Renamed MEGAQC_DEBUG to FLASK_DEBUG and tidied config profiles

.gitignore

@@ -4,6 +4,7 @@ uploads/*
 
 # Development stuff
 dev.db
+test.db
 dist/
 
 # Dev CSS

docs/installation-dev.md

@@ -26,20 +26,20 @@ conda install -c bioconda megaqc
 ```
 
 ## 2. (Optional) Set the variable for the development mode:
-Setting this bash variable tells MegaQC to show full Python exception
-tracebacks in the web browser, as well as additional Flask plugins
-which help with debugging and performance testing.
+Setting this bash variable runs MegaQC in development mode. This means
+that it will show full Python exception tracebacks in the web browser
+as well as additional Flask plugins which help with debugging and performance testing.
 
 This is only useful when actively developing MegaQC code and should
 be skipped if you're just trying MegaQC out.
 
 ```bash
-export MEGAQC_DEBUG=1
+export FLASK_DEBUG=1
 ```
 
 ## 3. Set up the database
 Running this command creates an empty SQLite MegaQC database file in the
-installation directory called `dev.db`.
+installation directory called `test.db` (`dev.db` if running in dev mode).
 
 ```bash
 megaqc initdb

megaqc/settings.py

@@ -67,7 +67,6 @@ def update_db_uri(self):
                 self.SQLALCHEMY_DATABASE
             )
 
-
 class ProdConfig(Config):
     """Production configuration."""
 
@@ -83,7 +82,7 @@ def __init__(self):
         super(ProdConfig, self).__init__()
         self.update_db_uri()
         # Log to the terminal
-        print("Env: Prod")
+        print(" * Environment: Prod")
         print(" * Database type: {}".format(self.SQLALCHEMY_DBMS))
         print(" * Database path: {}".format(self.SQLALCHEMY_DATABASE_URI_SAN))
 
@@ -107,7 +106,7 @@ def __init__(self):
         super(DevConfig, self).__init__()
         self.update_db_uri()
         # Log to the terminal
-        print("Env: dev")
+        print(" * Environment: dev")
         print(" * Database type: {}".format(self.SQLALCHEMY_DBMS))
         print(" * Database path: {}".format(self.SQLALCHEMY_DATABASE_URI_SAN))
 
@@ -126,6 +125,6 @@ def __init__(self):
         super(TestConfig, self).__init__()
         self.update_db_uri()
         # Log to the terminal
-        print("Env: test")
+        print(" * Environment: test")
         print(" * Database type: {}".format(self.SQLALCHEMY_DBMS))
         print(" * Database path: {}".format(self.SQLALCHEMY_DATABASE_URI_SAN))

megaqc/wsgi.py

@@ -3,7 +3,7 @@
 from megaqc.settings import TestConfig, DevConfig, ProdConfig
 
 
-if os.environ.get('MEGAQC_DEBUG', False):
+if os.environ.get('FLASK_DEBUG', False):
     CONFIG = DevConfig()
 elif os.environ.get('MEGAQC_PRODUCTION', False):
     CONFIG = ProdConfig()

scripts/megaqc

@@ -4,14 +4,15 @@
 """
 
 import click
+import os
 from flask.cli import FlaskGroup
 
 def create_megaqc_app(info):
     import os
     from megaqc.app import create_app
     from megaqc.settings import TestConfig, DevConfig, ProdConfig
 
-    if os.environ.get('MEGAQC_DEBUG', False):
+    if os.environ.get('FLASK_DEBUG', False):
         CONFIG = DevConfig()
     elif os.environ.get('MEGAQC_PRODUCTION', False):
         CONFIG = ProdConfig()
@@ -30,4 +31,9 @@ if __name__ == '__main__':
     import pkg_resources
     version = pkg_resources.get_distribution("megaqc").version
     print("This is MegaQC v{}\n".format(version))
+    if os.environ.get('FLASK_DEBUG', False):
+        print(' * Environment variable FLASK_DEBUG is true - running in dev mode')
+        os.environ['FLASK_ENV'] = 'dev'
+    elif not os.environ.get('MEGAQC_PRODUCTION', False):
+        os.environ['FLASK_ENV'] = 'test'
     cli()