From 634ebf832fbff1a0ef0527020772e2d65042d161 Mon Sep 17 00:00:00 2001
From: Marius1311 <marius.lange@bsse.ethz.ch>
Date: Mon, 19 Oct 2026 17:12:22 +0200
Subject: [PATCH] Name the Jupyter kernel after its pixi environment

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---
 {{cookiecutter.project_name}}/README.md                       | 2 +-
 .../analysis/ML-2026-01-27_demo_scRNA_workflow.ipynb          | 4 ++--
 {{cookiecutter.project_name}}/pixi.toml                       | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/{{cookiecutter.project_name}}/README.md b/{{cookiecutter.project_name}}/README.md
index 42af25f..f3e62f9 100644
--- a/{{cookiecutter.project_name}}/README.md
+++ b/{{cookiecutter.project_name}}/README.md
@@ -69,7 +69,7 @@ pixi run test                  # should pass (tests your package imports correct
 pixi run lab                   # opens Jupyter Lab
 ```
 
-In Jupyter Lab, check that your kernel appears (look for `{{ cookiecutter.project_name }} (pixi)`).
+In Jupyter Lab, check that your kernel appears (look for `{{ cookiecutter.project_name }} (pixi, default)`).
 
 🎉 **You're ready to start analyzing!**
 
diff --git a/{{cookiecutter.project_name}}/analysis/ML-2026-01-27_demo_scRNA_workflow.ipynb b/{{cookiecutter.project_name}}/analysis/ML-2026-01-27_demo_scRNA_workflow.ipynb
index b7e5af6..59d10dc 100644
--- a/{{cookiecutter.project_name}}/analysis/ML-2026-01-27_demo_scRNA_workflow.ipynb
+++ b/{{cookiecutter.project_name}}/analysis/ML-2026-01-27_demo_scRNA_workflow.ipynb
@@ -555,9 +555,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "{{ cookiecutter.project_name }} (pixi)",
+   "display_name": "{{ cookiecutter.project_name }} (pixi, default)",
    "language": "python",
-   "name": "{{ cookiecutter.project_name }}"
+   "name": "{{ cookiecutter.project_name }}-default"
   },
   "language_info": {
    "codemirror_mode": {
diff --git a/{{cookiecutter.project_name}}/pixi.toml b/{{cookiecutter.project_name}}/pixi.toml
index 9409b25..a8d27ba 100644
--- a/{{cookiecutter.project_name}}/pixi.toml
+++ b/{{cookiecutter.project_name}}/pixi.toml
@@ -9,7 +9,7 @@ platforms = ["osx-arm64", "linux-64"]
 [tasks]
 lab = "jupyter lab"
 test = "pytest"
-install-kernel = "python -m ipykernel install --user --name={{ cookiecutter.project_name }} --display-name='{{ cookiecutter.project_name }} (pixi)'"
+install-kernel = 'python -m ipykernel install --user --name={{ cookiecutter.project_name }}-$PIXI_ENVIRONMENT_NAME --display-name="{{ cookiecutter.project_name }} (pixi, $PIXI_ENVIRONMENT_NAME)"'
 install-hooks = { cmd = "pre-commit install --install-hooks", description = "Install pre-commit hooks (run once per clone)" }
 
 [dependencies]