python packages: convert to pure namespace packages

only directories in `lib/galaxy` & `packages/*/galaxy`
All other files removed or moved to their own module
All references to those files updated, especially galaxy/version.py

.github/workflows/test_galaxy_release.yaml

@@ -4,14 +4,14 @@ on:
     paths:
       - '.github/workflows/test_galaxy_release.yaml'
       - lib/galaxy/dependencies/**
-      - lib/galaxy/version.py
+      - lib/galaxy/version/__init__.py
       - scripts/release.sh
       - test/release.sh
   pull_request:
     paths:
       - '.github/workflows/test_galaxy_release.yaml'
       - lib/galaxy/dependencies/**
-      - lib/galaxy/version.py
+      - lib/galaxy/version/__init__.py
       - scripts/release.sh
       - test/release.sh
 concurrency:

Makefile

@@ -273,6 +273,9 @@ release-create: ## Create a release branch
 
 release-create-point: release-create ## Create a point release
 
+mypy:
+	cd lib && mypy . ../test
+
 .PHONY: help
 
 help:

client-api/README.md

@@ -155,7 +155,7 @@ To work on this package:
 3. Synchronize the version with Galaxy:
 
     ```bash
-    # Update the version in package.json from Galaxy's version.py
+    # Update the version in package.json from Galaxy's version/__init__.py
     npm run sync-version
     ```
 
@@ -174,7 +174,7 @@ To work on this package:
 
 ### Version Synchronization
 
-This package maintains version parity with Galaxy to indicate API compatibility. The version number in `package.json` is derived from Galaxy's `lib/galaxy/version.py` file but formatted to comply with npm's semver requirements.
+This package maintains version parity with Galaxy to indicate API compatibility. The version number in `package.json` is derived from Galaxy's `lib/galaxy/version/__init__.py` file but formatted to comply with npm's semver requirements.
 
 **Important:** npm does not allow republishing the same version, even for development versions. When making changes to the client API during development:
 
@@ -201,7 +201,7 @@ npm run sync-version
 
 The script will:
 
-1. Read the version from Galaxy's `version.py` file
+1. Read the version from Galaxy's `version/__init__.py` file
 2. Convert it to npm-compatible semver format
 3. Update the version in `package.json` if different
 

client-api/scripts/sync-version.js

@@ -3,7 +3,7 @@
 /**
  * Galaxy Client API Version Synchronization Script
  *
- * Reads Galaxy's version.py and updates package.json with a semver-compatible version.
+ * Reads Galaxy's version/__init__.py and updates package.json with a semver-compatible version.
  */
 
 import fs from "fs";
@@ -17,10 +17,10 @@ const galaxyRoot = process.env.GALAXY_ROOT || path.resolve(__dirname, "../..");
 const clientApiRoot = path.resolve(__dirname, "..");
 
 // File paths
-const galaxyVersionPath = path.join(galaxyRoot, "lib/galaxy/version.py");
+const galaxyVersionPath = path.join(galaxyRoot, "lib/galaxy/version/__init__.py");
 const packageJsonPath = path.join(clientApiRoot, "package.json");
 
-// Check if Galaxy version.py exists
+// Check if Galaxy version/__init__.py exists
 if (!fs.existsSync(galaxyVersionPath)) {
     console.error(`Galaxy version file not found at ${galaxyVersionPath}`);
     process.exit(1);
@@ -32,7 +32,7 @@ const majorMatch = versionPy.match(/VERSION_MAJOR\s*=\s*"([^"]+)"/);
 const minorMatch = versionPy.match(/VERSION_MINOR\s*=\s*"([^"]+)"/);
 
 if (!majorMatch) {
-    console.error("Could not find VERSION_MAJOR in version.py");
+    console.error("Could not find VERSION_MAJOR in version/__init__.py");
     process.exit(1);
 }
 

doc/source/dev/create_release.rst

@@ -18,7 +18,7 @@ The command is shipped with the `galaxy-release-util <https://pypi.org/project/g
 
 `galaxy-release-util create-release` will:
 
- - update lib/galaxy/version.py
+ - update lib/galaxy/version/__init__.py
  - create HISTORY.rst entries for all packages
  - build all packages
  - stage and commit all changes
@@ -28,7 +28,7 @@ The command is shipped with the `galaxy-release-util <https://pypi.org/project/g
 
 The script has 2 important arguments:
 
-    - `--new-version` is the new version as it will appear for PyPI packages and in lib/galaxy/version.py
+    - `--new-version` is the new version as it will appear for PyPI packages and in lib/galaxy/version/__init__.py
     - `--last-commit` indicates the first commit from which changes are to be included in the changelog.
 
 Before starting make sure local branches (all release branches and dev) are up to date and clean, and all release branches have been merged forward,

lib/galaxy/__init__.py

@@ -1,7 +0,0 @@
-"""
-Galaxy root package -- this is a namespace package.
-"""
-
-from pkgutil import extend_path
-
-__path__ = extend_path(__path__, __name__)

lib/galaxy/app/__init__.py

@@ -41,6 +41,7 @@ from galaxy.celery.base_task import (
 from galaxy.config import GalaxyAppConfiguration
 from galaxy.config_watchers import ConfigWatchers
 from galaxy.datatypes.registry import Registry
+from galaxy.di import Container
 from galaxy.files import (
     ConfiguredFileSources,
     ConfiguredFileSourcesConf,
@@ -141,6 +142,11 @@ from galaxy.short_term_storage import (
     ShortTermStorageManager,
     ShortTermStorageMonitor,
 )
+from galaxy.structured_app import (
+    BasicSharedApp,
+    MinimalManagerApp,
+    StructuredApp,
+)
 from galaxy.tool_shed.cache import ToolShedRepositoryCache
 from galaxy.tool_shed.galaxy_install.client import InstallationTarget
 from galaxy.tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
@@ -185,12 +191,6 @@ from galaxy.workflow import scheduling_manager
 from galaxy.workflow.completion_hooks import WorkflowCompletionHookRegistry
 from galaxy.workflow.completion_monitor import WorkflowCompletionMonitor
 from galaxy.workflow.trs_proxy import TrsProxy
-from .di import Container
-from .structured_app import (
-    BasicSharedApp,
-    MinimalManagerApp,
-    StructuredApp,
-)
 
 log = logging.getLogger(__name__)
 app = None

lib/galaxy/authnz/psa_authnz.py

@@ -22,6 +22,7 @@ from sqlalchemy import func
 from sqlalchemy.exc import IntegrityError
 
 from galaxy import exceptions as galaxy_exceptions
+from galaxy.config import GalaxyAppConfiguration
 from galaxy.exceptions import MalformedContents
 from galaxy.managers import users as user_managers
 from galaxy.model import (
@@ -44,7 +45,6 @@ from .oidc_utils import (
     is_oidc_backend,
     verify_oidc_response,
 )
-from ..config import GalaxyAppConfiguration
 
 if TYPE_CHECKING:
     from social_core.backends.oauth import BaseOAuth2

lib/galaxy/config/__init__.py

@@ -54,7 +54,7 @@ from galaxy.util.resources import (
     resource_path,
 )
 from galaxy.util.themes import flatten_theme
-from ..version import (
+from galaxy.version import (
     VERSION_MAJOR,
     VERSION_MINOR,
 )

lib/galaxy/datatypes/triples.py

@@ -5,18 +5,18 @@ Triple format classes
 import logging
 import re
 
+from galaxy.datatypes import (
+    binary,
+    data,
+    text,
+    xml,
+)
 from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes.protocols import DatasetProtocol
 from galaxy.datatypes.sniff import (
     build_sniff_from_prefix,
     FilePrefix,
 )
-from . import (
-    binary,
-    data,
-    text,
-    xml,
-)
 
 log = logging.getLogger(__name__)
 

lib/galaxy/main.py

@@ -1 +0,0 @@
-../../scripts/galaxy-main

lib/galaxy/main/__init__.py

@@ -0,0 +1 @@
+../../../scripts/galaxy-main

lib/galaxy/model/store/__init__.py

@@ -48,6 +48,7 @@ from sqlalchemy.orm.scoping import scoped_session
 from sqlalchemy.sql import expression
 from typing_extensions import Protocol
 
+from galaxy import model
 from galaxy.datatypes.registry import Registry
 from galaxy.exceptions import (
     MalformedContents,
@@ -122,7 +123,6 @@ from ..item_attrs import (
     add_item_annotation,
     get_item_annotation_str,
 )
-from ... import model
 
 if TYPE_CHECKING:
     from galaxy.managers.workflows import WorkflowContentsManager

lib/galaxy/util/properties.py

@@ -196,7 +196,7 @@ class NicerConfigParser(ConfigParser):
 
 
 def _running_from_source():
-    paths = ["run.sh", "lib/galaxy/__init__.py", "scripts/common_startup.sh"]
+    paths = ["run.sh", "lib/galaxy", "scripts/common_startup.sh"]
     return all(map(os.path.exists, paths))
 
 

mypy.ini

@@ -17,6 +17,7 @@ warn_redundant_casts = True
 warn_unreachable = True
 warn_unused_ignores = True
 platform = linux
+explicit_package_bases = True
 
 # green list - work on growing these please!
 [mypy-galaxy.jobs.job_destination]

packages/app/MANIFEST.in

@@ -1,4 +1,4 @@
-include *.rst *.txt LICENSE */py.typed
+include *.rst *.txt LICENSE galaxy/*/py.typed
 include galaxy/carbon_emissions/carbon_intensity.csv
 include galaxy/dependencies/*.txt
 include galaxy/dependencies/*.sh

packages/app/galaxy/__init__.py

@@ -1 +0,0 @@
-../../package.__init__.py

packages/app/galaxy/app

@@ -0,0 +1 @@
+../../../lib/galaxy/app

packages/app/galaxy/app.py

@@ -1 +0,0 @@
-../../../lib/galaxy/app.py

packages/app/galaxy/config_watchers

@@ -0,0 +1 @@
+../../../lib/galaxy/config_watchers

packages/app/galaxy/config_watchers.py

@@ -1 +0,0 @@
-../../../lib/galaxy/config_watchers.py

packages/app/galaxy/di

@@ -0,0 +1 @@
+../../../lib/galaxy/di

packages/app/galaxy/di.py

@@ -1 +0,0 @@
-../../../lib/galaxy/di.py

packages/app/galaxy/main

@@ -0,0 +1 @@
+../../../lib/galaxy/main

packages/app/galaxy/main.py

@@ -1 +0,0 @@
-../../../lib/galaxy/main.py

packages/app/galaxy/main_config

@@ -0,0 +1 @@
+../../../lib/galaxy/main_config

packages/app/galaxy/main_config.py

@@ -1 +0,0 @@
-../../../lib/galaxy/main_config.py

packages/app/galaxy/queue_worker

@@ -0,0 +1 @@
+../../../lib/galaxy/queue_worker

packages/app/galaxy/queue_worker.py

@@ -1 +0,0 @@
-../../../lib/galaxy/queue_worker.py

packages/app/galaxy/queues

@@ -0,0 +1 @@
+../../../lib/galaxy/queues

packages/app/galaxy/queues.py

@@ -1 +0,0 @@
-../../../lib/galaxy/queues.py

packages/app/galaxy/structured_app

@@ -0,0 +1 @@
+../../../lib/galaxy/structured_app

packages/app/galaxy/structured_app.py

@@ -1 +0,0 @@
-../../../lib/galaxy/structured_app.py

packages/auth/MANIFEST.in

@@ -1 +1 @@
-include *.rst *.txt LICENSE */py.typed
+include *.rst *.txt LICENSE galaxy/*/py.typed

packages/auth/galaxy/__init__.py

@@ -1 +0,0 @@
-../../package.__init__.py

packages/config/MANIFEST.in

@@ -1,4 +1,4 @@
-include *.rst *.txt LICENSE */py.typed
+include *.rst *.txt LICENSE galaxy/*/py.typed
 include galaxy/config/schemas/*.yml
 include galaxy/config/sample/*.sample*
 graft galaxy/config/templates/

packages/config/galaxy/__init__.py

@@ -1 +0,0 @@
-../../package.__init__.py

packages/data/MANIFEST.in

@@ -1,4 +1,4 @@
-include *.rst *.txt LICENSE */py.typed
+include *.rst *.txt LICENSE galaxy/*/py.typed
 include galaxy/datatypes/set_metadata_tool.xml
 include galaxy/datatypes/converters/*.xml
 graft galaxy/datatypes/display_applications/configs/

packages/data/galaxy/__init__.py

@@ -1 +0,0 @@
-../../package.__init__.py

packages/files/MANIFEST.in

@@ -1,2 +1,2 @@
-include *.rst *.txt LICENSE */py.typed
+include *.rst *.txt LICENSE galaxy/*/py.typed
 include galaxy/files/templates/examples/*yml

packages/files/galaxy/__init__.py

@@ -1 +0,0 @@
-../../package.__init__.py

packages/job_execution/MANIFEST.in

@@ -1,2 +1,2 @@
-include *.rst *.txt LICENSE */py.typed
+include *.rst *.txt LICENSE galaxy/*/py.typed
 

packages/job_execution/galaxy/__init__.py

@@ -1 +0,0 @@
-../../package.__init__.py

packages/job_metrics/MANIFEST.in

@@ -1 +1 @@
-include *.rst *.txt LICENSE */py.typed
+include *.rst *.txt LICENSE galaxy/*/py.typed