From dd64d40591b0418a51e99f27667dbbbeb45b5f2d Mon Sep 17 00:00:00 2001
From: Daniel Nachun <daniel.nachun@gmail.com>
Date: Mon, 31 Aug 2026 16:35:35 -0700
Subject: [PATCH 1/9] try to fix Linux setup

---
 pixi-setup.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pixi-setup.sh b/pixi-setup.sh
index 58f2b4c..f0de2c7 100755
--- a/pixi-setup.sh
+++ b/pixi-setup.sh
@@ -149,13 +149,13 @@ else
 
     install_global_packages <(extract_section "${_full_file}" "global")
 
-    if [[ "$OSTYPE" == "linux-gnu"* ]]; then
+    if [[ "$OSTYPE" =~ .*linux.* ]]; then
         safe_expose_remove util-linux kill
     fi
 
     install_global_packages <(echo "coreutils")
 
-    if [[ "$OSTYPE" == "linux-gnu"* ]]; then
+    if [[ "$OSTYPE" =~ .*linux.* ]]; then
         safe_expose_remove coreutils kill
         safe_expose_remove coreutils uptime
         install_global_packages <(extract_section "${_full_file}" "global_linux")
@@ -182,7 +182,7 @@ fi
 BB='\033[1;34m'
 RED='\033[1;31m'
 NC='\033[0m'
-if [[ "$OSTYPE" == "darwin"* ]]; then
+if [[ "$OSTYPE" == .*darwin.* ]]; then
     _shell_config="${HOME}/.zshrc"
 else
     _shell_config="${HOME}/.bashrc"

From 28e3512f0d405d38de0136668e5e91da0ea079b2 Mon Sep 17 00:00:00 2001
From: Daniel Nachun <daniel.nachun@gmail.com>
Date: Mon, 31 Aug 2026 16:39:27 -0700
Subject: [PATCH 2/9] try to fix Linux setup

---
 pixi-setup.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/pixi-setup.sh b/pixi-setup.sh
index f0de2c7..2a09b92 100755
--- a/pixi-setup.sh
+++ b/pixi-setup.sh
@@ -150,12 +150,14 @@ else
     install_global_packages <(extract_section "${_full_file}" "global")
 
     if [[ "$OSTYPE" =~ .*linux.* ]]; then
+        echo "Reached first removal"
         safe_expose_remove util-linux kill
     fi
 
     install_global_packages <(echo "coreutils")
 
     if [[ "$OSTYPE" =~ .*linux.* ]]; then
+        echo "Reached second removal"
         safe_expose_remove coreutils kill
         safe_expose_remove coreutils uptime
         install_global_packages <(extract_section "${_full_file}" "global_linux")

From 20421f9bc38979c8023ab765bc8df1e31c5cec2d Mon Sep 17 00:00:00 2001
From: Daniel Nachun <daniel.nachun@gmail.com>
Date: Mon, 31 Aug 2026 16:56:26 -0700
Subject: [PATCH 3/9] try to fix Linux setup

---
 pixi-setup.sh | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/pixi-setup.sh b/pixi-setup.sh
index 2a09b92..b2bb0cc 100755
--- a/pixi-setup.sh
+++ b/pixi-setup.sh
@@ -6,6 +6,7 @@ safe_expose_remove() {
     environment=$1
     executable=$2
     if [ -d ${PIXI_HOME}/envs/${environment} ]; then
+        echo "Reached removal"
         exposed_exes=$(pixi global list --environment ${environment} | tail -n 3 | head -n 1 | tr ',' '\n')
         if [[ " ${exposed_exes[*]} " =~ [[:space:]]${executable}[[:space:]] ]]; then
             pixi global expose remove ${executable}
@@ -150,14 +151,12 @@ else
     install_global_packages <(extract_section "${_full_file}" "global")
 
     if [[ "$OSTYPE" =~ .*linux.* ]]; then
-        echo "Reached first removal"
         safe_expose_remove util-linux kill
     fi
 
     install_global_packages <(echo "coreutils")
 
     if [[ "$OSTYPE" =~ .*linux.* ]]; then
-        echo "Reached second removal"
         safe_expose_remove coreutils kill
         safe_expose_remove coreutils uptime
         install_global_packages <(extract_section "${_full_file}" "global_linux")

From b73e941c96699915b38a6761a31031bc407dfade Mon Sep 17 00:00:00 2001
From: Daniel Nachun <daniel.nachun@gmail.com>
Date: Mon, 31 Aug 2026 17:10:07 -0700
Subject: [PATCH 4/9] try to fix Linux setup

---
 pixi-setup.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pixi-setup.sh b/pixi-setup.sh
index b2bb0cc..11ea39c 100755
--- a/pixi-setup.sh
+++ b/pixi-setup.sh
@@ -6,9 +6,9 @@ safe_expose_remove() {
     environment=$1
     executable=$2
     if [ -d ${PIXI_HOME}/envs/${environment} ]; then
-        echo "Reached removal"
         exposed_exes=$(pixi global list --environment ${environment} | tail -n 3 | head -n 1 | tr ',' '\n')
         if [[ " ${exposed_exes[*]} " =~ [[:space:]]${executable}[[:space:]] ]]; then
+            echo "Reached removal"
             pixi global expose remove ${executable}
         fi
     fi

From 547183ffbae47e2538c77ec073c415e019a89440 Mon Sep 17 00:00:00 2001
From: Daniel Nachun <daniel.nachun@gmail.com>
Date: Mon, 31 Aug 2026 17:46:43 -0700
Subject: [PATCH 5/9] try to fix Linux setup

---
 pixi-setup.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pixi-setup.sh b/pixi-setup.sh
index 11ea39c..569bfae 100755
--- a/pixi-setup.sh
+++ b/pixi-setup.sh
@@ -6,7 +6,7 @@ safe_expose_remove() {
     environment=$1
     executable=$2
     if [ -d ${PIXI_HOME}/envs/${environment} ]; then
-        exposed_exes=$(pixi global list --environment ${environment} | tail -n 3 | head -n 1 | tr ',' '\n')
+        exposed_exes=$(pixi global --json --environment coreutils | jq '.[].exposed.[].exposed_name' | tr -d '"')
         if [[ " ${exposed_exes[*]} " =~ [[:space:]]${executable}[[:space:]] ]]; then
             echo "Reached removal"
             pixi global expose remove ${executable}

From 2b6e76a385cee71950673073c7a84fc4072b0599 Mon Sep 17 00:00:00 2001
From: Daniel Nachun <daniel.nachun@gmail.com>
Date: Mon, 31 Aug 2026 17:49:42 -0700
Subject: [PATCH 6/9] try to fix Linux setup

---
 pixi-setup.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pixi-setup.sh b/pixi-setup.sh
index 569bfae..9137edc 100755
--- a/pixi-setup.sh
+++ b/pixi-setup.sh
@@ -6,7 +6,7 @@ safe_expose_remove() {
     environment=$1
     executable=$2
     if [ -d ${PIXI_HOME}/envs/${environment} ]; then
-        exposed_exes=$(pixi global --json --environment coreutils | jq '.[].exposed.[].exposed_name' | tr -d '"')
+        exposed_exes=$(pixi global list --json --environment coreutils | jq '.[].exposed.[].exposed_name' | tr -d '"')
         if [[ " ${exposed_exes[*]} " =~ [[:space:]]${executable}[[:space:]] ]]; then
             echo "Reached removal"
             pixi global expose remove ${executable}

From 0b618aa4584b163c18aec5d9755c6af50c558ad4 Mon Sep 17 00:00:00 2001
From: Daniel Nachun <daniel.nachun@gmail.com>
Date: Tue, 1 Sep 2026 01:28:36 -0700
Subject: [PATCH 7/9] try to fix Linux setup

---
 pixi-setup.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pixi-setup.sh b/pixi-setup.sh
index 9137edc..8158a46 100755
--- a/pixi-setup.sh
+++ b/pixi-setup.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-set -o nounset -o errexit -o pipefail
+set -o nounset -o errexit -o pipefail -o xtrace
 
 safe_expose_remove() {
     environment=$1
@@ -45,7 +45,7 @@ inject_packages() {
     if [ ! -d ${PIXI_HOME}/envs/${environment} ]; then
         missing_pkgs=$(cat ${package_list})
     else
-        missing_pkgs=$(comm -13 <(pixi global list --environment ${environment} | cut -f 1 -d ' ' | head -n -6 | tail -n +3 | sort -u) <(sort -u ${package_list}))
+        missing_pkgs=$(comm -13 <(pixi global list --json --environment r-base | jq '.[].dependencies.[].name' | tr -d '"') <(sort -u ${package_list}))
     fi
 
     if (( $(echo ${missing_pkgs} | wc -w) > 0 )); then

From 016c222b916a7c40af717d5139cc1d7276fb63ae Mon Sep 17 00:00:00 2001
From: Daniel Nachun <daniel.nachun@gmail.com>
Date: Tue, 1 Sep 2026 01:41:13 -0700
Subject: [PATCH 8/9] try to fix Linux setup

---
 pixi-setup.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pixi-setup.sh b/pixi-setup.sh
index 8158a46..7d7bf8a 100755
--- a/pixi-setup.sh
+++ b/pixi-setup.sh
@@ -1,12 +1,12 @@
 #!/usr/bin/env bash
 
-set -o nounset -o errexit -o pipefail -o xtrace
+set -o nounset -o errexit -o pipefail
 
 safe_expose_remove() {
     environment=$1
     executable=$2
     if [ -d ${PIXI_HOME}/envs/${environment} ]; then
-        exposed_exes=$(pixi global list --json --environment coreutils | jq '.[].exposed.[].exposed_name' | tr -d '"')
+        exposed_exes=$(pixi global list --json --environment ${environment} | jq '.[].exposed.[].exposed_name' | tr -d '"')
         if [[ " ${exposed_exes[*]} " =~ [[:space:]]${executable}[[:space:]] ]]; then
             echo "Reached removal"
             pixi global expose remove ${executable}
@@ -45,7 +45,7 @@ inject_packages() {
     if [ ! -d ${PIXI_HOME}/envs/${environment} ]; then
         missing_pkgs=$(cat ${package_list})
     else
-        missing_pkgs=$(comm -13 <(pixi global list --json --environment r-base | jq '.[].dependencies.[].name' | tr -d '"') <(sort -u ${package_list}))
+        missing_pkgs=$(comm -13 <(pixi global list --json --environment ${environment} | jq '.[].dependencies.[].name' | tr -d '"') <(sort -u ${package_list}))
     fi
 
     if (( $(echo ${missing_pkgs} | wc -w) > 0 )); then

From 133a6d3989cc2cdce32e70d543dc364e66551f3e Mon Sep 17 00:00:00 2001
From: Daniel Nachun <daniel.nachun@gmail.com>
Date: Tue, 1 Sep 2026 01:54:18 -0700
Subject: [PATCH 9/9] cleanup

---
 pixi-setup.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pixi-setup.sh b/pixi-setup.sh
index 7d7bf8a..ed2492e 100755
--- a/pixi-setup.sh
+++ b/pixi-setup.sh
@@ -8,7 +8,6 @@ safe_expose_remove() {
     if [ -d ${PIXI_HOME}/envs/${environment} ]; then
         exposed_exes=$(pixi global list --json --environment ${environment} | jq '.[].exposed.[].exposed_name' | tr -d '"')
         if [[ " ${exposed_exes[*]} " =~ [[:space:]]${executable}[[:space:]] ]]; then
-            echo "Reached removal"
             pixi global expose remove ${executable}
         fi
     fi