From d983a69c999681b47757254fda9c751097b4e816 Mon Sep 17 00:00:00 2001
From: Yaroslav Terentyev <17741549+YaroGitHubed@users.noreply.github.com>
Date: Fri, 17 Oct 2025 11:28:53 +0100
Subject: [PATCH 1/3] Fix NameError: add default PidentComments

---
 scripts/puppy-primers | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/scripts/puppy-primers b/scripts/puppy-primers
index 7fa2d0c..3a716cc 100644
--- a/scripts/puppy-primers
+++ b/scripts/puppy-primers
@@ -984,10 +984,17 @@ elif args.primers_type == "group":
             unintendedComment = "UNINTENDED AMPLIFICATION:\nWARNING - This gene amplifies unintended species in the defined community!"
 
         ## Comments about percentage identity of alignments:
-        if pidentSum == 100 * numTargets:
-            PidentComments = "ALIGNMENTS %ID:\nThis gene aligns perfectly (100% ID) to each target gene."
-        elif pidentSum < 100 * numTargets:
-            PidentComments = "ALIGNMENTS %ID:\nThis gene does not align perfectly (100% ID) to at least one target gene."
+        PidentComments = "ALIGNMENTS %ID:\nNo alignment information available."
+
+        if isinstance(pidentSum, (int, float)) and isinstance(numTargets, (int, float)):
+            if pidentSum == 100 * numTargets:
+                PidentComments = (
+                    "ALIGNMENTS %ID:\nThis gene aligns perfectly (100% ID) to each target gene."
+                )
+            elif pidentSum < 100 * numTargets:
+                PidentComments = (
+                    "ALIGNMENTS %ID:\nThis gene does not align perfectly (100% ID) to at least one target gene."
+                )
 
         ## Comments about alignments query coverage:
         if qcovSum == 1 * numTargets:

From 3505d6e0b5aa267601577b721c2b2fa22199ac2c Mon Sep 17 00:00:00 2001
From: Yaroslav Terentyev <17741549+YaroGitHubed@users.noreply.github.com>
Date: Tue, 28 Oct 2025 13:42:11 +0000
Subject: [PATCH 2/3] fix(puppy-primers): correct 0% identity logic for
 PidentComments

---
 scripts/puppy-primers | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)
 mode change 100644 => 100755 scripts/puppy-primers

diff --git a/scripts/puppy-primers b/scripts/puppy-primers
old mode 100644
new mode 100755
index 3a716cc..4e9dbc5
--- a/scripts/puppy-primers
+++ b/scripts/puppy-primers
@@ -987,7 +987,11 @@ elif args.primers_type == "group":
         PidentComments = "ALIGNMENTS %ID:\nNo alignment information available."
 
         if isinstance(pidentSum, (int, float)) and isinstance(numTargets, (int, float)):
-            if pidentSum == 100 * numTargets:
+            if not pidentSum or not numTargets:
+                PidentComments = (
+                    "ALIGNMENTS %ID:\nNo alignment information available."
+                )
+            elif pidentSum == 100 * numTargets:
                 PidentComments = (
                     "ALIGNMENTS %ID:\nThis gene aligns perfectly (100% ID) to each target gene."
                 )

From 2953f35829010ec19eef09de743443f8a7a68a5e Mon Sep 17 00:00:00 2001
From: Yaroslav Terentyev <17741549+YaroGitHubed@users.noreply.github.com>
Date: Fri, 31 Oct 2025 13:40:21 +0000
Subject: [PATCH 3/3] test(pidentcomments): add unit tests for pident_comment
 and constants

---
 my_tests/test_pidentcomments.py | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 my_tests/test_pidentcomments.py

diff --git a/my_tests/test_pidentcomments.py b/my_tests/test_pidentcomments.py
new file mode 100644
index 0000000..c8ab043
--- /dev/null
+++ b/my_tests/test_pidentcomments.py
@@ -0,0 +1,21 @@
+import math
+from my_tests.pidentcomments import pident_comment, DEFAULT, PERFECT, IMPERFECT
+
+def test_defaults_and_branches():
+    assert "No alignment" in pident_comment(None, 3)
+    assert "aligns perfectly" in pident_comment(100, 1)
+    assert "does not align perfectly" in pident_comment(99.9, 1)
+    # With 0 targets we fall back to DEFAULT
+    assert "No alignment" in pident_comment(0, 0)
+
+def test_never_raises_on_weird_inputs():
+    for pair in [("x","y"), ([],{}), (object(),object()), (-1,-1)]:
+        out = pident_comment(*pair)
+        assert isinstance(out, str)
+        assert "No alignment" in out
+
+def test_constants_are_strings():
+    for s in (DEFAULT, PERFECT, IMPERFECT):
+        assert isinstance(s, str)
+
+