From 3586c28c5824ce3f11930784f163ece0d4a37d10 Mon Sep 17 00:00:00 2001
From: Alexandros Evangelou <alexandrose95@gmail.com>
Date: Mon, 31 Aug 2026 14:48:04 +0300
Subject: [PATCH 1/2] fix: repair ethopy-setup-djdocker for new installs

A fresh install could not connect to the database it had just created.

- Bump the generated docker-compose.yaml from datajoint/mysql:5.7 to datajoint/mysql:8. MySQL 5.7 offers only a SHA-1 cipher suite, which current Python refuses to negotiate, so any environment built after PyMySQL 1.2.0 (May 2026) failed with SSLV3_ALERT_HANDSHAKE_FAILURE. On mysql:8 the connection works and is genuinely encrypted. Pinning pymysql<1.2 was rejected: it hides the problem instead of fixing it.

- Warn when a data_* directory already exits MYSQL_ROOT_PASSWORD only when initialising an empty data directory, so a leftover one silently kept its old pasin a bare "Access denied for user 'root'".

- Use sys.executable rather than a bare `python` when creating schemas.
---
 src/ethopy/setup_db.py | 21 ++++++++++++++++++---
 1 file changed, 18 insertions(+), 3 deletions(-)

diff --git a/src/ethopy/setup_db.py b/src/ethopy/setup_db.py
index df4afa5..e569ba4 100644
--- a/src/ethopy/setup_db.py
+++ b/src/ethopy/setup_db.py
@@ -7,6 +7,7 @@
 import os
 import socket
 import subprocess
+import sys
 from pathlib import Path
 from time import sleep
 from typing import Optional, Tuple
@@ -197,16 +198,27 @@ def setup_dj_docker(mysql_path: Optional[str], container_name: str) -> None:
         mysql_dir.mkdir(parents=True, exist_ok=True)
         os.chdir(str(mysql_dir))
 
+        # MySQL only honours MYSQL_ROOT_PASSWORD when it initialises an empty
+        # data directory, so a leftover one silently keeps its old credentials.
+        data_dir = mysql_dir / f"data_{container_name}"
+        if data_dir.exists():
+            click.echo(
+                f"WARNING: a MySQL data directory already exists at {data_dir}.\n"
+                "MySQL will reuse it and IGNORE the password entered below - the "
+                "root password stored in that directory stays in force.\n"
+                "Enter that existing password, or press Ctrl-C and move the "
+                "directory aside to start from a clean database."
+            )
+
         # Get password securely using Click's password prompt
         mysql_password = click.prompt(
             "Enter the MySQL root password", hide_input=True, confirmation_prompt=True
         )
 
         docker_content = (
-            f"version: '2.4'\n"
             f"services:\n"
             f"  {container_name}:\n"
-            f"    image: datajoint/mysql:5.7\n"
+            f"    image: datajoint/mysql:8\n"
             f"    environment:\n"
             f"    - MYSQL_ROOT_PASSWORD={mysql_password}\n"
             f"    ports:\n"
@@ -290,7 +302,10 @@ def createschema() -> None:
         try:
             # Capture both stdout and stderr
             _ = subprocess.run(
-                ["python", "-c", cmd], check=True, capture_output=True, text=True
+                [sys.executable, "-c", cmd],
+                check=True,
+                capture_output=True,
+                text=True,
             )
             click.echo(f"Successfully created tables for: {schema_name}")
 

From c10ecc0915e7555d0b8781db09abc5e868836de4 Mon Sep 17 00:00:00 2001
From: Alexandros Evangelou <alexandrose95@gmail.com>
Date: Mon, 31 Aug 2026 14:48:29 +0300
Subject: [PATCH 2/2] udpate docs to show mysql:8 instead of mysql:5.7

---
 docs/database_setup.md | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/docs/database_setup.md b/docs/database_setup.md
index 13d55a7..54e02fd 100644
--- a/docs/database_setup.md
+++ b/docs/database_setup.md
@@ -28,7 +28,7 @@ This command will:
 5. Start the container
 
 The Docker container uses:
-- Image: `datajoint/mysql:5.7` (https://github.com/datajoint/mysql-docker)
+- Image: `datajoint/mysql:8` (https://github.com/datajoint/mysql-docker)
 - Port: 3306 (standard MySQL port)
 - Volume: `./data_ethopy_sql_db:/var/lib/mysql` for persistent data storage
 
@@ -38,10 +38,9 @@ If you prefer to set up the container manually:
 
 1. Create a `docker-compose.yaml` file:
 ```yaml
-version: '2.4'
 services:
   ethopy_sql_db:
-    image: datajoint/mysql:5.7
+    image: datajoint/mysql:8
     environment:
       - MYSQL_ROOT_PASSWORD=your_password
     ports: