# HG changeset patch
# User francesco_lapi
# Date 1747755219 0
# Node ID d905439271faf6ac499d234c7d9a6f24d721512f
# Parent  81497dd6e4a0b3a2df1b4566718be452d4d01dc3
Uploaded

diff -r 81497dd6e4a0 -r d905439271fa COBRAxy/.gitignore
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COBRAxy/.gitignore	Tue May 20 15:33:39 2025 +0000
@@ -0,0 +1,6 @@
+__pycache__/
+cobraxy.egg-info/
+.venv/
+.vscode/
+outputs/
+build/
\ No newline at end of file
diff -r 81497dd6e4a0 -r d905439271fa COBRAxy/flux_simulation.xml
--- a/COBRAxy/flux_simulation.xml	Tue May 20 15:06:09 2025 +0000
+++ b/COBRAxy/flux_simulation.xml	Tue May 20 15:33:39 2025 +0000
@@ -10,7 +10,7 @@
 		<requirement type="package" version="0.29.0">cobra</requirement>
         <requirement type="package" version="5.2.2">lxml</requirement>
         <requirement type="package" version="1.4.2">joblib</requirement>
-        <requirement type="package" version="1.10.1">scipy</requirement>
+        <requirement type="package" version="1.11">scipy</requirement>
 	</requirements>
 
     <command detect_errors="exit_code">
diff -r 81497dd6e4a0 -r d905439271fa COBRAxy/flux_to_map.xml
--- a/COBRAxy/flux_to_map.xml	Tue May 20 15:06:09 2025 +0000
+++ b/COBRAxy/flux_to_map.xml	Tue May 20 15:33:39 2025 +0000
@@ -7,7 +7,7 @@
 		<requirement type="package" version="1.24.4">numpy</requirement>
         <requirement type="package" version="2.0.3">pandas</requirement>
 		<requirement type="package" version="0.13.0">seaborn</requirement>
-        <requirement type="package" version="1.10.1">scipy</requirement>
+        <requirement type="package" version="1.11">scipy</requirement>
 		<requirement type="package" version="1.5.1">svglib</requirement>
 		<requirement type="package" version="2.2.3">pyvips</requirement>
 		<requirement type="package" version="2.7.1">cairosvg</requirement>
diff -r 81497dd6e4a0 -r d905439271fa COBRAxy/marea.xml
--- a/COBRAxy/marea.xml	Tue May 20 15:06:09 2025 +0000
+++ b/COBRAxy/marea.xml	Tue May 20 15:33:39 2025 +0000
@@ -7,11 +7,14 @@
 		<requirement type="package" version="1.24.4">numpy</requirement>
         <requirement type="package" version="2.0.3">pandas</requirement>
         <requirement type="package" version="5.2.2">lxml</requirement>
-        <requirement type="package" version="1.10.1">scipy</requirement>
+        <requirement type="package" version="1.11">scipy</requirement>
 		<requirement type="package" version="1.5.1">svglib</requirement>
 		<requirement type="package" version="2.2.3">pyvips</requirement>
 		<requirement type="package" version="2.7.1">cairosvg</requirement>
 		<requirement type="package" version="0.29.0">cobra</requirement>
+		<requirement type="package" version="0.8.0">anndata</requirement>
+		<requirement type="package" version="1.11">scipy</requirement>
+		<requirement type="package" version="1.3.2">scikit-learn</requirement>
 		<requirement type="package" version="0.5.1">pydeseq2</requirement>
 	</requirements>
 	
diff -r 81497dd6e4a0 -r d905439271fa COBRAxy/marea_cluster.xml
--- a/COBRAxy/marea_cluster.xml	Tue May 20 15:06:09 2025 +0000
+++ b/COBRAxy/marea_cluster.xml	Tue May 20 15:33:39 2025 +0000
@@ -6,7 +6,7 @@
     <requirements>
 		<requirement type="package" version="1.24.4">numpy</requirement>
         <requirement type="package" version="2.0.3">pandas</requirement>
-		<requirement type="package" version="1.10.1">scipy</requirement>
+		<requirement type="package" version="1.11">scipy</requirement>
         <requirement type="package" version="1.3.2">scikit-learn</requirement>
         <requirement type="package" version="3.7.3">matplotlib</requirement>
 		<requirement type="package" version="5.2.2">lxml</requirement>