From bca6571c855ffd32c2dd54b67e4fcb9d5209e148 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Mon, 15 Jul 2024 17:24:58 +0200
Subject: [PATCH] Fix broken references in `pyhmmer` docstrings [ci skip]
---
pyhmmer/easel.pyx | 20 ++++++++++----------
pyhmmer/plan7.pyx | 10 +++++-----
2 files changed, 15 insertions(+), 15 deletions(-)
diff --git a/pyhmmer/easel.pyx b/pyhmmer/easel.pyx
index 8d7910b1..346a01db 100644
--- a/pyhmmer/easel.pyx
+++ b/pyhmmer/easel.pyx
@@ -476,9 +476,9 @@ cdef class GeneticCode:
translation_table (`int`): The translation table to use. Check the
`Wikipedia <https://w.wiki/47wo>`_ page listing all genetic
codes for the available values.
- nucleotide_alphabet (`pyhmmer.easel.Alphabet`): The nucleotide
+ nucleotide_alphabet (`~pyhmmer.easel.Alphabet`): The nucleotide
alphabet from which to translate the sequence.
- amino_alphabet (`pyhmmer.easel.Alphabet`): The target alphabet
+ amino_alphabet (`~pyhmmer.easel.Alphabet`): The target alphabet
into which to translate the sequence.
"""
@@ -579,7 +579,7 @@ cdef class GeneticCode:
`bytearray`, `~pyhmmer.easel.VectorU8`, etc.) may be given.
Returns:
- `pyhmmer.easel.VectorU8`: The translation of the input
+ `~pyhmmer.easel.VectorU8`: The translation of the input
sequence, as a raw digital sequence.
Raises:
@@ -5095,13 +5095,13 @@ cdef class DigitalSequence(Sequence):
"""Translate the sequence using the given genetic code.
Arguments:
- genetic_code (`pyhmmer.easel.GeneticCode`): The genetic code to
+ genetic_code (`~pyhmmer.easel.GeneticCode`): The genetic code to
use for translating the sequence. If none provided, the
default uses the standard translation table (1) and expects
DNA sequences.
Returns:
- `pyhmmer.easel.DigitalSequence`: The translation of the
+ `~pyhmmer.easel.DigitalSequence`: The translation of the
input sequence, in digital mode.
Raises:
@@ -5716,17 +5716,17 @@ cdef class DigitalSequenceBlock(SequenceBlock):
"""Translate the sequence block using the given genetic code.
Arguments:
- genetic_code (`pyhmmer.easel.GeneticCode`): The genetic code to
+ genetic_code (`~pyhmmer.easel.GeneticCode`): The genetic code to
use for translating the sequence. If none provided, the
default uses the standard translation table (1) and expects
DNA sequences.
Returns:
- `pyhmmer.easel.DigitalSequenceBlock`: The translation of
+ `~pyhmmer.easel.DigitalSequenceBlock`: The translation of
each sequence from the block, in digital mode.
Raises:
- `pyhmmer.errors.AlphabetMismatch`: When the ``genetic_code``
+ `~pyhmmer.errors.AlphabetMismatch`: When the ``genetic_code``
expects a different nucleotide alphabet than the one
currently for the sequences in the block.
`ValueError`: When a sequence from the block could not be
@@ -5734,8 +5734,8 @@ cdef class DigitalSequenceBlock(SequenceBlock):
recognized, or because the sequence has an invalid length.
See Also:
- `pyhmmer.easel.DigitalSequence.translate` for more information
- on how ambiguous nucleotides are handled.
+ `DigitalSequence.translate` for more information on how
+ ambiguous nucleotides are handled.
"""
assert self.alphabet is not None
diff --git a/pyhmmer/plan7.pyx b/pyhmmer/plan7.pyx
index 77049e45..73ead609 100644
--- a/pyhmmer/plan7.pyx
+++ b/pyhmmer/plan7.pyx
@@ -489,8 +489,8 @@ cdef class Background:
"""Create a new background model for the given ``alphabet``.
Arguments:
- alphabet (`pyhmmer.easel.Alphabet`): The alphabet to create the
- background model with.
+ alphabet (`~pyhmmer.easel.Alphabet`): The alphabet to create
+ the background model with.
uniform (`bool`): Whether or not to create the null model with
uniform frequencies. Defaults to `False`.
@@ -3041,9 +3041,9 @@ cdef class HMM:
"""Calculate the match occupancy for each match state.
Returns:
- `~easel.VectorF`: A vector of size :math:`M+1` containing the
- probability that each match state is used in a sample glocal
- path through the model.
+ `~pyhmmer.easel.VectorF`: A vector of size :math:`M+1`
+ containing the probability that each match state is used
+ in a sample glocal path through the model.
.. versionadded:: 0.4.10
--
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