Drop pkg_resources

lib/galaxy/eggs/__init__.py

@@ -1,8 +0,0 @@
-"""
-For backwards compatibility
-"""
-
-import pkg_resources
-
-
-require = pkg_resources.require

lib/galaxy/exceptions/error_codes.py

@@ -5,9 +5,7 @@ See the file error_codes.json for actual error code descriptions.
 from json import loads
 from typing import Dict
 
-from pkg_resources import resource_string
-
-from galaxy.util import unicodify
+from galaxy.util.resources import resource_string
 
 
 # Error codes are provided as a convience to Galaxy API clients, but at this
@@ -45,7 +43,7 @@ def _from_dict(entry):
     return (name, ErrorCode(code, message))
 
 
-error_codes_json = unicodify(resource_string(__name__, 'error_codes.json'))
+error_codes_json = resource_string(__name__.rsplit('.', 1)[0], 'error_codes.json')
 error_codes_by_name: Dict[str, ErrorCode] = {}
 
 for entry in loads(error_codes_json):

lib/galaxy/jobs/runners/util/job_script/__init__.py

@@ -5,26 +5,25 @@ import time
 from string import Template
 from typing import Any, Dict
 
-from pkg_resources import resource_string
-
 from galaxy.job_execution.setup import JobIO
 from galaxy.util import (
     RWXR_XR_X,
     unicodify,
 )
+from galaxy.util.resources import resource_string
 
 log = logging.getLogger(__name__)
 DEFAULT_SHELL = '/bin/bash'
 
 DEFAULT_JOB_FILE_TEMPLATE = Template(
-    unicodify(resource_string(__name__, 'DEFAULT_JOB_FILE_TEMPLATE.sh'))
+    resource_string(__name__, 'DEFAULT_JOB_FILE_TEMPLATE.sh')
 )
 
 SLOTS_STATEMENT_CLUSTER_DEFAULT = \
-    unicodify(resource_string(__name__, 'CLUSTER_SLOTS_STATEMENT.sh'))
+    resource_string(__name__, 'CLUSTER_SLOTS_STATEMENT.sh')
 
 MEMORY_STATEMENT_DEFAULT = \
-    unicodify(resource_string(__name__, 'MEMORY_STATEMENT.sh'))
+    resource_string(__name__, 'MEMORY_STATEMENT.sh')
 
 SLOTS_STATEMENT_SINGLE = """
 GALAXY_SLOTS="1"

lib/galaxy/managers/licenses.py

@@ -2,7 +2,6 @@ import json
 import logging
 from typing import List
 
-from pkg_resources import resource_string
 from pydantic import (
     BaseModel,
     Field,
@@ -10,6 +9,7 @@ from pydantic import (
 )
 
 from galaxy import exceptions
+from galaxy.util.resources import resource_string
 
 log = logging.getLogger(__name__)
 
@@ -85,7 +85,7 @@ RECOMMENDED_LICENSES = [
     "MPL-2.0",
     "PDDL-1.0",
 ]
-SPDX_LICENSES_STRING = resource_string(__name__, 'licenses.json').decode("UTF-8")
+SPDX_LICENSES_STRING = resource_string(__name__.rsplit('.', 1)[0], 'licenses.json')
 SPDX_LICENSES = json.loads(SPDX_LICENSES_STRING)
 for license in SPDX_LICENSES["licenses"]:
     license["recommended"] = license["licenseId"] in RECOMMENDED_LICENSES

lib/galaxy/managers/markdown_util.py

@@ -27,7 +27,6 @@ from typing import (
 )
 
 import markdown
-import pkg_resources
 try:
     import weasyprint
 except Exception:
@@ -47,6 +46,7 @@ from galaxy.managers.jobs import (
 from galaxy.model.item_attrs import get_item_annotation_str
 from galaxy.model.orm.now import now
 from galaxy.schema import PdfDocumentType
+from galaxy.util.resources import resource_string
 from galaxy.util.sanitize_html import sanitize_html
 from .markdown_parse import GALAXY_MARKDOWN_FUNCTION_CALL_LINE, validate_galaxy_markdown
 
@@ -596,7 +596,7 @@ def to_pdf_raw(basic_markdown: str, css_paths: Optional[List[str]] = None) -> by
         output_file.write(as_html)
         output_file.close()
         html = weasyprint.HTML(filename=index)
-        stylesheets = [weasyprint.CSS(string=pkg_resources.resource_string(__name__, 'markdown_export_base.css'))]
+        stylesheets = [weasyprint.CSS(string=resource_string(resource_string, 'markdown_export_base.css'))]
         for css_path in css_paths:
             with open(css_path) as f:
                 css_content = f.read()

lib/galaxy/selenium/data.py

@@ -1,10 +1,10 @@
 import yaml
-from pkg_resources import resource_string
 
+from galaxy.util.resources import resource_string
 from .components import Component
 
 
 def load_root_component() -> Component:
-    new_data_yaml = resource_string(__name__, 'navigation.yml').decode("UTF-8")
+    new_data_yaml = resource_string(__name__.rsplit('.', 1)[0], 'navigation.yml')
     navigation_raw = yaml.safe_load(new_data_yaml)
     return Component.from_dict("root", navigation_raw)

lib/galaxy/tools/__init__.py

@@ -30,7 +30,6 @@ import packaging.version
 import webob.exc
 from lxml import etree
 from mako.template import Template
-from pkg_resources import resource_string
 from webob.compat import cgi_FieldStorage
 
 from galaxy import (
@@ -112,6 +111,7 @@ from galaxy.util.dictifiable import Dictifiable
 from galaxy.util.expressions import ExpressionContext
 from galaxy.util.form_builder import SelectField
 from galaxy.util.json import safe_loads
+from galaxy.util.resources import resource_string
 from galaxy.util.rules_dsl import RuleSet
 from galaxy.util.template import (
     fill_template,
@@ -210,7 +210,7 @@ GALAXY_LIB_TOOLS_VERSIONED = {
     "winSplitter": packaging.version.parse("1.0.1"),
 }
 
-BIOTOOLS_MAPPING_CONTENT = resource_string(__name__, 'biotools_mappings.tsv').decode("UTF-8")
+BIOTOOLS_MAPPING_CONTENT = resource_string(__name__, 'biotools_mappings.tsv')
 BIOTOOLS_MAPPING: Dict[str, str] = dict([cast(Tuple[str, str], tuple(x.split("\t"))) for x in BIOTOOLS_MAPPING_CONTENT.splitlines() if not x.startswith("#")])
 
 REQUIRE_FULL_DIRECTORY = {

lib/galaxy/util/resources.py

@@ -0,0 +1,14 @@
+try:
+    from importlib.resources import files  # type: ignore[attr-defined]
+except ImportError:
+    # Python < 3.9
+    from importlib_resources import files  # type: ignore[no-redef]
+
+
+def resource_string(package_or_requirement, resource_name):
+    """
+    Return specified resource as a string.
+
+    Replacement function for pkg_resources.resource_string, but returns unicode string instead of bytestring.
+    """
+    return files(package_or_requirement).joinpath(resource_name).read_text()

lib/galaxy/util/rules_dsl.py

@@ -4,11 +4,12 @@ import re
 from typing import List, Type
 
 import yaml
-from pkg_resources import resource_stream
+
+from galaxy.util.resources import resource_string
 
 
 def get_rules_specification():
-    return yaml.safe_load(resource_stream(__name__, 'rules_dsl_spec.yml'))
+    return yaml.safe_load(resource_string(__name__.rsplit('.', 1)[0], 'rules_dsl_spec.yml'))
 
 
 def _ensure_rule_contains_keys(rule, keys):

lib/galaxy/webapps/__init__.py

@@ -1,3 +1,4 @@
 """Galaxy webapps root package -- this is a namespace package."""
 
-__import__("pkg_resources").declare_namespace(__name__)
+from pkgutil import extend_path
+__path__ = extend_path(__path__, __name__)  # type: ignore[has-type]

lib/galaxy_test/base/populators.py

@@ -69,7 +69,6 @@ from gxformat2 import (
     ImporterGalaxyInterface,
 )
 from gxformat2._yaml import ordered_load
-from pkg_resources import resource_string
 from requests.models import Response
 
 from galaxy.tool_util.client.staging import InteractorStaging
@@ -83,8 +82,8 @@ from galaxy.tool_util.verify.wait import (
 from galaxy.util import (
     DEFAULT_SOCKET_TIMEOUT,
     galaxy_root_path,
-    unicodify,
 )
+from galaxy.util.resources import resource_string
 from . import api_asserts
 from .api import ApiTestInteractor
 
@@ -92,10 +91,10 @@ from .api import ApiTestInteractor
 CWL_TOOL_DIRECTORY = os.path.join(galaxy_root_path, "test", "functional", "tools", "cwl_tools")
 
 # Simple workflow that takes an input and call cat wrapper on it.
-workflow_str = unicodify(resource_string(__name__, "data/test_workflow_1.ga"))
+workflow_str = resource_string(__name__.rsplit('.', 1)[0], "data/test_workflow_1.ga")
 # Simple workflow that takes an input and filters with random lines twice in a
 # row - first grabbing 8 lines at random and then 6.
-workflow_random_x2_str = unicodify(resource_string(__name__, "data/test_workflow_2.ga"))
+workflow_random_x2_str = resource_string(__name__.rsplit('.', 1)[0], "data/test_workflow_2.ga")
 
 
 DEFAULT_TIMEOUT = 60  # Secs to wait for state to turn ok
@@ -1124,7 +1123,7 @@ class BaseWorkflowPopulator(BasePopulator):
     def load_workflow_from_resource(self, name: str, filename: Optional[str] = None) -> dict:
         if filename is None:
             filename = f"data/{name}.ga"
-        content = unicodify(resource_string(__name__, filename))
+        content = resource_string(__name__.rsplit('.', 1)[0], filename)
         return self.load_workflow(name, content=content)
 
     def simple_workflow(self, name: str, **create_kwds) -> str:

packages/util/requirements.txt

@@ -1,6 +1,7 @@
 bleach
 boltons
 docutils
+importlib_resources
 markupsafe
 packaging
 pycryptodome

scripts/get_platforms.py

@@ -1,12 +0,0 @@
-#!/usr/bin/env python
-
-import os
-import sys
-
-assert sys.version_info[:2] >= (2, 6)
-
-lib = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib"))
-sys.path.insert(1, lib)
-
-import pkg_resources
-print(pkg_resources.get_platform())