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Refactor utility functions #55

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merged 15 commits into from
May 18, 2021
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Merged

Refactor utility functions #55

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b556c41
move operations and transform util files into a dedicated utils folder
gwaybio May 11, 2021
de4a799
move testing util files to a new test_utils folder
gwaybio May 11, 2021
2c33899
move assert_melt function to test_utils folder
gwaybio May 11, 2021
ec476eb
update util imports in all files
gwaybio May 11, 2021
6daa7dd
update util import statements in tests
gwaybio May 11, 2021
c7a6f69
split util files into better named files
gwaybio May 11, 2021
0328ceb
split util files into new test files
gwaybio May 11, 2021
e7aa8ed
fix assertion tolerance
gwaybio May 12, 2021
c730a0b
fix np builtin type deprecation in 1.2
gwaybio May 12, 2021
03c09ee
revert back to deprecated check_less_precise
gwaybio May 12, 2021
bdb9c78
add util init file
gwaybio May 18, 2021
ec01949
Update cytominer_eval/tests/test_operations/test_mp_value.py
gwaybio May 18, 2021
e450cff
Update cytominer_eval/tests/test_utils/test_availability_utils.py
gwaybio May 18, 2021
16df0c7
Update cytominer_eval/tests/test_utils/test_grit_utils.py
gwaybio May 18, 2021
5d2215c
Apply suggestions from code review
gwaybio May 18, 2021
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4 changes: 2 additions & 2 deletions cytominer_eval/evaluate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
from typing import List, Union

from cytominer_eval.transform import metric_melt
from cytominer_eval.transform.util import check_replicate_groups
from cytominer_eval.utils.transform_utils import check_replicate_groups
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For me, this line gives an error because utils are not imported here or in the init.py file. But I am unsure why the tests don't give that error?

This applies to all imports of util below

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oh interesting, what is the error?

Is it possible that your testing environment is out-of-date?

I also added a __init__.py file inside cytominer_eval/utils - so this might help. It should have been there in the first place, so thanks for making this note.

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Yea I know it works, for some reason pycharm is complaining about it. I think it's because if you run that file on its own, it won't find the util.
but all good

from cytominer_eval.operations import (
replicate_reproducibility,
precision_recall,
Expand All @@ -25,7 +25,7 @@ def evaluate(
replicate_groups: Union[List[str], dict],
operation: str = "replicate_reproducibility",
similarity_metric: str = "pearson",
replicate_reproducibility_quantile: np.float = 0.95,
replicate_reproducibility_quantile: float = 0.95,
replicate_reproducibility_return_median_cor: bool = False,
precision_recall_k: Union[int, List[int]] = 10,
grit_control_perts: List[str] = ["None"],
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11 changes: 4 additions & 7 deletions cytominer_eval/operations/enrichment.py
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Expand Up @@ -5,20 +5,17 @@
from typing import List, Union
import scipy

from .util import assign_replicates, calculate_grit, check_grit_replicate_summary_method
from cytominer_eval.transform.util import (
set_pair_ids,
set_grit_column_info,
assert_melt,
)
from cytominer_eval.utils.operation_utils import assign_replicates
from cytominer_eval.utils.transform_utils import set_pair_ids, assert_melt


def enrichment(
similarity_melted_df: pd.DataFrame,
replicate_groups: List[str],
percentile: Union[float, List[float]],
) -> pd.DataFrame:
"""Calculate the enrichment score. This score is based on the fisher exact odds score. Similar to the other functions, the closest connections are determined and checked with the replicates.
"""Calculate the enrichment score. This score is based on the fisher exact odds score.
Similar to the other functions, the closest connections are determined and checked with the replicates.
This score effectively calculates how much better the distribution of correct connections is compared to random.

Parameters
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9 changes: 5 additions & 4 deletions cytominer_eval/operations/grit.py
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Expand Up @@ -8,11 +8,12 @@
import pandas as pd
from typing import List

from .util import assign_replicates, calculate_grit, check_grit_replicate_summary_method
from cytominer_eval.transform.util import (
set_pair_ids,
from cytominer_eval.utils.operation_utils import assign_replicates
from cytominer_eval.utils.transform_utils import set_pair_ids, assert_melt
from cytominer_eval.utils.grit_utils import (
check_grit_replicate_summary_method,
set_grit_column_info,
assert_melt,
calculate_grit,
)


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2 changes: 1 addition & 1 deletion cytominer_eval/operations/mp_value.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
import pandas as pd
from typing import List

from .util import calculate_mp_value
from cytominer_eval.utils.mpvalue_utils import calculate_mp_value


def mp_value(
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5 changes: 3 additions & 2 deletions cytominer_eval/operations/precision_recall.py
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Expand Up @@ -6,8 +6,9 @@
import pandas as pd
from typing import List, Union

from .util import assign_replicates, calculate_precision_recall
from cytominer_eval.transform.util import set_pair_ids, assert_melt
from cytominer_eval.utils.precisionrecall_utils import calculate_precision_recall
from cytominer_eval.utils.operation_utils import assign_replicates
from cytominer_eval.utils.transform_utils import set_pair_ids, assert_melt


def precision_recall(
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8 changes: 4 additions & 4 deletions cytominer_eval/operations/replicate_reproducibility.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,16 +5,16 @@
import pandas as pd
from typing import List

from .util import assign_replicates, set_pair_ids
from cytominer_eval.transform.util import assert_melt
from cytominer_eval.utils.operation_utils import assign_replicates, set_pair_ids
from cytominer_eval.utils.transform_utils import assert_melt


def replicate_reproducibility(
similarity_melted_df: pd.DataFrame,
replicate_groups: List[str],
quantile_over_null: np.float = 0.95,
quantile_over_null: float = 0.95,
return_median_correlations: bool = False,
) -> np.float:
) -> float:
r"""Summarize pairwise replicate correlations

For a given pairwise similarity matrix, replicate information, and specific options,
Expand Down
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