
     py::array_t<T, py::array::f_style> inverted_displacement_map(displacement_map);
@@ -170,7 +182,7 @@ py::array_t<T, py::array::f_style> invert_displacement_field(py::array_t<T, py::
                                                              py::array_t<T, py::array::f_style> direction,
                                                              py::array_t<T, py::array::f_style> spacing,
                                                              ssize_t iterations, bool verbose) {
-    if (PyErr_CheckSignals() != 0) throw py::error_already_set();
+    WARPKIT_CHECK_SIGNALS();
 
     // Get the displacement field shape
     const ssize_t* shape = displacement_field.shape();
@@ -227,9 +239,9 @@ py::array_t<T, py::array::f_style> invert_displacement_field(py::array_t<T, py::
 
     // Get output
     typename DisplacementFieldType::Pointer inv_field = invert_displacement_filter->GetOutput();
-    if (PyErr_CheckSignals() != 0) throw py::error_already_set();
+    WARPKIT_CHECK_SIGNALS();
     inv_field->Update();
-    if (PyErr_CheckSignals() != 0) throw py::error_already_set();
+    WARPKIT_CHECK_SIGNALS();
     itk::ImageRegionConstIteratorWithIndex<DisplacementFieldType> inv_field_it(inv_field,
                                                                                inv_field->GetLargestPossibleRegion());
     py::array_t<T, py::array::f_style> inverted_displacement_field(displacement_field);
@@ -261,7 +273,7 @@ py::array_t<T, py::array::f_style> compute_jacobian_determinant(py::array_t<T, p
                                                                 py::array_t<T, py::array::f_style> origin,
                                                                 py::array_t<T, py::array::f_style> direction,
                                                                 py::array_t<T, py::array::f_style> spacing) {
-    if (PyErr_CheckSignals() != 0) throw py::error_already_set();
+    WARPKIT_CHECK_SIGNALS();
 
     // Get the displacement field shape
     const ssize_t* shape = displacement_field.shape();
@@ -315,9 +327,9 @@ py::array_t<T, py::array::f_style> compute_jacobian_determinant(py::array_t<T, p
     // Get the jacobian determinant fields
     typename DisplacementFieldJacobianDeterminantFilterType::OutputImagePointer jacobian_determinant =
         jacobian_filter->GetOutput();
-    if (PyErr_CheckSignals() != 0) throw py::error_already_set();
+    WARPKIT_CHECK_SIGNALS();
     jacobian_determinant->Update();
-    if (PyErr_CheckSignals() != 0) throw py::error_already_set();
+    WARPKIT_CHECK_SIGNALS();
 
     // Convert to numpy array
     py::array_t<T, py::array::f_style> jacobian_determinant_array({shape[0], shape[1], shape[2]});
@@ -461,9 +473,9 @@ py::array_t<T, py::array::f_style> resample(
 
     // Get the output
     typename OutputImageType::Pointer output_image = warp_filter->GetOutput();
-    if (PyErr_CheckSignals() != 0) throw py::error_already_set();
+    WARPKIT_CHECK_SIGNALS();
     output_image->Update();
-    if (PyErr_CheckSignals() != 0) throw py::error_already_set();
+    WARPKIT_CHECK_SIGNALS();
     itk::ImageRegionConstIteratorWithIndex<OutputImageType> output_iterator(output_image,
                                                                             output_image->GetLargestPossibleRegion());
     py::array_t<T, py::array::f_style> output_array({output_shape.at(0), output_shape.at(1), output_shape.at(2)});
@@ -481,7 +493,7 @@ T compute_hausdorff_distance(
     py::array_t<T, py::array::f_style> image1_direction, py::array_t<T, py::array::f_style> image1_spacing,
     py::array_t<T, py::array::f_style> image2, py::array_t<T, py::array::f_style> image2_origin,
     py::array_t<T, py::array::f_style> image2_direction, py::array_t<T, py::array::f_style> image2_spacing) {
-    if (PyErr_CheckSignals() != 0) throw py::error_already_set();
+    WARPKIT_CHECK_SIGNALS();
 
     // Setup types
     using ImageType = typename itk::Image<T, 3>;
@@ -545,7 +557,7 @@ T compute_hausdorff_distance(
     // Get the hausdorff distance
     hausdorff_filter->Update();
     T hausdorff_distance = hausdorff_filter->GetAverageHausdorffDistance();
-    if (PyErr_CheckSignals() != 0) throw py::error_already_set();
+    WARPKIT_CHECK_SIGNALS();
 
     // Return the hausdorff distance
     return hausdorff_distance;

{warpkit-1.2.1 → warpkit-1.2.2}/pyproject.toml

@@ -6,7 +6,7 @@ requires-python = ">=3.11"
 authors = [{ name = "Andrew Van", email = "vanandrew77@gmail.com" }]
 keywords = ["neuroimaging"]
 classifiers = ["Programming Language :: Python :: 3"]
-urls = { github = "https://github.com/vanandrew/warpkit" }
+urls = { github = "https://github.com/vanandrew/warpkit", paper = "https://doi.org/10.1162/IMAG.a.1262" }
 # include/romeo/LICENSE is the upstream MIT notice for the ROMEO C++ port; it
 # travels with the headers in source distributions and (via PEP 639
 # license-files) gets bundled into wheels under *.dist-info/licenses/.
@@ -122,9 +122,10 @@ command_line = "-m pytest"
 omit = ["tests/*"]
 
 [tool.cibuildwheel]
-# Skip musllinux (we ship manylinux only) and free-threaded CPython builds
-# (cp31Xt-*) — our pybind11 bindings + ITK haven't been audited for the no-GIL ABI.
-skip = "*musllinux* cp314t-*"
+# Skip musllinux (we ship manylinux only). Free-threaded (cp31Xt-*) builds
+# are kept: warps.h guards PyErr_CheckSignals() behind WARPKIT_CHECK_SIGNALS,
+# which is a no-op under Py_GIL_DISABLED.
+skip = "*musllinux*"
 build-frontend = "build"
 build-verbosity = 3
 

{warpkit-1.2.1 → warpkit-1.2.2}/src/warpkit.cpp

@@ -5,7 +5,7 @@
 
 namespace py = pybind11;
 
-PYBIND11_MODULE(warpkit_cpp, m) {
+PYBIND11_MODULE(warpkit_cpp, m, py::mod_gil_not_used()) {
     m.def("calculate_weights", &romeo::calculate_weights<float>,
           "ROMEO edge-weight map (3, nx, ny, nz) uint8. Exposed for port validation; not used by warpkit.",
           py::arg("phase"),