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from string import ascii_letters
import pandas as pd
import pytest
import numpy as np
from scipy import sparse
import anndata as ad
from anndata.tests.helpers import assert_equal, report_name, gen_adata
# Testing to see if all error types can have the key name appended.
# Currently fails for 22/118 since they have required arguments. Not sure what to do about that.
#
# @singledispatch
# def iswarning(x):
# return iswarning(type(x))
# @iswarning.register(type)
# def _notwarning(x):
# return False
# @iswarning.register(Warning)
# def _iswarning(x):
# return True
# @pytest.mark.parametrize("exception", list(filter(lambda t: not iswarning(t), Exception.__subclasses__())))
# def test_report_name_types(exception):
# def throw(e):
# raise e()
# tag = "".join(np.random.permutation(list(ascii_letters)))
# with pytest.raises(exception) as err:
# report_name(throw)(exception, _elem_name=tag)
# assert tag in str(err.value)
@pytest.fixture(scope="function")
def reusable_adata():
"""Reusable anndata for when tests shouldn’t mutate it"""
return gen_adata((10, 10))
# Does this work for every warning?
def test_report_name():
def raise_error():
raise Exception("an error occured!")
letters = np.array(list(ascii_letters))
tag = "".join(np.random.permutation(letters))
with pytest.raises(Exception) as e1:
raise_error()
with pytest.raises(Exception) as e2:
report_name(raise_error)(_elem_name=tag)
assert str(e2.value).startswith(str(e1.value))
assert tag in str(e2.value)
def test_assert_equal():
# ndarrays
assert_equal(np.ones((10, 10)), np.ones((10, 10)))
assert_equal( # Should this require an exact test?
np.ones((10, 10), dtype="i8"), np.ones((10, 10), dtype="f8")
)
assert_equal(
np.array(list(ascii_letters)), np.array(list(ascii_letters)), exact=True
)
with pytest.raises(AssertionError):
assert_equal(np.array(list(ascii_letters)), np.array(list(ascii_letters))[::-1])
adata = gen_adata((10, 10))
adata.raw = adata.copy()
assert_equal(adata, adata.copy(), exact=True)
# TODO: I’m not sure this is good behaviour, I’ve disabled in for now.
# assert_equal(
# adata,
# adata[
# np.random.permutation(adata.obs_names),
# np.random.permutation(adata.var_names),
# ].copy(),
# exact=False,
# )
adata2 = adata.copy()
to_modify = list(adata2.layers.keys())[0]
del adata2.layers[to_modify]
with pytest.raises(AssertionError) as missing_layer_error:
assert_equal(adata, adata2)
assert "layers" in str(missing_layer_error.value)
# `to_modify` will be in pytest info
adata2 = adata.copy()
adata2.layers[to_modify][0, 0] = adata2.layers[to_modify][0, 0] + 1
with pytest.raises(AssertionError) as changed_layer_error:
assert_equal(adata, adata2)
assert "layers" in str(changed_layer_error.value)
assert to_modify in str(changed_layer_error.value)
assert_equal(adata.obs, adata.obs.copy(), exact=True)
csr = sparse.random(100, 100, format="csr")
csc = csr.tocsc()
dense = csr.toarray()
assert_equal(csr, csc)
assert_equal(csc, dense)
assert_equal(dense, csc)
def test_assert_equal_raw():
base = gen_adata((10, 10))
orig = base.copy()
orig.raw = base.copy()
mod = base.copy()
mod.X[0, 0] = mod.X[0, 0] + 1
to_compare = base.copy()
to_compare.raw = mod.copy()
with pytest.raises(AssertionError):
assert_equal(orig, to_compare)
mod = base.copy()
mod.var["new_val"] = 1
to_compare = base.copy()
to_compare.raw = mod.copy()
with pytest.raises(AssertionError):
assert_equal(orig, to_compare)
# TODO: Should views be equal to actual?
# Should they not be if an exact comparison is made?
def test_assert_equal_aligned_mapping():
adata1 = gen_adata((10, 10))
adata2 = adata1.copy()
for attr in ["obsm", "varm", "layers", "obsp", "varp"]:
assert_equal(getattr(adata1, attr), getattr(adata2, attr))
# Checking that subsetting other axis only changes some attrs
obs_subset = adata2[:5, :]
for attr in ["obsm", "layers", "obsp"]:
with pytest.raises(AssertionError):
assert_equal(getattr(adata1, attr), getattr(obs_subset, attr))
for attr in ["varm", "varp"]:
assert_equal(getattr(adata1, attr), getattr(obs_subset, attr))
var_subset = adata2[:, 5:]
for attr in ["varm", "layers", "varp"]:
with pytest.raises(AssertionError):
assert_equal(getattr(adata1, attr), getattr(var_subset, attr))
for attr in ["obsm", "obsp"]:
assert_equal(getattr(adata1, attr), getattr(var_subset, attr))
def test_assert_equal_aligned_mapping_empty():
chars = np.array(list(ascii_letters))
adata = ad.AnnData(
X=np.zeros((10, 10)),
obs=pd.DataFrame([], index=np.random.choice(chars[:20], 10, replace=False)),
var=pd.DataFrame([], index=np.random.choice(chars[:20], 10, replace=False)),
)
diff_idx = ad.AnnData(
X=np.zeros((10, 10)),
obs=pd.DataFrame([], index=np.random.choice(chars[20:], 10, replace=False)),
var=pd.DataFrame([], index=np.random.choice(chars[20:], 10, replace=False)),
)
same_idx = ad.AnnData(adata.X, obs=adata.obs.copy(), var=adata.var.copy())
for attr in ["obsm", "varm", "layers", "obsp", "varp"]:
with pytest.raises(AssertionError):
assert_equal(getattr(adata, attr), getattr(diff_idx, attr))
assert_equal(getattr(adata, attr), getattr(same_idx, attr))
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