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Update Readme and fix the import path of Banksy_py submodules #8

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Update Readme and fix the import path of Banksy_py submodules #8

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5455501
fix the import path of Banksy_py submodules
B0nn1eLa1 Jun 17, 2026
30f388e
Fix typo in README for cloning instructions
B0nn1eLa1 Jun 17, 2026
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11 changes: 8 additions & 3 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ https://doi.org/10.5281/zenodo.11120922
To download:

```
cd ~/xenium_benchmark
cd ~/benchmark-spatial-transcriptomics
bash download_data.sh
```

Expand All @@ -26,7 +26,7 @@ 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
Expand All @@ -36,6 +36,11 @@ cd benchmark-spatial-transcriptomics
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/
Expand All @@ -48,7 +53,7 @@ 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
```
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11 changes: 6 additions & 5 deletions run_xenium_benchmark.py
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Expand Up @@ -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
Expand All @@ -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 *
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