diff --git a/environment.yml b/environment.yml
index 6d961b74..61a94cc6 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,4 +1,4 @@
-name: gubbins_env
+name: test_gubbins_env
 channels:
   - conda-forge
   - bioconda
@@ -6,7 +6,7 @@ channels:
   - r
 dependencies:
 # python
-  - python>=3.8
+  - python>=3.8,<3.11
 # installation
   - autoconf
   - automake
@@ -26,8 +26,9 @@ dependencies:
   - dendropy
   - biopython
   - multiprocess
-  - numpy<=1.23.0
-  - numba
+  - llvmlite=0.41.0
+  - numpy>=1.25,<1.26
+  - numba=0.58.0
 # phylogenetics
   - raxml=8.2.12
   - iqtree>=2.2
diff --git a/python/gubbins/PreProcessFasta.py b/python/gubbins/PreProcessFasta.py
index bb91fa7e..5714cd1a 100644
--- a/python/gubbins/PreProcessFasta.py
+++ b/python/gubbins/PreProcessFasta.py
@@ -1,3 +1,6 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
 import sys
 import hashlib
 from Bio import AlignIO
diff --git a/python/gubbins/ValidateFastaAlignment.py b/python/gubbins/ValidateFastaAlignment.py
index 85d3c0a1..5be757f2 100644
--- a/python/gubbins/ValidateFastaAlignment.py
+++ b/python/gubbins/ValidateFastaAlignment.py
@@ -1,3 +1,6 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
 import os
 import re
 import sys
diff --git a/python/gubbins/__init__.py b/python/gubbins/__init__.py
index 06010447..6aed4ed7 100644
--- a/python/gubbins/__init__.py
+++ b/python/gubbins/__init__.py
@@ -1,4 +1,5 @@
-#! /usr/bin/env python3
+#!/usr/bin/env python
+# encoding: utf-8
 
 """
 Imports into the `gubbins` namespace all fundamental
diff --git a/python/gubbins/common.py b/python/gubbins/common.py
index c9e3bf39..08c6dcf5 100644
--- a/python/gubbins/common.py
+++ b/python/gubbins/common.py
@@ -1,4 +1,6 @@
+#!/usr/bin/env python
 # encoding: utf-8
+#
 # Wellcome Trust Sanger Institute
 # Copyright (C) 2013  Wellcome Trust Sanger Institute
 # 
diff --git a/python/gubbins/pyjar.py b/python/gubbins/pyjar.py
index 982889c4..2cdc15a7 100755
--- a/python/gubbins/pyjar.py
+++ b/python/gubbins/pyjar.py
@@ -1,5 +1,6 @@
-#!/usr/bin/env python3
-
+#!/usr/bin/env python
+# encoding: utf-8
+#
 # pyjar written by Simon Harris
 # code modified from https://github.com/simonrharris/pyjar
 # pyjar is free software, licensed under GPLv3.
diff --git a/python/gubbins/run_gubbins.py b/python/gubbins/run_gubbins.py
index 96e5f544..61969272 100755
--- a/python/gubbins/run_gubbins.py
+++ b/python/gubbins/run_gubbins.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/env python
 # encoding: utf-8
 #
 # Wellcome Trust Sanger Institute
diff --git a/python/gubbins/treebuilders.py b/python/gubbins/treebuilders.py
index 01546e71..5f531a53 100644
--- a/python/gubbins/treebuilders.py
+++ b/python/gubbins/treebuilders.py
@@ -1,4 +1,6 @@
+#!/usr/bin/env python
 # encoding: utf-8
+#
 # Wellcome Trust Sanger Institute
 # Copyright (C) 2013  Wellcome Trust Sanger Institute
 #
diff --git a/python/gubbins/utils.py b/python/gubbins/utils.py
index fdc4dbd3..dc19a8fe 100644
--- a/python/gubbins/utils.py
+++ b/python/gubbins/utils.py
@@ -1,4 +1,6 @@
+#!/usr/bin/env python
 # encoding: utf-8
+#
 # Wellcome Trust Sanger Institute
 # Copyright (C) 2013  Wellcome Trust Sanger Institute
 #