make profile a Version

lib/galaxy/tool_util/deps/container_classes.py

@@ -364,7 +364,7 @@ def add_var(name, value):
                 defaults += ",$tool_directory:default_ro"
             if self.job_info.job_directory:
                 defaults += ",$job_directory:default_ro,$job_directory/outputs:rw"
-                if Version(str(self.tool_info.profile)) <= Version("19.09"):
+                if self.tool_info.profile <= Version("19.09"):
                     defaults += ",$job_directory/configs:rw"
             if self.job_info.home_directory is not None:
                 defaults += ",$home_directory:rw"

lib/galaxy/tool_util/deps/dependencies.py

@@ -6,6 +6,8 @@
     Union,
 )
 
+from packaging.version import Version
+
 from galaxy.tool_util.deps.requirements import (
     ContainerDescription,
     ToolRequirement,
@@ -62,7 +64,7 @@ def __init__(
         guest_ports=None,
         tool_id: Optional[str] = None,
         tool_version: Optional[str] = None,
-        profile: float = -1,
+        profile: Version = Version("0"),
     ):
         if env_pass_through is None:
             env_pass_through = ["GALAXY_SLOTS", "GALAXY_MEMORY_MB", "GALAXY_MEMORY_MB_PER_SLOT"]

lib/galaxy/tool_util/linters/general.py

@@ -66,10 +66,10 @@ def lint_general(tool_source, lint_ctx):
         lint_ctx.valid(VALID_ID_MSG % tool_id, node=tool_node)
 
     profile = tool_source.parse_profile()
-    profile_valid = PROFILE_PATTERN.match(profile) is not None
+    profile_valid = PROFILE_PATTERN.match(str(profile)) is not None
     if not profile_valid:
         lint_ctx.error(PROFILE_INVALID_MSG % profile, node=tool_node)
-    elif Version(profile) == Version("16.01"):
+    elif profile == Version("16.01"):
         lint_ctx.valid(PROFILE_INFO_DEFAULT_MSG, node=tool_node)
     else:
         lint_ctx.valid(PROFILE_INFO_SPECIFIED_MSG % profile, node=tool_node)

lib/galaxy/tool_util/linters/inputs.py

@@ -346,7 +346,7 @@ def lint_inputs(tool_source: "ToolSource", lint_ctx: "LintContext"):
         if param_type == "boolean":
             truevalue = param_attrib.get("truevalue", "true")
             falsevalue = param_attrib.get("falsevalue", "false")
-            problematic_booleans_allowed = Version(profile) < Version("23.1")
+            problematic_booleans_allowed = profile < Version("23.1")
             lint_level = lint_ctx.warn if problematic_booleans_allowed else lint_ctx.error
             if truevalue == falsevalue:
                 lint_level(

lib/galaxy/tool_util/linters/outputs.py

@@ -96,7 +96,7 @@ def lint_output(tool_source: "ToolSource", lint_ctx: "LintContext"):
     lint_ctx.info(f"{num_outputs} outputs found.", node=outputs[0])
 
 
-def __check_format(node, lint_ctx, profile: str, allow_ext=False):
+def __check_format(node, lint_ctx, profile: Version, allow_ext=False):
     """
     check if format/ext/format_source attribute is set in a given node
     issue a warning if the value is input
@@ -119,7 +119,7 @@ def __check_format(node, lint_ctx, profile: str, allow_ext=False):
         fmt = node.attrib.get("format")
     if fmt == "input":
         message = f"Using format='input' on {node.tag} is deprecated. Use the format_source attribute."
-        if Version(str(profile)) <= Version("16.01"):
+        if profile <= Version("16.01"):
             lint_ctx.warn(message, node=node)
         else:
             lint_ctx.error(message, node=node)

lib/galaxy/tool_util/linters/stdio.py

@@ -22,7 +22,7 @@ def lint_stdio(tool_source, lint_ctx):
     if not stdios:
         command = get_command(tool_xml) if tool_xml else None
         if command is None or not command.get("detect_errors"):
-            if Version(tool_source.parse_profile()) <= Version("16.01"):
+            if tool_source.parse_profile() <= Version("16.01"):
                 lint_ctx.info(
                     "No stdio definition found, tool indicates error conditions with output written to stderr.",
                     node=tool_node,

lib/galaxy/tool_util/parser/cwl.py

@@ -3,7 +3,7 @@
 import math
 from typing import Optional
 
-import packaging.version
+from packaging.version import Version
 
 from galaxy.tool_util.cwl.parser import (
     tool_proxy,
@@ -163,8 +163,8 @@ def parse_requirements_and_containers(self):
             resource_requirements=resource_requirements,
         )
 
-    def parse_profile(self):
-        return "17.09"
+    def parse_profile(self) -> Version:
+        return Version("17.09")
 
     def parse_xrefs(self):
         return []
@@ -173,7 +173,7 @@ def parse_license(self):
         return None
 
     def parse_python_template_version(self):
-        return packaging.version.Version("3.5")
+        return Version("3.5")
 
     def to_string(self):
         return json.dumps(self.tool_proxy.to_persistent_representation())

lib/galaxy/tool_util/parser/interface.py

@@ -16,7 +16,7 @@
     Union,
 )
 
-import packaging.version
+from packaging.version import Version
 from typing_extensions import TypedDict
 
 from galaxy.util.path import safe_walk
@@ -276,15 +276,15 @@ def parse_help(self) -> Optional[str]:
         """
 
     @abstractmethod
-    def parse_profile(self):
+    def parse_profile(self) -> Version:
         """Return tool profile version as Galaxy major e.g. 16.01 or 16.04."""
 
     @abstractmethod
     def parse_license(self):
         """Return license corresponding to tool wrapper."""
 
     @abstractmethod
-    def parse_python_template_version(self) -> Optional[packaging.version.Version]:
+    def parse_python_template_version(self) -> Optional[Version]:
         """
         Return minimum python version that the tool template has been developed against.
         """

lib/galaxy/tool_util/parser/xml.py

@@ -130,7 +130,7 @@ def __init__(self, xml_tree: ElementTree, source_path=None, macro_paths=None):
         self.root = self.xml_tree.getroot()
         self._source_path = source_path
         self._macro_paths = macro_paths or []
-        self.legacy_defaults = Version(self.parse_profile()) == Version("16.01")
+        self.legacy_defaults = self.parse_profile() == Version("16.01")
         self._string = xml_to_string(self.root)
 
     def to_string(self):
@@ -250,7 +250,7 @@ def parse_environment_variables(self):
         return environment_variables
 
     def parse_home_target(self):
-        target = "job_home" if Version(self.parse_profile()) >= Version("18.01") else "shared_home"
+        target = "job_home" if self.parse_profile() >= Version("18.01") else "shared_home"
         command_el = self._command_el
         command_legacy = (command_el is not None) and command_el.get("use_shared_home", None)
         if command_legacy is not None:
@@ -397,7 +397,7 @@ def parse_provided_metadata_style(self):
             style = out_elem.attrib["provided_metadata_style"]
 
         if style is None:
-            style = "legacy" if Version(self.parse_profile()) < Version("17.09") else "default"
+            style = "legacy" if self.parse_profile() < Version("17.09") else "default"
 
         assert style in ["legacy", "default"]
         return style
@@ -539,7 +539,7 @@ def _parse_output(
         output.filters = data_elem.findall("filter")
         output.tool = tool
         output.from_work_dir = data_elem.get("from_work_dir", None)
-        if output.from_work_dir and Version(str(getattr(tool, "profile", 0))) < Version("21.09"):
+        if output.from_work_dir and getattr(tool, "profile", Version("16.01")) < Version("21.09"):
             # We started quoting from_work_dir outputs in 21.09.
             # Prior to quoting, trailing spaces had no effect.
             # This ensures that old tools continue to work.
@@ -616,7 +616,7 @@ def parse_stdio(self):
 
     def parse_strict_shell(self):
         command_el = self._command_el
-        if Version(self.parse_profile()) < Version("20.09"):
+        if self.parse_profile() < Version("20.09"):
             default = "False"
         else:
             default = "True"
@@ -649,14 +649,14 @@ def parse_tests_to_dict(self) -> ToolSourceTests:
 
         return rval
 
-    def parse_profile(self) -> str:
+    def parse_profile(self) -> Version:
         # Pre-16.04 or default XML defaults
         # - Use standard error for error detection.
         # - Don't run shells with -e
         # - Auto-check for implicit multiple outputs.
         # - Auto-check for $param_file.
         # - Enable buggy interpreter attribute.
-        return self.root.get("profile", "16.01")
+        return Version(self.root.get("profile", "16.01"))
 
     def parse_license(self):
         return self.root.get("license")
@@ -687,7 +687,7 @@ def parse_creator(self):
         return creators
 
 
-def _test_elem_to_dict(test_elem, i, profile=None) -> ToolSourceTest:
+def _test_elem_to_dict(test_elem, i, profile: Optional[Version] = None) -> ToolSourceTest:
     rval: ToolSourceTest = dict(
         outputs=__parse_output_elems(test_elem),
         output_collections=__parse_output_collection_elems(test_elem, profile=profile),
@@ -760,7 +760,7 @@ def __parse_element_tests(parent_element, profile=None):
         element_tests[identifier] = __parse_test_attributes(
             element, element_attrib, parse_elements=True, profile=profile
         )
-        if profile and Version(profile) >= Version("20.09"):
+        if profile and profile >= Version("20.09"):
             element_tests[identifier][1]["expected_sort_order"] = idx
 
     return element_tests

lib/galaxy/tools/__init__.py

@@ -913,10 +913,10 @@ def requires_galaxy_python_environment(self):
         if self.tool_type not in ["default", "manage_data", "interactive", "data_source"]:
             return True
 
-        if self.tool_type == "manage_data" and Version(str(self.profile)) < Version("18.09"):
+        if self.tool_type == "manage_data" and self.profile < Version("18.09"):
             return True
 
-        if self.tool_type == "data_source" and Version(str(self.profile)) < Version("21.09"):
+        if self.tool_type == "data_source" and self.profile < Version("21.09"):
             return True
 
         config = self.app.config
@@ -1000,7 +1000,7 @@ def parse(self, tool_source: ToolSource, guid=None, dynamic=False):
         """
         Read tool configuration from the element `root` and fill in `self`.
         """
-        self.profile = float(tool_source.parse_profile())
+        self.profile = tool_source.parse_profile()
         # Get the UNIQUE id for the tool
         self.old_id = tool_source.parse_id()
         if guid is None:
@@ -1011,15 +1011,14 @@ def parse(self, tool_source: ToolSource, guid=None, dynamic=False):
         if not dynamic and not self.id:
             raise Exception(f"Missing tool 'id' for tool at '{tool_source}'")
 
-        profile = Version(str(self.profile))
-        if self.app.name == "galaxy" and profile >= Version("16.04") and Version(VERSION_MAJOR) < profile:
+        if self.app.name == "galaxy" and self.profile >= Version("16.04") and Version(VERSION_MAJOR) < self.profile:
             message = f"The tool [{self.id}] targets version {self.profile} of Galaxy, you should upgrade Galaxy to ensure proper functioning of this tool."
             raise Exception(message)
 
         self.python_template_version = tool_source.parse_python_template_version()
         if self.python_template_version is None:
             # If python_template_version not specified we assume tools with profile versions >= 19.05 are python 3 ready
-            if profile >= Version("19.05"):
+            if self.profile >= Version("19.05"):
                 self.python_template_version = Version("3.5")
             else:
                 self.python_template_version = Version("2.7")
@@ -1033,7 +1032,7 @@ def parse(self, tool_source: ToolSource, guid=None, dynamic=False):
 
         self.version = tool_source.parse_version()
         if not self.version:
-            if profile < Version("16.04"):
+            if self.profile < Version("16.04"):
                 # For backward compatibility, some tools may not have versions yet.
                 self.version = "1.0.0"
             else:

lib/galaxy/tools/actions/__init__.py

@@ -419,7 +419,7 @@ def execute(
         # format='input" previously would give you a random extension from
         # the input extensions, now it should just give "input" as the output
         # format.
-        input_ext = "data" if Version(str(tool.profile)) < Version("16.04") else "input"
+        input_ext = "data" if tool.profile < Version("16.04") else "input"
         input_dbkey = incoming.get("dbkey", "?")
         for name, data in reversed(list(inp_data.items())):
             if not data:
@@ -431,7 +431,7 @@ def execute(
                 data = data.to_history_dataset_association(None)
                 inp_data[name] = data
 
-            if Version(str(tool.profile)) < Version("16.04"):
+            if tool.profile < Version("16.04"):
                 input_ext = data.ext
 
             if data.dbkey not in [None, "?"]:

lib/galaxy/tools/evaluation.py

@@ -731,7 +731,7 @@ def _build_param_file(self):
         param_dict = self.param_dict
         directory = self.local_working_directory
         command = self.tool.command
-        if Version(str(self.tool.profile)) < Version("16.04") and command and "$param_file" in command:
+        if self.tool.profile < Version("16.04") and command and "$param_file" in command:
             with tempfile.NamedTemporaryFile(mode="w", dir=directory, delete=False) as param:
                 for key, value in param_dict.items():
                     # parameters can be strings or lists of strings, coerce to list

lib/galaxy/tools/execute.py

@@ -311,7 +311,7 @@ def output_name(self, trans, history, params, output):
         return output_collection_name
 
     def sliced_input_collection_structure(self, input_name):
-        unqualified_recurse = Version(str(self.tool.profile)) < Version("18.09") and "|" not in input_name
+        unqualified_recurse = self.tool.profile < Version("18.09") and "|" not in input_name
 
         def find_collection(input_dict, input_name):
             for key, value in input_dict.items():

lib/galaxy/tools/parameters/basic.py

@@ -595,7 +595,7 @@ def __init__(self, tool, input_source):
         super().__init__(tool, input_source)
         truevalue = input_source.get("truevalue", "true")
         falsevalue = input_source.get("falsevalue", "false")
-        if tool and Version(str(tool.profile)) >= Version("23.1"):
+        if tool and tool.profile >= Version("23.1"):
             if truevalue == falsevalue:
                 raise ParameterValueError("Cannot set true and false to the same value", self.name)
             if truevalue.lower() == "false":
@@ -1023,7 +1023,7 @@ def from_json(self, value, trans, other_values=None, require_legal_value=True):
                 "an invalid option (None) was selected, please verify", self.name, None, is_dynamic=self.is_dynamic
             )
         elif not legal_values:
-            if self.optional and Version(str(self.tool.profile)) < Version("18.09"):
+            if self.optional and self.tool.profile < Version("18.09"):
                 # Covers optional parameters with default values that reference other optional parameters.
                 # These will have a value but no legal_values.
                 # See https://github.com/galaxyproject/tools-iuc/pull/1842#issuecomment-394083768 for context.

lib/galaxy/tools/wrappers.py

@@ -122,15 +122,15 @@ def __init__(
         input: "ToolParameter",
         value: Optional[str],
         other_values: Optional[Dict[str, str]] = None,
-        profile: Optional[float] = None,
+        profile: Optional[Version] = None,
     ) -> None:
         self.input = input
         if (
             value is None
             and input.type == "text"
             and input.optional
             and input.optionality_inferred
-            and (profile is None or Version(str(profile)) < Version("23.0"))
+            and (profile is None or profile < Version("23.0"))
         ):
             # Tools with old profile versions may treat an optional text parameter as `""`
             value = ""

test/unit/app/tools/test_evaluation.py

@@ -1,5 +1,7 @@
 import os
 
+from packaging.version import Version
+
 from galaxy.app_unittest_utils.tools_support import UsesApp
 from galaxy.job_execution.compute_environment import SimpleComputeEnvironment
 from galaxy.job_execution.datasets import DatasetPath
@@ -297,7 +299,7 @@ def get_file_sources_dict(self):
 
 class MockTool:
     def __init__(self, app):
-        self.profile = 16.01
+        self.profile = Version("16.01")
         self.python_template_version = "2.7"
         self.app = app
         self.hooks_called = []

test/unit/app/tools/test_wrappers.py

@@ -4,6 +4,7 @@
 from unittest.mock import Mock
 
 import pytest
+from packaging.version import Version
 
 from galaxy.datatypes.metadata import MetadataSpecCollection
 from galaxy.job_execution.compute_environment import ComputeEnvironment
@@ -320,7 +321,7 @@ class MockTool:
     def __init__(self, app):
         self.app = app
         self.options = Mock(sanitize=False)
-        self.profile = 23.0
+        self.profile = Version("23.0")
 
 
 class MockApp: