From 2330fa0526bc7a4754e35033d59398fa6cc25e31 Mon Sep 17 00:00:00 2001
From: Albert Lie <alberttri23@gmail.com>
Date: Thu, 12 Nov 2026 17:38:20 -0500
Subject: [PATCH] Declare runtime dependencies in pyproject.toml

pip install ScreenPro2 installed no dependencies, so importing the
package or running the screenpro CLI failed with ModuleNotFoundError.
List every package the code imports, with the pins environment.yml
already uses (pandas<2, matplotlib<3.7) plus the ones those pins imply
(numpy<2, pydeseq2<0.5, pyarrow<26, Python <3.12).

Fixes #112
---
 pyproject.toml | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 9c47f2b..a68543d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -18,7 +18,22 @@ packages = [
 dynamic = ["version"]
 
 [tool.poetry.dependencies]
-python = ">=3.9"
+python = ">=3.9,<3.12"
+pandas = "<2.0"
+numpy = "<2.0"
+scipy = "*"
+matplotlib = "<3.7"
+bokeh = "*"
+anndata = "*"
+scanpy = "*"
+polars = ">0.20"
+pyarrow = "<26"
+biobear = "*"
+pydeseq2 = "<0.5"
+statsmodels = "*"
+scikit-learn = "*"
+simple_colors = "*"
+adjustText = "*"
 
 [tool.poetry.scripts]
 screenpro = "screenpro.main:main"