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Document the backend parameter to pyhmmer.hmmer functions
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althonos committed Oct 14, 2024
1 parent 92babdf commit 15c6bdb
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Showing 5 changed files with 16 additions and 1 deletion.
3 changes: 3 additions & 0 deletions src/pyhmmer/hmmer/_hmmscan.py
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Expand Up @@ -129,6 +129,9 @@ def hmmscan(
background (`pyhmmer.plan7.Background`, *optional*): A background
object to use for configuring the profiles. If `None` given,
create a default one.
backend (`str`): The parallel backend to use for workers to be
executed. Supports ``threading`` to use thread-based parallelism,
or ``multiprocessing`` to use process-based parallelism.
Yields:
`~pyhmmer.plan7.TopHits`: An object reporting *top hits* for each
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6 changes: 6 additions & 0 deletions src/pyhmmer/hmmer/_hmmsearch.py
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Expand Up @@ -135,6 +135,9 @@ def hmmsearch(
callback (callable): A callback that is called everytime a query is
processed with two arguments: the query, and the total number
of queries. This can be used to display progress in UI.
backend (`str`): The parallel backend to use for workers to be
executed. Supports ``threading`` to use thread-based parallelism,
or ``multiprocessing`` to use process-based parallelism.
Yields:
`~pyhmmer.plan7.TopHits`: An object reporting *top hits* for each
Expand All @@ -154,6 +157,9 @@ def hmmsearch(
>>> hits[0].score
8.601...
Since *version 0.11.0*, ``mypy`` should be able to detection which
keywords can be passed to `hmmsearch` using a `TypedDict` annotation.
.. versionadded:: 0.1.0
.. versionchanged:: 0.4.9
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2 changes: 1 addition & 1 deletion src/pyhmmer/hmmer/_jackhmmer.py
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Expand Up @@ -306,7 +306,7 @@ def jackhmmer(
builder (`~pyhmmer.plan7.Builder`, optional): A builder to configure
how the queries are converted to HMMs. Passing `None` will create
a default instance.
backend (`str`): The parallel backend to use for workers to be
backend (`str`): The parallel backend to use for workers to be
executed. Supports ``threading`` to use thread-based parallelism,
or ``multiprocessing`` to use process-based parallelism.
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3 changes: 3 additions & 0 deletions src/pyhmmer/hmmer/_nhmmer.py
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Expand Up @@ -162,6 +162,9 @@ def nhmmer(
builder (`~pyhmmer.plan7.Builder`, optional): A builder to configure
how the queries are converted to HMMs. Passing `None` will create
a default instance.
backend (`str`): The parallel backend to use for workers to be
executed. Supports ``threading`` to use thread-based parallelism,
or ``multiprocessing`` to use process-based parallelism.
Yields:
`~pyhmmer.plan7.TopHits`: A *top hits* instance for each query,
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3 changes: 3 additions & 0 deletions src/pyhmmer/hmmer/_phmmer.py
Original file line number Diff line number Diff line change
Expand Up @@ -128,6 +128,9 @@ def phmmer(
builder (`~pyhmmer.plan7.Builder`, optional): A builder to configure
how the queries are converted to HMMs. Passing `None` will create
a default instance.
backend (`str`): The parallel backend to use for workers to be
executed. Supports ``threading`` to use thread-based parallelism,
or ``multiprocessing`` to use process-based parallelism.
Yields:
`~pyhmmer.plan7.TopHits`: A *top hits* instance for each query,
Expand Down

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