galaxyproject · nsoranzo · Mar 2, 2022 · Feb 27, 2022 · Feb 28, 2022 · Mar 1, 2022
diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
diff --git a/lib/galaxy/web/formatting.py b/lib/galaxy/web/formatting.py
diff --git a/lib/galaxy/web_stack/__init__.py b/lib/galaxy/web_stack/__init__.py
@@ -633,10 +633,6 @@ def get_app_kwds(config_section, app_name=None):
     return application_stack_class().get_app_kwds(config_section, app_name=app_name)
 
 
-def get_stack_facts(config=None):
-    return application_stack_instance(config=config).facts
-
-
 def _uwsgi_configured_mules():
     mules = uwsgi.opt.get('mule', [])
     return [mules] if isinstance(mules, str) or mules is True else mules

diff --git a/lib/tool_shed/webapp/config.py b/lib/tool_shed/webapp/config.py
@@ -12,11 +12,11 @@
     CommonConfigurationMixin,
     get_database_engine_options,
 )
+from galaxy.config import expand_pretty_datetime_format
 from galaxy.config.schema import AppSchema
 from galaxy.exceptions import ConfigurationError
 from galaxy.util import string_as_bool
 from galaxy.version import VERSION, VERSION_MAJOR, VERSION_MINOR
-from galaxy.web.formatting import expand_pretty_datetime_format
 
 try:
     from importlib.resources import files  # type: ignore[attr-defined]

diff --git a/packages/app/MANIFEST.in b/packages/app/MANIFEST.in
@@ -1,5 +1,3 @@
 include *.rst *.txt LICENSE
-include galaxy/config/schemas/*.yml
-include galaxy/config/sample/*.sample*
 include galaxy/jobs/runners/util/job_script/*.sh
 include galaxy/tools/*tsv
diff --git a/packages/app/requirements.txt b/packages/app/requirements.txt
@@ -1,4 +1,5 @@
 galaxy-auth
+galaxy-config
 galaxy-data
 galaxy-job-execution
 galaxy-job-metrics

diff --git a/packages/app/setup.py b/packages/app/setup.py
@@ -34,7 +34,6 @@ def get_var(var_name):
     'galaxy.actions',
     'galaxy.app_unittest_utils',
     'galaxy.authnz',
-    'galaxy.config',
     'galaxy.dependencies',
     'galaxy.forms',
     'galaxy.jobs',
@@ -95,14 +94,9 @@ def get_var(var_name):
 ENTRY_POINTS = '''
         [console_scripts]
         galaxy-main=galaxy.main:main
-        galaxy-config=galaxy.config.script:main
 '''
 PACKAGE_DATA = {
     # Be sure to update MANIFEST.in for source dist.
-    'galaxy': [
-        'config/schemas/*.yml',
-        'config/sample/*',
-    ],
     'tool_shed': [
         'scripts/bootstrap_tool_shed/user_info.xml',
     ],

diff --git a/packages/config/HISTORY.rst b/packages/config/HISTORY.rst
@@ -0,0 +1,11 @@
+.. :changelog:
+
+History
+-------
+
+.. to_doc
+
+---------------------
+22.1.0.dev0
+---------------------
+Initial release
diff --git a/packages/config/LICENSE b/packages/config/LICENSE
@@ -0,0 +1 @@
+../MIT_LICENSE.txt
diff --git a/packages/config/MANIFEST.in b/packages/config/MANIFEST.in
@@ -0,0 +1,3 @@
+include *.rst *.txt LICENSE
+include galaxy/config/schemas/*.yml
+include galaxy/config/sample/*.sample*
diff --git a/packages/config/Makefile b/packages/config/Makefile
@@ -0,0 +1 @@
+../package.Makefile
diff --git a/packages/config/README.rst b/packages/config/README.rst
@@ -0,0 +1,14 @@
+
+.. image:: https://badge.fury.io/py/galaxy-config.svg
+   :target: https://pypi.org/project/galaxy-config/
+
+
+Overview
+--------
+
+The Galaxy_ config module.
+
+* Free software: Academic Free License version 3.0
+* Code: https://github.com/galaxyproject/galaxy
+
+.. _Galaxy: http://galaxyproject.org/
diff --git a/packages/config/dev-requirements.txt b/packages/config/dev-requirements.txt
@@ -0,0 +1 @@
+../package-dev-requirements.txt
diff --git a/packages/config/galaxy/__init__.py b/packages/config/galaxy/__init__.py
@@ -0,0 +1 @@
+__path__ = __import__('pkgutil').extend_path(__path__, __name__)  # type: ignore[has-type]
diff --git a/packages/app/galaxy/config → packages/config/galaxy/config b/packages/app/galaxy/config → packages/config/galaxy/config
diff --git a/packages/config/galaxy/project_galaxy_util.py b/packages/config/galaxy/project_galaxy_util.py
@@ -0,0 +1,11 @@
+__version__ = "22.1.0rc1"
+
+PROJECT_NAME = "galaxy-config"
+PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
+PROJECT_URL = "https://github.com/galaxyproject/galaxy"
+PROJECT_AUTHOR = 'Galaxy Project and Community'
+PROJECT_DESCRIPTION = 'Galaxy Generic Utilities'
+PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org'
+RAW_CONTENT_URL = "https://raw.github.com/{}/{}/master/".format(
+    PROJECT_USERAME, PROJECT_NAME
+)
diff --git a/packages/config/requirements.txt b/packages/config/requirements.txt
@@ -0,0 +1,2 @@
+galaxy-containers
+pykwalify
diff --git a/packages/config/scripts b/packages/config/scripts
@@ -0,0 +1 @@
+../build_scripts
diff --git a/packages/config/setup.cfg b/packages/config/setup.cfg
@@ -0,0 +1 @@
+../../setup.cfg
diff --git a/packages/config/setup.py b/packages/config/setup.py
@@ -0,0 +1,99 @@
+#!/usr/bin/env python
+
+import ast
+import os
+import re
+try:
+    from setuptools import setup
+except ImportError:
+    from distutils.core import setup
+
+SOURCE_DIR = "galaxy"
+
+_version_re = re.compile(r'__version__\s+=\s+(.*)')
+
+with open('%s/project_galaxy_util.py' % SOURCE_DIR, 'rb') as f:
+    init_contents = f.read().decode('utf-8')
+
+    def get_var(var_name):
+        pattern = re.compile(r'%s\s+=\s+(.*)' % var_name)
+        match = pattern.search(init_contents).group(1)
+        return str(ast.literal_eval(match))
+
+    version = get_var("__version__")
+    PROJECT_NAME = get_var("PROJECT_NAME")
+    PROJECT_URL = get_var("PROJECT_URL")
+    PROJECT_AUTHOR = get_var("PROJECT_AUTHOR")
+    PROJECT_EMAIL = get_var("PROJECT_EMAIL")
+    PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION")
+
+TEST_DIR = 'tests'
+PACKAGES = [
+    'galaxy',
+    'galaxy.config',
+]
+ENTRY_POINTS = '''
+        [console_scripts]
+        galaxy-config=galaxy.config.script:main
+'''
+PACKAGE_DATA = {
+    # Be sure to update MANIFEST.in for source dist.
+    'galaxy': [
+        'config/schemas/*.yml',
+        'config/sample/*',
+    ],
+}
+PACKAGE_DIR = {
+    SOURCE_DIR: SOURCE_DIR,
+}
+
+readme = open('README.rst').read()
+history = open('HISTORY.rst').read().replace('.. :changelog:', '')
+
+if os.path.exists("requirements.txt"):
+    requirements = open("requirements.txt").read().split("\n")
+else:
+    # In tox, it will cover them anyway.
+    requirements = []
+
+
+test_requirements = open("test-requirements.txt").read().split("\n")
+
+
+setup(
+    name=PROJECT_NAME,
+    version=version,
+    description=PROJECT_DESCRIPTION,
+    long_description=readme + '\n\n' + history,
+    long_description_content_type='text/x-rst',
+    author=PROJECT_AUTHOR,
+    author_email=PROJECT_EMAIL,
+    url=PROJECT_URL,
+    packages=PACKAGES,
+    entry_points=ENTRY_POINTS,
+    package_data=PACKAGE_DATA,
+    package_dir=PACKAGE_DIR,
+    include_package_data=True,
+    install_requires=requirements,
+    license="MIT",
+    zip_safe=False,
+    keywords='galaxy',
+    classifiers=[
+        'Development Status :: 5 - Production/Stable',
+        'Intended Audience :: Developers',
+        'Environment :: Console',
+        'License :: OSI Approved :: MIT License',
+        'Operating System :: POSIX',
+        'Topic :: Software Development',
+        'Topic :: Software Development :: Code Generators',
+        'Topic :: Software Development :: Testing',
+        'Natural Language :: English',
+        "Programming Language :: Python :: 3",
+        'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: 3.8',
+        'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+    ],
+    test_suite=TEST_DIR,
+    tests_require=test_requirements
+)
diff --git a/packages/config/test-data b/packages/config/test-data
@@ -0,0 +1 @@
+../../test-data
diff --git a/packages/config/test-requirements.txt b/packages/config/test-requirements.txt
@@ -0,0 +1,2 @@
+pytest<6.1
+responses
diff --git a/test/unit/config/config_manage/__init__.py → packages/config/tests/__init__.py b/test/unit/config/config_manage/__init__.py → packages/config/tests/__init__.py
diff --git a/packages/config/tests/config b/packages/config/tests/config
@@ -0,0 +1 @@
+../../../test/unit/config
diff --git a/packages/config/tests/util b/packages/config/tests/util
@@ -0,0 +1 @@
+../../../test/unit/util
diff --git a/packages/test.sh b/packages/test.sh
@@ -23,6 +23,7 @@ PACKAGE_DIRS=(
     objectstore
     job_metrics
     containers
+    config
     files
     tool_util
     data

diff --git a/packages/util/galaxy/version.py b/packages/util/galaxy/version.py
@@ -0,0 +1 @@
+../../../lib/galaxy/version.py
diff --git a/test/unit/config/test_config_dataset_storage.py b/test/unit/config/test_config_dataset_storage.py
@@ -1,34 +1,24 @@
 import os.path
 
-import pytest
-
 from galaxy import config
 from galaxy.config import BaseAppConfiguration
 
 
-@pytest.fixture
-def mock_config_file(monkeypatch):
-    # Patch this; otherwise tempfile.tempdir will be set, which is a global variable that
-    # defines the value of the default `dir` argument to the functions in Python's
-    # tempfile module - which breaks multiple tests.
-    monkeypatch.setattr(config.GalaxyAppConfiguration, '_override_tempdir', lambda a, b: None)
-
-
-def test_object_store_store_by_set(mock_config_file, monkeypatch):
+def test_object_store_store_by_set():
     # object_store_store_by set by admin
     appconfig = config.GalaxyAppConfiguration(object_store_store_by='id')
     assert appconfig.object_store_store_by == 'id'
 
 
-def test_uuid_1(mock_config_file, monkeypatch):
+def test_uuid_1():
     # object_store_store_by not set
     # file_path set by admin to `objects` (no need for the dir to exist)
     appconfig = config.GalaxyAppConfiguration(file_path='objects')
 
     assert appconfig.object_store_store_by == 'uuid'
 
 
-def test_uuid_2(mock_config_file, monkeypatch):
+def test_uuid_2(monkeypatch):
     # object_store_store_by not set
     # file_path not set, `files` dir doesn't exist
     monkeypatch.setattr(BaseAppConfiguration, '_path_exists', lambda self, path: False)
@@ -37,15 +27,15 @@ def test_uuid_2(mock_config_file, monkeypatch):
     assert appconfig.object_store_store_by == 'uuid'
 
 
-def test_id_1(mock_config_file, monkeypatch):
+def test_id_1():
     # object_store_store_by not set
     # file_path set by admin to `not_objects` (no need for the dir to exist)
     appconfig = config.GalaxyAppConfiguration(file_path='not_objects')
 
     assert appconfig.object_store_store_by == 'id'
 
 
-def test_id_2(mock_config_file, monkeypatch):
+def test_id_2(monkeypatch):
     # object_store_store_by not set
     # file_path not set, `files` dir exists
     monkeypatch.setattr(BaseAppConfiguration, '_path_exists', lambda self, path: True if os.path.basename(path) == 'files' else False)