From 2c6706e09fbfa59ef5068af635fb7ebe5bea5159 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gwendolyn=20O=2E=20D=C3=B6bel?=
 <81755070+GwennyGit@users.noreply.github.com>
Date: Mon, 11 Nov 2024 15:07:16 +0100
Subject: [PATCH 1/2] Updated regexes to raw strings

---
 src/refinegems/utility/databases.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/refinegems/utility/databases.py b/src/refinegems/utility/databases.py
index 6d33722..8eec169 100644
--- a/src/refinegems/utility/databases.py
+++ b/src/refinegems/utility/databases.py
@@ -114,9 +114,9 @@ def is_valid_database(db_cursor: sqlite3.Cursor) -> int:
    db_cursor.execute("SELECT name FROM sqlite_master WHERE type='table';")
    tables = [string[0] for string in db_cursor.fetchall()]
    
-   bigg_tables_contained = len([s for s in tables if re.match('^bigg_(?!to)(.*?)', s, re.IGNORECASE)]) == 2
-   sbo_tables_contained = len([s for s in tables if re.match('(.*?)_sbo$', s, re.IGNORECASE)]) == 2
-   media_tables_contained = len([s for s in tables if re.match('^medium(.*?)|^substance(.*?)|^subset(.*?)', s, re.IGNORECASE)]) == 6
+   bigg_tables_contained = len([s for s in tables if re.match(r'^bigg_(?!to)(.*?)', s, re.IGNORECASE)]) == 2
+   sbo_tables_contained = len([s for s in tables if re.match(r'(.*?)_sbo$', s, re.IGNORECASE)]) == 2
+   media_tables_contained = len([s for s in tables if re.match(r'^medium(.*?)|^substance(.*?)|^subset(.*?)', s, re.IGNORECASE)]) == 6
    sbo_media_tables_contained = sbo_tables_contained and media_tables_contained  # These can only occur together
    modelseed_cmpd_tbl_contained = len([s for s in tables if s == 'modelseed_compounds']) == 1
    

From f28bba081ae3ab1350eb0a972130d65f9f860ce9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gwendolyn=20O=2E=20D=C3=B6bel?=
 <81755070+GwennyGit@users.noreply.github.com>
Date: Mon, 11 Nov 2024 15:12:07 +0100
Subject: [PATCH 2/2] Removed deprecated dsplay_version flag from conf.py

---
 docs/source/conf.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 6778a3c..ec42dc1 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -82,7 +82,6 @@
 html_logo = str(Path('images','refineGEMs_logo.png'))
 html_theme_options = {
     'logo_only': True,
-    'display_version': False,
 	'flyout_display': 'attached'
 }