From a76540883b998fd8bb67d35c84909bf378d19082 Mon Sep 17 00:00:00 2001
From: schereme <schereme@mpi-cbg.de>
Date: Mon, 18 May 2026 15:12:21 +0200
Subject: [PATCH 1/2] Fixed dependencies and Python version requirements in
 pyproject.toml, README.md, and requirements.txt

---
 README.md        | 12 ++++++++++--
 pyproject.toml   | 13 +++++++------
 requirements.txt |  4 +---
 3 files changed, 18 insertions(+), 11 deletions(-)

diff --git a/README.md b/README.md
index c7f0ac9..bb470f2 100644
--- a/README.md
+++ b/README.md
@@ -26,6 +26,9 @@ MobiDB-lite is also available as Docker container [MobiDB-lite_docker](https://g
 
 
 ## Installation
+
+Supported Python versions: >=3.11,<3.15
+
 You can use the tool simply cloning this repo and running `__main__.py` Python script. 
 which implements a command line interface.
 To avoid import errors you need to add the source root folder 
@@ -41,10 +44,15 @@ From GitHub:
     git clone https://github.com/BioComputingUP/MobiDB-lite.git
     pip install .
 
-To install the dependencies:  
+### How to install MobiDB-lite using Conda?
 
-    pip install -r requirements.txt
+You can create a Conda environment and install MobiDB-lite using the following commands:
 
+```bash
+conda create -n mobidb_lite python=3.12
+conda activate mobidb_lite
+pip install .
+```
 
 ## Usage
 
diff --git a/pyproject.toml b/pyproject.toml
index c079f94..50160ba 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,15 +13,16 @@ authors = [
   {name = "Damiano Piovesan", email = "damiano.piovesan@unipd.it"},
   {name = "Mahta Mehdiabadi", email = "mahta.mehdiabadi@studenti.unipd.it"}
 ]
-requires-python = ">=3.12.3"
-dependencies = []
-
-[project.optional-dependencies]
-nu = [
+requires-python = ">=3.11.3,<3.15"
+dependencies = [
+  "joblib >= 1.5.2",
+  "numba >= 0.61.2",
+  "pandas >= 2.3.2",
   "scikit-learn >= 1.4.2",
-  "numba >= 0.59.1"
 ]
 
+[project.optional-dependencies]
+
 [tool.setuptools.packages.find]
 where = ["src"]
 namespaces = false
diff --git a/requirements.txt b/requirements.txt
index 823b71f..371439d 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,6 +1,4 @@
 joblib==1.5.2
 numba==0.61.2
-numpy==2.3.2
 pandas==2.3.2
-scikit-learn==1.4.2
-setuptools==59.6.0
+scikit-learn==1.4.2
\ No newline at end of file

From faf2edc89a099d136ec2146f210898b2607a1030 Mon Sep 17 00:00:00 2001
From: schereme <schereme@mpi-cbg.de>
Date: Mon, 18 May 2026 15:28:09 +0200
Subject: [PATCH 2/2] Update installation instructions in README.md to include
 virtual environment setup

---
 README.md | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index bb470f2..a4056d9 100644
--- a/README.md
+++ b/README.md
@@ -41,8 +41,16 @@ in this case.
 
 From GitHub:
 
-    git clone https://github.com/BioComputingUP/MobiDB-lite.git
-    pip install .
+```bash
+git clone https://github.com/BioComputingUP/MobiDB-lite.git
+
+# one-off
+python3 -m venv .venv
+
+source .venv/bin/activate
+    
+pip install .
+```
 
 ### How to install MobiDB-lite using Conda?