From a65fcac9af56fc9c9994c29600a27b9900c0e3d6 Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Wed, 23 Apr 2025 15:22:20 +0200
Subject: [PATCH 1/2] add support for freeze requirements file in
 replace_alphax.sh

---
 alphatesting/replace_alphax.sh | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/alphatesting/replace_alphax.sh b/alphatesting/replace_alphax.sh
index 14955da9..cf6879cf 100755
--- a/alphatesting/replace_alphax.sh
+++ b/alphatesting/replace_alphax.sh
@@ -21,8 +21,9 @@ else
 fi
 
 LOOSE_REQUIREMENTS_FILE=${REQUIREMENTS_FILE/.txt/_loose.txt}
+FREEZE_REQUIREMENTS_FILE=${REQUIREMENTS_FILE/requirements.txt/_requirements_freeze.txt}
 
-echo using $REQUIREMENTS_FILE $LOOSE_REQUIREMENTS_FILE
+echo using $REQUIREMENTS_FILE $LOOSE_REQUIREMENTS_FILE $FREEZE_REQUIREMENTS_FILE
 
 # Add any alphaX packages that others depend on here. Use the name like it is given in the requirements file!
 for a in alphabase alphatims alpharaw peptdeep alphatims alphaviz directlfq; do
@@ -31,6 +32,9 @@ for a in alphabase alphatims alpharaw peptdeep alphatims alphaviz directlfq; do
   if [ -f $LOOSE_REQUIREMENTS_FILE ]; then
       sed -i "s/$a/### $a/" $LOOSE_REQUIREMENTS_FILE
   fi
+  if [ -f $FREEZE_REQUIREMENTS_FILE ]; then
+      sed -i "s/$a/### $a/" $FREEZE_REQUIREMENTS_FILE
+  fi
 done
 
 echo $REQUIREMENTS_FILE:

From 3a0e968215fdf66365d22ea2f42370c740598c95 Mon Sep 17 00:00:00 2001
From: mschwoerer <82171591+mschwoer@users.noreply.github.com>
Date: Wed, 23 Apr 2025 16:11:38 +0200
Subject: [PATCH 2/2] fix free file name

---
 alphatesting/replace_alphax.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/alphatesting/replace_alphax.sh b/alphatesting/replace_alphax.sh
index cf6879cf..5cee4130 100755
--- a/alphatesting/replace_alphax.sh
+++ b/alphatesting/replace_alphax.sh
@@ -21,7 +21,7 @@ else
 fi
 
 LOOSE_REQUIREMENTS_FILE=${REQUIREMENTS_FILE/.txt/_loose.txt}
-FREEZE_REQUIREMENTS_FILE=${REQUIREMENTS_FILE/requirements.txt/_requirements_freeze.txt}
+FREEZE_REQUIREMENTS_FILE=${REQUIREMENTS_FILE/requirements.txt/_requirements.freeze.txt}
 
 echo using $REQUIREMENTS_FILE $LOOSE_REQUIREMENTS_FILE $FREEZE_REQUIREMENTS_FILE