brkraw 0.5.5__tar.gz → 0.5.6__tar.gz

{brkraw-0.5.5 → brkraw-0.5.6}/.github/workflows/release.yml

@@ -14,6 +14,8 @@ on:
 permissions:
   contents: write
   discussions: write
+  id-token: write
+  actions: write
 
 jobs:
   release:
@@ -148,21 +150,26 @@ jobs:
             echo "Zenodo badge update attempt $i/10"
             python3 scripts/update_zenodo_badge.py --up-to-date-exit-code 2
             exit_code=$?
+            set -e
+
             if [ "$exit_code" -eq 0 ]; then
               echo "Zenodo badge updated."
               exit 0
             fi
+
             if [ "$exit_code" -ne 2 ]; then
               exit "$exit_code"
             fi
+            
             sleep 60
           done
+          
           echo "Zenodo badge still up to date after 10 attempts; giving up."
 
-  publish:
-    if: ${{ github.repository == 'BrkRaw/brkraw' && (needs.release.outputs.prerelease == 'true' || needs.release.outputs.zenodo_success == 'true') }}
-    needs: [release]
-    uses: ./.github/workflows/publish.yml
-    with:
-      target: ${{ needs.release.outputs.prerelease == 'true' && 'testpypi' || 'pypi' }}
-      tag: ${{ needs.release.outputs.tag }}
+      - name: Trigger publish workflow
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          target="${{ steps.prerelease.outputs.value == 'true' && 'testpypi' || 'pypi' }}"
+          tag="${{ steps.tag.outputs.value }}"
+          gh workflow run publish.yml -f target="$target" -f tag="$tag"

{brkraw-0.5.5 → brkraw-0.5.6}/.github/workflows/release_on_merge.yml

@@ -6,6 +6,7 @@ on:
 
 permissions:
   contents: write
+  actions: write
 
 jobs:
   tag_release:
@@ -116,3 +117,10 @@ jobs:
           fi
           git tag "$tag" "${{ github.sha }}"
           git push origin "$tag"
+      - name: Trigger release workflow
+        if: ${{ steps.version.outputs.changed == 'true' }}
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          tag="${{ steps.version.outputs.value }}"
+          gh workflow run release.yml -f tag="$tag"

{brkraw-0.5.5 → brkraw-0.5.6}/CITATION.cff

@@ -34,4 +34,4 @@ keywords:
   - BIDS
   - neuroimaging
 
-version: "0.5.5"
+version: "0.5.6"

{brkraw-0.5.5 → brkraw-0.5.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: brkraw
-Version: 0.5.5
+Version: 0.5.6
 Summary: Toolkit for loading Bruker Paravision datasets, mapping metadata, and exporting NIfTI
 Project-URL: Homepage, https://brkraw.github.io
 Maintainer-email: SungHo Lee <shlee@unc.edu>
@@ -49,7 +49,7 @@ Description-Content-Type: text/markdown
 
 A modular toolkit for Bruker MRI raw-data handling.
 
-BrkRaw (v0.5.5) converts raw data into standardized, neuroimaging-ready
+BrkRaw (v0.5.6) converts raw data into standardized, neuroimaging-ready
 datasets, with extensible rules/specs and plugin hooks.
 
 - Documentation: [brkraw.github.io](https://brkraw.github.io/)
@@ -70,7 +70,7 @@ If you use BrkRaw in your research, please cite it.
 @software{brkraw,
   author = {Lee, Sung-Ho and Devenyi, Gabriel A. and Ban, Woomi and Shih, Yen-Yu Ian},
   title = {BrkRaw: A modular toolkit for Bruker MRI raw-data handling},
-  version = {0.5.5},
+  version = {0.5.6},
   doi = {10.5281/zenodo.3818614},
   url = {https://github.com/BrkRaw/brkraw},
   note = {Documentation: https://brkraw.github.io},

{brkraw-0.5.5 → brkraw-0.5.6}/README.md

@@ -10,7 +10,7 @@
 
 A modular toolkit for Bruker MRI raw-data handling.
 
-BrkRaw (v0.5.5) converts raw data into standardized, neuroimaging-ready
+BrkRaw (v0.5.6) converts raw data into standardized, neuroimaging-ready
 datasets, with extensible rules/specs and plugin hooks.
 
 - Documentation: [brkraw.github.io](https://brkraw.github.io/)
@@ -31,7 +31,7 @@ If you use BrkRaw in your research, please cite it.
 @software{brkraw,
   author = {Lee, Sung-Ho and Devenyi, Gabriel A. and Ban, Woomi and Shih, Yen-Yu Ian},
   title = {BrkRaw: A modular toolkit for Bruker MRI raw-data handling},
-  version = {0.5.5},
+  version = {0.5.6},
   doi = {10.5281/zenodo.3818614},
   url = {https://github.com/BrkRaw/brkraw},
   note = {Documentation: https://brkraw.github.io},

brkraw-0.5.6/RELEASE_NOTES.md

@@ -0,0 +1,14 @@
+# Release v0.5.6
+
+Date: 2026-01-29
+Changes since 0.5.5
+
+- chore: prepare release v0.5.6 (3a23f42)
+- docs: update contributors (b36012b)
+- ci: replace the locaiton of gh command to get pr number (e522e6b)
+- fix: cast NIfTI dataobj shape (f0bae05)
+- fix: make type aliases explicit (ad1d065)
+- ci: add actions:write permission to trigger other workflow. (2a4a71d)
+- ci: fix Zenodo badge update retry logic (ff66a7d)
+- Update Zenodo DOI badge (a6d453e)
+- ci(release): allow OIDC by granting id-token permission (db29a36)

{brkraw-0.5.5 → brkraw-0.5.6}/brkraw/__init__.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-__version__ = '0.5.5'
+__version__ = '0.5.6'
 from .apps.loader import BrukerLoader
 
 

{brkraw-0.5.5 → brkraw-0.5.6}/brkraw/apps/loader/types.py

@@ -28,10 +28,10 @@ if TYPE_CHECKING:
     from ...resolver.nifti import Nifti1HeaderContents, XYZUNIT, TUNIT
 
 
-InfoScope = Literal['full', 'study', 'scan']
+InfoScope: TypeAlias = Literal['full', 'study', 'scan']
 Dataobjs = Optional[Union[NDArray, Tuple[NDArray, ...]]]
 Affines = Optional[Union[NDArray, Tuple[NDArray, ...]]]
-AffineSpace = Literal["raw", "scanner", "subject_ras"]
+AffineSpace: TypeAlias = Literal["raw", "scanner", "subject_ras"]
 ConvertedObj = Optional[Union["ToFilename", Tuple["ToFilename", ...]]]
 Metadata = Optional[Union[Dict, Tuple[Optional[Dict], ...]]]
 HookArgs = Optional[Mapping[str, Mapping[str, Any]]]

{brkraw-0.5.5 → brkraw-0.5.6}/brkraw/resolver/affine.py

@@ -1,6 +1,13 @@
 from __future__ import annotations
-from typing import Optional, Union, TypedDict, Tuple, Literal, List, Any
-from typing import cast, TYPE_CHECKING
+from typing import Optional, Union, TypedDict, Tuple, Literal, List, Any, TYPE_CHECKING
+from typing import cast
+if TYPE_CHECKING:
+    from typing_extensions import TypeAlias
+else:
+    try:
+        from typing import TypeAlias
+    except ImportError:  # pragma: no cover - fallback for Python 3.8
+        from typing_extensions import TypeAlias
 from .helpers import get_file, get_reco, return_alt_val_if_none
 import logging
 import numpy as np
@@ -11,8 +18,8 @@ if TYPE_CHECKING:
     from ..dataclasses import Scan, Reco
     from ..core.parameters import Parameters
 
-SubjectType = Literal["Biped", "Quadruped", "Phantom", "Other", "OtherAnimal"]
-SubjectPose = Literal[
+SubjectType: TypeAlias = Literal["Biped", "Quadruped", "Phantom", "Other", "OtherAnimal"]
+SubjectPose: TypeAlias = Literal[
     "Head_Supine", "Head_Prone", "Head_Left", "Head_Right",
     "Foot_Supine", "Foot_Prone", "Foot_Left", "Foot_Right",
 ]

{brkraw-0.5.5 → brkraw-0.5.6}/brkraw/resolver/nifti.py

@@ -260,7 +260,7 @@ def resolve(
     
     if num_cycles > 1:
         time_step = cast(float, image_info['time_per_cycle']) / 1000.0
-        num_slices = image_info['dataobj'].shape[2]
+        num_slices = cast(np.ndarray, image_info['dataobj']).shape[2]
         slice_duration = time_step / num_slices
     else:
         time_step = None

{brkraw-0.5.5 → brkraw-0.5.6}/docs/assets/zenodo_badge.svg

@@ -26,10 +26,10 @@
             </text>
             <text x="110.609375"
             y="15" fill="#010101" fill-opacity=".3">
-                10.5281/zenodo.18329489
+                10.5281/zenodo.18392548
             </text>
             <text x="110.609375" y="14">
-                10.5281/zenodo.18329489
+                10.5281/zenodo.18392548
             </text>
         </g>
     </svg>

{brkraw-0.5.5 → brkraw-0.5.6}/docs/dev/contributors.md

@@ -39,4 +39,4 @@ This page is auto-generated from GitHub contributors.
 [ricardorios46]: https://github.com/RicardoRios46
 [ricardorios46-avatar]: https://avatars.githubusercontent.com/u/43252153?s=96
 
-Last updated: 2026-01-27
+Last updated: 2026-01-29

brkraw-0.5.5/RELEASE_NOTES.md

@@ -1,17 +0,0 @@
-# Release v0.5.5
-
-Date: 2026-01-27
-Changes since 0.5.4
-
-- chore: prepare release v0.5.5 (c3260df)
-- docs: update contributors (a7bf3ef)
-- update: vscode, auto activate environment setting. (95e6868)
-- Chore: wire release → publish workflow (3419d97)
-- Use VS Code interpreter for venv setup task (5aed156)
-- Update release workflow and scripts for Zenodo badge + bibtex generation (e63e007)
-- Patch for brkraw-viewer lazy loading (avoid eager data resolution) (c916625)
-- chore(api): config module (2fa90fc)
-- chore(api): hook resolver (9c36e95)
-- chore(api): minor remapping (f2ef87e)
-- chore(api): ensure naming consistency (9010542)
-- refactor(loader): improve hook handling logic (5c5a0e7)

{brkraw-0.5.5 → brkraw-0.5.6}/scripts/release_pr.py

@@ -474,16 +474,6 @@ def main() -> int:
     title = args.pr_title or f"Release v{args.version}"
     initial_body = args.pr_body or build_pr_body(args.version, "- (pending)")
 
-    pr_number = ensure_pr(
-        upstream_repo_full=upstream_repo_full,
-        base_branch=base_branch,
-        head_ref=head_ref,
-        title=title,
-        body=initial_body,
-        no_pr=args.no_pr,
-        dry_run=args.dry_run,
-    )
-
     # 1) contributors
     run_update_contributors(upstream_repo_full)
     commit_if_changed(
@@ -518,6 +508,16 @@ def main() -> int:
     if not args.dry_run:
         run_git(["push", args.remote_origin, f"HEAD:{branch}"], check=True)
 
+    pr_number = ensure_pr(
+        upstream_repo_full=upstream_repo_full,
+        base_branch=base_branch,
+        head_ref=head_ref,
+        title=title,
+        body=initial_body,
+        no_pr=args.no_pr,
+        dry_run=args.dry_run,
+    )
+
     # PR body update + label (if enabled)
     if pr_number and (not args.no_pr):
         changed_files = get_changed_files(args.base)