Release v0.5.5

.github/workflows/publish.yml

@@ -12,6 +12,16 @@ on:
         description: "Tag to publish (optional, e.g. v1.2.3)"
         required: false
         type: string
+  workflow_call:
+    inputs:
+      target:
+        description: "Publish target"
+        type: string
+        default: testpypi
+      tag:
+        description: "Tag to publish (optional, e.g. v1.2.3)"
+        required: false
+        type: string
 
 permissions:
   contents: read

.github/workflows/release.yml

@@ -19,6 +19,10 @@ jobs:
   release:
     if: ${{ github.repository == 'BrkRaw/brkraw' }}
     runs-on: ubuntu-latest
+    outputs:
+      prerelease: ${{ steps.prerelease.outputs.value }}
+      tag: ${{ steps.tag.outputs.value }}
+      zenodo_success: ${{ steps.zenodo.outcome == 'success' }}
     steps:
       - name: Resolve tag
         id: tag
@@ -127,3 +131,38 @@ jobs:
           if url:
               print(f"Created discussion: {url}")
           PY
+      - name: Checkout main for Zenodo badge update
+        uses: actions/checkout@v4
+        with:
+          ref: main
+      - name: Set up git identity
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+      - name: Update Zenodo badge
+        id: zenodo
+        if: ${{ steps.prerelease.outputs.value != 'true' }}
+        continue-on-error: true
+        run: |
+          for i in $(seq 1 10); do
+            echo "Zenodo badge update attempt $i/10"
+            python3 scripts/update_zenodo_badge.py --up-to-date-exit-code 2
+            exit_code=$?
+            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 }}

.gitignore

@@ -21,6 +21,5 @@ site/
 .direnv/
 .envrc
 .idea/
-.vscode/
 *.lock
 .tmp

.vscode/settings.json

@@ -1,3 +1,4 @@
 {
-  "python.defaultInterpreterPath": "${workspaceFolder}/.venv/bin/python"
+  "python.defaultInterpreterPath": "${workspaceFolder}/.venv/bin/python",
+  "python.terminal.activateEnvironment": true
 }

.vscode/tasks.json

@@ -11,9 +11,9 @@
     {
       "label": "Standard: Setup venv + deps",
       "type": "shell",
-      "command": "python3 -m venv .venv && . .venv/bin/activate && python -m pip install -U pip && python -m pip install -e \".[dev]\"",
+      "command": "\"${command:python.interpreterPath}\" -m venv .venv && .venv/bin/python -m pip install -U pip && .venv/bin/python -m pip install -e \".[dev]\"",
       "windows": {
-        "command": "py -m venv .venv; .venv\\Scripts\\Activate.ps1; python -m pip install -U pip; python -m pip install -e \".[dev]\"",
+        "command": "\"${command:python.interpreterPath}\" -m venv .venv; .venv\\Scripts\\python -m pip install -U pip; .venv\\Scripts\\python -m pip install -e \".[dev]\"",
         "options": {
           "shell": {
             "executable": "pwsh"

CITATION.cff

@@ -34,4 +34,4 @@ keywords:
   - BIDS
   - neuroimaging
 
-version: "0.5.4"
+version: "0.5.5"

README.md

@@ -10,7 +10,7 @@
 
 A modular toolkit for Bruker MRI raw-data handling.
 
-BrkRaw (v0.5.4) converts raw data into standardized, neuroimaging-ready
+BrkRaw (v0.5.5) 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 = {0.5.4},
+  version = {0.5.5},
   doi = {10.5281/zenodo.3818614},
   url = {https://github.com/BrkRaw/brkraw},
   note = {Documentation: https://brkraw.github.io},

RELEASE_NOTES.md

@@ -1,38 +1,17 @@
-# Release v0.5.4
+# Release v0.5.5
 
-Date: 2026-01-26
-Changes since 0.5.2
+Date: 2026-01-27
+Changes since 0.5.4
 
-- chore: prepare release v0.5.4 (7634b95)
-- docs: update contributors (7fa7594)
-- feat(api): introduce public API layer (d38b088)
-- perf: improve loader efficiency and reduce overhead (8998d68)
-- prevent update of num_cycle when slice (e0932a7)
-- Handle single-cycle datasets (09d37f6)
-- update types in loader app (a921da7)
-- patch wrapped get_dataobj in loader takes kwargs (4945816)
-- perf: introduce lazy scan/image loading and enable partial cycle reads (3185440)
-- update docstrings on cache.py (a23b8ae)
-- bug: unit of cached files, updated (6d4323c)
-- feat: add central cache management (CLI 'cache' command and core API) (5898e03)
-- missing kwargs input (59c72fa)
-- expose additional types for hook development (e25c52e)
-- add opiotion to input version using argument (1b02ab6)
-- Make Paravision path detection robust using pdata anchor (691c81b)
-- Handle convert hook errors per scan (c4afa3d)
-- Improve ci workflow and zenodo badge mapping (efeb725)
-- Update Zenodo DOI badge (f6a531a)
-- Refine GitHub Actions and release preparation scripts (d4dcde0)
-- Normalize __version__ regex to use hex escapes for quotes (061d3c5)
-- script: patch issue in finding version from the __init__.py (6ae9ea3)
-- fix: parse __version__ regex in release workflow (73745d5)
-- fix: send labels as array in gh api (23b5391)
-- docs: release notes for v0.5.3 (20dc0a6)
-- fix: avoid gh pr graphql in release_pr (6311e09)
-- docs: release notes for v0.5.3 (2e427de)
-- chore: prepare release v0.5.3 (15e1158)
-- docs: update contributors (83d68bf)
-- Add debug logging for converter hooks (db8943d)
-- refactor: drop flip_x from nifti header (14e5304)
-- refactor: route hook kwargs by signature and drop format option (4c3f4d6)
-- readme.md biblatex update (b39e11d)
+- 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)

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: 2026-01-26
+Last updated: 2026-01-27