Enable warn_unreachable mypy option

.pre-commit-config.yaml.sample

@@ -1,10 +1,10 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 22.10.0
+    rev: 24.1.1
     hooks:
     - id: black
   - repo: https://github.com/pycqa/flake8
-    rev: 5.0.4
+    rev: 7.0.0
     hooks:
     - id: flake8
   - repo: https://github.com/pre-commit/mirrors-prettier
@@ -16,7 +16,7 @@ repos:
         additional_dependencies:
           - [email protected] # Workaround. See https://github.com/pre-commit/mirrors-prettier/issues/29
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0  # Use the ref you want to point at
+    rev: v4.5.0  # Use the ref you want to point at
     hooks:
       - id: trailing-whitespace
       - id: check-merge-conflict
@@ -30,7 +30,7 @@ repos:
     - id: shell-lint
       args: [--format=json]
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.27.3
+    rev: 0.27.4
     hooks:
       - id: check-github-workflows
   - repo: local

lib/galaxy/datatypes/blast.py

@@ -261,7 +261,7 @@ def merge(split_files: List[str], output_file: str) -> None:
         raise NotImplementedError("Merging BLAST databases is non-trivial (do this via makeblastdb?)")
 
     @classmethod
-    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Dict) -> None:
+    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Optional[Dict]) -> None:
         """Split a BLAST database (not implemented for now)."""
         if split_params is None:
             return None

lib/galaxy/datatypes/data.py

@@ -1110,7 +1110,7 @@ def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
             dataset.blurb = "file purged from disk"
 
     @classmethod
-    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Dict) -> None:
+    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Optional[Dict]) -> None:
         """
         Split the input files by line.
         """

lib/galaxy/datatypes/molecules.py

@@ -5,6 +5,7 @@
     Callable,
     Dict,
     List,
+    Optional,
 )
 
 from galaxy.datatypes import metadata
@@ -261,7 +262,7 @@ def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> N
         dataset.metadata.number_of_molecules = count_special_lines(r"^\$\$\$\$$", dataset.get_file_name())
 
     @classmethod
-    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Dict) -> None:
+    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Optional[Dict]) -> None:
         """
         Split the input files by molecule records.
         """
@@ -344,7 +345,7 @@ def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> N
         dataset.metadata.number_of_molecules = count_special_lines("@<TRIPOS>MOLECULE", dataset.get_file_name())
 
     @classmethod
-    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Dict) -> None:
+    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Optional[Dict]) -> None:
         """
         Split the input files by molecule records.
         """
@@ -430,7 +431,7 @@ def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> N
         dataset.metadata.number_of_molecules = count_special_lines("^#", dataset.get_file_name(), invert=True)
 
     @classmethod
-    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Dict) -> None:
+    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Optional[Dict]) -> None:
         """
         Split the input files by fingerprint records.
         """
@@ -554,7 +555,7 @@ def merge(split_files: List[str], output_file: str) -> None:
         raise NotImplementedError("Merging Fastsearch indices is not supported.")
 
     @classmethod
-    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Dict) -> None:
+    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Optional[Dict]) -> None:
         """Splitting Fastsearch indices is not supported."""
         if split_params is None:
             return None
@@ -1631,7 +1632,7 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         return True
 
     @classmethod
-    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Dict) -> None:
+    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Optional[Dict]) -> None:
         """
         Split the input files by molecule records.
         """

lib/galaxy/datatypes/msa.py

@@ -6,6 +6,7 @@
     Callable,
     Dict,
     List,
+    Optional,
 )
 
 from galaxy.datatypes.binary import Binary
@@ -205,7 +206,7 @@ def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> N
         )
 
     @classmethod
-    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Dict) -> None:
+    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Optional[Dict]) -> None:
         """
 
         Split the input files by model records.

lib/galaxy/datatypes/sequence.py

@@ -217,7 +217,7 @@ def get_subdir(idx):
         return directories
 
     @classmethod
-    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Dict) -> None:
+    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Optional[Dict]) -> None:
         """Split a generic sequence file (not sensible or possible, see subclasses)."""
         if split_params is None:
             return None
@@ -335,7 +335,7 @@ class Alignment(data.Text):
     )
 
     @classmethod
-    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Dict) -> None:
+    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Optional[Dict]) -> None:
         """Split a generic alignment file (not sensible or possible, see subclasses)."""
         if split_params is None:
             return None
@@ -405,7 +405,7 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         return False
 
     @classmethod
-    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Dict) -> None:
+    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Optional[Dict]) -> None:
         """Split a FASTA file sequence by sequence.
 
         Note that even if split_mode="number_of_parts", the actual number of
@@ -792,7 +792,7 @@ def display_data(
             return Sequence.display_data(self, trans, dataset, preview, filename, to_ext, **kwd)
 
     @classmethod
-    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Dict) -> None:
+    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Optional[Dict]) -> None:
         """
         FASTQ files are split on cluster boundaries, in increments of 4 lines
         """

lib/galaxy/datatypes/spaln.py

@@ -172,7 +172,7 @@ def merge(split_files: List[str], output_file: str) -> None:
         raise NotImplementedError("Merging spaln databases is not possible")
 
     @classmethod
-    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Dict) -> None:
+    def split(cls, input_datasets: List, subdir_generator_function: Callable, split_params: Optional[Dict]) -> None:
         """Split a spaln database (not implemented)."""
         if split_params is None:
             return None

lib/galaxy/datatypes/text.py

@@ -1113,7 +1113,6 @@ def _looks_like_yaml(self, file_prefix: FilePrefix) -> bool:
                 return True
             except yaml.YAMLError:
                 return False
-            return False
 
 
 @build_sniff_from_prefix

lib/galaxy/jobs/runners/state_handlers/_safe_eval.py

@@ -1,5 +1,4 @@
 from ast import (
-    Module,
     parse,
     walk,
 )
@@ -127,8 +126,6 @@ def _check_expression(text, allowed_variables=None):
     except SyntaxError:
         return False
 
-    if not isinstance(module, Module):
-        return False
     statements = module.body
     if not len(statements) == 1:
         return False

lib/galaxy/selenium/context.py

@@ -41,7 +41,7 @@ def screenshot(self, label: str):
         return target
 
     @abstractmethod
-    def _screenshot_path(self, label: str, extension=".png") -> str:
+    def _screenshot_path(self, label: str, extension=".png") -> Optional[str]:
         """Path to store screenshots in."""
 
 

lib/galaxy/tool_util/cwl/parser.py

@@ -293,6 +293,7 @@ class ExpressionToolProxy(CommandLineToolProxy):
 
 class JobProxy:
     def __init__(self, tool_proxy, input_dict, output_dict, job_directory):
+        assert RuntimeContext is not None, "cwltool is not installed, cannot run CWL jobs"
         self._tool_proxy = tool_proxy
         self._input_dict = input_dict
         self._output_dict = output_dict
@@ -327,12 +328,8 @@ def _ensure_cwl_job_initialized(self):
                 beta_relaxed_fmt_check=beta_relaxed_fmt_check,
             )
 
-            args = []
+            args = [RuntimeContext(job_args)]
             kwargs: Dict[str, str] = {}
-            if RuntimeContext is not None:
-                args.append(RuntimeContext(job_args))
-            else:
-                kwargs = job_args
             self._cwl_job = next(self._tool_proxy._tool.job(self._input_dict, self._output_callback, *args, **kwargs))
             self._is_command_line_job = hasattr(self._cwl_job, "command_line")
 

lib/galaxy/tool_util/data/__init__.py

@@ -26,6 +26,7 @@
     Dict,
     List,
     Optional,
+    overload,
     Set,
     Tuple,
     Type,
@@ -878,7 +879,15 @@ def to_dict(self, view: str = "collection", value_mapper: Optional[Dict[str, Cal
         return rval
 
 
-def _expand_here_template(content: str, here: Optional[str]) -> str:
+@overload
+def _expand_here_template(content: str, here: Optional[str]) -> str: ...
+
+
+@overload
+def _expand_here_template(content: None, here: Optional[str]) -> None: ...
+
+
+def _expand_here_template(content: Optional[str], here: Optional[str]) -> Optional[str]:
     if here and content:
         content = string.Template(content).safe_substitute({"__HERE__": here})
     return content

lib/galaxy/tool_util/deps/conda_compat.py

@@ -6,7 +6,6 @@
 """
 
 import os
-from collections.abc import Hashable
 
 import yaml
 
@@ -31,10 +30,6 @@ def __init__(self, func):
         self.cache = {}
 
     def __call__(self, *args):
-        if not isinstance(args, Hashable):
-            # uncacheable. a list, for instance.
-            # better to not cache than blow up.
-            return self.func(*args)
         if args in self.cache:
             return self.cache[args]
         else:

lib/galaxy/tool_util/deps/docker_util.py

@@ -110,7 +110,7 @@ def build_docker_run_command(
     auto_rm: bool = DEFAULT_AUTO_REMOVE,
     set_user: Optional[str] = DEFAULT_SET_USER,
     host: Optional[str] = DEFAULT_HOST,
-    guest_ports: Union[bool, List[str]] = False,
+    guest_ports: Union[bool, str, List[str]] = False,
     container_name: Optional[str] = None,
 ) -> str:
     env_directives = env_directives or []

lib/galaxy/tool_util/linters/xml_order.py

@@ -4,6 +4,8 @@
 https://github.com/galaxy-iuc/standards.
 """
 
+from typing import Optional
+
 # https://github.com/galaxy-iuc/standards
 # https://github.com/galaxy-iuc/standards/pull/7/files
 TAG_ORDER = [
@@ -54,7 +56,7 @@ def lint_xml_order(tool_xml, lint_ctx):
         tag_ordering = TAG_ORDER
 
     last_tag = None
-    last_key = None
+    last_key: Optional[int] = None
     for elem in tool_root:
         tag = elem.tag
         if tag in tag_ordering:

lib/galaxy/tool_util/parser/output_actions.py

@@ -324,7 +324,7 @@ def apply_action(self, output_dataset, other_values) -> None:
             else:
                 # fallback when Cheetah not available, equivalent to how this was handled prior 23.0
                 # definitely not needed for CWL tool parsing
-                log.warning("Cheetah not installed, falling back to legacy 'apply_action' behavior.")
+                log.warning("Cheetah not installed, falling back to legacy 'apply_action' behavior.")  # type: ignore[unreachable]
                 value = self.default
         if value is not None:
             setattr(output_dataset.metadata, self.name, value)

lib/galaxy/tool_util/toolbox/base.py

@@ -763,9 +763,6 @@ def has_tool(self, tool_id: str, tool_version: Optional[str] = None, exact: bool
 
     def is_missing_shed_tool(self, tool_id: str) -> bool:
         """Confirm that the tool ID does reference a shed tool and is not installed."""
-        if tool_id is None:
-            # This is not a tool ID.
-            return False
         if "repos" not in tool_id:
             # This is not a shed tool.
             return False

lib/galaxy/tool_util/verify/__init__.py

@@ -39,7 +39,7 @@
 def verify(
     item_label: str,
     output_content: bytes,
-    attributes: Dict[str, Any],
+    attributes: Optional[Dict[str, Any]],
     filename: Optional[str] = None,
     get_filecontent: Optional[Callable[[str], bytes]] = None,
     get_filename: Optional[Callable[[str], str]] = None,
@@ -51,6 +51,7 @@ def verify(
 
     Throw an informative assertion error if any of these tests fail.
     """
+    attributes = attributes or {}
     if get_filename is None:
         get_filecontent_: Callable[[str], bytes]
         if get_filecontent is None:
@@ -67,7 +68,7 @@ def get_filename(filename: str) -> str:
 
     # Check assertions...
     assertions = attributes.get("assert_list", None)
-    if attributes is not None and assertions is not None:
+    if assertions is not None:
         try:
             verify_assertions(output_content, attributes["assert_list"], attributes.get("decompress", False))
         except AssertionError as err:
@@ -95,9 +96,6 @@ def get_filename(filename: str) -> str:
             errmsg += unicodify(err)
             raise AssertionError(errmsg)
 
-    if attributes is None:
-        attributes = {}
-
     # expected object might be None, so don't pull unless available
     has_expected_object = "object" in attributes
     if has_expected_object:

lib/galaxy/tools/__init__.py

@@ -789,7 +789,7 @@ def __init__(
         # tool_data_table_conf.xml entries exist.
         self.input_params: List[ToolParameter] = []
         # Attributes of tools installed from Galaxy tool sheds.
-        self.tool_shed = None
+        self.tool_shed: Optional[str] = None
         self.repository_name = None
         self.repository_owner = None
         self.changeset_revision = None
@@ -1659,6 +1659,7 @@ def populate_resource_parameters(self, tool_source):
     def populate_tool_shed_info(self, tool_shed_repository):
         if tool_shed_repository:
             self.tool_shed = tool_shed_repository.tool_shed
+            assert self.tool_shed
             self.repository_name = tool_shed_repository.name
             self.repository_owner = tool_shed_repository.owner
             self.changeset_revision = tool_shed_repository.changeset_revision

lib/galaxy/tools/cache.py

@@ -271,23 +271,13 @@ def __init__(self, path: str, modtime: Optional[float] = None, lazy_hash: bool =
             self.hash  # noqa: B018
 
     def modtime_less_than(self, other_modtime: float):
-        if self._modtime is None:
-            # For the purposes of the tool cache,
-            # if we haven't seen the modtime we consider it not equal
-            return True
         return self._modtime < other_modtime
 
     def hash_equals(self, other_hash: Optional[str]):
-        if self._tool_hash is None or other_hash is None:
-            # For the purposes of the tool cache,
-            # if we haven't seen the hash yet we consider it not equal
-            return False
         return self.hash == other_hash
 
     @property
     def modtime(self) -> float:
-        if self._modtime is None:
-            self._modtime = os.path.getmtime(self.path)
         return self._modtime
 
     @modtime.setter