From 84cdfe2c866249ce5fa467ed79abf06eae8eafbd Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 17 Oct 2024 15:12:29 -0400
Subject: [PATCH 1/3] fix: reconfig needs to use platform-specific configfile

---
 charlie | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/charlie b/charlie
index ca9e827..4588c8c 100755
--- a/charlie
+++ b/charlie
@@ -295,7 +295,7 @@ function reconfig(){
   # this is only for dev purposes when new key-value pairs are being added to the config file
   check_essential_files
   sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" -e "s/WORKDIR/${WORKDIR//\//\\/}/g" \
-  ${PIPELINE_HOME}/config/config.yaml |\
+  ${PIPELINE_HOME}/config/$PLATFORM/config.yaml |\
   cat - ${PIPELINE_HOME}/config/containers.yaml > $WORKDIR/config.yaml
   echo "$WORKDIR/config.yaml has been updated!"
 }

From 8cb66bc6b9de6f8e40d91a451895b1692e833ad5 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 17 Oct 2024 15:15:42 -0400
Subject: [PATCH 2/3] fix: update reconfig to use SED for variables

---
 charlie | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/charlie b/charlie
index 4588c8c..a79d429 100755
--- a/charlie
+++ b/charlie
@@ -294,9 +294,13 @@ function reconfig(){
   # rebuild config file and replace the config.yaml in the WORKDIR
   # this is only for dev purposes when new key-value pairs are being added to the config file
   check_essential_files
-  sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" -e "s/WORKDIR/${WORKDIR//\//\\/}/g" \
-  ${PIPELINE_HOME}/config/$PLATFORM/config.yaml |\
-  cat - ${PIPELINE_HOME}/config/containers.yaml > $WORKDIR/config.yaml
+  sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" \
+    -e "s/WORKDIR/${WORKDIR//\//\\/}/g" \
+    -e "s/HOST/${HOST}/g" \
+    -e "s/ADDITIVES/${ADDITIVES}/g" \
+    -e "s/VIRUSES/${VIRUSES}/g" \
+    ${PIPELINE_HOME}/config/$PLATFORM/config.yaml |\
+    cat - ${PIPELINE_HOME}/config/containers.yaml > $CONFIGFILE
   echo "$WORKDIR/config.yaml has been updated!"
 }
 

From f7a0837b5f7e6b9c4c56d523278cd4ca3d9d43d1 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Thu, 17 Oct 2024 15:16:27 -0400
Subject: [PATCH 3/3] chore: update CHANGELOG.md

---
 CHANGELOG.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b51ad1c..3cbc750 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,9 @@
 
 - CHARLIE was falsely throwing a file permissions error for tempdir values containing bash variables. (#118, @kelly-sovacool)
 - Singularity bind paths were not being set properly. (#119, @kelly-sovacool)
+- Update docker containers to set `$PYTHONPATH`. (#119, @kelly-sovacool)
+  - Otherwise, this environment variable can be carried over and cause package conflicts when singularity is not run with `-C`.
+- Fix `reconfig` to correctly replace variables in the config file. (#121, @kelly-sovacool)
 
 ## CHARLIE 0.11.0