From 1ed54d69796a874a623dc689fe801ea7c1752e63 Mon Sep 17 00:00:00 2001
From: Daniel Weilandt <daniel.weilandt@princeton.edu>
Date: Tue, 10 May 2022 21:14:13 -0400
Subject: [PATCH] MTN: Fixup dependencies + version tag

---
 README.rst              | 9 +++++++--
 docker/requirements.txt | 2 +-
 setup.py                | 4 ++--
 3 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/README.rst b/README.rst
index cbb5950..4109f72 100644
--- a/README.rst
+++ b/README.rst
@@ -110,18 +110,23 @@ This module was developed in Python 3.9, and it is recommended to run Python 3.9
 The module also was tested in Python 3.8.
 
 Further the following pip-python packages are required
-    - sympy >= 1.1.
+    - sympy >=1.1 <=1.5
     - pytest
     - scipy
     - numpy
     - bokeh
     - pandas
     - Cython
-    - scikits.odes
+    - markupsafe <=2.0.1
+    - bokeh >=0.12.0
+    - scikits.odes ==2.6.3
     - deap
     - dill
     - h5py
     - escher
+    - pytfa
+    - cobra <=0.24.0
+
 
 The installation requires additionaly the following libraries:
   - gcc
diff --git a/docker/requirements.txt b/docker/requirements.txt
index 473f638..489012f 100644
--- a/docker/requirements.txt
+++ b/docker/requirements.txt
@@ -23,7 +23,7 @@ dill
 h5py
 # extras ORACLE:
 pytfa
-cobra <= 0.24.0
+cobra <=0.24.0
 escher==1.7.0
 # Additional things that are useful in RabLab
 python-libsbml
diff --git a/setup.py b/setup.py
index 1933242..dd14ea5 100644
--- a/setup.py
+++ b/setup.py
@@ -31,8 +31,8 @@
     os.path.join(d, "flint") for d in default_include_dirs
 ]
 
-# Current version 0.9,1-beta
-version_tag = '0.9.1-beta'
+# Current version 1.0.1
+version_tag = '1.0.1'
 
 
 extensions = [