Update branch with optimised C code

VERSION

@@ -1 +1 @@
-3.3.1
+3.3.5

environment.yml

@@ -6,7 +6,7 @@ channels:
   - r
 dependencies:
 # python
-  - python>=3.8
+  - python>=3.8,<3.11
 # installation
   - autoconf
   - automake

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
 # 
@@ -224,7 +226,7 @@ def parse_and_run(input_args, program_description=""):
     printer.print("...done. Run time: {:.2f} s".format(time.time() - start_time))
 
     # Find all SNP sites with Gubbins
-    gubbins_command = " ".join([gubbins_exec, input_args.alignment_filename])
+    gubbins_command = f"{gubbins_exec} \"{input_args.alignment_filename}\""
     printer.print(["\nRunning Gubbins to detect SNPs...", gubbins_command])
     try:
         subprocess.check_call(gubbins_command, shell=True)

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
 #