Move scripts to top-level gn_auth package.

In preparation for migrating to pyproject.toml (from setup.py and
friends) we need to have only one top-level package. This will also
help in improving testing and checks down the line, since everything
will be relative to one single top-level directory.

11 files changed, 6 insertions, 7 deletions

diff --git a/README.md b/README.md
index 963b5c5..07937eb 100644
--- a/README.md
+++ b/README.md
@@ -268,7 +268,7 @@ The checks we do are
 ### Linting
 
 ```bash
-pylint *py tests gn_auth scripts
+pylint *py tests gn_auth
 ```
 
 ### Type-Checking
diff --git a/gn_auth/auth/authorisation/data/views.py b/gn_auth/auth/authorisation/data/views.py
index ef3d119..fc1849f 100644
--- a/gn_auth/auth/authorisation/data/views.py
+++ b/gn_auth/auth/authorisation/data/views.py
@@ -244,7 +244,7 @@ def __search_phenotypes__():
         job_id = uuid.uuid4()
         selected = __request_key__("selected_traits", [])
         command =[
-            sys.executable, "-m", "scripts.search_phenotypes",
+            sys.executable, "-m", "gn_auth.scripts.search_phenotypes",
             __request_key__("species_name"),
             __request_key__("query"),
             str(job_id),
diff --git a/gn_auth/scripts/__init__.py b/gn_auth/scripts/__init__.py
new file mode 100644
index 0000000..5be56d8
--- /dev/null
+++ b/gn_auth/scripts/__init__.py
@@ -0,0 +1 @@
+"""These are command-line scripts to be run manually or in the background."""
diff --git a/scripts/assign_data_to_default_admin.py b/gn_auth/scripts/assign_data_to_default_admin.py
index 69fc50c..69fc50c 100644
--- a/scripts/assign_data_to_default_admin.py
+++ b/gn_auth/scripts/assign_data_to_default_admin.py
diff --git a/scripts/batch_assign_data_to_default_admin.py b/gn_auth/scripts/batch_assign_data_to_default_admin.py
index a468019..95d9794 100644
--- a/scripts/batch_assign_data_to_default_admin.py
+++ b/gn_auth/scripts/batch_assign_data_to_default_admin.py
@@ -15,8 +15,7 @@ from gn_auth.auth.db import sqlite3 as authdb
 from gn_auth.auth.authentication.users import User
 from gn_auth.auth.authorisation.resources.groups.models import (
     Group, db_row_to_group)
-
-from scripts.assign_data_to_default_admin import (
+from gn_auth.scripts.assign_data_to_default_admin import (
     default_resources, assign_data_to_resource)
 
 
diff --git a/scripts/link_inbredsets.py b/gn_auth/scripts/link_inbredsets.py
index c78a050..ad743f5 100644
--- a/scripts/link_inbredsets.py
+++ b/gn_auth/scripts/link_inbredsets.py
@@ -10,7 +10,7 @@ from gn_libs import mysqldb as biodb
 
 import gn_auth.auth.db.sqlite3 as authdb
 
-from scripts.assign_data_to_default_admin import (
+from gn_auth.scripts.assign_data_to_default_admin import (
     sys_admins, admin_group, select_sys_admin)
 
 def linked_inbredsets(conn):
diff --git a/scripts/register_sys_admin.py b/gn_auth/scripts/register_sys_admin.py
index 06aa845..06aa845 100644
--- a/scripts/register_sys_admin.py
+++ b/gn_auth/scripts/register_sys_admin.py
diff --git a/scripts/search_phenotypes.py b/gn_auth/scripts/search_phenotypes.py
index eee112d..eee112d 100644
--- a/scripts/search_phenotypes.py
+++ b/gn_auth/scripts/search_phenotypes.py
diff --git a/scripts/worker.py b/gn_auth/scripts/worker.py
index 0a77d41..0a77d41 100644
--- a/scripts/worker.py
+++ b/gn_auth/scripts/worker.py
diff --git a/gn_auth/wsgi.py b/gn_auth/wsgi.py
index e05ef0d..f2f17f1 100644
--- a/gn_auth/wsgi.py
+++ b/gn_auth/wsgi.py
@@ -16,8 +16,7 @@ from gn_auth.auth.db import sqlite3 as db
 from gn_auth.auth.errors import NotFoundError
 from gn_auth.auth.authentication.users import user_by_id, hash_password
 from gn_auth.auth.authorisation.users.admin.models import make_sys_admin
-
-from scripts import register_sys_admin as rsysadm# type: ignore[import]
+from gn_auth.scripts import register_sys_admin as rsysadm# type: ignore[import]
 
 
 app = create_app()
diff --git a/scripts/__init__.py b/scripts/__init__.py
deleted file mode 100644
index e69de29..0000000
--- a/scripts/__init__.py
+++ /dev/null