brkraw 0.5.6__tar.gz → 0.5.7__tar.gz

{brkraw-0.5.6 → brkraw-0.5.7}/.github/workflows/release_on_merge.yml

@@ -3,6 +3,19 @@ name: Release On Merge
 on:
   push:
     branches: [main]
+  workflow_dispatch:
+    inputs:
+      tag:
+        description: "Tag to create and push (e.g., v0.4.2)"
+        required: true
+      run_release:
+        description: "Trigger release workflow after tagging"
+        required: false
+        default: "true"
+        type: choice
+        options:
+          - "true"
+          - "false"
 
 permissions:
   contents: write
@@ -29,12 +42,6 @@ jobs:
           # Default outputs
           echo "changed=false" >> "$GITHUB_OUTPUT"
 
-          # Only proceed for merge commits ("Merge pull request ...")
-          if [[ "${{ github.event.head_commit.message }}" != Merge\ pull\ request* ]]; then
-            echo "Not a merge commit. Skipping." 
-            exit 0
-          fi
-
           # Find the PR associated with this merge commit and ensure it has the 'release' label.
           api="https://api.github.com/repos/${REPO}/commits/${SHA}/pulls"
           pr_json=$(curl -fsSL \
@@ -59,7 +66,8 @@ jobs:
           )
 
           if [[ -z "${pr_number}" ]]; then
-            echo "No PR associated with ${SHA}. Skipping." 
+            echo "No PR associated with ${SHA}. Skipping."
+            echo "This can happen for direct pushes, API failures, or insufficient token scopes."
             exit 0
           fi
 
@@ -79,7 +87,8 @@ jobs:
           )
 
           if [[ "${has_release}" != "true" ]]; then
-            echo "PR #${pr_number} does not have 'release' label. Skipping." 
+            echo "PR #${pr_number} does not have 'release' label. Skipping."
+            echo "If this was a squash/rebase merge, ensure the PR is labeled before merging."
             exit 0
           fi
 
@@ -107,10 +116,18 @@ jobs:
           echo "changed=true" >> "$GITHUB_OUTPUT"
           echo "value=$version" >> "$GITHUB_OUTPUT"
         shell: bash
+      - name: Manual tag inputs
+        id: manual
+        if: ${{ github.event_name == 'workflow_dispatch' }}
+        run: |
+          set -euo pipefail
+          echo "changed=true" >> "$GITHUB_OUTPUT"
+          echo "value=${{ inputs.tag }}" >> "$GITHUB_OUTPUT"
+          echo "run_release=${{ inputs.run_release }}" >> "$GITHUB_OUTPUT"
       - name: Create and push tag
-        if: ${{ steps.version.outputs.changed == 'true' }}
+        if: ${{ steps.version.outputs.changed == 'true' || steps.manual.outputs.changed == 'true' }}
         run: |
-          tag="${{ steps.version.outputs.value }}"
+          tag="${{ steps.manual.outputs.value || steps.version.outputs.value }}"
           if git rev-parse "$tag" >/dev/null 2>&1; then
             echo "Tag $tag already exists. Skipping."
             exit 0
@@ -118,9 +135,9 @@ jobs:
           git tag "$tag" "${{ github.sha }}"
           git push origin "$tag"
       - name: Trigger release workflow
-        if: ${{ steps.version.outputs.changed == 'true' }}
+        if: ${{ (steps.version.outputs.changed == 'true') || (steps.manual.outputs.changed == 'true' && steps.manual.outputs.run_release == 'true') }}
         env:
           GH_TOKEN: ${{ github.token }}
         run: |
-          tag="${{ steps.version.outputs.value }}"
+          tag="${{ steps.manual.outputs.value || steps.version.outputs.value }}"
           gh workflow run release.yml -f tag="$tag"

{brkraw-0.5.6 → brkraw-0.5.7}/.markdownlint.yaml

@@ -4,3 +4,4 @@ MD013:
   tables: false
 MD022: false
 MD032: false
+MD033: false

brkraw-0.5.7/.vscode/settings.json

@@ -0,0 +1,5 @@
+{
+  "python.defaultInterpreterPath": "${workspaceFolder}/.venv/bin/python",
+  "python.terminal.activateEnvironment": true,
+  "terminal.integrated.defaultProfile.osx": "zsh"
+}

brkraw-0.5.7/.vscode/tasks.json

@@ -0,0 +1,86 @@
+{
+  "version": "2.0.0",
+  "inputs": [
+    {
+      "id": "releaseVersion",
+      "type": "promptString",
+      "description": "Release version (e.g., 1.0.0)"
+    }
+  ],
+  "tasks": [
+    {
+      "label": "Standard: Setup venv + deps",
+      "type": "shell",
+      "command": "\"${workspaceFolder}/.venv/bin/python\" -m venv .venv && \"${workspaceFolder}/.venv/bin/python\" -m pip install -U pip && \"${workspaceFolder}/.venv/bin/python\" -m pip install -e \".[dev]\"",
+      "windows": {
+        "command": "\"${workspaceFolder}\\.venv\\Scripts\\python\" -m venv .venv; \"${workspaceFolder}\\.venv\\Scripts\\python\" -m pip install -U pip; \"${workspaceFolder}\\.venv\\Scripts\\python\" -m pip install -e \".[dev]\"",
+        "options": {
+          "shell": {
+            "executable": "pwsh"
+          }
+        }
+      },
+      "group": "build",
+      "problemMatcher": []
+    },
+    {
+      "label": "Standard: Release Prep PR (2-step)",
+      "type": "shell",
+      "command": "\"${workspaceFolder}/.venv/bin/python\" scripts/release_pr.py --version ${input:releaseVersion} --base upstream/main --remote-upstream upstream --remote-origin origin",
+      "group": "build",
+      "problemMatcher": []
+    },
+    {
+      "label": "DryRun: Release Prep PR (2-step)",
+      "type": "shell",
+      "command": "\"${workspaceFolder}/.venv/bin/python\" scripts/release_pr.py --dry-run --version ${input:releaseVersion} --base upstream/main --remote-upstream upstream --remote-origin origin",
+      "group": "build",
+      "problemMatcher": []
+    },
+    {
+      "label": "Standard: MkDocs Serve",
+      "type": "shell",
+      "command": "\"${workspaceFolder}/.venv/bin/python\" -m mkdocs serve",
+      "group": "build",
+      "problemMatcher": []
+    },
+    {
+      "label": "Optional: Release Prep (bump + notes)",
+      "type": "shell",
+      "command": "\"${workspaceFolder}/.venv/bin/python\" scripts/update_contributors.py --source github --repo brkraw/brkraw --output docs/dev/contributors.md && \"${workspaceFolder}/.venv/bin/python\" scripts/release_prep.py --version ${input:releaseVersion} --fetch-tags --remote upstream",
+      "windows": {
+        "command": "pwsh -NoProfile -Command \"& \\\"${workspaceFolder}\\.venv\\Scripts\\python\\\" scripts/update_contributors.py --source github --repo brkraw/brkraw --output docs/dev/contributors.md; if ($LASTEXITCODE -ne 0) { exit $LASTEXITCODE }; & \\\"${workspaceFolder}\\.venv\\Scripts\\python\\\" scripts/release_prep.py --version ${input:releaseVersion} --fetch-tags --remote upstream\""
+      },
+      "group": "build",
+      "problemMatcher": []
+    },
+    {
+      "label": "Optional: Release Notes Only",
+      "type": "shell",
+      "command": "\"${workspaceFolder}/.venv/bin/python\" scripts/release_notes.py --fetch-tags --remote upstream",
+      "group": "build",
+      "problemMatcher": []
+    },
+    {
+      "label": "Optional: Release Tag + Push (upstream)",
+      "type": "shell",
+      "command": "\"${workspaceFolder}/.venv/bin/python\" scripts/tag_and_push.py",
+      "group": "build",
+      "problemMatcher": []
+    },
+    {
+      "label": "Optional: Docs Update Contributors (git)",
+      "type": "shell",
+      "command": "\"${workspaceFolder}/.venv/bin/python\" scripts/update_contributors.py --source git --output docs/dev/contributors.md",
+      "group": "build",
+      "problemMatcher": []
+    },
+    {
+      "label": "Optional: Docs Update Contributors (GitHub API)",
+      "type": "shell",
+      "command": "\"${workspaceFolder}/.venv/bin/python\" scripts/update_contributors.py --source github --repo brkraw/brkraw --output docs/dev/contributors.md",
+      "group": "build",
+      "problemMatcher": []
+    }
+  ]
+}

{brkraw-0.5.6 → brkraw-0.5.7}/CITATION.cff

@@ -34,4 +34,4 @@ keywords:
   - BIDS
   - neuroimaging
 
-version: "0.5.6"
+version: "0.5.7"

{brkraw-0.5.6 → brkraw-0.5.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: brkraw
-Version: 0.5.6
+Version: 0.5.7
 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 (v0.5.6) converts raw data into standardized, neuroimaging-ready
+BrkRaw (v0.5.7) 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 = {0.5.6},
+  version = {0.5.7},
   doi = {10.5281/zenodo.3818614},
   url = {https://github.com/BrkRaw/brkraw},
   note = {Documentation: https://brkraw.github.io},

{brkraw-0.5.6 → brkraw-0.5.7}/README.md

@@ -10,7 +10,7 @@
 
 A modular toolkit for Bruker MRI raw-data handling.
 
-BrkRaw (v0.5.6) converts raw data into standardized, neuroimaging-ready
+BrkRaw (v0.5.7) 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 = {0.5.6},
+  version = {0.5.7},
   doi = {10.5281/zenodo.3818614},
   url = {https://github.com/BrkRaw/brkraw},
   note = {Documentation: https://brkraw.github.io},

brkraw-0.5.7/RELEASE_NOTES.md

@@ -0,0 +1,15 @@
+# Release v0.5.7
+
+Date: 2026-02-03
+Changes since 0.5.6
+
+- docs: release notes for v0.5.7 (0fbaf73)
+- chore: prepare release v0.5.7 (3e98477)
+- docs: update contributors (3f18c3b)
+- doc: markdown lint (2fde999)
+- Fix hook spec documentation (5c271e1)
+- update (dev): CI workflow / dev configurations (502c98a)
+- patch(info_spec): added missing slice info (13fbc3e)
+- fix(cli): ensure to make outout directory during convertion (6dfb153)
+- Fix hook uninstall deps, affine slicepacks, and info stdout (da01975)
+- fix (spec): typo in Study info spec (ef6c980)

{brkraw-0.5.6 → brkraw-0.5.7}/brkraw/__init__.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-__version__ = '0.5.6'
+__version__ = '0.5.7'
 from .apps.loader import BrukerLoader
 
 

{brkraw-0.5.6 → brkraw-0.5.7}/brkraw/apps/addon/dependencies.py

@@ -17,11 +17,23 @@ RULE_KEYS = {"info_spec", "metadata_spec", "converter_hook"}
 _SPEC_EXTS = (".yaml", ".yml")
 
 
-def warn_dependencies(target: Path, *, kind: str, root: Optional[Union[str, Path]]) -> bool:
+def warn_dependencies(
+    target: Path,
+    *,
+    kind: str,
+    root: Optional[Union[str, Path]],
+    ignore_rules_dir: Optional[Path] = None,
+    ignore_specs_dir: Optional[Path] = None,
+) -> bool:
     paths = config_core.paths(root=root)
     warned = False
     if kind == "spec":
-        used_by_rules = rules_using_spec(target.name, paths.rules_dir)
+        used_by_rules = rules_using_spec(
+            target,
+            paths.rules_dir,
+            root=paths.root,
+            ignore_dir=ignore_rules_dir,
+        )
         if used_by_rules:
             logger.warning(
                 "Spec %s is referenced by rules: %s",
@@ -29,7 +41,11 @@ def warn_dependencies(target: Path, *, kind: str, root: Optional[Union[str, Path
                 ", ".join(sorted(used_by_rules)),
             )
             warned = True
-        included_by = specs_including_spec(target.name, paths.specs_dir)
+        included_by = specs_including_spec(
+            target,
+            paths.specs_dir,
+            ignore_dir=ignore_specs_dir,
+        )
         if included_by:
             logger.warning(
                 "Spec %s is included by: %s",
@@ -54,12 +70,34 @@ def warn_dependencies(target: Path, *, kind: str, root: Optional[Union[str, Path
     return warned
 
 
-def rules_using_spec(spec_name: str, rules_dir: Path) -> Set[str]:
+def _is_under(path: Path, base: Optional[Path]) -> bool:
+    if base is None:
+        return False
+    try:
+        path.relative_to(base)
+    except ValueError:
+        return False
+    return True
+
+
+def rules_using_spec(
+    target: Union[str, Path],
+    rules_dir: Path,
+    *,
+    root: Optional[Union[str, Path]] = None,
+    ignore_dir: Optional[Path] = None,
+) -> Set[str]:
     used_by: Set[str] = set()
     if not rules_dir.exists():
         return used_by
+    if isinstance(target, Path):
+        target_path = target.resolve()
+    else:
+        target_path = None
     files = list(rules_dir.rglob("*.yaml")) + list(rules_dir.rglob("*.yml"))
     for path in files:
+        if _is_under(path, ignore_dir):
+            continue
         data = yaml.safe_load(path.read_text(encoding="utf-8"))
         if not isinstance(data, dict):
             continue
@@ -70,17 +108,46 @@ def rules_using_spec(spec_name: str, rules_dir: Path) -> Set[str]:
                 if not isinstance(item, dict):
                     continue
                 use = item.get("use")
-                if isinstance(use, str) and Path(use).name == spec_name:
+                if not isinstance(use, str):
+                    continue
+                if target_path is None:
+                    if Path(use).name == str(target):
+                        used_by.add(path.name)
+                    continue
+                if root is None:
+                    continue
+                version = item.get("version") if isinstance(item.get("version"), str) else None
+                try:
+                    resolved = resolve_spec_reference(
+                        use,
+                        category=key,
+                        version=version,
+                        root=root,
+                    )
+                except Exception:
+                    continue
+                if resolved.resolve() == target_path:
                     used_by.add(path.name)
     return used_by
 
 
-def specs_including_spec(spec_name: str, specs_dir: Path) -> Set[str]:
+def specs_including_spec(
+    target: Union[str, Path],
+    specs_dir: Path,
+    *,
+    ignore_dir: Optional[Path] = None,
+) -> Set[str]:
     included_by: Set[str] = set()
     if not specs_dir.exists():
         return included_by
+    if isinstance(target, Path):
+        target_path = target.resolve()
+    else:
+        target_path = None
     files = list(specs_dir.rglob("*.yaml")) + list(specs_dir.rglob("*.yml"))
     for path in files:
+        if _is_under(path, ignore_dir):
+            continue
         data = yaml.safe_load(path.read_text(encoding="utf-8"))
         if not isinstance(data, dict):
             continue
@@ -92,8 +159,17 @@ def specs_including_spec(spec_name: str, specs_dir: Path) -> Set[str]:
                 include_list = [include]
             elif isinstance(include, list) and all(isinstance(item, str) for item in include):
                 include_list = include
-        if any(Path(item).name == spec_name for item in include_list):
-            included_by.add(path.name)
+        for item in include_list:
+            inc_path = Path(item)
+            if not inc_path.is_absolute():
+                inc_path = (path.parent / inc_path).resolve()
+            if target_path is None:
+                if inc_path.name == str(target):
+                    included_by.add(path.name)
+                    break
+            elif inc_path == target_path:
+                included_by.add(path.name)
+                break
     return included_by
 
 

{brkraw-0.5.6 → brkraw-0.5.7}/brkraw/apps/hook/core.py

@@ -150,12 +150,18 @@ def uninstall_hook(
         "transforms": [],
     }
     root_path = config_core.resolve_root(root)
+    namespace = entry.get("namespace") if isinstance(entry, dict) else None
     for kind in ("specs", "pruner_specs", "rules", "transforms"):
         for relpath in entry.get(kind, []) if isinstance(entry, dict) else []:
             target_path = root_path / relpath
             if not target_path.exists():
                 continue
-            if _has_dependencies(target_path, kind, root=root_path) and not force:
+            if _has_dependencies(
+                target_path,
+                kind,
+                root=root_path,
+                namespace=namespace,
+            ) and not force:
                 raise RuntimeError("Dependencies found; use --force to remove.")
             target_path.unlink()
             removed[kind].append(relpath)
@@ -587,9 +593,22 @@ def _has_dependencies(
     kind: str,
     *,
     root: Optional[Union[str, Path]],
+    namespace: Optional[str] = None,
 ) -> bool:
     try:
-        return addon_deps.warn_dependencies(target, kind=_kind_to_remove(kind), root=root)
+        ignore_rules_dir = None
+        ignore_specs_dir = None
+        if namespace:
+            paths = config_core.paths(root=root)
+            ignore_rules_dir = paths.rules_dir / namespace
+            ignore_specs_dir = paths.specs_dir / namespace
+        return addon_deps.warn_dependencies(
+            target,
+            kind=_kind_to_remove(kind),
+            root=root,
+            ignore_rules_dir=ignore_rules_dir,
+            ignore_specs_dir=ignore_specs_dir,
+        )
     except Exception:
         return False
 

{brkraw-0.5.6 → brkraw-0.5.7}/brkraw/apps/loader/core.py

@@ -565,7 +565,6 @@ class BrukerLoader:
 
             if scope == 'scan':
                 if not as_dict:
-                    config_core.configure_logging(root=base, stream=sys.stdout)
                     text = format_info_tables(
                         {"Scan(s)": scan_info},
                         width=width,
@@ -574,7 +573,7 @@ class BrukerLoader:
                         scan_transpose=scan_transpose,
                         float_decimals=float_decimals,
                     )
-                    logger.info("%s", text)
+                    print(text)
                     return None
                 return scan_info
         
@@ -586,19 +585,17 @@ class BrukerLoader:
         
         if scope == 'study':
             if not as_dict:
-                config_core.configure_logging(root=base, stream=sys.stdout)
                 text = format_info_tables(
                     study_info,
                     width=width,
                     float_decimals=float_decimals,
                 )
-                logger.info("%s", text)
+                print(text)
                 return None
             return study_info
         
         study_info['Scan(s)'] = scan_info
         if not as_dict:
-            config_core.configure_logging(root=base, stream=sys.stdout)
             text = format_info_tables(
                 study_info,
                 width=width,
@@ -607,7 +604,7 @@ class BrukerLoader:
                 scan_transpose=scan_transpose,
                 float_decimals=float_decimals,
             )
-            logger.info("%s", text)
+            print(text)
             return None
         return study_info
 

{brkraw-0.5.6 → brkraw-0.5.7}/brkraw/apps/loader/info/scan.yaml

@@ -56,6 +56,10 @@ FOV (mm):
     - file: method
       key: PVM_Fov
   transform: convert_to_list
+Num Slices:
+  sources:
+    - file: acqp
+      key: NSLICES
 NumSlicePack:
   sources:
     - file: method

{brkraw-0.5.6 → brkraw-0.5.7}/brkraw/apps/loader/info/study.yaml

@@ -5,7 +5,7 @@ study:
     description: "Study-level info mapping for Bruker datasets."
     category: "info_spec"
     transforms_source: "transform.py"
-  Study.Opperator:
+  Study.Operator:
     sources:
       - file: subject
         key: SUBJECT_referral
@@ -91,7 +91,7 @@ scan:
     description: "Scan-level fallback info mapping for Bruker datasets."
     category: "info_spec"
     transforms_source: "transform.py"
-  Study.Opperator:
+  Study.Operator:
     sources:
       - file: visu_pars
         key: VisuStudyReferringPhysician

{brkraw-0.5.6 → brkraw-0.5.7}/brkraw/cli/commands/convert.py

@@ -12,7 +12,7 @@ import logging
 import os
 import re
 from pathlib import Path
-from typing import Any, Mapping, Optional, Dict, List, Tuple, cast, get_args
+from typing import Any, Mapping, Optional, Dict, List, Tuple, Sequence, cast, get_args
 
 import numpy as np
 from brkraw.cli.utils import load
@@ -387,6 +387,8 @@ def cmd_convert(args: argparse.Namespace) -> int:
             for path in output_paths:
                 reserved_paths.add(path)
 
+            _ensure_output_dirs(output_paths)
+
             sidecar_meta = None
             if args.sidecar:
                 sidecar_meta = loader.get_metadata(
@@ -397,12 +399,10 @@ def cmd_convert(args: argparse.Namespace) -> int:
 
             if args.no_convert:
                 for path in output_paths:
-                    path.parent.mkdir(parents=True, exist_ok=True)
                     _write_sidecar(path, sidecar_meta)
                     total_written += 1
             else:
                 for path, obj in zip(output_paths, nii_list):
-                    path.parent.mkdir(parents=True, exist_ok=True)
                     obj.to_filename(str(path))
                     logger.info("Wrote NIfTI: %s", path)
                     total_written += 1
@@ -713,6 +713,15 @@ def _parse_hook_args(values: List[str]) -> Dict[str, Dict[str, Any]]:
     return parsed
 
 
+def _ensure_output_dirs(paths: Sequence[Path]) -> None:
+    for path in paths:
+        try:
+            path.parent.mkdir(parents=True, exist_ok=True)
+        except OSError as exc:
+            logger.error("Failed to create output directory %s: %s", path.parent, exc)
+            raise
+
+
 def _uses_counter_tag(
     *,
     layout_template: Optional[str],

{brkraw-0.5.6 → brkraw-0.5.7}/brkraw/cli/commands/hook.py

@@ -274,7 +274,8 @@ def cmd_preset(args: argparse.Namespace) -> int:
         return 2
     preset = _infer_hook_preset(entry)
     payload = {"hooks": {args.target: preset}}
-    text = yaml.safe_dump(payload, sort_keys=False)
+    normalized = _normalize_yaml_payload(payload)
+    text = yaml.safe_dump(normalized, sort_keys=False)
     if args.output:
         Path(args.output).expanduser().write_text(text, encoding="utf-8")
         logger.info("Wrote preset: %s", args.output)
@@ -283,6 +284,18 @@ def cmd_preset(args: argparse.Namespace) -> int:
     return 0
 
 
+def _normalize_yaml_payload(value: Any) -> Any:
+    if isinstance(value, Path):
+        return str(value)
+    if dataclasses.is_dataclass(value) and not isinstance(value, type):
+        return _normalize_yaml_payload(dataclasses.asdict(value))
+    if isinstance(value, dict):
+        return {key: _normalize_yaml_payload(item) for key, item in value.items()}
+    if isinstance(value, (list, tuple, set)):
+        return [_normalize_yaml_payload(item) for item in value]
+    return value
+
+
 def register(subparsers: argparse._SubParsersAction) -> None:  # type: ignore[name-defined]
     hook_parser = subparsers.add_parser(
         "hook",

{brkraw-0.5.6 → brkraw-0.5.7}/brkraw/cli/commands/info.py

@@ -39,7 +39,7 @@ def cmd_info(args: argparse.Namespace) -> int:
         width=width,
     )
     if text is not None:
-        logger.info("%s", text)
+        print(text)
     return 0
 
 

{brkraw-0.5.6 → brkraw-0.5.7}/brkraw/cli/commands/prune.py

@@ -97,7 +97,7 @@ def register(subparsers: argparse._SubParsersAction) -> None:  # type: ignore[na
         "--output",
         dest="output",
         type=str,
-        help="Output zip path (default: <input>_pruned.*).",
+        help="Output zip path (default: ./<root_name>.zip when omitted).",
     )
     prune_parser.add_argument(
         "--no-validate",

{brkraw-0.5.6 → brkraw-0.5.7}/brkraw/cli/utils.py

@@ -7,6 +7,7 @@ from __future__ import annotations
 
 import itertools
 import logging
+import sys
 import threading
 import time
 from contextlib import contextmanager
@@ -26,7 +27,7 @@ def spinner(prefix: str = "Loading") -> Iterator[None]:
     Yields:
         None.
     """
-    if logger.isEnabledFor(logging.DEBUG):
+    if logger.isEnabledFor(logging.DEBUG) or not sys.stdout.isatty():
         yield
         return
 
@@ -35,7 +36,11 @@ def spinner(prefix: str = "Loading") -> Iterator[None]:
 
     def run() -> None:
         while not stop_event.is_set():
-            print(f"\r{prefix} {next(seq)}", end="", flush=True)
+            try:
+                print(f"\r{prefix} {next(seq)}", end="", flush=True)
+            except BrokenPipeError:
+                stop_event.set()
+                break
             time.sleep(0.08)
 
     thread = threading.Thread(target=run, daemon=True)
@@ -45,7 +50,10 @@ def spinner(prefix: str = "Loading") -> Iterator[None]:
     finally:
         stop_event.set()
         thread.join()
-        print("\r" + " " * (len(prefix) + 2) + "\r", end="", flush=True)
+        try:
+            print("\r" + " " * (len(prefix) + 2) + "\r", end="", flush=True)
+        except BrokenPipeError:
+            pass
 
 
 def load(path, *, prefix: str = "Loading") -> BrukerLoader: