From b01ffb887b0399e15a37814945016186483957d4 Mon Sep 17 00:00:00 2001
From: Sharif Haason <sharif.haason@gmail.com>
Date: Sun, 22 Mar 2026 19:57:05 -0400
Subject: [PATCH 1/2] Add minimum version constraints to all dependencies
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Empirically tested each of the 14 core dependencies by installing
progressively older versions on Python 3.10 and running the full
test suite (38 tests) to find the oldest version that passes.

Also updates ReadTheDocs build: ubuntu-20.04 (EOL) → ubuntu-22.04,
Python 3.10 → 3.12.

Closes #19

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 .readthedocs.yaml |  4 ++--
 pyproject.toml    | 32 ++++++++++++++++----------------
 2 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index bb285f7..edf50ed 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -1,9 +1,9 @@
 # https://docs.readthedocs.io/en/stable/config-file/v2.html
 version: 2
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python: "3.12"
 
 sphinx:
   configuration: docs/conf.py
diff --git a/pyproject.toml b/pyproject.toml
index 27b9cb4..8ced7a0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -30,24 +30,24 @@ classifiers = [
   "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
-  "anndata",
-  "igraph",
-  "loguru",
-  "matplotlib",
-  "mudata",
-  "numba",
-  "numpy",
-  "pandas",
-  "readfcs",
-  "scanpy",
-  "scikit-learn",
-  "scipy",
-  "seaborn",
+  "anndata>=0.10",
+  "igraph>=0.9.8",
+  "loguru>=0.5",
+  "matplotlib>=3.5",
+  "mudata>=0.3.1",
+  "numba>=0.56",
+  "numpy>=1.23",
+  "pandas>=1.4",
+  "readfcs>=1.1",
+  "scanpy>=1.9.3",
+  "scikit-learn>=1.2",
+  "scipy>=1.8",
+  "seaborn>=0.12",
   # for debug logging (referenced from the issue template)
-  "session-info2",
+  "session-info2>=0.1",
 ]
 
-optional-dependencies.dev = [ "pre-commit", "twine>=4.0.2" ]
+optional-dependencies.dev = [ "pre-commit>=3.0", "twine>=4.0.2" ]
 optional-dependencies.doc = [
   "docutils>=0.8,!=0.18.*,!=0.19.*",
   # For notebooks
@@ -67,7 +67,7 @@ optional-dependencies.doc = [
   "sphinxcontrib-bibtex>=1",
   "sphinxext-opengraph",
 ]
-optional-dependencies.test = [ "coverage", "pyflowsom>=0.1.5", "pytest" ]
+optional-dependencies.test = [ "coverage>=7.0", "pyflowsom>=0.1.5", "pytest>=7.0" ]
 urls.Documentation = "https://flowsom.readthedocs.io/en/latest/"
 urls.Home-page = "https://github.com/saeyslab/FlowSOM_Python"
 urls.Source = "https://github.com/saeyslab/FlowSOM_Python"

From 623317e5b67b0e38a7e92f66c57b73efb96db0f6 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sun, 22 Mar 2026 23:57:42 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 8ced7a0..101abf4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -47,7 +47,7 @@ dependencies = [
   "session-info2>=0.1",
 ]
 
-optional-dependencies.dev = [ "pre-commit>=3.0", "twine>=4.0.2" ]
+optional-dependencies.dev = [ "pre-commit>=3", "twine>=4.0.2" ]
 optional-dependencies.doc = [
   "docutils>=0.8,!=0.18.*,!=0.19.*",
   # For notebooks
@@ -67,7 +67,7 @@ optional-dependencies.doc = [
   "sphinxcontrib-bibtex>=1",
   "sphinxext-opengraph",
 ]
-optional-dependencies.test = [ "coverage>=7.0", "pyflowsom>=0.1.5", "pytest>=7.0" ]
+optional-dependencies.test = [ "coverage>=7", "pyflowsom>=0.1.5", "pytest>=7" ]
 urls.Documentation = "https://flowsom.readthedocs.io/en/latest/"
 urls.Home-page = "https://github.com/saeyslab/FlowSOM_Python"
 urls.Source = "https://github.com/saeyslab/FlowSOM_Python"