Update python version used

environment.yml

@@ -1,12 +1,12 @@
-name: gubbins_env
+name: test_gubbins_env
 channels:
   - conda-forge
   - bioconda
   - defaults
   - 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

python/gubbins/PreProcessFasta.py

@@ -1,3 +1,6 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
 import sys
 import hashlib
 from Bio import AlignIO

python/gubbins/ValidateFastaAlignment.py

@@ -1,3 +1,6 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
 import os
 import re
 import sys

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

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
 # 

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.

python/gubbins/run_gubbins.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/env python
 # encoding: utf-8
 #
 # Wellcome Trust Sanger Institute

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
 #

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
 #