From 92262dc43cd721bf10b1bf734f8cfd045d12c84e Mon Sep 17 00:00:00 2001
From: sof202 <s.o.fletcher@exeter.ac.uk>
Date: Fri, 22 Nov 2024 10:16:46 +0000
Subject: [PATCH 1/3] build: add execution permissions

---
 Setup/setup | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 Setup/setup

diff --git a/Setup/setup b/Setup/setup
old mode 100644
new mode 100755

From 16e295f59e3fdeb64e15fc008976573f3ba6d329 Mon Sep 17 00:00:00 2001
From: sof202 <s.o.fletcher@exeter.ac.uk>
Date: Fri, 22 Nov 2024 10:19:50 +0000
Subject: [PATCH 2/3] fix: only show usage if -h or --help is argument

---
 Setup/setup | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Setup/setup b/Setup/setup
index 42f6abd..d69a3ce 100755
--- a/Setup/setup
+++ b/Setup/setup
@@ -15,7 +15,7 @@ EOF
     exit 0
 }
 
-if [ "$#" -eq 0 ]; then usage; fi 
+if [[ $1 == "-h" || $1 == "--help" ]]; then usage; fi 
 
 REPO_DIR=$(dirname "$0")/..
 

From c65f21f51b4e0a9de3c708b02e113515ccd1141c Mon Sep 17 00:00:00 2001
From: sof202 <s.o.fletcher@exeter.ac.uk>
Date: Fri, 22 Nov 2024 10:20:35 +0000
Subject: [PATCH 3/3] fix: only read CONDA_SHELL if previous path failed

---
 Setup/setup | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/Setup/setup b/Setup/setup
index d69a3ce..28a6982 100755
--- a/Setup/setup
+++ b/Setup/setup
@@ -43,9 +43,8 @@ fi
 CONDA_SHELL="${CONDA_EXE%/bin/conda}/etc/profile.d/conda.sh"
 source "${CONDA_SHELL}" || { echo "Could not find conda shell at:
 ${CONDA_SHELL}. Please provide the path to this file
-(.../conda/etc/profile.d/conda.sh"; }
+(.../conda/etc/profile.d/conda.sh"; read -r CONDA_SHELL; }
 
-read -r CONDA_SHELL
 source "${CONDA_SHELL}" || { echo "Could not find conda shell at:
 ${CONDA_SHELL}"; exit 1; }