TYP: add missing type annotations to enable mypy's strict mode

pyproject.toml

@@ -111,11 +111,10 @@ exclude_lines = [
 
 [tool.mypy]
 python_version = '3.10'
+strict = true
 show_error_codes = true
-warn_unused_configs = true
-warn_unused_ignores = true
-warn_unreachable = true
 show_error_context = true
+warn_unused_ignores = true
 
 [tool.pytest.ini_options]
 minversion = "6.0"

src/idefix_cli/_backports.py

@@ -1,3 +1,5 @@
+# type: ignore
+
 import os
 import sys
 

src/idefix_cli/_commands/clean.py

@@ -66,7 +66,7 @@ def add_arguments(parser: ArgumentParser) -> None:
 
 
 def command(
-    directory, clean_all: bool = False, dry: bool = False, confirm: bool = True
+    directory: str, clean_all: bool = False, dry: bool = False, confirm: bool = True
 ) -> int:
     origin = os.path.abspath(os.curdir)
     with chdir(directory):

src/idefix_cli/_commands/clone.py

@@ -5,6 +5,8 @@
 import os
 import shutil
 import sys
+from argparse import ArgumentParser
+from collections.abc import Generator, Sequence
 from pathlib import Path
 from tempfile import TemporaryDirectory
 from typing import TYPE_CHECKING
@@ -81,14 +83,14 @@ def exists(self) -> bool:
             return self._path.exists()
 
         @property
-        def parent(self):
+        def parent(self) -> Path:
             return self._path.parent
 
         @property
-        def parents(self):
+        def parents(self) -> Sequence[Path]:
             return self._path.parents
 
-        def glob(self, *args):
+        def glob(self, *args: str) -> Generator[Path, None, None]:
             return self._path.glob(*args)
 
         def __str__(self) -> str:
@@ -105,7 +107,7 @@ def get_include_from_conf() -> list[str]:
     return raw.split()
 
 
-def add_arguments(parser) -> None:
+def add_arguments(parser: ArgumentParser) -> None:
     parser.add_argument(
         "source",
         default="",
@@ -156,7 +158,7 @@ def command(
         include = []
 
     files_and_dirs_to_copy = files_from_patterns(
-        str(source),
+        Path(str(source)),
         *BASE_INCLUDE,
         *include,
         *get_include_from_conf(),

src/idefix_cli/_commands/conf.py

@@ -224,7 +224,7 @@ def substitute_cmake_args(args: list[str]) -> list[str]:
     return args
 
 
-def add_arguments(parser) -> None:
+def add_arguments(parser: ArgumentParser) -> None:
     parser.add_argument("--dir", dest="directory", default=".", help="target directory")
 
     parser.add_argument(

src/idefix_cli/_commands/digest.py

@@ -5,14 +5,14 @@
 from argparse import ArgumentParser
 from pathlib import Path
 from time import monotonic_ns
-from typing import Any
+from typing import Any, TextIO
 
 from idefix_cli.lib import print_error
 
 _LOG_LINE_REGEXP = re.compile(r"^(?P<trailer>TimeIntegrator:)(?P<data>.*\|.*)")
 
 
-def _log_to_data(log: list[str]):
+def _log_to_data(log: list[str]) -> dict[str, list[Any]]:
     columns: dict[str, list[Any]] = {name.strip(): [] for name in log[0].split("|")}
     tokenized_log = [line.replace("N/A", "NaN").split("|") for line in log[1:]]
     for i, name in enumerate(columns.keys()):
@@ -87,11 +87,11 @@ def add_arguments(parser: ArgumentParser) -> None:
 def command(
     dir: str,
     input_: list[str] | None = None,
-    output=sys.stdout,
+    output: TextIO = sys.stdout,
     all_files: bool = False,
     timeit: bool = False,
     *,
-    _log_line_regexp=_LOG_LINE_REGEXP,
+    _log_line_regexp: re.Pattern[str] = _LOG_LINE_REGEXP,
 ) -> int:
     pdir = Path(dir)
     if not pdir.is_dir():

src/idefix_cli/_commands/read.py

@@ -3,14 +3,15 @@
 from __future__ import annotations
 
 import json
+from argparse import ArgumentParser
 from pathlib import Path
 
 import inifix
 
 from idefix_cli.lib import print_error
 
 
-def add_arguments(parser) -> None:
+def add_arguments(parser: ArgumentParser) -> None:
     parser.add_argument("inifile", type=str, help="target inifile")
     parser.add_argument(
         "--indent", type=int, help="indentation in spaces (default is flat output)"

src/idefix_cli/_commands/run.py

@@ -6,6 +6,7 @@
 import re
 import subprocess
 import sys
+from argparse import ArgumentParser
 from copy import deepcopy
 from enum import auto
 from math import prod
@@ -38,7 +39,7 @@
 else:
     from typing_extensions import assert_never
 
-    from idefix_cli._backports import StrEnum
+    from idefix_cli._backports import StrEnum  # type: ignore [attr-defined]
     from idefix_cli.lib import chdir
 
 MAIN_LOG_FILE = "idefix.0.log"
@@ -124,7 +125,7 @@ def get_command(
     return cmd
 
 
-class RebuildMode(StrEnum):
+class RebuildMode(StrEnum):  # type: ignore [misc]
     ALWAYS = auto()
     PROMPT = auto()
 
@@ -156,11 +157,11 @@ def get_cpu_count() -> int:
 
 
 def get_highest_power_of_two(n_max: int) -> int:
-    return 2 ** (n_max.bit_length() - 1)
+    return 1 << (n_max.bit_length() - 1)
 
 
 @requires_idefix()
-def build_idefix(directory) -> int:
+def build_idefix(directory: str) -> int:
     ncpus = min(8, get_highest_power_of_two(get_cpu_count()))
     cmd = ["make", "-j", str(ncpus)]
     return run_subcommand(cmd, loc=Path(directory), err="failed to build idefix")
@@ -189,7 +190,7 @@ def parse_ncycles(unknown_args: tuple[str, ...], ncycles: int) -> tuple[str, ...
         return unknown_args
 
 
-def add_arguments(parser) -> None:
+def add_arguments(parser: ArgumentParser) -> None:
     parser.add_argument("--dir", dest="directory", default=".", help="target directory")
     parser.add_argument(
         "-i",
@@ -358,11 +359,11 @@ def command(
         rebuild_mode = RebuildMode(rebuild_mode_str)
     except ValueError:
         print_warning(
-            f"Expected [idfx run].recompile to be any of {[str(_) for _ in RebuildMode]}"
+            f"Expected [idfx run].recompile to be any of {[str(_) for _ in RebuildMode]}"  # type: ignore [attr-defined]
             f"Got {rebuild_mode_str!r} from {get_config_file()}\n"
         )
         print_warning("Falling back to 'prompt' mode.")
-        rebuild_mode = RebuildMode.PROMPT
+        rebuild_mode = RebuildMode.PROMPT  # type: ignore [assignment]
 
     build_is_required: bool = True
     if rebuild_mode is RebuildMode.ALWAYS:

src/idefix_cli/_commands/switch.py

@@ -1,12 +1,13 @@
 """switch git branch in $IDEFIX_DIR using git checkout"""
 
 import os
+from argparse import ArgumentParser
 from pathlib import Path
 
 from idefix_cli.lib import print_error, requires_idefix, run_subcommand
 
 
-def add_arguments(parser):
+def add_arguments(parser: ArgumentParser) -> None:
     parser.add_argument(
         "branch",
         default="-",

src/idefix_cli/_commands/write.py

@@ -2,6 +2,7 @@
 
 import json
 import sys
+from argparse import ArgumentParser
 from contextlib import ExitStack
 from io import TextIOBase
 from pathlib import Path
@@ -11,7 +12,7 @@
 from idefix_cli.lib import print_error
 
 
-def add_arguments(parser) -> None:
+def add_arguments(parser: ArgumentParser) -> None:
     parser.add_argument("dest", type=str, help="dest inifile")
     parser.add_argument(
         "source",

src/idefix_cli/_theme.py

@@ -1,5 +1,6 @@
 import sys
 import unicodedata
+from collections.abc import Generator
 from contextlib import contextmanager
 from dataclasses import dataclass
 from typing import Literal, TypedDict
@@ -34,7 +35,7 @@ def register(
         symbols: SymbolSet,
         enter: str | None = None,
         exit: str | None = None,
-    ):
+    ) -> None:
         self._registry[name] = Theme(
             name=name, symbols=symbols, enter_msg=enter, exit_msg=exit
         )
@@ -79,7 +80,7 @@ def get_symbol(key: Literal["LAUNCH", "SUCCESS", "WARNING", "ERROR", "HINT"]) ->
 
 
 @contextmanager
-def theme_ctx(name: str):
+def theme_ctx(name: str) -> Generator[None, None, None]:
     global THEME
     old_name = THEME.name
     THEME = themes[name]

src/idefix_cli/lib.py

@@ -22,7 +22,7 @@
 if sys.version_info >= (3, 11):
     from enum import StrEnum
 else:
-    from idefix_cli._backports import StrEnum
+    from idefix_cli._backports import StrEnum  # type: ignore[attr-defined]
 
 # workaround mypy not being confortable around decorator preserving signatures
 # adapted from
@@ -53,14 +53,14 @@
 __all__.append("chdir")
 
 
-class _WindowsTree(StrEnum):
+class _WindowsTree(StrEnum):  # type: ignore [misc]
     TRUNK = "|"
     FORK = "|-"
     ANGLE = "'-"
     BRANCH = "-"
 
 
-class _PosixTree(StrEnum):
+class _PosixTree(StrEnum):  # type: ignore [misc]
     TRUNK = "│"
     FORK = "├"
     ANGLE = "└"
@@ -102,7 +102,7 @@ class requires_idefix:
 
     def __call__(self, f: TFun) -> TFun:
         @wraps(f)
-        def wrapper(*args, **kwargs) -> Any:
+        def wrapper(*args: Any, **kwargs: Any) -> Any:
             if (IDEFIX_DIR := os.getenv("IDEFIX_DIR")) is None:
                 print_error(
                     "this functionality requires $IDEFIX_DIR to be defined",
@@ -260,8 +260,8 @@ def run_subcommand(
 
 
 def files_from_patterns(
-    source,
-    *patterns,
+    source: os.PathLike[str],
+    *patterns: str,
     recursive: bool = False,
     excludes: list[str] | None = None,
 ) -> list[str]:
@@ -447,17 +447,17 @@ def prompt_ask(prompt: str, /) -> bool:
         print("Please enter y or n", file=sys.stderr)
 
 
-def __getattr__(attr: str):
+def __getattr__(attr: str) -> Any:
     # avoid leaking more than intended from the standard library
     if attr == "chdir":
         if sys.version_info >= (3, 11):
             from contextlib import chdir
         else:
-            from idefix_cli._backports import chdir
+            from idefix_cli._backports import chdir  # type: ignore [attr-defined]
         return chdir
     else:
         raise AttributeError(f"Unknown attribute {attr!r}")
 
 
-def __dir__():
+def __dir__() -> list[str]:
     return list(globals()) + ["chdir"]

tests/test_app_structure.py

@@ -81,7 +81,9 @@ def test_plugins(isolated_conf_dir, tmp_path, capsys):
             dedent(
                 """
                 'test extension command'
-                def add_arguments(parser) -> None:
+                from argparse import ArgumentParser
+
+                def add_arguments(parser: ArgumentParser) -> None:
                     return
 
                 def command() -> int: