From 72b6a4bfb834354c45e98775806910fcae839f6f Mon Sep 17 00:00:00 2001
From: Tristan Kuehn <tkuehn@uwo.ca>
Date: Wed, 25 Jan 2023 10:40:15 -0500
Subject: [PATCH 1/2] Update gitignore

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 46c0d93..262cf90 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,3 @@
 # Local poetry config
 poetry.toml
+**/__pycache__

From a173e24424e4e1d21c7c7f0d5f4b0295e09e624e Mon Sep 17 00:00:00 2001
From: Tristan Kuehn <tkuehn@uwo.ca>
Date: Wed, 25 Jan 2023 16:53:25 -0500
Subject: [PATCH 2/2] Use source metadata instead of images to build metadata

Also, pre-commit went off on the workflows
---
 .github/release-drafter.yml               | 27 ++++++-----------------
 .github/workflows/deploy.yml              |  6 ++---
 .github/workflows/quality.yml             |  8 ++-----
 labelmerge/workflow/scripts/labelmerge.py | 20 +++++++++++++----
 4 files changed, 28 insertions(+), 33 deletions(-)

diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml
index e6cc139..ffb42f5 100644
--- a/.github/release-drafter.yml
+++ b/.github/release-drafter.yml
@@ -8,22 +8,15 @@ template: |
   $CHANGES
 categories:
   - title: 🚀 Features
-    labels:
-      - breaking
-      - enhancement
+    labels: [breaking, enhancement]
   - title: 🐛 Bug Fixes
-    labels:
-      - bug
+    labels: [bug]
   - title: 🧰 Maintenance
-    labels:
-      - maintenance
-      - test
+    labels: [maintenance, test]
   - title: 📝 Documentation
-    labels:
-      - documentation
+    labels: [documentation]
 
-exclude-labels:
-  - skip_changelog
+exclude-labels: [skip_changelog]
 
 change-template: '- $TITLE @$AUTHOR (#$NUMBER)'
 change-title-escapes: \<*_&    # You can add  # and @ to disable mentions, and add ` to disable code blocks.
@@ -33,13 +26,7 @@ version-resolver:
   #   labels:
   #     - 'breaking'
   minor:
-    labels:
-      - breaking
-      - enhancement
+    labels: [breaking, enhancement]
   patch:
-    labels:
-      - maintenance
-      - bug
-      - test
-      - documentation
+    labels: [maintenance, bug, test, documentation]
   default: patch
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index 234d86b..b3e2354 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -91,9 +91,9 @@ jobs:
   #       with:
   #         python-version: '3.9'
 
-  #     #----------------------------------------------
-  #     #  -----  install & configure poetry  -----
-  #     #----------------------------------------------
+  #  #----------------------------------------------
+  #  #  -----  install & configure poetry  -----
+  #  #----------------------------------------------
   #     - name: Install Poetry
   #       uses: snok/install-poetry@v1
   #       with:
diff --git a/.github/workflows/quality.yml b/.github/workflows/quality.yml
index ac472f9..ffe18b2 100644
--- a/.github/workflows/quality.yml
+++ b/.github/workflows/quality.yml
@@ -3,13 +3,9 @@ name: Lint workflow
 
 on:
   push:
-    branches:
-      - '*'
-      - '!push-action/*'
+    branches: ['*', '!push-action/*']
   pull_request:
-    branches:
-      - '*'
-      - '!push-action/*'
+    branches: ['*', '!push-action/*']
 
 jobs:
   quality:
diff --git a/labelmerge/workflow/scripts/labelmerge.py b/labelmerge/workflow/scripts/labelmerge.py
index 1e8d150..4a39fbb 100644
--- a/labelmerge/workflow/scripts/labelmerge.py
+++ b/labelmerge/workflow/scripts/labelmerge.py
@@ -4,6 +4,7 @@
 from argparse import ArgumentParser
 from os import PathLike
 from pathlib import Path
+from typing import Optional
 
 import nibabel as nib
 import numpy as np
@@ -15,7 +16,7 @@
 def load_atlas(atlas_path: PathLike):
     """Loading relevant atlas data"""
     atlas = nib.load(atlas_path)
-    data = atlas.get_fdata().astype(np.ushort)
+    data = atlas.get_fdata().astype(np.int_)
     header = atlas.header
     affine = atlas.affine
 
@@ -49,14 +50,25 @@ def split_labels(
     atlas: np.ndarray,
     metadata: pd.DataFrame,
     prefix: str = "",
-    exceptions: list[str] = [],
+    exceptions: Optional[list[str]] = None,
 ) -> list[xr.Dataset]:
+    if exceptions is None:
+        exceptions = []
     unique_vals = np.unique(atlas[atlas > 0])
+    all_labels: pd.Series[int] = metadata["index"]
+    if not set(unique_vals) <= set(all_labels):
+        unlabeled_vals = ", ".join(
+            str(val) for val in set(unique_vals) - set(all_labels)
+        )
+        raise MetadataError(
+            f"Labels with indices {unlabeled_vals} from {prefix}atlas not "
+            "found in metadata table"
+        )
     normal_ds = xr.Dataset(
         dict(
             [
                 assemble_mask(atlas, metadata, label, prefix)
-                for label in unique_vals
+                for label in all_labels
                 if label not in exceptions
             ]
         )
@@ -67,7 +79,7 @@ def split_labels(
         dict(
             [
                 assemble_mask(atlas, metadata, label, prefix)
-                for label in unique_vals
+                for label in all_labels
                 if label in exceptions
             ]
         )