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Fix get_required_parameters_for_parameter_table #340

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Merged
dweindl merged 1 commit into from
Dec 11, 2024
Merged

Fix get_required_parameters_for_parameter_table #340

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5 changes: 2 additions & 3 deletions petab/v1/parameters.py
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Original file line number Diff line number Diff line change
Expand Up @@ -332,9 +332,8 @@ def append_overrides(overrides):
if not model.has_entity_with_id(p):
parameter_ids[p] = None

# remove parameters that occur in the condition table and are overridden
# for ALL conditions
for p in condition_df.columns[~condition_df.isnull().any()]:
# parameters that are overridden via the condition table are not allowed
for p in condition_df.columns:
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@dilpath dilpath Dec 11, 2024

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Instead of try-except, could do one of these, but fine as is

for p in set(condition_df.columns).intersection(parameter_ids):
    del parameter_ids[p]

for p in condition_df.columns:
    if p in parameter_ids:
        del parameter_ids[p]

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@dweindl dweindl Dec 11, 2024

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Right, but then one has to look up each element twice.

try:
del parameter_ids[p]
except KeyError:
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7 changes: 2 additions & 5 deletions petab/v2/lint.py
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Expand Up @@ -621,11 +621,8 @@ def append_overrides(overrides):
if not problem.model.has_entity_with_id(p)
)

# remove parameters that occur in the condition table and are overridden
# for ALL conditions
for p in problem.condition_df.columns[
~problem.condition_df.isnull().any()
]:
# parameters that are overridden via the condition table are not allowed
for p in problem.condition_df.columns:
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@dilpath dilpath Dec 11, 2024

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Since parameter IDs is now a set, can change try-except/loop to

parameter_ids -= set(condition_df.columns)

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@dweindl dweindl Dec 11, 2024

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Right, but parameter_ids is still an OrderedDict (we wanted to preserve order here). Only the returned DictKeyView (or similar) acts like a set.

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@dweindl dweindl Dec 11, 2024

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Since it's right before returning, it could be done just on the keys, but then future modifications might easily mess up the ordering. I'd leave it as is until Python has a proper OrderedSet.

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@dilpath dilpath Dec 11, 2024

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Where does it become OrderedDict? In the v1 code it's initialized as an OrderedDict, but here as a set?

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@dweindl dweindl Dec 11, 2024 •
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You are right. I was in v1.
Not sure why I changed it to set there in the first place.

try:
parameter_ids.remove(p)
except KeyError:
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8 changes: 6 additions & 2 deletions petab/v2/problem.py
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Expand Up @@ -32,7 +32,7 @@
from . import experiments

if TYPE_CHECKING:
from ..v2.lint import ValidationIssue, ValidationResultList, ValidationTask
from ..v2.lint import ValidationResultList, ValidationTask


__all__ = ["Problem"]
Expand Down Expand Up @@ -722,7 +722,11 @@ def validate(
Returns:
A list of validation results.
"""
from ..v2.lint import ValidationIssueSeverity, ValidationResultList
from ..v2.lint import (
ValidationIssue,
ValidationIssueSeverity,
ValidationResultList,
)

validation_results = ValidationResultList()
if self.extensions_config:
Expand Down
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