From aed6b51be4f356db8d7f9e536621aa3c119a12d4 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Tue, 16 Jul 2024 11:19:18 +0200
Subject: [PATCH] Fix some remaining issues in Sphinx documentation [ci skip]
---
docs/api/errors/mem.rst | 2 ++
docs/api/errors/runtime.rst | 4 +++-
docs/api/errors/value.rst | 3 ++-
docs/api/hmmer/iter.rst | 4 +++-
docs/conf.py | 2 ++
docs/examples/index.rst | 2 +-
6 files changed, 13 insertions(+), 4 deletions(-)
diff --git a/docs/api/errors/mem.rst b/docs/api/errors/mem.rst
index 8fc7c42d..f6271220 100644
--- a/docs/api/errors/mem.rst
+++ b/docs/api/errors/mem.rst
@@ -1,6 +1,8 @@
Memory Errors
-------------
+.. currentmodule:: pyhmmer.errors
+
.. autoexception:: AllocationError(MemoryError)
:special-members: __init__
:members:
diff --git a/docs/api/errors/runtime.rst b/docs/api/errors/runtime.rst
index bc5b07b4..ddb60190 100644
--- a/docs/api/errors/runtime.rst
+++ b/docs/api/errors/runtime.rst
@@ -1,6 +1,8 @@
Runtime Errors
--------------
+.. currentmodule:: pyhmmer.errors
+
.. autoexception:: UnexpectedError(RuntimeError)
:special-members: __init__
:members:
@@ -11,4 +13,4 @@ Runtime Errors
.. autoexception:: ServerError(RuntimeError)
:special-members: __init__
- :members:
\ No newline at end of file
+ :members:
diff --git a/docs/api/errors/value.rst b/docs/api/errors/value.rst
index 443bdcd9..21b2e60a 100644
--- a/docs/api/errors/value.rst
+++ b/docs/api/errors/value.rst
@@ -1,6 +1,7 @@
Value Errors
------------
+.. currentmodule:: pyhmmer.errors
.. autoexception:: AlphabetMismatch(ValueError)
:special-members: __init__
@@ -16,4 +17,4 @@ Value Errors
.. autoexception:: InvalidParameter(ValueError)
:special-members: __init__
- :members:
\ No newline at end of file
+ :members:
diff --git a/docs/api/hmmer/iter.rst b/docs/api/hmmer/iter.rst
index 97517e81..9f43fcba 100644
--- a/docs/api/hmmer/iter.rst
+++ b/docs/api/hmmer/iter.rst
@@ -1,4 +1,6 @@
Iterative Searches
==================
-.. autofunction:: pyhmmer.hmmer.jackhmmer(queries, sequences, cpus=0, allback=None, builder=None, max_iterations=5, select_hits=None, checkpoints=False, **options)
+.. currentmodule:: pyhmmer.hmmer
+
+.. autofunction:: pyhmmer.hmmer.jackhmmer(queries, sequences, *, max_iterations=5, select_hits=None, checkpoints=False, cpus=0, callback=None, builder=None, **options)
diff --git a/docs/conf.py b/docs/conf.py
index 29873591..95a01a96 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -190,6 +190,8 @@ napoleon_use_rtype = False
autoclass_content = "class"
autodoc_member_order = 'groupwise'
autosummary_generate = []
+autodoc_typehints = 'none'
+autodoc_class_signature = 'separated'
# -- Options for intersphinx extension ---------------------------------------
diff --git a/docs/examples/index.rst b/docs/examples/index.rst
index 590b2f59..6c370c07 100644
--- a/docs/examples/index.rst
+++ b/docs/examples/index.rst
@@ -13,7 +13,7 @@ examples, and running with the latest version of the PyHMMER interface.
Build an HMM from an multiple sequence alignment <msa_to_hmm>
Analyse the active site of an enzymatic domain <active_site>
- Fetch Marker Genes from a genome <fetchmgs>
+ Fetch marker genes from a genome <fetchmgs>
Run an iterative search to build a HMM for rhodopsins <iterative_search>
--
GitLab