Reorganize documentation to use the PyData theme

docs/_static/css/custom.css

+code-data#setup span.caption-text {
+    display: none;
+}
\ No newline at end of file

docs/_static/js/custom-icon.js

+/*******************************************************************************
+ * Set a custom icon for pypi as it's not available in the fa built-in brands
+ */
+FontAwesome.library.add(
+  (faListOldStyle = {
+    prefix: "fa-custom",
+    iconName: "pypi",
+    icon: [
+      17.313, // viewBox width
+      19.807, // viewBox height
+      [], // ligature
+      "e001", // unicode codepoint - private use area
+      "m10.383 0.2-3.239 1.1769 3.1883 1.1614 3.239-1.1798zm-3.4152 1.2411-3.2362 1.1769 3.1855 1.1614 3.2369-1.1769zm6.7177 0.00281-3.2947 1.2009v3.8254l3.2947-1.1988zm-3.4145 1.2439-3.2926 1.1981v3.8254l0.17548-0.064132 3.1171-1.1347zm-6.6564 0.018325v3.8247l3.244 1.1805v-3.8254zm10.191 0.20931v2.3137l3.1777-1.1558zm3.2947 1.2425-3.2947 1.1988v3.8254l3.2947-1.1988zm-8.7058 0.45739c0.00929-1.931e-4 0.018327-2.977e-4 0.027485 0 0.25633 0.00851 0.4263 0.20713 0.42638 0.49826 1.953e-4 0.38532-0.29327 0.80469-0.65542 0.93662-0.36226 0.13215-0.65608-0.073306-0.65613-0.4588-6.28e-5 -0.38556 0.2938-0.80504 0.65613-0.93662 0.068422-0.024919 0.13655-0.038114 0.20156-0.039466zm5.2913 0.78369-3.2947 1.1988v3.8247l3.2947-1.1981zm-10.132 1.239-3.2362 1.1769 3.1883 1.1614 3.2362-1.1769zm6.7177 0.00213-3.2926 1.2016v3.8247l3.2926-1.2009zm-3.4124 1.2439-3.2947 1.1988v3.8254l3.2947-1.1988zm-6.6585 0.016195v3.8275l3.244 1.1805v-3.8254zm16.9 0.21143-3.2947 1.1988v3.8247l3.2947-1.1981zm-3.4145 1.2411-3.2926 1.2016v3.8247l3.2926-1.2009zm-3.4145 1.2411-3.2926 1.2016v3.8247l3.2926-1.2009zm-3.4124 1.2432-3.2947 1.1988v3.8254l3.2947-1.1988zm-6.6585 0.019027v3.8247l3.244 1.1805v-3.8254zm13.485 1.4497-3.2947 1.1988v3.8247l3.2947-1.1981zm-3.4145 1.2411-3.2926 1.2016v3.8247l3.2926-1.2009zm2.4018 0.38127c0.0093-1.83e-4 0.01833-3.16e-4 0.02749 0 0.25633 0.0085 0.4263 0.20713 0.42638 0.49826 1.97e-4 0.38532-0.29327 0.80469-0.65542 0.93662-0.36188 0.1316-0.65525-0.07375-0.65542-0.4588-1.95e-4 -0.38532 0.29328-0.80469 0.65542-0.93662 0.06842-0.02494 0.13655-0.03819 0.20156-0.03947zm-5.8142 0.86403-3.244 1.1805v1.4201l3.244 1.1805z", // svg path (https://simpleicons.org/icons/pypi.svg)
+    ],
+  }),
+);

docs/api/daemon.rst → docs/api/daemon/client.rst

-Daemon
-======
-
-.. currentmodule:: pyhmmer.daemon
-
-
-.. automodule:: pyhmmer.daemon
-
-
-
 Client
-------
+======
 
 .. autoclass:: pyhmmer.daemon.Client
    :special-members: __init__
    :members:
 
-
-IterativeSearch
----------------
-
 .. autoclass:: pyhmmer.daemon.IterativeSearch
    :special-members: __init__
-   :members:
+   :members:
\ No newline at end of file

docs/api/daemon/index.rst

+Daemon
+======
+
+.. currentmodule:: pyhmmer.daemon
+
+.. automodule:: pyhmmer.daemon
+
+
+Client
+------
+
+.. autosummary::
+
+   Client
+   IterativeSearch
+
+.. toctree::
+    :hidden:
+    :caption: Client
+
+    Client <client>
\ No newline at end of file

docs/api/easel.rst

-Easel
-=====
-
-.. currentmodule:: pyhmmer.easel
-
-
-.. automodule:: pyhmmer.easel
-
-
-Data Structures
----------------
-
-Bitfield
-^^^^^^^^
-
-.. autoclass:: pyhmmer.easel.Bitfield
-   :special-members: __init__
-   :members:
-
-KeyHash
-^^^^^^^
-
-.. autoclass:: pyhmmer.easel.KeyHash
-   :special-members: __init__
-   :members:
-
-
-Sequences
----------
-
-Sequence
-^^^^^^^^
-
-.. autoclass:: pyhmmer.easel.Sequence
-   :members:
-
-TextSequence
-^^^^^^^^^^^^
-
-.. autoclass:: pyhmmer.easel.TextSequence(Sequence)
-   :special-members: __init__
-   :members:
-
-DigitalSequence
-^^^^^^^^^^^^^^^
-
-.. autoclass:: pyhmmer.easel.DigitalSequence(Sequence)
-   :special-members: __init__
-   :members:
-
-
-Sequence Blocks
----------------
-
-SequenceBlock
-^^^^^^^^^^^^^
-
-.. autoclass:: pyhmmer.easel.SequenceBlock
-   :members:
-
-TextSequenceBlock
-^^^^^^^^^^^^^^^^^
-
-.. autoclass:: pyhmmer.easel.TextSequenceBlock(SequenceBlock)
-   :special-members: __init__
-   :members:
-
-DigitalSequenceBlock
-^^^^^^^^^^^^^^^^^^^^
-
-.. autoclass:: pyhmmer.easel.DigitalSequenceBlock(SequenceBlock)
-   :special-members: __init__
-   :members:
-
-
-SequenceFile
-------------
-
-SequenceFile
-^^^^^^^^^^^^
-
-.. autoclass:: pyhmmer.easel.SequenceFile
-  :special-members: __init__
-  :members:
-
-
-Alignments
-----------
-
-MSA
-^^^
-
-.. autoclass:: pyhmmer.easel.MSA
-   :members:
-
-TextMSA
-^^^^^^^
-
-.. autoclass:: pyhmmer.easel.TextMSA(MSA)
-   :special-members: __init__
-   :members:
-
-DigitalMSA
-^^^^^^^^^^
-
-.. autoclass:: pyhmmer.easel.DigitalMSA(MSA)
-   :special-members: __init__
-   :members:
-
-MSAFile
-^^^^^^^
-
-.. autoclass:: pyhmmer.easel.MSAFile
-   :special-members: __init__
-   :members:
-
-
-Linear Algebra
---------------
-
-Vector
-^^^^^^
-
-.. autoclass:: pyhmmer.easel.Vector
-   :members:
-
-VectorF
-^^^^^^^
-
-.. autoclass:: pyhmmer.easel.VectorF
-   :special-members: __init__
-   :members:
-
-VectorU8
-^^^^^^^^
-
-.. autoclass:: pyhmmer.easel.VectorU8
-   :special-members: __init__
-   :members:
-
-Matrix
-^^^^^^
-
-.. autoclass:: pyhmmer.easel.Matrix
-   :members:
-
-MatrixF
-^^^^^^^
-
-.. autoclass:: pyhmmer.easel.MatrixF
-   :special-members: __init__
-   :members:
-
-MatrixU8
-^^^^^^^^
-
-.. autoclass:: pyhmmer.easel.MatrixU8
-   :special-members: __init__
-   :members:
-
-
-Miscellaneous
--------------
-
-Alphabet
-^^^^^^^^
-
-.. autoclass:: pyhmmer.easel.Alphabet
-   :members:
-
-GeneticCode
-^^^^^^^^^^^
-
-.. autoclass:: pyhmmer.easel.GeneticCode
-   :members:
-
-Randomness
-^^^^^^^^^^
-
-.. autoclass:: pyhmmer.easel.Randomness
-   :special-members: __init__
-   :members:
-
-Sequence / Subsequence Index
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. autoclass:: pyhmmer.easel.SSIReader
-   :special-members: __init__
-   :members:
-
-.. autoclass:: pyhmmer.easel.SSIWriter
-   :special-members: __init__
-   :members:

docs/api/easel/block.rst

+Blocks
+======
+
+.. autoclass:: pyhmmer.easel.SequenceBlock
+   :members:
+
+.. autoclass:: pyhmmer.easel.TextSequenceBlock(SequenceBlock)
+   :members:
+   :special-members: __init__
+
+.. autoclass:: pyhmmer.easel.DigitalSequenceBlock(SequenceBlock)
+   :members:
+   :special-members: __init__
\ No newline at end of file

docs/api/easel/data.rst

+Data Structures
+===============
+
+.. autoclass:: pyhmmer.easel.Bitfield
+   :special-members: __init__
+   :members:
+
+.. autoclass:: pyhmmer.easel.KeyHash
+   :special-members: __init__
+   :members:
\ No newline at end of file

docs/api/easel/index.rst

+Easel
+=====
+
+.. currentmodule:: pyhmmer.easel
+
+
+.. automodule:: pyhmmer.easel
+
+
+Data Structures
+---------------
+
+.. autosummary::
+
+   Bitfield
+   KeyHash
+
+.. toctree::
+   :caption: Data Structures
+   :maxdepth: 1
+   :hidden:
+
+   Data Structures <data>
+
+
+Sequences
+---------
+
+.. autosummary::
+
+   Sequence
+   TextSequence
+   DigitalSequence
+
+.. toctree::
+   :caption: Sequences
+   :maxdepth: 1
+   :hidden:
+
+   Sequences <seq>
+
+
+Sequence Blocks
+---------------
+
+.. autosummary::
+
+   SequenceBlock
+   TextSequenceBlock
+   DigitalSequenceBlock
+
+.. toctree::
+   :caption: Sequence Blocks
+   :maxdepth: 1
+   :hidden:
+
+   Sequence Blocks <block>
+
+
+Alignments
+----------
+
+.. autosummary::
+
+   MSA
+   TextMSA
+   DigitalMSA
+
+.. toctree::
+   :caption: Alignments
+   :maxdepth: 1
+   :hidden:
+
+   Alignments <msa>
+
+
+Parsers
+-------
+
+.. autosummary::
+
+   SequenceFile
+   MSAFile
+
+.. toctree::
+   :caption: Parsers
+   :maxdepth: 1
+   :hidden:
+
+   Parsers <parsers>
+
+
+Linear Algebra
+--------------
+
+.. autosummary::
+
+   Vector
+   VectorF
+   VectorU8
+   Matrix
+   MatrixF
+   MatrixU8
+
+.. toctree::
+   :caption: Linear Algebra
+   :maxdepth: 1
+   :hidden:
+
+   Linear Algebra <linalg>
+
+
+Miscellaneous
+-------------
+
+.. autosummary::
+
+   Alphabet
+   GeneticCode
+   Randomness
+   SSIReader
+   SSIWriter
+
+.. toctree::
+   :caption: Miscellaneous
+   :maxdepth: 1
+   :hidden:
+
+   Miscellaneous <misc>
+

docs/api/easel/linalg.rst

+Linear Algebra
+==============
+
+Vectors
+-------
+
+.. autoclass:: pyhmmer.easel.Vector
+   :members:
+
+.. autoclass:: pyhmmer.easel.VectorF(Vector)
+   :special-members: __init__
+   :members:
+
+.. autoclass:: pyhmmer.easel.VectorU8(Vector)
+   :special-members: __init__
+   :members:
+
+
+Matrix
+------
+
+.. autoclass:: pyhmmer.easel.Matrix
+   :members:
+
+.. autoclass:: pyhmmer.easel.MatrixF
+   :special-members: __init__
+   :members:
+
+.. autoclass:: pyhmmer.easel.MatrixU8
+   :special-members: __init__
+   :members:
\ No newline at end of file

docs/api/easel/misc.rst

+Miscellaneous
+=============
+
+.. autoclass:: pyhmmer.easel.Alphabet
+   :members:
+
+.. autoclass:: pyhmmer.easel.GeneticCode
+   :special-members: __init__
+   :members:
+
+.. autoclass:: pyhmmer.easel.Randomness
+   :special-members: __init__
+   :members:
+
+.. autoclass:: pyhmmer.easel.SSIReader
+   :special-members: __init__
+   :members:
+
+.. autoclass:: pyhmmer.easel.SSIWriter
+   :special-members: __init__
+   :members:

docs/api/easel/msa.rst

+Alignments
+==========
+
+.. autoclass:: pyhmmer.easel.MSA
+   :members:
+
+.. autoclass:: pyhmmer.easel.TextMSA(MSA)
+   :special-members: __init__
+   :members:
+
+.. autoclass:: pyhmmer.easel.DigitalMSA(MSA)
+   :special-members: __init__
+   :members:
\ No newline at end of file

docs/api/easel/parsers.rst

+MSAFile
+=======
+
+.. autoclass:: pyhmmer.easel.SequenceFile
+   :special-members: __init__
+   :members:
+
+.. autoclass:: pyhmmer.easel.MSAFile
+   :special-members: __init__
+   :members:
+

docs/api/easel/seq.rst

+Sequence
+========
+
+.. autoclass:: pyhmmer.easel.Sequence
+   :members:
+
+.. autoclass:: pyhmmer.easel.TextSequence
+   :special-members: __init__
+   :members:
+
+.. autoclass:: pyhmmer.easel.DigitalSequence
+   :special-members: __init__
+   :members:
\ No newline at end of file

docs/api/errors/index.rst

+Errors
+======
+
+.. currentmodule:: pyhmmer.errors
+
+.. automodule:: pyhmmer.errors
+
+
+Memory Errors
+-------------
+
+.. autosummary::
+
+   AllocationError
+
+.. toctree::
+    :hidden:
+    :caption: Memory Errors
+
+    Memory Errors <mem>
+
+
+Value Errors
+------------
+
+.. autosummary::
+
+   AlphabetMismatch
+   MissingCutoffs
+   InvalidHMM
+   InvalidParameter
+
+.. toctree::
+    :hidden:
+    :caption: Memory Errors
+
+    Value Errors <value>
+
+
+Runtime Errors
+--------------
+
+.. autosummary::
+
+   UnexpectedError
+   EaselError
+   ServerError
+
+.. toctree::
+    :hidden:
+    :caption: Runtime Errors
+
+    Runtime Errors <runtime>
\ No newline at end of file

docs/api/errors/mem.rst

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

docs/api/errors/runtime.rst

+Runtime Errors
+--------------
+
+.. autoexception:: UnexpectedError(RuntimeError)
+   :special-members: __init__
+   :members:
+
+.. autoexception:: EaselError(RuntimeError)
+   :special-members: __init__
+   :members:
+
+.. autoexception:: ServerError(RuntimeError)
+   :special-members: __init__
+   :members:
\ No newline at end of file

docs/api/errors.rst → docs/api/errors/value.rst

-Errors
-======
+Value Errors
+------------
 
-.. currentmodule:: pyhmmer.errors
-
-.. automodule:: pyhmmer.errors
-
-
-AllocationError
----------------
-
-.. autoexception:: AllocationError(MemoryError)
-   :special-members: __init__
-   :members:
-
-
-UnexpectedError
----------------
-
-.. autoexception:: UnexpectedError(RuntimeError)
-   :special-members: __init__
-   :members:
-
-
-EaselError
-----------
-
-.. autoexception:: EaselError(RuntimeError)
-   :special-members: __init__
-   :members:
-
-
-AlphabetMismatch
-----------------
 
 .. autoexception:: AlphabetMismatch(ValueError)
    :special-members: __init__
    :members:
 
-
-ServerError
------------
-
-.. autoexception:: ServerError(RuntimeError)
-   :special-members: __init__
-   :members:
-
-
-MissingCutoffs
---------------
-
 .. autoexception:: MissingCutoffs(ValueError)
    :special-members: __init__
    :members:
 
-
-InvalidParameter
-----------------
-
-.. autoexception:: InvalidParameter(ValueError)
+.. autoexception:: InvalidHMM(ValueError)
    :special-members: __init__
    :members:
 
-
-InvalidHMM
-----------
-
-.. autoexception:: InvalidHMM(ValueError)
+.. autoexception:: InvalidParameter(ValueError)
    :special-members: __init__
-   :members:
+   :members:
\ No newline at end of file

docs/api/hmmer.rst

-HMMER
-=====
-
-.. currentmodule:: pyhmmer.hmmer
-
-
-.. automodule:: pyhmmer.hmmer
-
-
-hmmsearch
----------
-
-.. autofunction:: pyhmmer.hmmer.hmmsearch(queries, sequences, cpus=0, callback=None, **options)
-
-
-hmmscan
--------
-
-.. autofunction:: pyhmmer.hmmer.hmmscan(queries, profiles, cpus=0, callback=None, background=None, **options)
-
-
-phmmer
-------
-
-.. autofunction:: pyhmmer.hmmer.phmmer(queries, sequences, cpus=0, callback=None, builder=None, **options)
-
-
-nhmmer
-------
-
-.. autofunction:: pyhmmer.hmmer.nhmmer(queries, sequences, cpus=0, callback=None, builder=None, **options)
-
-
-hmmpress
---------
-
-.. autofunction:: pyhmmer.hmmer.hmmpress(hmms, output)
-
-
-hmmalign
---------
-
-.. autofunction:: pyhmmer.hmmer.hmmalign(hmm, sequences, trim=False, digitize=False, all_consensus_cols=True)
-
-
-jackhmmer
----------
-
-.. autofunction:: pyhmmer.hmmer.jackhmmer(queries, sequences, cpus=0, allback=None, builder=None, max_iterations=5, select_hits=None, checkpoints=False, **options)

docs/api/hmmer/index.rst

+HMMER
+=====
+
+.. currentmodule:: pyhmmer.hmmer
+
+
+Profile Searches
+----------------
+
+.. toctree::
+    :hidden:
+    :caption: Sequence Searches
+
+    Sequence Searches <seq>
+
+.. autosummary::
+
+    hmmsearch
+    hmmscan
+
+
+Sequence Searches
+-----------------
+
+.. toctree::
+    :hidden:
+    :caption: Profile Searches
+
+    Profile Searches <profile>
+
+.. autosummary::
+
+    phmmer
+    nhmmer
+
+
+Iterative Searches
+------------------
+
+.. toctree::
+    :hidden:
+    :caption: Iterative Searches
+
+    IterativeSearch <iter>
+
+.. autosummary::
+
+    jackhmmer
+
+
+Utilities
+---------
+
+.. toctree::
+    :hidden:
+    :caption: Utilities
+
+    Utilities <utils>
+
+.. autosummary::
+
+    hmmpress
+    hmmalign
+
+
+
+
+
+
+

docs/api/hmmer/jackhmmer.rst

+Iterative Searches
+==================
+
+.. autofunction:: pyhmmer.hmmer.jackhmmer(queries, sequences, cpus=0, allback=None, builder=None, max_iterations=5, select_hits=None, checkpoints=False, **options)