From 5ad28e246084af96361ea4904517c03a2c952262 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Tue, 8 Oct 2024 14:46:15 +0200
Subject: [PATCH] Add deprecation warnings to old `TopHits` query properties
---
pyhmmer/plan7.pyx | 29 +++++++++++++++++++++++++++++
1 file changed, 29 insertions(+)
diff --git a/pyhmmer/plan7.pyx b/pyhmmer/plan7.pyx
index eb5204b2..c78060dc 100644
--- a/pyhmmer/plan7.pyx
+++ b/pyhmmer/plan7.pyx
@@ -7924,6 +7924,12 @@ cdef class TopHits:
Use ``TopHits.query`` to access the original query directly.
"""
+ warnings.warn(
+ "TopHits.query_name has been deprecated in v0.10.10 and will be "
+ "removed in v0.11.0, use TopHits.query to access the properties of "
+ "the original query object directly",
+ DeprecationWarning,
+ )
if self._query is None:
return None
return self._query.name
@@ -7938,6 +7944,12 @@ cdef class TopHits:
Use ``TopHits.query`` to access the original query directly.
"""
+ warnings.warn(
+ "TopHits.query_accession has been deprecated in v0.10.10 and will be "
+ "removed in v0.11.0, use TopHits.query to access the properties of "
+ "the original query object directly",
+ DeprecationWarning,
+ )
if self._query is None:
return None
return self._query.accession
@@ -7952,6 +7964,12 @@ cdef class TopHits:
Use ``TopHits.query`` to access the original query directly.
"""
+ warnings.warn(
+ "TopHits.query_length has been deprecated in v0.10.10 and will be "
+ "removed in v0.11.0, use TopHits.query to access the properties of "
+ "the original query object directly",
+ DeprecationWarning,
+ )
if self._query is None:
return 0
return self._query.M if isinstance(self._query, HMM) else len(self._query)
@@ -7959,6 +7977,17 @@ cdef class TopHits:
@property
def query(self):
"""`object`: The query object these hits were obtained for.
+
+ The actual type of `TopHits.query` depends on the query that was given
+ to the `Pipeline`, or the `~pyhmmer.hmmer` function, that created the
+ object::
+
+ >>> hits = next(pyhmmer.hmmsearch(thioesterase, proteins))
+ >>> hits.query
+ <HMM alphabet=Alphabet.amino() M=243 name=b'Thioesterase'>
+
+ .. versionadded 0.10.10
+
"""
return self._query
--
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