Fix some remaining issues in Sphinx documentation [ci skip]

docs/api/errors/mem.rst

 Memory Errors
 -------------
 
+.. currentmodule:: pyhmmer.errors
+
 .. autoexception:: AllocationError(MemoryError)
    :special-members: __init__
    :members:

docs/api/errors/runtime.rst

 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:

docs/api/errors/value.rst

 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:

docs/api/hmmer/iter.rst

 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)

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 ---------------------------------------
 

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>