From 7d443ff80364108d238adb9e0d0ba5ea1c41ad53 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Tue, 28 Jul 2026 13:11:02 +0200
Subject: [PATCH 1/2] write metric_ids and metric_values as lists

* average_batch_r2 and flowsom_mapping_similarity wrote them as scalars
---
 src/metrics/average_batch_r2/script.py          | 4 ++--
 src/metrics/flowsom_mapping_similarity/script.R | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/metrics/average_batch_r2/script.py b/src/metrics/average_batch_r2/script.py
index 93fbd6204..80b1c12e9 100644
--- a/src/metrics/average_batch_r2/script.py
+++ b/src/metrics/average_batch_r2/script.py
@@ -84,8 +84,8 @@
     uns={
         "dataset_id": integrated_s1.uns["dataset_id"],
         "method_id": integrated_s1.uns["method_id"],
-        "metric_ids": "average_batch_r2_ct",
-        "metric_values": average_batch_r2_ct,
+        "metric_ids": ["average_batch_r2_ct"],
+        "metric_values": [average_batch_r2_ct],
         "r2_collection_ct": r2_collection_ct,
     }
 )
diff --git a/src/metrics/flowsom_mapping_similarity/script.R b/src/metrics/flowsom_mapping_similarity/script.R
index fa1a268a9..2e246b831 100644
--- a/src/metrics/flowsom_mapping_similarity/script.R
+++ b/src/metrics/flowsom_mapping_similarity/script.R
@@ -144,8 +144,8 @@ output <- anndata::AnnData(
   uns = list(
     dataset_id = integrated_s1$uns$dataset_id,
     method_id = integrated_s1$uns$method_id,
-    metric_ids = "flowsom_mean_mapping_similarity",
-    metric_values = fs_mapping_similarity_avg,
+    metric_ids = list("flowsom_mean_mapping_similarity"),
+    metric_values = list(fs_mapping_similarity_avg),
     fsom_absdiff_by_donor_refsplit = fsom_absdiff_by_donor_refsplit,
     fsom_parameters = list(
       "xdim" = grid_xdim,

From 21bed4c9c5dede3af652986221896722e24c2a79 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Tue, 28 Jul 2026 13:11:12 +0200
Subject: [PATCH 2/2] update changelog

---
 CHANGELOG.md | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 271fda0d5..39f5a35f0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -239,4 +239,7 @@
   and thus can't be directly overriden (new values given by get_donor_batch_map is int) (PR #119).
 
 * Update flowsom mapping similarity so we subset to just markers to correct, and lisi to remove control samples
-  and unlabelled cells (PR #119).
\ No newline at end of file
+  and unlabelled cells (PR #119).
+
+* Fix `average_batch_r2` and `flowsom_mapping_similarity` writing `metric_ids` and `metric_values`
+  as scalars instead of lists, as required by `file_score.yaml` (PR #130).