Merge pull request #18301 from nsoranzo/release_24.1_fix_packages

[24.1] Fix various packages' issues
galaxyproject · Jun 3, 2024 · 60fbf43 · 60fbf43
2 parents fa9af6f + 80701f4
commit 60fbf43
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Showing 39 changed files with 68 additions and 24 deletions.
diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
@@ -28,6 +28,7 @@
     jobs,
     tools,
 )
+from galaxy.carbon_emissions import get_carbon_intensity_entry
 from galaxy.celery.base_task import (
     GalaxyTaskBeforeStart,
     GalaxyTaskBeforeStartUserRateLimitPostgres,
@@ -556,6 +557,10 @@ def __init__(self, configure_logging=True, use_converters=True, use_display_appl
         self.application_stack = self._register_singleton(ApplicationStack, application_stack_instance(app=self))
         if configure_logging:
             config.configure_logging(self.config, self.application_stack.facts)
+        # Carbon emissions configuration
+        carbon_intensity_entry = get_carbon_intensity_entry(self.config.geographical_server_location_code)
+        self.carbon_intensity = carbon_intensity_entry["carbon_intensity"]
+        self.geographical_server_location_name = carbon_intensity_entry["location_name"]
         # Initialize job metrics manager, needs to be in place before
         # config so per-destination modifications can be made.
         self.job_metrics = self._register_singleton(

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
@@ -34,7 +34,6 @@
 
 import yaml
 
-from galaxy.carbon_emissions import get_carbon_intensity_entry
 from galaxy.config.schema import AppSchema
 from galaxy.exceptions import ConfigurationError
 from galaxy.util import (
@@ -700,15 +699,13 @@ class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
 
     allowed_origin_hostnames: List[str]
     builds_file_path: str
-    carbon_intensity: float
     container_resolvers_config_file: str
     database_connection: str
     drmaa_external_runjob_script: str
     email_from: Optional[str]
     enable_tool_shed_check: bool
     galaxy_data_manager_data_path: str
     galaxy_infrastructure_url: str
-    geographical_server_location_name: str
     hours_between_check: int
     integrated_tool_panel_config: str
     involucro_path: str
@@ -814,11 +811,6 @@ def _process_config(self, kwargs: Dict[str, Any]) -> None:
         else:
             self.version_extra = extra_info
 
-        # Carbon emissions configuration
-        carbon_intensity_entry = get_carbon_intensity_entry(kwargs.get("geographical_server_location_code", ""))
-        self.carbon_intensity = carbon_intensity_entry["carbon_intensity"]
-        self.geographical_server_location_name = carbon_intensity_entry["location_name"]
-
         # Database related configuration
         self.check_migrate_databases = string_as_bool(kwargs.get("check_migrate_databases", True))
         if not self.database_connection:  # Provide default if not supplied by user

diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py
@@ -183,8 +183,8 @@ def _config_is_truthy(item, key, **context):
             "interactivetools_enable": _use_config,
             "aws_estimate": _use_config,
             "carbon_emission_estimates": _defaults_to(True),
-            "carbon_intensity": _use_config,
-            "geographical_server_location_name": _use_config,
+            "carbon_intensity": lambda item, key, **context: self.app.carbon_intensity,
+            "geographical_server_location_name": lambda item, key, **context: self.app.geographical_server_location_name,
             "geographical_server_location_code": _use_config,
             "power_usage_effectiveness": _use_config,
             "message_box_content": _use_config,

diff --git a/lib/galaxy/structured_app.py b/lib/galaxy/structured_app.py
@@ -101,8 +101,10 @@ class MinimalApp(BasicSharedApp):
 
 class MinimalManagerApp(MinimalApp):
     # Minimal App that is sufficient to run Celery tasks
+    carbon_intensity: float
     file_sources: ConfiguredFileSources
     genome_builds: GenomeBuilds
+    geographical_server_location_name: str
     dataset_collection_manager: "DatasetCollectionManager"
     tool_data_tables: "ToolDataTableManager"
     history_manager: "HistoryManager"

diff --git a/packages/app/pytest.ini b/packages/app/pytest.ini
diff --git a/packages/app/pytest.ini b/packages/app/pytest.ini
@@ -0,0 +1 @@
+../package-pytest.ini
diff --git a/packages/auth/pytest.ini b/packages/auth/pytest.ini
@@ -0,0 +1 @@
+../package-pytest.ini
diff --git a/packages/config/pytest.ini b/packages/config/pytest.ini
@@ -0,0 +1 @@
+../package-pytest.ini
diff --git a/packages/data/pytest.ini b/packages/data/pytest.ini
@@ -0,0 +1 @@
+../package-pytest.ini
diff --git a/packages/files/pytest.ini b/packages/files/pytest.ini
@@ -0,0 +1 @@
+../package-pytest.ini
diff --git a/packages/job_execution/pytest.ini b/packages/job_execution/pytest.ini
@@ -0,0 +1 @@
+../package-pytest.ini
diff --git a/packages/job_metrics/pytest.ini b/packages/job_metrics/pytest.ini
@@ -0,0 +1 @@
+../package-pytest.ini
diff --git a/packages/meta/pytest.ini b/packages/meta/pytest.ini
@@ -0,0 +1 @@
+../package-pytest.ini
diff --git a/packages/navigation/pytest.ini b/packages/navigation/pytest.ini
@@ -0,0 +1 @@
+../package-pytest.ini
diff --git a/packages/objectstore/pytest.ini b/packages/objectstore/pytest.ini
@@ -0,0 +1 @@
+../package-pytest.ini
diff --git a/packages/package-pytest.ini b/packages/package-pytest.ini
@@ -0,0 +1,6 @@
+[pytest]
+# Prevent execution of alembic/env.py at test collection stage (alembic.context not set).
+# Also ignore functional tests (galaxy_test/ and tool_shed/test/).
+addopts = --doctest-modules --ignore=galaxy/model/migrations/alembic/ --ignore=galaxy/tools/bundled/ --ignore=galaxy_test/ --ignore=tool_shed/test/ --ignore=tool_shed/webapp/model/migrations/alembic/ --doctest-continue-on-failure --verbosity=1
+asyncio_mode = auto
+log_level = DEBUG
diff --git a/packages/schema/pytest.ini b/packages/schema/pytest.ini
@@ -0,0 +1 @@
+../package-pytest.ini
diff --git a/packages/selenium/pytest.ini b/packages/selenium/pytest.ini
@@ -0,0 +1 @@
+../package-pytest.ini
diff --git a/packages/test.sh b/packages/test.sh
@@ -63,11 +63,8 @@ while read -r package_dir || [ -n "$package_dir" ]; do  # https://stackoverflow.
     else
         marker_args=()
     fi
-    # Prevent execution of alembic/env.py at test collection stage (alembic.context not set)
-    # Also ignore functional tests (galaxy_test/ and tool_shed/test/).
-    unit_extra=(--doctest-modules --ignore=galaxy/model/migrations/alembic/ --ignore=galaxy_test/ --ignore=tool_shed/test/ --ignore=tool_shed/webapp/model/migrations/alembic/ "${marker_args[@]}")
     # Ignore exit code 5 (no tests ran)
-    pytest "${unit_extra[@]}" . || test $? -eq 5
+    pytest "${marker_args[@]}" . || test $? -eq 5
     if [ $FOR_PULSAR -eq 0 ]; then
         make mypy
     fi

diff --git a/packages/test_api/pytest.ini b/packages/test_api/pytest.ini
@@ -0,0 +1 @@
+../package-pytest.ini
diff --git a/packages/test_base/pytest.ini b/packages/test_base/pytest.ini
@@ -0,0 +1 @@
+../package-pytest.ini
diff --git a/packages/test_driver/pytest.ini b/packages/test_driver/pytest.ini
@@ -0,0 +1 @@
+../package-pytest.ini
diff --git 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/test_selenium/pytest.ini b/packages/test_selenium/pytest.ini
@@ -0,0 +1 @@
+../package-pytest.ini
diff --git 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/pytest.ini b/packages/tool_shed/pytest.ini
@@ -0,0 +1 @@
+../package-pytest.ini
diff --git 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/tool_util/pytest.ini b/packages/tool_util/pytest.ini
@@ -0,0 +1 @@
+../package-pytest.ini
diff --git a/packages/tours/pytest.ini b/packages/tours/pytest.ini
@@ -0,0 +1 @@
+../package-pytest.ini
diff --git a/packages/util/pytest.ini b/packages/util/pytest.ini
@@ -0,0 +1 @@
+../package-pytest.ini
diff --git 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
diff --git a/packages/web_apps/pytest.ini b/packages/web_apps/pytest.ini
@@ -0,0 +1 @@
+../package-pytest.ini
diff --git 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/packages/web_framework/pytest.ini b/packages/web_framework/pytest.ini
@@ -0,0 +1 @@
+../package-pytest.ini
diff --git a/packages/web_stack/pytest.ini b/packages/web_stack/pytest.ini
@@ -0,0 +1 @@
+../package-pytest.ini
diff --git 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/carbon_emissions/__init__.py → test/unit/app/carbon_emissions/__init__.py b/test/unit/carbon_emissions/__init__.py → test/unit/app/carbon_emissions/__init__.py
diff --git a/...ssions/test_get_carbon_intensity_entry.py → ...ssions/test_get_carbon_intensity_entry.py b/...ssions/test_get_carbon_intensity_entry.py → ...ssions/test_get_carbon_intensity_entry.py
diff --git a/test/unit/webapps/test_tool_validation.py → test/unit/tool_shed/test_tool_validation.py b/test/unit/webapps/test_tool_validation.py → test/unit/tool_shed/test_tool_validation.py
Original file line number	Diff line number	Diff line change
		@@ -1 +1,2 @@
		include .rst .txt LICENSE */py.typed
		graft tool_shed/webapp/templates/