From 54555013d2a84c0b4e2f7b5c394c191e5e08b710 Mon Sep 17 00:00:00 2001
From: B0nn1eLa1 <b09b02011@ntu.edu.tw>
Date: Wed, 17 Jun 2026 14:53:27 +0000
Subject: [PATCH 1/2] fix the import path of Banksy_py submodules

---
 README.md               | 12 ++++++++++--
 run_xenium_benchmark.py | 11 ++++++-----
 2 files changed, 16 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index 1ca9013..69d9acb 100644
--- a/README.md
+++ b/README.md
@@ -17,7 +17,7 @@ https://doi.org/10.5281/zenodo.11120922
 To download:
 
 ```
-cd ~/xenium_benchmark
+cd ~/benchmark-spatial-transcriptomics
 bash download_data.sh
 ```
 
@@ -31,11 +31,19 @@ Clone this repository along with the origianl Xenium benchmarking pipeline:
 ```
 git clone --recurse-submodules https://github.com/CBDatCMU/benchmark-spatial-transcriptomics.git
 cd benchmark-spatial-transcriptomics
+
+# Update the submodule
+git submodule update --init --recursive
 ```
 
 Install the conda environment:
  
 ```
+# Make sure that the current shell session is able to use conda
+# This must be run once per login session.
+source ~/miniconda3/etc/profile.d/conda.sh
+
+# create and activate the conda environment
 conda env create --file Xenium_benchmarking/xenium_benchmarking.yml --prefix ./envs/xb
 conda activate ./envs/xb
 pip install -e Xenium_benchmarking/
@@ -48,7 +56,7 @@ pip install -e Xenium_benchmarking/
 sbatch submit_xenium.sh
 
 # Run directly
-cd ~/xenium_benchmark
+cd ~/benchmark-spatial-transcriptomics
 conda activate ~/xenium_benchmark/envs/xb
 python run_xenium_benchmark.py
 ```
diff --git a/run_xenium_benchmark.py b/run_xenium_benchmark.py
index 243aee2..ff9f710 100644
--- a/run_xenium_benchmark.py
+++ b/run_xenium_benchmark.py
@@ -2,6 +2,12 @@
 
 import os
 import sys
+
+# ── Banksy submodule path ──────────────────────────────────────────────────────
+_repo = os.path.dirname(os.path.abspath(__file__))
+sys.path.insert(0, os.path.join(_repo, 'Xenium_benchmarking'))
+sys.path.insert(0, os.path.join(_repo, 'Xenium_benchmarking', 'Banksy_py'))
+
 import time
 import logging
 import numpy as np
@@ -13,11 +19,6 @@
 import matplotlib.pyplot as plt
 import squidpy as sq
 
-# ── Banksy submodule path ──────────────────────────────────────────────────────
-banksy_path = os.path.join(os.path.expanduser('~'), 'xenium_benchmark', 'Xenium_benchmarking', 'Banksy_py')
-if banksy_path not in sys.path:
-    sys.path.insert(0, banksy_path)
-
 # ── xb package imports ─────────────────────────────────────────────────────────
 from xb.formatting import *
 from xb.plotting import *

From 30f388ec95d4c9c49b2e1b7b8f257db85a571798 Mon Sep 17 00:00:00 2001
From: B0nn1eLa1 <163808399+B0nn1eLa1@users.noreply.github.com>
Date: Wed, 17 Jun 2026 15:28:09 -0400
Subject: [PATCH 2/2] Fix typo in README for cloning instructions

---
 README.md | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 69d9acb..6137b91 100644
--- a/README.md
+++ b/README.md
@@ -26,14 +26,11 @@ This will place the data at `data/example_spinal_chord_inactive/`. If that folde
 If automatic download fails, download `example_spinal_chord_inactive.zip` manually from the link above and extract it into `data/`.
 
 ## Setup
-Clone this repository along with the origianl Xenium benchmarking pipeline:
+Clone this repository along with the original Xenium benchmarking pipeline:
  
 ```
 git clone --recurse-submodules https://github.com/CBDatCMU/benchmark-spatial-transcriptomics.git
 cd benchmark-spatial-transcriptomics
-
-# Update the submodule
-git submodule update --init --recursive
 ```
 
 Install the conda environment: