diff --git a/src/coverup/codeinfo.py b/src/coverup/codeinfo.py
index f48cf53..6cbddbd 100644
--- a/src/coverup/codeinfo.py
+++ b/src/coverup/codeinfo.py
@@ -7,9 +7,19 @@
 _debug = lambda x: None
 
 
+class Module(ast.Module):
+    def __init__(self, original: ast.Module, path: Path):
+        super().__init__(original.body, original.type_ignores)
+        self.path = path
+
+    def __reduce__(self):
+        # for pickle/deepcopy
+        return (self.__class__, (ast.Module(self.body, self.type_ignores), self.path))
+
+
 # TODO use 'ast' alternative that retains comments?
 
-def _package_path(file: Path) -> T.Optional[T.List[str]]:
+def _package_path(file: Path) -> Path|None:
     """Returns a Python source file's path relative to its package"""
     import sys
 
@@ -18,6 +28,7 @@ def _package_path(file: Path) -> T.Optional[T.List[str]]:
 
     parents = list(file.parents)
 
+    path: str|Path
     for path in sys.path:
         path = Path(path)
         if not path.is_absolute():
@@ -27,33 +38,35 @@ def _package_path(file: Path) -> T.Optional[T.List[str]]:
             if p == path:
                 return file.relative_to(p)
 
+    return None
 
-def _get_fqn(file: Path) -> T.Optional[T.List[str]]:
+
+def _get_fqn(file: Path) -> T.Sequence[str]|None:
     """Returns a source file's Python Fully Qualified Name, as a list name parts."""
     if not (path := _package_path(file)):
-        return none
+        return None
 
     path = path.parent if path.name == '__init__.py' else path.parent / path.stem
     return path.parts
 
 
-def _resolve_from_import(file: Path, imp: ast.ImportFrom) -> str:
+def _resolve_from_import(file: Path, imp: ast.ImportFrom) -> str|None:
     """Resolves the module name in a `from X import Y` statement."""
 
     if imp.level > 0:  # relative import
         if not (pkg_path := _package_path(file)):
             return None
 
-        pkg_path = pkg_path.parts
-        if imp.level > len(pkg_path):
+        pkg_path_parts = pkg_path.parts
+        if imp.level > len(pkg_path_parts):
             return None # would go beyond top-level package
 
-        return ".".join(pkg_path[:-imp.level]) + (f".{imp.module}" if imp.module else "")
+        return ".".join(pkg_path_parts[:-imp.level]) + (f".{imp.module}" if imp.module else "")
 
     return imp.module # absolute from ... import 
 
 
-def _load_module(module_name: str) -> ast.Module | None:
+def _load_module(module_name: str) -> Module | None:
     try:
         if ((spec := importlib.util.find_spec(module_name))
             and spec.origin and spec.origin.endswith('.py')):
@@ -78,10 +91,10 @@ def helper(*args):
     return helper
 
 
-def _handle_import(module: ast.Module, node: ast.Import | ast.ImportFrom, name: T.List[str],
-                   *, paths_seen: T.Set[Path] = None) -> T.Optional[T.List[ast.AST]]:
+def _handle_import(module: Module, node: ast.Import | ast.ImportFrom, name: T.List[str],
+                   *, paths_seen: T.Set[Path]|None = None) -> T.Optional[T.List[ast.AST]]:
 
-    def transition(node: ast.Import | ast.ImportFrom, alias: ast.alias, mod: ast.Module) -> T.List:
+    def transition(node: ast.Import | ast.ImportFrom, alias: ast.alias, mod: Module) -> T.List:
         imp = copy.copy(node)
         imp.names = [alias]
         return [imp, mod]
@@ -127,7 +140,7 @@ def transition(node: ast.Import | ast.ImportFrom, alias: ast.alias, mod: ast.Mod
                     return transition(node, alias, mod) + path
 
 
-def _find_name_path(module: ast.Module, name: T.List[str], *, paths_seen: T.Set[Path] = None) -> T.List[ast.AST]:
+def _find_name_path(module: Module, name: T.List[str], *, paths_seen: T.Set[Path]|None = None) -> T.List[ast.AST]|None:
     """Looks for a symbol's definition by its name, returning the "path" of ast.ClassDef, ast.Import, etc.,
        crossed to find it.
     """
@@ -207,7 +220,7 @@ def _summarize(path: T.List[ast.AST]) -> ast.AST:
                 # Leave "__init__" unmodified as it's likely to contain important member information
                 c.body = [ast.Expr(ast.Constant(value=ast.literal_eval("...")))]
 
-    elif isinstance(path[-1], ast.Module):
+    elif isinstance(path[-1], Module):
         path[-1] = copy.deepcopy(path[-1])
         for c in ast.iter_child_nodes(path[-1]):
             if isinstance(c, (ast.ClassDef, ast.FunctionDef, ast.AsyncFunctionDef)):
@@ -217,7 +230,8 @@ def _summarize(path: T.List[ast.AST]) -> ast.AST:
     for i in reversed(range(len(path)-1)):
         if isinstance(path[i], ast.ClassDef):
             path[i] = copy.copy(path[i])
-            path[i].body = [
+            path_i = T.cast(ast.ClassDef, path[i])
+            path_i.body = [
                 ast.Expr(ast.Constant(value=ast.literal_eval("..."))),
                 path[i+1]
             ]
@@ -225,22 +239,19 @@ def _summarize(path: T.List[ast.AST]) -> ast.AST:
     return path[0]
 
 
-def parse_file(file: Path) -> ast.AST:
+def parse_file(file: Path) -> Module:
     """Reads a python source file, annotating it with its path/filename."""
     with file.open("r") as f:
         tree = ast.parse(f.read())
 
-    assert isinstance(tree, ast.Module)
-    tree._attributes = (*tree._attributes, 'path')
-    tree.path = file
-    return tree
+    return Module(tree, file)
 
 
 def _common_prefix_len(a: T.List[str], b: T.List[str]) -> int:
     return next((i for i, (x, y) in enumerate(zip(a, b)) if x != y), min(len(a), len(b)))
 
 
-def get_global_imports(module: ast.Module, node: ast.AST) -> T.List[ast.Import | ast.ImportFrom]:
+def get_global_imports(module: Module, node: ast.AST) -> T.List[ast.Import | ast.ImportFrom]:
     """Looks for module-level `import`s that (may) define the names seen in "node"."""
 
     def get_names(node: ast.AST):
@@ -291,15 +302,17 @@ def get_imports(n: ast.AST):
     return imports
 
 
-def _find_excerpt(module: ast.Module, line: int) -> ast.AST:
+def _find_excerpt(module: ast.Module, line: int) -> ast.AST|None:
     for node in ast.walk(module):
         if isinstance(node, (ast.FunctionDef, ast.AsyncFunctionDef, ast.ClassDef)):
             begin = min([node.lineno] + [d.lineno for d in node.decorator_list])
             if begin <= line <= node.end_lineno:
                 return node
 
+    return None
+
 
-def get_info(module: ast.Module, name: str, *, line: int = 0, generate_imports: bool = True) -> T.Optional[str]:
+def get_info(module: Module, name: str, *, line: int = 0, generate_imports: bool = True) -> T.Optional[str]:
     """Returns summarized information on a class or function, following imports if necessary."""
 
     key = name.split('.')
diff --git a/src/coverup/coverup.py b/src/coverup/coverup.py
index d9e54a9..9c21ce2 100644
--- a/src/coverup/coverup.py
+++ b/src/coverup/coverup.py
@@ -17,7 +17,7 @@
 from .utils import summary_coverage
 
 
-def get_prompters() -> dict[str, Prompter]:
+def get_prompters() -> dict[str, T.Callable[[T.Any], Prompter]]:
     # in the future, we may dynamically load based on file names.
 
     from .prompt.gpt_v1 import GptV1Prompter
@@ -207,20 +207,19 @@ def positive_int(value):
     return args
 
 
-def test_file_path(test_seq: int) -> Path:
+def test_file_path(args, test_seq: int) -> Path:
     """Returns the Path for a test's file, given its sequence number."""
-    global args
     return args.tests_dir / f"test_{args.prefix}_{test_seq}.py"
 
 
-test_seq = 1
-def new_test_file():
+test_seq: int = 1
+def new_test_file(args):
     """Creates a new test file, returning its Path."""
 
-    global test_seq, args
+    global test_seq
 
     while True:
-        p = test_file_path(test_seq)
+        p = test_file_path(args, test_seq)
         if not (p.exists() or (p.parent / ("disabled_" + p.name)).exists()):
             try:
                 p.touch(exist_ok=False)
@@ -254,7 +253,7 @@ def clean_error(error: str) -> str:
 def log_write(seg: CodeSegment, m: str) -> None:
     """Writes to the log file, opening it first if necessary."""
 
-    global log_file
+    global log_file, args
     if not log_file:
         log_file = open(args.log_file, "a", buffering=1)    # 1 = line buffered
 
@@ -265,6 +264,7 @@ def check_whole_suite() -> None:
     """Check whole suite and disable any polluting/failing tests."""
     import pytest_cleanslate.reduce as reduce
 
+    global args
     pytest_args = (*(("--count", str(args.repeat_tests)) if args.repeat_tests else ()), *args.pytest_args.split())
 
     while True:
@@ -599,7 +599,7 @@ async def improve_coverage(chatter: llm.Chatter, prompter: Prompter, seg: CodeSe
         asked = {'lines': sorted(seg.missing_lines), 'branches': sorted(seg.missing_branches)}
         gained = {'lines': sorted(gained_lines), 'branches': sorted(gained_branches)}
 
-        new_test = new_test_file()
+        new_test = new_test_file(args)
         new_test.write_text(f"# file: {seg.identify()}\n" +\
                             f"# asked: {json.dumps(asked)}\n" +\
                             f"# gained: {json.dumps(gained)}\n\n" +\
diff --git a/src/coverup/llm.py b/src/coverup/llm.py
index 7782377..7b02a04 100644
--- a/src/coverup/llm.py
+++ b/src/coverup/llm.py
@@ -6,6 +6,7 @@
 import textwrap
 import json
 import traceback
+from aiolimiter import AsyncLimiter
 
 with warnings.catch_warnings():
     # ignore pydantic warnings https://github.com/BerriAI/litellm/issues/2832
@@ -88,7 +89,7 @@
 }
 
 
-def token_rate_limit_for_model(model_name: str) -> T.Tuple[int, int]:
+def token_rate_limit_for_model(model_name: str) -> T.Tuple[int, int]|None:
     if model_name.startswith('openai/'):
         model_name = model_name[7:]
 
@@ -107,7 +108,7 @@ def token_rate_limit_for_model(model_name: str) -> T.Tuple[int, int]:
     return None
 
 
-def compute_cost(usage: dict, model_name: str) -> float:
+def compute_cost(usage: dict, model_name: str) -> float|None:
     from math import ceil
 
     if model_name.startswith('openai/'):
@@ -121,7 +122,7 @@ def compute_cost(usage: dict, model_name: str) -> float:
     return None
 
 
-_token_encoding_cache = dict()
+_token_encoding_cache: dict[str, T.Any] = dict()
 def count_tokens(model_name: str, completion: dict):
     """Counts the number of tokens in a chat completion request."""
     import tiktoken
@@ -151,14 +152,15 @@ def __init__(self, model: str) -> None:
         Chatter._validate_model(model)
 
         self._model = model
-        self._model_temperature = None
+        self._model_temperature: float|None = None
         self._max_backoff = 64 # seconds
+        self.token_rate_limit: AsyncLimiter|None
         self.set_token_rate_limit(token_rate_limit_for_model(model))
         self._add_cost = lambda cost: None
         self._log_msg = lambda ctx, msg: None
         self._log_json = lambda ctx, j: None
         self._signal_retry = lambda: None
-        self._functions = dict()
+        self._functions: dict[str, dict[str, T.Any]] = dict()
         self._max_func_calls_per_chat = 50
 
 
@@ -206,7 +208,6 @@ def set_model_temperature(self, temperature: T.Optional[float]) -> None:
 
     def set_token_rate_limit(self, limit: T.Union[T.Tuple[int, int], None]) -> None:
         if limit:
-            from aiolimiter import AsyncLimiter
             self.token_rate_limit = AsyncLimiter(*limit)
         else:
             self.token_rate_limit = None
@@ -239,10 +240,10 @@ def set_signal_retry(self, signal_retry: T.Callable) -> None:
     def add_function(self, function: T.Callable) -> None:
         """Makes a function availabe to the LLM."""
         if not litellm.supports_function_calling(self._model):
-            raise ChatterError(f"The {f._model} model does not support function calling.")
+            raise ChatterError(f"The {self._model} model does not support function calling.")
 
         try:
-            schema = json.loads(function.__doc__)
+            schema = json.loads(getattr(function, "__doc__", ""))
             if 'name' not in schema:
                 raise ChatterError("Name missing from function {function} schema.")
         except json.decoder.JSONDecodeError as e:
@@ -263,7 +264,7 @@ def _request(self, messages: T.List[dict]) -> dict:
         }
 
 
-    async def _send_request(self, request: dict, ctx: object) -> dict:
+    async def _send_request(self, request: dict, ctx: object) -> litellm.ModelResponse|None:
         """Sends the LLM chat request, handling common failures and returning the response."""
 
         sleep = 1
@@ -319,7 +320,7 @@ async def _send_request(self, request: dict, ctx: object) -> dict:
                 return None # gives up this segment
 
 
-    def _call_function(self, ctx: object, tool_call: dict) -> str:
+    def _call_function(self, ctx: object, tool_call: litellm.ModelResponse) -> str:
         args = json.loads(tool_call.function.arguments)
         function = self._functions[tool_call.function.name]
 
@@ -335,7 +336,7 @@ def _call_function(self, ctx: object, tool_call: dict) -> str:
             return f'Error executing function: {e}'
 
 
-    async def chat(self, messages: list, *, ctx: T.Optional[object] = None) -> dict:
+    async def chat(self, messages: list, *, ctx: T.Optional[object] = None) -> dict|None:
         """Chats with the LLM, sending the given messages, handling common failures and returning the response.
            Automatically calls any tool functions requested."""
 
diff --git a/src/coverup/prompt/claude.py b/src/coverup/prompt/claude.py
index 0b8daca..4a68b32 100644
--- a/src/coverup/prompt/claude.py
+++ b/src/coverup/prompt/claude.py
@@ -1,5 +1,6 @@
 import typing as T
 from .prompter import Prompter, CodeSegment, mk_message, get_module_name
+from ..utils import lines_branches_do
 
 
 class ClaudePrompter(Prompter):
diff --git a/src/coverup/prompt/gpt_v1.py b/src/coverup/prompt/gpt_v1.py
index c53809e..7cbd5f9 100644
--- a/src/coverup/prompt/gpt_v1.py
+++ b/src/coverup/prompt/gpt_v1.py
@@ -1,5 +1,6 @@
 import typing as T
 from .prompter import Prompter, CodeSegment, mk_message, get_module_name
+from ..utils import lines_branches_do
 
 
 class GptV1Prompter(Prompter):
diff --git a/src/coverup/prompt/prompter.py b/src/coverup/prompt/prompter.py
index a142899..dc33eec 100644
--- a/src/coverup/prompt/prompter.py
+++ b/src/coverup/prompt/prompter.py
@@ -34,7 +34,7 @@ def get_functions(self) -> T.List[T.Callable]:
         return []
 
 
-def get_module_name(src_file: Path, base_dir: Path) -> str:
+def get_module_name(src_file: Path, base_dir: Path) -> str|None:
     # assumes both src_file and src_dir Path.resolve()'d
     try:
         relative = src_file.relative_to(base_dir)
diff --git a/src/coverup/utils.py b/src/coverup/utils.py
index 6f15171..c9ef6a8 100644
--- a/src/coverup/utils.py
+++ b/src/coverup/utils.py
@@ -49,7 +49,7 @@ def lines_branches_do(lines: T.Set[int], neg_lines: T.Set[int], branches: T.Set[
     return s
 
 
-async def subprocess_run(args: str, check: bool = False, timeout: T.Optional[int] = None) -> subprocess.CompletedProcess:
+async def subprocess_run(args: T.Sequence[str], check: bool = False, timeout: T.Optional[int] = None) -> subprocess.CompletedProcess:
     """Provides an asynchronous version of subprocess.run"""
     import asyncio
 
@@ -75,10 +75,11 @@ async def subprocess_run(args: str, check: bool = False, timeout: T.Optional[int
             timeout_f = 0.0
         raise subprocess.TimeoutExpired(args, timeout_f) from None
 
-    if check and process.returncode != 0:
+    if check and process.returncode:
         raise subprocess.CalledProcessError(process.returncode, args, output=output)
 
-    return subprocess.CompletedProcess(args=args, returncode=process.returncode, stdout=output)
+    # process.returncode is None iff the process hasn't terminated yet
+    return subprocess.CompletedProcess(args=args, returncode=T.cast(int, process.returncode), stdout=output)
 
 
 def summary_coverage(cov: dict, sources: T.List[Path]) -> str:
diff --git a/tests/test_coverup_13.py b/tests/test_coverup_13.py
index 860eb12..5dbdb4d 100644
--- a/tests/test_coverup_13.py
+++ b/tests/test_coverup_13.py
@@ -1,35 +1,19 @@
-# file src/coverup/coverup.py:142-145
-# lines [145]
-# branches []
-
 import pytest
 from pathlib import Path
 from unittest.mock import MagicMock
 
-# Assuming the 'args' is part of a larger module or context, we'll need to mock it
-# For the purpose of this example, let's assume 'args' is an attribute of a module named 'coverup'
-# We will also assume that 'coverup.args' has 'tests_dir' and 'prefix' attributes
 
-# Mocking the 'coverup' module
 class MockArgs:
     def __init__(self, tests_dir, prefix):
         self.tests_dir = Path(tests_dir)
         self.prefix = prefix
 
-@pytest.fixture
-def mock_args(monkeypatch):
-    # Setup the mock
-    mock_args = MockArgs('/tmp', 'mock_prefix')
-    monkeypatch.setattr('coverup.coverup.args', mock_args, raising=False)
-    # Teardown code to clean up after the test
-    yield
-    # No teardown needed as monkeypatch will undo the patching after the test
 
-def test_file_path_executes_line_145(mock_args):
+def test_file_path():
     from coverup.coverup import test_file_path
+    mock_args = MockArgs('/tmp', 'mock_prefix')
 
     test_seq = 1
-    expected_path = Path('/tmp') / f"test_mock_prefix_{test_seq}.py"
-    actual_path = test_file_path(test_seq)
+    actual_path = test_file_path(mock_args, test_seq)
     
-    assert actual_path == expected_path, "The test_file_path function did not return the expected file path"
+    assert actual_path == Path('/tmp') / f"test_mock_prefix_{test_seq}.py"