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WIP: check for unknown kwargs in Index.select #2663

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WIP: check for unknown kwargs in Index.select #2663

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291ece7
check for unknown kwargs in select
ctb Jun 28, 2023
8f58a1f
Merge branch 'try-submanifest' into more_submanifest
ctb Sep 4, 2023
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16 changes: 16 additions & 0 deletions src/sourmash/index/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,13 @@
flatten_and_downsample_num,
flatten_and_intersect_scaled)

def _check_for_unknown_select_params(kwargs):
legit_param_names = { 'ksize', 'moltype', 'scaled', 'num', 'abund',
'containment', 'picklist', 'filter_manifest' } # @CTB picklist
kk = set(kwargs.keys())
assert kk.issubset(legit_param_names), kk - legit_param_names


Comment on lines +52 to +58
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Might be relevant: in #2726 I defined a Selection TypedDict to be able to

  1. use type checking
  2. being able to more easily convert a selection to Rust (the _selection_as_rust function).

Then the method signature for select becomes
def select(self, **kwargs: Unpack[Selection]):

(This is slightly annoying because the select method needs to extract the values from kwargs...)

PEP-692 has more details

# generic return tuple for Index.search and Index.gather
IndexSearchResult = namedtuple('Result', 'score, signature, location')

Expand Down Expand Up @@ -413,6 +420,8 @@ def select(self, **kwargs):

Does not raise ValueError, but may return an empty Index.
"""
_check_for_unknown_select_params(kwargs)

siglist = []
for ss in self._signatures:
if select_signature(ss, **kwargs):
Expand Down Expand Up @@ -484,6 +493,8 @@ def select(self, **kwargs):

Does not raise ValueError, but may return an empty Index.
"""
_check_for_unknown_select_params(kwargs)

selection_dict = dict(self.selection_dict)
for k, v in kwargs.items():
if k in selection_dict:
Expand Down Expand Up @@ -644,6 +655,7 @@ def signatures(self):

def select(self, **kwargs):
"Select signatures in zip file based on ksize/moltype/etc."
_check_for_unknown_select_params(kwargs)

# if we have a manifest, run 'select' on the manifest.
manifest = self.manifest
Expand Down Expand Up @@ -1055,6 +1067,8 @@ def save(self, *args):

def select(self, **kwargs):
"Run 'select' on the manifest."
_check_for_unknown_select_params(kwargs)

new_manifest = self.manifest.select_to_manifest(**kwargs)
return MultiIndex(new_manifest, self.parent,
prepend_location=self.prepend_location)
Expand Down Expand Up @@ -1164,6 +1178,8 @@ def insert(self, *args):

def select(self, **kwargs):
"Run 'select' on the manifest."
_check_for_unknown_select_params(kwargs)

new_manifest = self.manifest.select_to_manifest(**kwargs)
return StandaloneManifestIndex(new_manifest, self._location,
prefix=self.prefix)
3 changes: 2 additions & 1 deletion src/sourmash/sbt.py
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Original file line number Diff line number Diff line change
Expand Up @@ -192,7 +192,8 @@ def _signatures_with_internal(self):
yield ss, k._path

def select(self, ksize=None, moltype=None, num=0, scaled=0,
containment=False, abund=None, picklist=None, filter_manifest=None):
containment=False, abund=None, picklist=None,
filter_manifest=None):
"""Make sure this database matches the requested requirements.

Will always raise ValueError if a requirement cannot be met.
Expand Down