From 1174bbe8f47aa238615a1366b3598f5cf2b89220 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Sun, 2 Jun 2024 19:39:05 +0100
Subject: [PATCH] Fix packages' dependencies and MANIFEST.in files

Also:
- Add missing `graphene` and `graphql-core` dependencies to
  `pyproject.toml` (already installed as other dependencies' deps,
  but explicitly imported by ToolShed code).
- Move `test_tool_validation.py` unit tests to the galaxy-tool-shed
  package.
---
 packages/test_driver/setup.cfg                |  2 --
 packages/tool_shed/MANIFEST.in                |  1 +
 packages/tool_shed/setup.cfg                  | 25 +++++++++++++++++++
 packages/web_apps/MANIFEST.in                 |  2 --
 .../datatypes/display_applications/configs    |  1 -
 packages/web_apps/setup.cfg                   |  2 --
 pyproject.toml                                |  4 ++-
 .../test_tool_validation.py                   |  0
 8 files changed, 29 insertions(+), 8 deletions(-)
 delete mode 120000 packages/web_apps/galaxy/datatypes/display_applications/configs
 rename test/unit/{webapps => tool_shed}/test_tool_validation.py (100%)

diff --git a/packages/test_driver/setup.cfg b/packages/test_driver/setup.cfg
index 6f4efce2cfab..5c3292823c1b 100644
--- a/packages/test_driver/setup.cfg
+++ b/packages/test_driver/setup.cfg
@@ -40,8 +40,6 @@ install_requires =
     galaxy-util
     galaxy-web-apps
     pytest
-    graphene-sqlalchemy==3.0.0rc1  # these are only needed by tool shed - which we've split out but the test driver loads
-    starlette-graphene3
 packages = find:
 python_requires = >=3.8
 
diff --git a/packages/tool_shed/MANIFEST.in b/packages/tool_shed/MANIFEST.in
index 12302eb8dff0..d9a9578d12ba 100644
--- a/packages/tool_shed/MANIFEST.in
+++ b/packages/tool_shed/MANIFEST.in
@@ -1 +1,2 @@
 include *.rst *.txt LICENSE */py.typed
+graft tool_shed/webapp/templates/
diff --git a/packages/tool_shed/setup.cfg b/packages/tool_shed/setup.cfg
index 4e78a7c84c29..9ec024a7992c 100644
--- a/packages/tool_shed/setup.cfg
+++ b/packages/tool_shed/setup.cfg
@@ -32,8 +32,33 @@ version = 23.2.dev0
 [options]
 include_package_data = True
 install_requires =
+    galaxy-app
+    galaxy-auth
+    galaxy-config
+    galaxy-data
+    galaxy-util
+    galaxy-web-framework
     galaxy-web-stack
     galaxy-web-apps
+    a2wsgi
+    alembic
+    fastapi>=0.101.0
+    graphene
+    graphene-sqlalchemy>=3.0.0rc1
+    graphql-core
+    Mako
+    MarkupSafe
+    mercurial
+    Paste
+    pydantic>=2,!=2.6.0,!=2.6.1
+    Routes
+    SQLAlchemy>=2.0,<2.1
+    starlette
+    starlette-context
+    starlette-graphene3
+    typing-extensions
+    WebOb
+    Whoosh
 packages = find:
 python_requires = >=3.8
 
diff --git a/packages/web_apps/MANIFEST.in b/packages/web_apps/MANIFEST.in
index fe784b101c20..9c04be40d0fd 100644
--- a/packages/web_apps/MANIFEST.in
+++ b/packages/web_apps/MANIFEST.in
@@ -7,5 +7,3 @@ prune galaxy/webapps/base/static/plugins/
 exclude galaxy/webapps/base/static/style/base.css
 exclude galaxy/webapps/base/static/welcome.html
 graft galaxy/webapps/base/templates/
-include tool_shed/webapp/model/migrate/migrate.cfg
-graft tool_shed/webapp/templates/
diff --git a/packages/web_apps/galaxy/datatypes/display_applications/configs b/packages/web_apps/galaxy/datatypes/display_applications/configs
deleted file mode 120000
index bd4fe9cae4ab..000000000000
--- a/packages/web_apps/galaxy/datatypes/display_applications/configs
+++ /dev/null
@@ -1 +0,0 @@
-../../../../../lib/galaxy/datatypes/display_applications/configs
\ No newline at end of file
diff --git a/packages/web_apps/setup.cfg b/packages/web_apps/setup.cfg
index 53ef00625581..02b2a8005312 100644
--- a/packages/web_apps/setup.cfg
+++ b/packages/web_apps/setup.cfg
@@ -49,7 +49,6 @@ install_requires =
     importlib-resources;python_version<'3.9'
     Mako
     MarkupSafe
-    mercurial
     Paste
     pydantic>=2,!=2.6.0,!=2.6.1
     PyJWT
@@ -67,7 +66,6 @@ install_requires =
     uvicorn
     uvloop
     WebOb
-    Whoosh
 packages = find:
 python_requires = >=3.8
 
diff --git a/pyproject.toml b/pyproject.toml
index f927c91fc45c..2f7355735122 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -61,7 +61,9 @@ fastapi-slim = ">=0.111.0"
 fs = "*"
 future = ">=1.0.0"  # Python 3.12 support
 galaxy_sequence_utils = "*"
-graphene-sqlalchemy = "3.0.0rc1"  # need a beta release to be compat. with starlette plugin
+graphene = "*"
+graphene-sqlalchemy = ">=3.0.0rc1"  # need a beta release to be compat. with starlette plugin
+graphql-core = "*"
 gravity = ">=1.0.4"
 gunicorn = "*"
 gxformat2 = "*"
diff --git a/test/unit/webapps/test_tool_validation.py b/test/unit/tool_shed/test_tool_validation.py
similarity index 100%
rename from test/unit/webapps/test_tool_validation.py
rename to test/unit/tool_shed/test_tool_validation.py