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from __future__ import annotations
import importlib
import os
import re
import types
from enum import Enum
from pathlib import Path
import pytest
import anndata as ad
from anndata._settings import (
SettingsManager,
check_and_get_bool,
check_and_get_environ_var,
validate_bool,
)
option = "test_var"
default_val = False
description = "My doc string!"
option_2 = "test_var_2"
default_val_2 = False
description_2 = "My doc string 2!"
option_3 = "test_var_3"
default_val_3 = [1, 2]
description_3 = "My doc string 3!"
type_3 = list[int]
def validate_int_list(val: list, settings: SettingsManager) -> bool:
if not isinstance(val, list) or not [isinstance(type(e), int) for e in val]:
msg = f"{val!r} is not a valid int list"
raise TypeError(msg)
return True
@pytest.fixture
def settings() -> SettingsManager:
settings = SettingsManager()
settings.register(
option,
default_value=default_val,
description=description,
validate=validate_bool,
)
settings.register(
option_2,
default_value=default_val_2,
description=description_2,
validate=validate_bool,
)
settings.register(
option_3,
default_value=default_val_3,
description=description_3,
validate=validate_int_list,
option_type=type_3,
)
return settings
def test_register_option_default(settings: SettingsManager):
assert getattr(settings, option) == default_val
assert description in settings.describe(option)
def test_register_with_env(settings: SettingsManager, monkeypatch: pytest.MonkeyPatch):
option_env = "test_var_env"
default_val_env = False
description_env = "My doc string env!"
option_env_var = "ANNDATA_" + option_env.upper()
monkeypatch.setenv(option_env_var, "1")
settings.register(
option_env,
default_value=default_val_env,
description=description_env,
validate=validate_bool,
get_from_env=check_and_get_bool,
)
assert settings.test_var_env
def test_register_with_env_enum(
settings: SettingsManager, monkeypatch: pytest.MonkeyPatch
):
option_env = "test_var_env"
default_val_env = False
description_env = "My doc string env!"
option_env_var = "ANNDATA_" + option_env.upper()
monkeypatch.setenv(option_env_var, "b")
class TestEnum(Enum):
a = False
b = True
def check_and_get_bool_enum(option, default_value):
return check_and_get_environ_var(
"ANNDATA_" + option.upper(), "a", cast=TestEnum
).value
settings.register(
option_env,
default_value=default_val_env,
description=description_env,
validate=validate_bool,
get_from_env=check_and_get_bool_enum,
)
assert settings.test_var_env
def test_register_bad_option(settings: SettingsManager):
with pytest.raises(TypeError, match=r"'foo' is not a valid int list"):
settings.register(
"test_var_4",
default_value="foo", # should be a list of ints
description=description_3,
validate=validate_int_list,
option_type=type_3,
)
def test_set_option(settings: SettingsManager):
setattr(settings, option, not default_val)
assert getattr(settings, option) == (not default_val)
settings.reset(option)
assert getattr(settings, option) == default_val
def test_dir(settings: SettingsManager):
assert {option, option_2, option_3} <= set(dir(settings))
assert dir(settings) == sorted(dir(settings))
def test_reset_multiple(settings: SettingsManager):
setattr(settings, option, not default_val)
setattr(settings, option_2, not default_val_2)
settings.reset([option, option_2])
assert getattr(settings, option) == default_val
assert getattr(settings, option_2) == default_val_2
def test_get_unregistered_option(settings: SettingsManager):
with pytest.raises(AttributeError):
setattr(settings, option + "_different", default_val)
def test_override(settings: SettingsManager):
with settings.override(**{option: not default_val}):
assert getattr(settings, option) == (not default_val)
assert getattr(settings, option) == default_val
def test_override_multiple(settings: SettingsManager):
with settings.override(**{option: not default_val, option_2: not default_val_2}):
assert getattr(settings, option) == (not default_val)
assert getattr(settings, option_2) == (not default_val_2)
assert getattr(settings, option) == default_val
assert getattr(settings, option_2) == default_val_2
def test_deprecation(settings: SettingsManager):
warning = "This is a deprecation warning!"
version = "0.1.0"
settings.deprecate(option, version, warning)
described_option = settings.describe(option, should_print_description=False)
# first line is message, second two from deprecation
default_deprecation_message = f"{option} will be removed in {version}.*"
assert described_option.endswith(default_deprecation_message)
described_option = (
described_option.rstrip().removesuffix(default_deprecation_message).rstrip()
)
assert described_option.endswith(warning)
with pytest.warns(
FutureWarning,
match=r"'test_var' will be removed in 0\.1\.0\. This is a deprecation warning!",
):
assert getattr(settings, option) == default_val
def test_deprecation_no_message(settings: SettingsManager):
version = "0.1.0"
settings.deprecate(option, version)
described_option = settings.describe(option, should_print_description=False)
# first line is message, second from deprecation version
assert described_option.endswith(f"{option} will be removed in {version}.*")
def test_option_typing(settings: SettingsManager):
assert settings._registered_options[option_3].type == type_3
assert str(type_3) in settings.describe(option_3, should_print_description=False)
def test_check_and_get_environ_var(monkeypatch: pytest.MonkeyPatch):
option_env_var = "ANNDATA_OPTION"
assert hash("foo") == check_and_get_environ_var(
option_env_var, "foo", ["foo", "bar"], lambda x: hash(x)
)
monkeypatch.setenv(option_env_var, "bar")
assert hash("bar") == check_and_get_environ_var(
option_env_var, "foo", ["foo", "bar"], lambda x: hash(x)
)
monkeypatch.setenv(option_env_var, "Not foo or bar")
with pytest.warns(
match=f"Value '{re.escape(os.environ[option_env_var])}' is not in allowed"
):
check_and_get_environ_var(
option_env_var, "foo", ["foo", "bar"], lambda x: hash(x)
)
assert hash("Not foo or bar") == check_and_get_environ_var(
option_env_var, "foo", cast=lambda x: hash(x)
)
def test_check_and_get_bool(monkeypatch: pytest.MonkeyPatch):
option_env_var = f"ANNDATA_{option.upper()}"
assert not check_and_get_bool(option, default_val)
monkeypatch.setenv(option_env_var, "1")
assert check_and_get_bool(option, default_val)
monkeypatch.setenv(option_env_var, "Not 0 or 1")
with pytest.warns(
match=f"Value '{re.escape(os.environ[option_env_var])}' is not in allowed"
):
check_and_get_bool(option, default_val)
def test_check_and_get_bool_enum(monkeypatch: pytest.MonkeyPatch):
option_env_var = f"ANNDATA_{option.upper()}"
monkeypatch.setenv(option_env_var, "b")
class TestEnum(Enum):
a = False
b = True
assert check_and_get_environ_var(option_env_var, "a", cast=TestEnum).value
@pytest.mark.parametrize(
("as_rst", "expected"),
[
pytest.param(
True,
(
".. attribute:: settings.test_var_3\n"
" :type: list[int]\n"
" :value: [1, 2]\n"
"\n"
" My doc string 3!"
),
id="rst",
),
pytest.param(
False,
"test_var_3: `list[int]`\n My doc string 3! (default: `[1, 2]`).",
id="plain",
),
],
)
def test_describe(*, as_rst: bool, expected: str, settings: SettingsManager):
assert settings.describe("test_var_3", as_rst=as_rst) == expected
def test_hints():
settings = ad.settings
types_loader = importlib.machinery.SourceFileLoader(
"settings_types",
Path(ad.__file__).parent / "_settings.pyi",
)
settings_types_mod = types.ModuleType(types_loader.name)
types_loader.exec_module(settings_types_mod)
obj_attrs, typing_attrs = (
{k for k in dir(o) if not k.startswith("_")}
for o in (settings, settings_types_mod._AnnDataSettingsManager)
)
assert obj_attrs == typing_attrs
|
