other location to adjust for gtdb cert failure (in my currently grossly redundant code)

Author: Mike Lee

bin/gtt-check-or-setup-GTDB-files

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 """
-This is a helper program of GToTree (https://github.com/AstrobioMike/GToTree/wiki) 
+This is a helper program of GToTree (https://github.com/AstrobioMike/GToTree/wiki)
 for setting up reference files for the glorious Genome Taxonomy Database (gtdb.ecogenomic.org/).
 
 For examples, please visit the GToTree wiki here: https://github.com/AstrobioMike/GToTree/wiki/example-usage
@@ -13,6 +13,12 @@ import urllib.request
 import pandas as pd
 import textwrap
 import argparse
+import ssl
+###########
+# temp fix for certificate failure: https://github.com/AstrobioMike/GToTree/issues/107
+ssl._create_default_https_context = ssl._create_unverified_context
+###########
+
 
 parser = argparse.ArgumentParser(description="This is a helper program to facilitate setting up the reference files for the \
                                               glorious Genome Taxonomy Database (gtdb.ecogenomic.org). It's really meant for internal \
@@ -50,7 +56,7 @@ def color_text(text, color='green'):
 
 
 def wprint(text):
-    print(textwrap.fill(text, width=80, initial_indent="  ", 
+    print(textwrap.fill(text, width=80, initial_indent="  ",
           subsequent_indent="  ", break_on_hyphens=False))
 
 
@@ -155,7 +161,7 @@ def check_and_or_get_gtdb_files(GTDB_dir):
     else:
         wprint(color_text("Downloading and parsing archaeal and bacterial metadata tables from GTDB (only needs to be done once)...", "yellow"))
         print("")
-        
+
         gen_gtdb_tab(GTDB_dir)