diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index c3d640d..16d8c21 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -261,11 +261,14 @@ jobs:
             # test ungathered_v2 default name
             upgrade-db .github/workflows/log_ungathered_v2.sqlite
 
+            # utilize nogather flag to ensure schema is from modification
+            # instead of gathering, which builds schema v3
             runalyzer .github/workflows/log_ungathered_v2_upgrade.sqlite -c 'db.print_cursor(db.q("select * from warnings"))' --nogather
             runalyzer .github/workflows/log_ungathered_v2_upgrade.sqlite -c 'print([l[0] for l in q("select * from warnings").description])' --nogather
             runalyzer .github/workflows/log_ungathered_v2_upgrade.sqlite -c 'print([l[0] for l in q("select * from logging").description])' --nogather
             runalyzer .github/workflows/log_ungathered_v2_upgrade.sqlite -c 'assert "unixtime" in [l[0] for l in q("select * from warnings").description]' --nogather
             runalyzer .github/workflows/log_ungathered_v2_upgrade.sqlite -c 'assert "rank" in [l[0] for l in q("select * from warnings").description]' --nogather
+            runalyzer .github/workflows/log_ungathered_v2_upgrade.sqlite -c 'assert [l[0] for l in q("select schema_version")][0] == 3'
 
 
             # test gathered_v2 default name
@@ -276,6 +279,7 @@ jobs:
             runalyzer .github/workflows/log_gathered_v2_upgrade.sqlite -c 'print([l[0] for l in q("select * from logging").description])' --nogather
             runalyzer .github/workflows/log_gathered_v2_upgrade.sqlite -c 'assert "unixtime" in [l[0] for l in q("select * from warnings").description]' --nogather
             runalyzer .github/workflows/log_gathered_v2_upgrade.sqlite -c 'assert "rank" in [l[0] for l in q("select * from warnings").description]' --nogather
+            runalyzer .github/workflows/log_gathered_v2_upgrade.sqlite -c 'assert [l[0] for l in q("select schema_version")][0] == 3'
 
 
             # test gathered custom name
@@ -286,6 +290,7 @@ jobs:
             runalyzer .github/workflows/log_gathered_v2_new.sqlite -c 'print([l[0] for l in q("select * from logging").description])' --nogather
             runalyzer .github/workflows/log_gathered_v2_new.sqlite -c 'assert "unixtime" in [l[0] for l in q("select * from warnings").description]' --nogather
             runalyzer .github/workflows/log_gathered_v2_new.sqlite -c 'assert "rank" in [l[0] for l in q("select * from warnings").description]' --nogather
+            runalyzer .github/workflows/log_gathered_v2_new.sqlite -c 'assert [l[0] for l in q("select schema_version")][0] == 3'
 
         - name: Upgrade V3 to V3
           # Tests upgrades on current version for stability and allows users
@@ -296,11 +301,14 @@ jobs:
             # test ungathered_v3 default name
             upgrade-db .github/workflows/log_ungathered_v3.sqlite
 
+            # utilize nogather flag to ensure schema is from modification
+            # instead of gathering, which builds schema v3
             runalyzer .github/workflows/log_ungathered_v3_upgrade.sqlite -c 'db.print_cursor(db.q("select * from warnings"))' --nogather
             runalyzer .github/workflows/log_ungathered_v3_upgrade.sqlite -c 'print([l[0] for l in q("select * from warnings").description])' --nogather
             runalyzer .github/workflows/log_ungathered_v3_upgrade.sqlite -c 'print([l[0] for l in q("select * from logging").description])' --nogather
             runalyzer .github/workflows/log_ungathered_v3_upgrade.sqlite -c 'assert "unixtime" in [l[0] for l in q("select * from warnings").description]' --nogather
             runalyzer .github/workflows/log_ungathered_v3_upgrade.sqlite -c 'assert "rank" in [l[0] for l in q("select * from warnings").description]' --nogather
+            runalyzer .github/workflows/log_ungathered_v3_upgrade.sqlite -c 'assert [l[0] for l in q("select schema_version")][0] == 3'
 
             # test gathered_v3 default name
             upgrade-db .github/workflows/log_gathered_v3.sqlite
@@ -310,6 +318,7 @@ jobs:
             runalyzer .github/workflows/log_gathered_v3_upgrade.sqlite -c 'print([l[0] for l in q("select * from logging").description])' --nogather
             runalyzer .github/workflows/log_gathered_v3_upgrade.sqlite -c 'assert "unixtime" in [l[0] for l in q("select * from warnings").description]' --nogather
             runalyzer .github/workflows/log_gathered_v3_upgrade.sqlite -c 'assert "rank" in [l[0] for l in q("select * from warnings").description]' --nogather
+            runalyzer .github/workflows/log_gathered_v3_upgrade.sqlite -c 'assert [l[0] for l in q("select schema_version")][0] == 3'
 
             # test gathered custom name
             upgrade-db .github/workflows/log_gathered_v3.sqlite --suffix '_new'
@@ -319,3 +328,4 @@ jobs:
             runalyzer .github/workflows/log_gathered_v3_new.sqlite -c 'print([l[0] for l in q("select * from logging").description])' --nogather
             runalyzer .github/workflows/log_gathered_v3_new.sqlite -c 'assert "unixtime" in [l[0] for l in q("select * from warnings").description]' --nogather
             runalyzer .github/workflows/log_gathered_v3_new.sqlite -c 'assert "rank" in [l[0] for l in q("select * from warnings").description]' --nogather
+            runalyzer .github/workflows/log_gathered_v3_new.sqlite -c 'assert [l[0] for l in q("select schema_version")][0] == 3'
diff --git a/bin/runalyzer b/bin/runalyzer
index e21dc30..58849e3 100755
--- a/bin/runalyzer
+++ b/bin/runalyzer
@@ -17,7 +17,10 @@ def main() -> None:
     parser.add_argument("--script", type=str,
                         help="script file to read")
     parser.add_argument("--nogather", action="store_true",
-                        help="do not automatically gather files")
+                        help="""
+                        Do not automatically gather files. Primarily
+                        used internally to view database schema.
+                        """)
     args = parser.parse_args()
 
     from logpyle.runalyzer import make_runalyzer_symbols, make_wrapped_db
diff --git a/logpyle/runalyzer.py b/logpyle/runalyzer.py
index 724dc36..00782f8 100644
--- a/logpyle/runalyzer.py
+++ b/logpyle/runalyzer.py
@@ -533,7 +533,7 @@ def make_wrapped_db(
     if gather:
         db = auto_gather(filenames)
     else:
-        assert len(filenames) == 1, "Enable autogather to support multiple infiles"
+        assert len(filenames) == 1, "Enable autogather to support multiple input files"
         db = sqlite3.connect(filenames[0])
     db.create_aggregate("stddev", 1, StdDeviation)  # type: ignore[arg-type]
     db.create_aggregate("var", 1, Variance)
diff --git a/logpyle/upgrade_db.py b/logpyle/upgrade_db.py
index 3ac2b54..31341e8 100644
--- a/logpyle/upgrade_db.py
+++ b/logpyle/upgrade_db.py
@@ -2,6 +2,9 @@
 Database Upgrade Functions
 --------------------------------
 .. autofunction:: upgrade_db
+.. note::
+   Currently, upgrades all schema versions to version 3.
+   Upgrading from version 1 is untested.
 
 .. list-table:: Overview of known changes between schema versions
    :widths: 25 25 50
@@ -71,6 +74,16 @@ def upgrade_conn(conn: sqlite3.Connection) -> sqlite3.Connection:
                 ADD run_id integer;
                              """)
 
+    from pickle import dumps
+    schema_version = 3
+    value = bytes(dumps(schema_version))
+    if gathered:
+        conn.execute("UPDATE runs SET schema_version=3")
+        # conn.execute("UPDATE runs SET schema_version = ?", (value,))
+    else:
+        # conn.execute("UPDATE constants SET value=3 WHERE name='schema_version'")
+        conn.execute("UPDATE constants SET value = ? WHERE name='schema_version'", (value,))
+
     return conn