From be90bf05cbb7989e18098b08c9e59f56e6434560 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Thu, 4 Jun 2026 13:49:08 -0400
Subject: [PATCH] Fix missing console scripts in built wheels

When [project] is defined in pyproject.toml, setuptools does not include
[options.entry_points] from setup.cfg in the built wheel.

Solution: move console script definitions to [project.scripts] in
pyproject.toml for all affected packages.
---
 packages/app/pyproject.toml           |  4 ++++
 packages/config/pyproject.toml        |  3 +++
 packages/data/pyproject.toml          |  8 ++++++++
 packages/files/pyproject.toml         |  3 +++
 packages/job_execution/pyproject.toml |  4 ++++
 packages/selenium/pyproject.toml      |  3 +++
 packages/tool_util/pyproject.toml     | 12 ++++++++++++
 packages/tours/pyproject.toml         |  3 +++
 packages/web_apps/pyproject.toml      |  3 +++
 packages/web_client/pyproject.toml    |  3 +++
 10 files changed, 46 insertions(+)

diff --git a/packages/app/pyproject.toml b/packages/app/pyproject.toml
index 47134ec526e..471d8999398 100644
--- a/packages/app/pyproject.toml
+++ b/packages/app/pyproject.toml
@@ -14,3 +14,7 @@ dynamic = [
     "version",
 ]
 name = "galaxy-app"
+
+[project.scripts]
+galaxy-main = "galaxy.main:main"
+galaxy-dependencies = "galaxy.dependencies.script:main"
diff --git a/packages/config/pyproject.toml b/packages/config/pyproject.toml
index 122dd8a20a2..70e99ed32fd 100644
--- a/packages/config/pyproject.toml
+++ b/packages/config/pyproject.toml
@@ -14,3 +14,6 @@ dynamic = [
     "version",
 ]
 name = "galaxy-config"
+
+[project.scripts]
+galaxy-config = "galaxy.config.script:main"
diff --git a/packages/data/pyproject.toml b/packages/data/pyproject.toml
index cc90e5906eb..134d4d6d343 100644
--- a/packages/data/pyproject.toml
+++ b/packages/data/pyproject.toml
@@ -14,3 +14,11 @@ dynamic = [
     "version",
 ]
 name = "galaxy-data"
+
+[project.scripts]
+galaxy-build-objects = "galaxy.model.store.build_objects:main"
+galaxy-load-objects = "galaxy.model.store.load_objects:main"
+galaxy-manage-db = "galaxy.model.orm.scripts:manage_db"
+galaxy-prune-histories = "galaxy.model.scripts:prune_history_table"
+galaxy-delete-sessions = "galaxy.model.scripts:delete_galaxy_sessions"
+galaxy-delete-job-metrics = "galaxy.model.scripts:delete_job_metrics"
diff --git a/packages/files/pyproject.toml b/packages/files/pyproject.toml
index e91dbb41933..28ab2d700b0 100644
--- a/packages/files/pyproject.toml
+++ b/packages/files/pyproject.toml
@@ -14,3 +14,6 @@ dynamic = [
     "version",
 ]
 name = "galaxy-files"
+
+[project.scripts]
+galaxy-file-sources-conf-validation = "galaxy.files.validate.script:main"
diff --git a/packages/job_execution/pyproject.toml b/packages/job_execution/pyproject.toml
index a772ff3f331..22723da8dd5 100644
--- a/packages/job_execution/pyproject.toml
+++ b/packages/job_execution/pyproject.toml
@@ -14,3 +14,7 @@ dynamic = [
     "version",
 ]
 name = "galaxy-job-execution"
+
+[project.scripts]
+galaxy-set-metadata = "galaxy.metadata.set_metadata:set_metadata"
+galaxy-container-monitor = "galaxy.job_execution.container_monitor:main"
diff --git a/packages/selenium/pyproject.toml b/packages/selenium/pyproject.toml
index a868d63ae73..3b9255ecd02 100644
--- a/packages/selenium/pyproject.toml
+++ b/packages/selenium/pyproject.toml
@@ -14,3 +14,6 @@ dynamic = [
     "version",
 ]
 name = "galaxy-selenium"
+
+[project.scripts]
+gx-dump-tour = "galaxy.selenium.scripts.dump_tour:main"
diff --git a/packages/tool_util/pyproject.toml b/packages/tool_util/pyproject.toml
index ed167eede19..2c1d4b73077 100644
--- a/packages/tool_util/pyproject.toml
+++ b/packages/tool_util/pyproject.toml
@@ -14,3 +14,15 @@ dynamic = [
     "version",
 ]
 name = "galaxy-tool-util"
+
+[project.scripts]
+galaxy-tool-test = "galaxy.tool_util.verify.script:main"
+galaxy-tool-test-case-validation = "galaxy.tool_util.parameters.scripts.validate_test_cases:main"
+galaxy-tool-upgrade-advisor = "galaxy.tool_util.upgrade.script:main"
+validate-test-format = "galaxy.tool_util.validate_test_format:main"
+mulled-build = "galaxy.tool_util.deps.mulled.mulled_build:main"
+mulled-build-channel = "galaxy.tool_util.deps.mulled.mulled_build_channel:main"
+mulled-build-files = "galaxy.tool_util.deps.mulled.mulled_build_files:main"
+mulled-build-tool = "galaxy.tool_util.deps.mulled.mulled_build_tool:main"
+mulled-hash = "galaxy.tool_util.deps.mulled.mulled_hash:main"
+mulled-list = "galaxy.tool_util.deps.mulled.mulled_list:main"
diff --git a/packages/tours/pyproject.toml b/packages/tours/pyproject.toml
index a6752b88225..71389b1beea 100644
--- a/packages/tours/pyproject.toml
+++ b/packages/tours/pyproject.toml
@@ -14,3 +14,6 @@ dynamic = [
     "version",
 ]
 name = "galaxy-tours"
+
+[project.scripts]
+gx-validate-tours = "galaxy.tours.validate:main"
diff --git a/packages/web_apps/pyproject.toml b/packages/web_apps/pyproject.toml
index 0396a77b34e..42a54a92ea7 100644
--- a/packages/web_apps/pyproject.toml
+++ b/packages/web_apps/pyproject.toml
@@ -14,3 +14,6 @@ dynamic = [
     "version",
 ]
 name = "galaxy-web-apps"
+
+[project.scripts]
+galaxy-web = "galaxy.webapps.galaxy.script:main"
diff --git a/packages/web_client/pyproject.toml b/packages/web_client/pyproject.toml
index e3b99d0a761..e5f8e5d96e2 100644
--- a/packages/web_client/pyproject.toml
+++ b/packages/web_client/pyproject.toml
@@ -14,3 +14,6 @@ dynamic = [
     "version",
 ]
 name = "galaxy-web-client"
+
+[project.scripts]
+galaxy-web-client-install = "galaxy.web_client.install:main"