From c67934730fdae7e42e86c29c947b4b722a72fced Mon Sep 17 00:00:00 2001
From: Arjun Prasad <aprasad@ncbi.nlm.nih.gov>
Date: Fri, 31 May 2024 15:09:07 -0400
Subject: [PATCH 1/3] Removed excess code from test_stxtyper.sh

---
 test_stxtyper.sh | 25 -------------------------
 1 file changed, 25 deletions(-)

diff --git a/test_stxtyper.sh b/test_stxtyper.sh
index 436015f..7a836f2 100755
--- a/test_stxtyper.sh
+++ b/test_stxtyper.sh
@@ -46,31 +46,6 @@ function test_input_file {
     fi
 }
 
-function test_amrfinder_output {
-    local test_base=$1
-    if ! $STXTYPER --amrfinder -n "test/$test_base.fa" > "test/$test_base.amr.got"
-    then
-        echo "not ok: $STXTYPER returned a non-zero exit value indicating a failure of the software"
-        echo "#  $STXTYPER -n test/$test_base.fa > test/$test_base.amr.got"
-        return 1
-    else
-        if ! diff -q "test/$test_base.amr.expected" "test/$test_base.amr.got"
-            ###### STOPPED HERE ######
-        then
-            echo "not ok: $STXTYPER returned output different from expected"
-            echo "#  $STXTYPER -n test/$test_base.fa > test/$test_base.got"
-            echo "# diff test/$test_base.expected test/$test_base.got"
-            diff "test/$test_base.expected" "test/$test_base.got"
-            echo "#  To approve run:"
-            echo "#     mv test/$test_base.got test/$test_base.expected "
-            return 1
-        else
-            echo "ok: test/$test_base.fa"
-            return 0
-        fi
-    fi
-}
-
 
 test_input_file 'basic'
 FAILURES=$(( $? + $FAILURES ))

From d69b5df0ac66638ea56a4ae987363e907710c2c2 Mon Sep 17 00:00:00 2001
From: Arjun Prasad <aprasad@ncbi.nlm.nih.gov>
Date: Mon, 24 Jun 2024 13:16:15 -0400
Subject: [PATCH 2/3] Update README.md, clarify EXTENDED

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 8c037f2..83286bd 100644
--- a/README.md
+++ b/README.md
@@ -76,8 +76,8 @@ The output of StxTyper is a tab-delimited file with the following fields, all pe
       terminating at contig boundaries
     - __PARTIAL_CONTIG_END__ for partial operons that could be split by contig
       boundaries due to sequencing or assembly artifacts
-    - __EXTENDED__ Where the coding sequence would extend beyond the stop codon
-      for the reference protein
+    - __EXTENDED__ The coding sequence extends beyond the reference stop codon
+      for one or both of the reference proteins
     - __INTERNAL_STOP__ for Stx operons where one of the subunits has a
       nonsense mutation
     - __FRAMESHIFT__ where StxTyper detected an indel in the coding sequence

From 9b666d38109edec875d18bd21865c4feaa8708ef Mon Sep 17 00:00:00 2001
From: Arjun Prasad <aprasad@ncbi.nlm.nih.gov>
Date: Mon, 24 Jun 2024 13:18:05 -0400
Subject: [PATCH 3/3] Switch actions to only trigger on "push"

---
 .github/workflows/linux-cpp.yml | 1 -
 .github/workflows/mac-cpp.yml   | 1 -
 2 files changed, 2 deletions(-)

diff --git a/.github/workflows/linux-cpp.yml b/.github/workflows/linux-cpp.yml
index 82a5a27..e453006 100644
--- a/.github/workflows/linux-cpp.yml
+++ b/.github/workflows/linux-cpp.yml
@@ -3,7 +3,6 @@ name: Linux C++ CI
 on:
   workflow_dispatch:
   push:
-  pull_request:
 
 jobs:
   build:
diff --git a/.github/workflows/mac-cpp.yml b/.github/workflows/mac-cpp.yml
index 3cf225b..c8fb09c 100644
--- a/.github/workflows/mac-cpp.yml
+++ b/.github/workflows/mac-cpp.yml
@@ -3,7 +3,6 @@ name: MacOS C++ CI
 on:
     workflow_dispatch:
     push:
-    pull_request:
 
 jobs:
     build: