add patch for UMI-tools 1.1.4 and 1.1.5 to resolve pandas incompatibility warning

easybuild/easyconfigs/u/UMI-tools/UMI-tools-1.1.4-foss-2023a.eb

@@ -22,9 +22,14 @@ exts_list = [
         'checksums': ['eec0037cdd3d7553e6d72435a4379bede64be17c6712f149e485169638154d2b'],
     }),
     (name, version, {
+        'patches': ['UMI-tools-1.1.4_fix_pandas_warning.patch'],
         'source_tmpl': '%(version)s.tar.gz',
         'source_urls': ['https://github.com/CGATOxford/UMI-tools/archive/'],
-        'checksums': ['945c4c98e2007369c301a7a009c6f9deb0fda74b0117cd14e14bd134164a4ff6'],
+        'checksums': [
+            {'1.1.4.tar.gz': '945c4c98e2007369c301a7a009c6f9deb0fda74b0117cd14e14bd134164a4ff6'},
+            {'UMI-tools-1.1.4_fix_pandas_warning.patch':
+             '6ed8f436b50b316a795b09cb95bb9e4f29bebdedf8d2620a84d48d73a172cec1'},
+        ],
     }),
 ]
 

easybuild/easyconfigs/u/UMI-tools/UMI-tools-1.1.4_fix_pandas_warning.patch

@@ -0,0 +1,37 @@
+Backport https://github.com/CGATOxford/UMI-tools/pull/628 from UMI-tools 1.1.6
+See https://github.com/CGATOxford/UMI-tools/issues/615
+
+From d4bf10ced10e9d7b34523fd1de71c0fe8b2c09e4 Mon Sep 17 00:00:00 2001
+From: Tom Smith <[email protected]>
+Date: Mon, 4 Mar 2024 13:28:11 +0000
+Subject: [PATCH] resolves pandas aggregation warnings
+
+---
+ umi_tools/dedup.py | 6 ++++--
+ 1 file changed, 4 insertions(+), 2 deletions(-)
+
+diff --git a/umi_tools/dedup.py b/umi_tools/dedup.py
+index a518fc6..2b8e5ee 100644
+--- a/umi_tools/dedup.py
++++ b/umi_tools/dedup.py
+@@ -167,7 +167,7 @@ def aggregateStatsDF(stats_df):
+
+     grouped = stats_df.groupby("UMI")
+
+-    agg_dict = {'counts': [np.median, len, np.sum]}
++    agg_dict = {'counts': ['median', len, 'sum']}
+     agg_df = grouped.agg(agg_dict)
+
+     agg_df.columns = ['median_counts', 'times_observed', 'total_counts']
+@@ -444,8 +444,10 @@ def tallyCounts(binned_cluster, max_edit_distance):
+             columns=["unique", "unique_null", options.method,
+                      "%s_null" % options.method, "edit_distance"])
+
++        edit_distance_df['edit_distance'] = edit_distance_df['edit_distance'].astype(str)
++
+         # TS - set lowest bin (-1) to "Single_UMI"
+-        edit_distance_df['edit_distance'][0] = "Single_UMI"
++        edit_distance_df.loc[0, 'edit_distance'] = "Single_UMI"
+
+         edit_distance_df.to_csv(options.stats + "_edit_distance.tsv",
+                                 index=False, sep="\t")

easybuild/easyconfigs/u/UMI-tools/UMI-tools-1.1.5-foss-2023b.eb

@@ -22,9 +22,14 @@ exts_list = [
         'checksums': ['eec0037cdd3d7553e6d72435a4379bede64be17c6712f149e485169638154d2b'],
     }),
     (name, version, {
+        'patches': ['UMI-tools-1.1.4_fix_pandas_warning.patch'],
         'source_tmpl': '%(version)s.tar.gz',
         'source_urls': ['https://github.com/CGATOxford/UMI-tools/archive/'],
-        'checksums': ['2a87b75364ebe3e6ccf467d3b6d0501c458a48f3e6c8ab8b7c4dfb3fd7627fab'],
+        'checksums': [
+            {'1.1.5.tar.gz': '2a87b75364ebe3e6ccf467d3b6d0501c458a48f3e6c8ab8b7c4dfb3fd7627fab'},
+            {'UMI-tools-1.1.4_fix_pandas_warning.patch':
+             '6ed8f436b50b316a795b09cb95bb9e4f29bebdedf8d2620a84d48d73a172cec1'},
+        ],
     }),
 ]