Merge branch 'docs-pydata'

CONTRIBUTING.md

-# Contributing to pyHMMER
+# Contributing to PyHMMER
 
 For bug fixes or new features, please file an issue before submitting a
 pull request. If the change isn't trivial, it may be best to wait for

README.md

@@ -50,7 +50,7 @@ HMMER internals, which has the following advantages over CLI wrappers
   loaded in memory, for instance because you obtained them from another
   Python library (such as [Pyrodigal](https://github.com/althonos/pyrodigal)
   or [Biopython](https://biopython.org/)).
-- **no output formatting**: HMMER3 is notorious for its numerous output files
+- **no output parsing**: HMMER3 is notorious for its numerous output files
   and its fixed-width tabular output, which is hard to parse (even
   [`Bio.SearchIO.HmmerIO`](https://biopython.org/docs/dev/api/Bio.SearchIO.HmmerIO.html)
   is struggling on some sequences).

docs/_images/logo.png

+../../static/logo.png
\ No newline at end of file

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: [
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+      19.807, // viewBox height
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+      "e001", // unicode codepoint - private use area
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+    ],
+  }),
+);
+
+FontAwesome.library.add(
+  (faListOldStyle = {
+    prefix: "fa-custom",
+    iconName: "sword",
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+      256, // viewBox width
+      256, // viewBox height
+      [], // ligature
+      "e002", // unicode codepoint - private use area
+      "M221.65723,34.34326A8.00246,8.00246,0,0,0,216,32h-.02539l-63.79883.20117A8.00073,8.00073,0,0,0,146.0332,35.106L75.637,120.32275,67.31348,111.999A16.02162,16.02162,0,0,0,44.68555,112L32.001,124.68555A15.99888,15.99888,0,0,0,32,147.31348l20.88672,20.88769L22.94531,198.14258a16.01777,16.01777,0,0,0,.001,22.62695l12.28418,12.28418a16.00007,16.00007,0,0,0,22.62793,0L87.79883,203.1123,108.68652,224.001A16.02251,16.02251,0,0,0,131.31445,224L143.999,211.31445A15.99888,15.99888,0,0,0,144,188.68652l-8.32324-8.32324,85.21679-70.39648a8.00125,8.00125,0,0,0,2.90528-6.14258L224,40.02539A8.001,8.001,0,0,0,221.65723,34.34326Zm-13.84668,65.67822-83.49829,68.97706L111.314,156l54.34327-54.34277a8.00053,8.00053,0,0,0-11.31446-11.31446L100,144.686,87.00195,131.6875,155.97852,48.189l51.99609-.16357Z", // svg path (https://simpleicons.org/icons/pypi.svg)
+    ],
+  }),
+);
+
+FontAwesome.library.add(
+  (faListOldStyle = {
+    prefix: "fa-custom",
+    iconName: "knife",
+    icon: [
+      256, // viewBox width
+      256, // viewBox height
+      [], // ligature
+      "e003", // unicode codepoint - private use area
+      "M231.79883,32.2002a28.05536,28.05536,0,0,0-39.667.06933L18.27441,210.41211a8,8,0,0,0,3.92676,13.38281,155.06019,155.06019,0,0,0,34.957,4.00293c33.4209-.001,66.877-10.86914,98.32813-32.1748,31.74512-21.50391,50.14551-45.79981,50.91406-46.82325a8.00114,8.00114,0,0,0-.74316-10.457L186.919,119.60547l44.97753-47.90332A28.03445,28.03445,0,0,0,231.79883,32.2002ZM189.207,144.52148a225.51045,225.51045,0,0,1-43.10351,38.13184c-34.46973,23.23145-69.999,32.665-105.83887,28.13477l106.29492-108.915,23.30176,23.30175q.208.22852.43847.44434l.082.07617Z", // 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
+==============
+
+.. autoclass:: pyhmmer.easel.Vector
+   :members:
+
+.. autoclass:: pyhmmer.easel.VectorF(Vector)
+   :special-members: __init__
+   :members:
+
+.. autoclass:: pyhmmer.easel.VectorU8(Vector)
+   :special-members: __init__
+   :members:
+
+
+.. 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
+-------------
+
+.. 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:
+
+.. autoexception:: EaselError(RuntimeError)
+   :special-members: __init__
+   :members:
+
+.. autoexception:: ServerError(RuntimeError)
+   :special-members: __init__
+   :members: