diff --git a/docs/api/errors/mem.rst b/docs/api/errors/mem.rst index 8fc7c42d2f312636d244847e49d582a6e8edeb77..f627122038e083db1563f98fd81a72f3167ac1d4 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 bc5b07b4cafb78515bf1ea79f3da72fd175a7c41..ddb6019010348c9dd50e647ef708194bdd141e05 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 443bdcd9c95f481b633a4ce8b7a0a46d487dd2ae..21b2e60a3c0cf18ee59577de7bbb3c6b80d45ae7 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 97517e8133d32bf2993bd2736b0d80cd9411ded2..9f43fcbae2f67d6a60988bdb2eeeb90caae63380 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 29873591907b774752d7a4b642f70f149c21fd6e..95a01a965a001c36596b3e2889a35e6c56cfbf72 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 590b2f5967890da9c993466db639baa716e732f9..6c370c073841ec91d833b1b6193dbf97d99155a1 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>