From 12320fb63d8d16f9800c505345c6e3f30798455f Mon Sep 17 00:00:00 2001
From: Leonardo Schwarz <leonardo.schwarz@fgcz.ethz.ch>
Date: Wed, 23 Oct 2024 11:57:20 +0200
Subject: [PATCH] fix installation problems

---
 .gitignore     | 1 +
 README.md      | 6 ++++--
 pyproject.toml | 4 ++--
 3 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/.gitignore b/.gitignore
index b1781c9..d1db0e3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,6 +9,7 @@
 .task
 .venv
 .vscode
+.python-version
 dist
 __pycache__
 
diff --git a/README.md b/README.md
index 4517d51..c80ea32 100644
--- a/README.md
+++ b/README.md
@@ -13,6 +13,8 @@ This project is in an early state of development. If you are interested, it's be
 
 ## Setup dev environment
 
+Currently, Python 3.12 is required, 3.13 is not compatible yet (missing wheels and e.g. llvmlite).
+
 ### Using `uv` (recommended)
 
 Install the `pyproject.toml` in editable mode, tested with
@@ -20,7 +22,7 @@ Install the `pyproject.toml` in editable mode, tested with
 
 ```bash
 uv venv
-uv pip install -e ".[dev,testing]"
+uv pip install -e ".[dev]"
 ```
 
 ### Using `conda`
@@ -28,7 +30,7 @@ uv pip install -e ".[dev,testing]"
 ```bash
 conda create -n exp-2024-05-depiction python=3.11
 conda activate exp-2024-05-depiction
-pip install -e ".[dev,testing]"
+pip install -e ".[dev]"
 ```
 
 ## Geometry Conventions
diff --git a/pyproject.toml b/pyproject.toml
index bad62cf..99726b4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,7 +7,6 @@ readme = "README.md"
 license = { text = "Apache-2.0" }
 
 dependencies = [
-    "setuptools",
     "alphapept>=0.5.2",
     # TODO investigate
     "altair<5.4.0",
@@ -62,6 +61,7 @@ testing = [
     "pytest-mock"
 ]
 dev = [
+    "depiction[testing]",
     "bokeh>=3.3.2",
     "hvplot>=0.9.0",
     "jupyterlab>=4.0.9",
@@ -73,7 +73,7 @@ dev = [
     "licensecheck",
     "hdbscan",
     "nox[uv]",
-    "spatialdata",
+    "spatialdata>=0.2.3",
     "spatialdata-plot>=0.2.1",
     "types-tqdm",
     "rpy2",