From fc7072823c2a03a03ac9c48190ff8cc1c9fe4f72 Mon Sep 17 00:00:00 2001
From: pierremillard <millard@insa-toulouse.fr>
Date: Thu, 2 Nov 2023 12:36:40 +0100
Subject: [PATCH] remove distutils for py312

---
 README.md             | 6 +++---
 doc/index.rst         | 2 +-
 isocor/__init__.py    | 2 +-
 isocor/ui/isocordb.py | 3 +--
 setup.cfg             | 4 ++++
 5 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index 9cd8442..566d4e8 100644
--- a/README.md
+++ b/README.md
@@ -19,7 +19,7 @@ The output of IsoCor is the isotopologue distribution of the molecule
 of isotopic substitutions of the tracer). IsoCor also calculates
 the mean enrichment (i.e. the mean isotopic content in the molecule) in metabolites.
 
-It is one of the routine tools that we use at the [MetaSys team](http://www.lisbp.fr/en/research/molecular-physiology-and-metabolism/metasys.html) and [MetaToul platform](http://www.metatoul.fr) in isotopic studies of metabolic systems.
+It is one of the routine tools that we use at the [MetaSys team](https://www.toulouse-biotechnology-institute.fr/en/poles/equipe-metasys/) and [MetaToul platform](https://www.metabohub.fr/home.html) in isotopic studies of metabolic systems.
 
 The code is open-source, and available under a GPLv3 license. Additional information can be found in [IsoCor publication](https://doi.org/10.1093/bioinformatics/btz209).
 
@@ -34,12 +34,12 @@ Check out the [Tutorials](https://isocor.readthedocs.io/en/latest/tutorials.html
 * can be applied to singly- and multiply-charged ions
 * can be used with any tracer element (having two or more isotopes)
 * account for the contribution of derivatization steps (if any),
-* generate isotopic InChIs of the tracer isotopologues,
+* generate isotopic InChIs of tracer isotopologues,
 * open-source, free and easy to install everywhere where Python 3 and pip run,
 * biologist-friendly.
 
 ## Quick-start
-IsoCor requires Python 3.5 or higher and run on all plate-forms.
+IsoCor requires Python 3.6 or higher and run on all platforms.
 Please check [the documentation](https://isocor.readthedocs.io/en/latest/quickstart.html) for complete
 installation and usage instructions.
 
diff --git a/doc/index.rst b/doc/index.rst
index 13e39ee..10eb4ab 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -18,7 +18,7 @@ The output of IsoCor is the :ref:`isotopologue distribution <isotopologue distri
 of isotopic substitutions of the tracer) of the molecule. IsoCor also calculates
 the mean enrichment (i.e. the mean isotopic content in the molecule) in metabolites.
 
-It is one of the routine tools that we use at the `MetaSys team <http://www.toulouse-biotechnology-institute.fr/en/research/molecular-physiology-and-metabolism/metasys.html>`_ and `MetaToul platform <http://www.metatoul.fr>`_ in isotopic studies of metabolic systems.
+It is one of the routine tools that we use at the `MetaSys team <https://www.toulouse-biotechnology-institute.fr/en/poles/equipe-metasys/>`_ and `MetaToul platform <https://www.metabohub.fr/home.html>`_ in isotopic studies of metabolic systems.
 
 The code is open-source, and available on `GitHub <https://github.com/MetaSys-LISBP/IsoCor/>`_ under a :ref:`GPLv3 license <license>`.
 
diff --git a/isocor/__init__.py b/isocor/__init__.py
index 6cad3f2..11afbb1 100644
--- a/isocor/__init__.py
+++ b/isocor/__init__.py
@@ -5,7 +5,7 @@
 """
 
 # Version number MUST be maintained here (x.y.z format)
-__version__ = '2.2.1'
+__version__ = '2.2.2'
 
 from isocor.mscorrectors import MetaboliteCorrectorFactory
 from isocor.mscorrectors import LowResMetaboliteCorrector, HighResMetaboliteCorrector
diff --git a/isocor/ui/isocordb.py b/isocor/ui/isocordb.py
index c79a5d4..2f18ee4 100644
--- a/isocor/ui/isocordb.py
+++ b/isocor/ui/isocordb.py
@@ -3,7 +3,6 @@
 from os.path import expanduser
 import isocor as hr
 from decimal import Decimal
-from distutils.dir_util import copy_tree
 import shutil
 import numpy as np
 import pkg_resources
@@ -28,7 +27,7 @@ def initializeDB(self):
                 if not Path(self.default_db, i).is_file():
                     shutil.copy(Path(self.example_db, i), self.default_db)
         else:
-            copy_tree(str(self.example_db), str(self.default_db))
+            shutil.copytree(str(self.example_db), str(self.default_db))
 
     def initializeEnv(self):
         self.home = self.home
diff --git a/setup.cfg b/setup.cfg
index c489381..1f289f8 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -11,6 +11,10 @@ classifiers =
     Programming Language :: Python :: 3.6
     Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
     License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
     Operating System :: OS Independent
     Intended Audience :: Science/Research