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Add the n_protocol_dag_results property to ProtocolResult #381

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merged 12 commits into from
Nov 26, 2024
Merged

Add the n_protocol_dag_results property to ProtocolResult #381

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bab5f38
Added the n_protocol_dag_results property to ProtocolResult
ianmkenney Oct 30, 2024
dc48543
Merge remote-tracking branch 'origin/main' into feature/protocolresul…
ianmkenney Oct 30, 2024
d97cf22
Modified test and fixed typo
ianmkenney Oct 30, 2024
2aa451f
Added a test for the infinite generator guardrail
ianmkenney Oct 30, 2024
ef9c926
Merge branch 'main' into feature/protocolresult_n_protocol_dag_results
IAlibay Oct 31, 2024
3b5ca83
Replaced Optional[int] (default None) with int (default 0)
ianmkenney Oct 31, 2024
1c8bf8c
Added more tests for the ProtocolResult
ianmkenney Oct 31, 2024
32a8d1a
Merge remote-tracking branch 'origin/main' into feature/protocolresul…
ianmkenney Nov 1, 2024
8fe3e24
Refactor ProtocolResult._from_dict
ianmkenney Nov 21, 2024
8d7f3b7
Add test for creating a ProtocolResult from dict with missing data
ianmkenney Nov 21, 2024
3bac74d
Merge remote-tracking branch 'upstream/main' into feature/protocolres…
ianmkenney Nov 21, 2024
6cdbb72
Merge branch 'main' into feature/protocolresult_n_protocol_dag_results
ianmkenney Nov 26, 2024
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20 changes: 17 additions & 3 deletions gufe/protocols/protocol.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
"""

import abc
from typing import Optional, Iterable, Any, Union
from typing import Optional, Iterable, Any, Union, Sized
from openff.units import Quantity
import warnings

Expand All @@ -32,8 +32,11 @@ class ProtocolResult(GufeTokenizable):
- `get_uncertainty`
"""

def __init__(self, **data):
def __init__(self, n_protocol_dag_results: Optional[int] = None, **data):
self._data = data
self._n_protocol_dag_results = (
n_protocol_dag_results if n_protocol_dag_results is not None else 0
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I'm trying to wrap my head around the use case here, could you explain the case where None happens? I.e. at first glance setting None to zero seems incorrect if None means that the gather method did not pass through a value. In that case None means undefined and it's much cleaner than getting 0 with the idea that you got no results (but you do).

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I think in the context of a Protocol's gather, you'll never see a None passed in. I can see instances where ProtocolResults are used directly, incorrectly or not, and a None would make sense. But of course I immediately throw away the None in the code you highlighted above. I suppose there is still some indecision on my part what the right signature should be and which values the ProtocolResult holds on to. I'm tempted to just drop Optional[int] and use int with default 0.

Just from the tests, I see instances where someone would make a ProtocolResult directly and I'll probably do something similar in testing parts of stratocaster downstream:

class DummyProtocolResult(gufe.ProtocolResult):
    def get_estimate(self):
        return self.data['estimate']

    def get_uncertainty(self):
        return self.data['uncertainty']


class TestProtocolResult(GufeTokenizableTestsMixin):
    cls = DummyProtocolResult
    key = 'DummyProtocolResult-b7b854b39c1e37feabec58b4000680a0'
    repr = f'<{key}>'

    @pytest.fixture
    def instance(self):
        return DummyProtocolResult(
            estimate=4.2 * unit.kilojoule_per_mole,
            uncertainty=0.2 * unit.kilojoule_per_mole,
        )

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Thanks @ianmkenney - is this a time critical thing? I would like to spend a bit of time to check what this means for the existing Protocols, but I don't think I'll have time until Monday :(

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Not necessarily. I'll be testing stratocaster strategies based on this branch until it's merged in the hopes that we get some solution that's close in spirit to what we have here.

)

@classmethod
def _defaults(cls):
Expand All @@ -46,6 +49,10 @@ def _to_dict(self):
def _from_dict(cls, dct: dict):
return cls(**dct['data'])

@property
def n_protocol_dag_results(self) -> int:
return self._n_protocol_dag_results

@property
def data(self) -> dict[str, Any]:
"""
Expand Down Expand Up @@ -254,7 +261,14 @@ def gather(
ProtocolResult
Aggregated results from many `ProtocolDAGResult`s from a given `Protocol`.
"""
return self.result_cls(**self._gather(protocol_dag_results))
# Iterable does not implement __len__ and makes no guarantees that
# protocol_dag_results is finite, checking both in method signature
# doesn't appear possible, explicitly check for __len__ through the
# Sized type
if not isinstance(protocol_dag_results, Sized):
raise ValueError("`protocol_dag_results` must implement `__len__`")
return self.result_cls(n_protocol_dag_results=len(protocol_dag_results),
**self._gather(protocol_dag_results))

@abc.abstractmethod
def _gather(
Expand Down
22 changes: 21 additions & 1 deletion gufe/tests/test_protocol.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
import datetime
import itertools
from openff.units import unit
from typing import Optional, Iterable, List, Dict, Any, Union
from typing import Optional, Iterable, List, Dict, Any, Union, Sized
from collections import defaultdict
import pathlib

Expand Down Expand Up @@ -328,11 +328,31 @@ def test_create_execute_gather(self, protocol_dag):
# gather aggregated results of interest
protocolresult = protocol.gather([dagresult])

assert protocolresult.n_protocol_dag_results == 1
assert len(protocolresult.data['logs']) == 1
assert len(protocolresult.data['logs'][0]) == 21 + 1

assert protocolresult.get_estimate() == 95500.0

def test_gather_infinite_iterable_guardrail(self, protocol_dag):
protocol, dag, dagresult = protocol_dag

assert dagresult.ok()

# we want an infinite generator, but one that would actually stop early in case
# the guardrail doesn't work, but the type system doesn't know that
def infinite_generator():
while True:
yield dag
break

gen = infinite_generator()
assert isinstance(gen, Iterable)
assert not isinstance(gen, Sized)

with pytest.raises(ValueError, match="`protocol_dag_results` must implement `__len__`"):
protocol.gather(infinite_generator())

def test_deprecation_warning_on_dict_mapping(self, instance, vacuum_ligand, solvated_ligand):
lig = solvated_ligand.components['ligand']
mapping = gufe.LigandAtomMapping(lig, lig, componentA_to_componentB={})
Expand Down
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