Reorganize documentation to use the PyData theme

docs/api/hmmer/profile.rst

+Profile Searches
+================
+
+.. autofunction:: pyhmmer.hmmer.hmmsearch(queries, sequences, cpus=0, callback=None, **options)
+
+.. autofunction:: pyhmmer.hmmer.hmmscan(queries, profiles, cpus=0, callback=None, background=None, **options)

docs/api/hmmer/seq.rst

+Sequence Searches
+=================
+
+.. autofunction:: pyhmmer.hmmer.phmmer(queries, sequences, cpus=0, callback=None, builder=None, **options)
+
+.. autofunction:: pyhmmer.hmmer.nhmmer(queries, sequences, cpus=0, callback=None, builder=None, **options)

docs/api/hmmer/utils.rst

+Utilities
+=========
+
+.. autofunction:: pyhmmer.hmmer.hmmpress(hmms, output)
+
+.. autofunction:: pyhmmer.hmmer.hmmalign(hmm, sequences, trim=False, digitize=False, all_consensus_cols=True)

docs/api/index.rst

 API Reference
 ==============
 
-.. toctree::
-   :hidden:
-
-   hmmer <hmmer>
-   easel <easel>
-   plan7 <plan7>
-   daemon <daemon>
-   errors <errors>
-
-
 .. currentmodule:: pyhmmer
 
 .. automodule:: pyhmmer
 
+.. toctree::
+   :maxdepth: 2
 
-.. only:: html
-
-    HMMER
-    -----
-
-    .. autosummary::
-        :nosignatures:
-
-        pyhmmer.hmmer.hmmsearch
-        pyhmmer.hmmer.hmmscan
-        pyhmmer.hmmer.phmmer
-        pyhmmer.hmmer.nhmmer
-        pyhmmer.hmmer.hmmpress
-        pyhmmer.hmmer.hmmalign
-
-
-    Easel
-    -----
-
-    Data Structures
-    ^^^^^^^^^^^^^^^
-
-    .. autosummary::
-       :nosignatures:
-
-       pyhmmer.easel.Bitfield
-       pyhmmer.easel.KeyHash
-
-
-    Sequences
-    ^^^^^^^^^
-
-    .. autosummary::
-       :nosignatures:
-
-       pyhmmer.easel.Sequence
-       pyhmmer.easel.TextSequence
-       pyhmmer.easel.DigitalSequence
-
-
-    Sequence Blocks
-    ^^^^^^^^^^^^^^^
-
-    .. autosummary::
-       :nosignatures:
-
-       pyhmmer.easel.SequenceBlock
-       pyhmmer.easel.TextSequenceBlock
-       pyhmmer.easel.DigitalSequenceBlock
-
-
-    Sequence File
-    ^^^^^^^^^^^^^
-
-    .. autosummary::
-       :nosignatures:
-
-       pyhmmer.easel.SequenceFile
-
-
-    Alignments
-    ^^^^^^^^^^
-
-    .. autosummary::
-       :nosignatures:
-
-       pyhmmer.easel.MSA
-       pyhmmer.easel.TextMSA
-       pyhmmer.easel.DigitalMSA
-
-
-    Alignment File
-    ^^^^^^^^^^^^^^
-
-    .. autosummary::
-       :nosignatures:
-
-       pyhmmer.easel.MSAFile
-
-
-    Linear Algebra
-    ^^^^^^^^^^^^^^
-
-    .. autosummary::
-       :nosignatures:
-
-       pyhmmer.easel.Vector
-       pyhmmer.easel.VectorF
-       pyhmmer.easel.VectorU8
-       pyhmmer.easel.Matrix
-       pyhmmer.easel.MatrixF
-       pyhmmer.easel.MatrixU8
-
-
-    Miscellaneous
-    ^^^^^^^^^^^^^
-
-    .. autosummary::
-       :nosignatures:
-
-       pyhmmer.easel.Alphabet
-       pyhmmer.easel.Randomness
-       pyhmmer.easel.SSIReader
-       pyhmmer.easel.SSIWriter
-
-
-
-    Plan7
-    -----
-
-    Profile HMMs
-    ^^^^^^^^^^^^
-
-    .. autosummary::
-        :nosignatures:
-
-        pyhmmer.plan7.HMM
-        pyhmmer.plan7.Profile
-        pyhmmer.plan7.OptimizedProfile
-        pyhmmer.plan7.OptimizedProfileBlock
-
-
-    HMM Files
-    ^^^^^^^^^
-
-    .. autosummary::
-        :nosignatures:
-
-        pyhmmer.plan7.HMMFile
-        pyhmmer.plan7.HMMPressedFile
-
-
-    Pipelines
-    ^^^^^^^^^
-
-    .. autosummary::
-        :nosignatures:
-
-        pyhmmer.plan7.Pipeline
-        pyhmmer.plan7.LongTargetsPipeline
-        pyhmmer.plan7.Builder
-        pyhmmer.plan7.Background
-
-
-    Results
-    ^^^^^^^
-
-    .. autosummary::
-        :nosignatures:
-
-        pyhmmer.plan7.TopHits
-        pyhmmer.plan7.Hit
-        pyhmmer.plan7.Domains
-        pyhmmer.plan7.Domain
-        pyhmmer.plan7.Alignment
-
-
-    Traces
-    ^^^^^^^
-
-    .. autosummary::
-        :nosignatures:
-
-        pyhmmer.plan7.TraceAligner
-        pyhmmer.plan7.Traces
-        pyhmmer.plan7.Trace
-
-
-    Iterative Searches
-    ^^^^^^^^^^^^^^^^^^
-
-    .. autosummary::
-       :nosignatures:
-
-       pyhmmer.plan7.IterativeSearch
-       pyhmmer.plan7.IterationResult
-
-
-    Miscellaneous
-    ^^^^^^^^^^^^^
-
-    .. autosummary::
-        :nosignatures:
-
-        pyhmmer.plan7.Cutoffs
-        pyhmmer.plan7.EvalueParameters
-        pyhmmer.plan7.Offsets
-        pyhmmer.plan7.Transitions
-
-
-    Daemon
-    ------
-
-    .. autosummary::
-        :nosignatures:
-
-        pyhmmer.daemon.Client
-        pyhmmer.daemon.IterativeSearch
-
-
-    Errors
-    ------
-
-    .. autosummary::
-       :nosignatures:
+   HMMER <hmmer/index>
+   Easel <easel/index>
+   Plan7 <plan7/index>
+   Daemon <daemon/index>
+   Errors <errors/index>
 
-       pyhmmer.errors.AllocationError
-       pyhmmer.errors.UnexpectedError
-       pyhmmer.errors.EaselError
-       pyhmmer.errors.AlphabetMismatch
-       pyhmmer.errors.ServerError
-       pyhmmer.errors.MissingCutoffs
-       pyhmmer.errors.InvalidParameter
-       pyhmmer.errors.InvalidHMM

docs/api/plan7.rst

-Plan7
-=====
-
-.. currentmodule:: pyhmmer.plan7
-
-
-.. automodule:: pyhmmer.plan7
-
-
-Profile HMMs
-------------
-
-HMM
-^^^
-
-.. autoclass:: pyhmmer.plan7.HMM
-   :special-members: __init__
-   :members:
-
-Profile
-^^^^^^^
-
-.. autoclass:: pyhmmer.plan7.Profile
-   :special-members: __init__
-   :members:
-
-OptimizedProfile
-^^^^^^^^^^^^^^^^
-
-.. autoclass:: pyhmmer.plan7.OptimizedProfile
-   :special-members: __init__
-   :members:
-
-
-OptimizedProfileBlock
-^^^^^^^^^^^^^^^^^^^^^
-
-.. autoclass:: pyhmmer.plan7.OptimizedProfileBlock
-   :special-members: __init__
-   :members:
-
-
-HMM Files
----------
-
-HMMFile
-^^^^^^^
-
-.. autoclass:: pyhmmer.plan7.HMMFile
-   :special-members: __init__
-   :members:
-
-HMMPressedFile
-^^^^^^^^^^^^^^
-
-.. autoclass:: pyhmmer.plan7.HMMPressedFile
-   :special-members: __init__
-   :members:
-
-
-Pipelines
----------
-
-Pipeline
-^^^^^^^^
-
-.. autoclass:: pyhmmer.plan7.Pipeline
-   :special-members: __init__
-   :members:
-
-LongTargetsPipeline
-^^^^^^^^^^^^^^^^^^^
-
-.. autoclass:: pyhmmer.plan7.LongTargetsPipeline(Pipeline)
-  :special-members: __init__
-  :members:
-
-
-Builder
-^^^^^^^
-
-.. autoclass:: pyhmmer.plan7.Builder
-  :special-members: __init__
-  :members:
-
-
-Background
-^^^^^^^^^^
-
-.. autoclass:: pyhmmer.plan7.Background
-   :special-members: __init__
-   :members:
-
-
-
-Results
--------
-
-TopHits
-^^^^^^^
-
-.. autoclass:: pyhmmer.plan7.TopHits
-   :special-members: __init__
-   :members:
-
-Hit
-^^^
-
-.. autoclass:: pyhmmer.plan7.Hit
-   :special-members: __init__
-   :members:
-
-Domains
-^^^^^^^
-
-.. autoclass:: pyhmmer.plan7.Domains
-   :special-members: __init__
-   :members:
-
-Domain
-^^^^^^
-
-.. autoclass:: pyhmmer.plan7.Domain
-   :special-members: __init__
-   :members:
-
-Alignment
-^^^^^^^^^
-
-.. autoclass:: pyhmmer.plan7.Alignment
-   :special-members: __init__
-   :members:
-
-
-Traces
-------
-
-TraceAligner
-^^^^^^^^^^^^
-
-.. autoclass:: pyhmmer.plan7.TraceAligner
-   :special-members: __init__
-   :members:
-
-Traces
-^^^^^^
-
-.. autoclass:: pyhmmer.plan7.Traces
-   :special-members: __init__
-   :members:
-
-Trace
-^^^^^
-
-.. autoclass:: pyhmmer.plan7.Trace
-   :special-members: __init__
-   :members:
-
-
-Iterative Searches
-------------------
-
-IterativeSearch
-^^^^^^^^^^^^^^^
-
-.. autoclass:: pyhmmer.plan7.IterativeSearch
-    :special-members: __init__
-    :members:
-
-
-IterationResult
-^^^^^^^^^^^^^^^
-
-.. autoclass:: pyhmmer.plan7.IterationResult
-    :special-members: __init__
-    :members:
-
-
-Miscellaneous
--------------
-
-Cutoffs
-^^^^^^^
-
-.. autoclass:: pyhmmer.plan7.Cutoffs
-   :members:
-
-EvalueParameters
-^^^^^^^^^^^^^^^^
-
-.. autoclass:: pyhmmer.plan7.EvalueParameters
-   :members:
-
-Offsets
-^^^^^^^
-
-.. autoclass:: pyhmmer.plan7.Offsets
-   :members:
-
-
-Transitions
-^^^^^^^^^^^
-
-.. autoclass:: pyhmmer.plan7.Transitions(enum.IntEnum)
-
-   .. autoattribute:: MM
-
-   .. autoattribute:: MI
-
-   .. autoattribute:: MD
-
-   .. autoattribute:: IM
-
-   .. autoattribute:: II
-
-   .. autoattribute:: DM
-
-   .. autoattribute:: DD
-

docs/api/plan7/hmms.rst

+Profile Hidden Markov Models
+============================
+
+.. autoclass:: pyhmmer.plan7.HMM
+   :special-members: __init__
+   :members:
+
+.. autoclass:: pyhmmer.plan7.Profile
+   :special-members: __init__
+   :members:
+
+.. autoclass:: pyhmmer.plan7.OptimizedProfile
+   :special-members: __init__
+   :members:
+
+.. autoclass:: pyhmmer.plan7.OptimizedProfileBlock
+   :special-members: __init__
+   :members:
\ No newline at end of file

docs/api/plan7/index.rst

+Plan7
+=====
+
+.. currentmodule:: pyhmmer.plan7
+
+.. automodule:: pyhmmer.plan7
+
+
+Profile Hidden Markov Models
+----------------------------
+
+.. autosummary::
+
+    HMM
+    Profile
+    OptimizedProfile
+    OptimizedProfileBlock
+
+.. toctree::
+    :caption: Profile Hidden Markov Models
+    :maxdepth: 1
+    :hidden:
+
+    Profile Hidden Markov Models <hmms>
+
+
+Parsers
+-------
+
+.. autosummary::
+
+    HMMFile
+    HMMPressedFile
+
+.. toctree::
+    :caption: Parsers
+    :maxdepth: 1
+    :hidden:
+
+    Parsers <parsers>
+
+
+Pipelines
+---------
+
+.. autosummary::
+
+    Pipeline
+    LongTargetsPipeline
+    Builder
+    Background
+
+.. toctree::
+    :caption: Pipelines
+    :maxdepth: 1
+    :hidden:
+
+    Pipelines <pli>
+
+
+Results
+-------
+
+.. autosummary::
+
+    TopHits
+    Hit
+    Domains
+    Domain
+    Alignment
+
+.. toctree::
+    :caption: Results
+    :maxdepth: 1
+    :hidden:
+
+    Results <results>
+
+
+Traces
+------
+
+.. autosummary::
+
+    TraceAligner
+    Traces
+    Trace
+
+.. toctree::
+    :caption: Traces
+    :maxdepth: 1
+    :hidden:
+
+    Traces <traces>
+
+
+Iterative Searches
+------------------
+
+.. autosummary::
+
+    IterativeSearch
+    IterationResult
+
+.. toctree::
+    :caption: Iterative Searches
+    :maxdepth: 1
+    :hidden:
+
+    Iterative Searches <iter>
+
+
+Miscellaneous
+-------------
+
+.. autosummary::
+
+    Cutoffs
+    EvalueParameters
+    Offsets
+    Transitions
+
+.. toctree::
+    :caption: Miscellaneous
+    :maxdepth: 1
+    :hidden:
+
+    Miscellaneous <misc>

docs/api/plan7/iter.rst

+Iterative Searches
+==================
+
+.. autoclass:: pyhmmer.plan7.IterativeSearch
+    :special-members: __init__
+    :members:
+
+.. autoclass:: pyhmmer.plan7.IterationResult
+    :special-members: __init__
+    :members:
\ No newline at end of file

docs/api/plan7/misc.rst

+Miscellaneous
+=============
+
+.. autoclass:: pyhmmer.plan7.Cutoffs
+   :members:
+
+.. autoclass:: pyhmmer.plan7.EvalueParameters
+   :members:
+
+.. autoclass:: pyhmmer.plan7.Offsets
+   :members:
+
+.. autoclass:: pyhmmer.plan7.Transitions(enum.IntEnum)
+   .. autoattribute:: MM
+   .. autoattribute:: MI
+   .. autoattribute:: MD
+   .. autoattribute:: IM
+   .. autoattribute:: II
+   .. autoattribute:: DM
+   .. autoattribute:: DD
\ No newline at end of file

docs/api/plan7/parsers.rst

+Parsers
+=======
+
+.. autoclass:: pyhmmer.plan7.HMMFile
+   :special-members: __init__
+   :members:
+
+.. autoclass:: pyhmmer.plan7.HMMPressedFile
+   :special-members: __init__
+   :members:
\ No newline at end of file

docs/api/plan7/pli.rst

+Pipelines
+=========
+
+.. autoclass:: pyhmmer.plan7.Pipeline
+   :special-members: __init__
+   :members:
+
+.. autoclass:: pyhmmer.plan7.LongTargetsPipeline(Pipeline)
+   :special-members: __init__
+   :members:
+
+.. autoclass:: pyhmmer.plan7.Builder
+   :special-members: __init__
+   :members:
+
+.. autoclass:: pyhmmer.plan7.Background
+   :special-members: __init__
+   :members:
\ No newline at end of file

docs/api/plan7/results.rst

+Results
+=======
+
+.. autoclass:: pyhmmer.plan7.TopHits
+   :special-members: __init__
+   :members:
+
+.. autoclass:: pyhmmer.plan7.Hit
+   :special-members: __init__
+   :members:
+
+.. autoclass:: pyhmmer.plan7.Domains
+   :special-members: __init__
+   :members:
+
+.. autoclass:: pyhmmer.plan7.Domain
+   :special-members: __init__
+   :members:
+
+.. autoclass:: pyhmmer.plan7.Alignment
+   :special-members: __init__
+   :members:
\ No newline at end of file

docs/api/plan7/traces.rst

+Traces
+======
+
+.. autoclass:: pyhmmer.plan7.TraceAligner
+   :special-members: __init__
+   :members:
+
+.. autoclass:: pyhmmer.plan7.Traces
+   :special-members: __init__, __getitem__
+   :members:
+
+.. autoclass:: pyhmmer.plan7.Trace
+   :special-members: __init__
+   :members:
\ No newline at end of file

docs/changes.md

-../CHANGELOG.md
\ No newline at end of file

docs/conf.py

@@ -30,8 +30,9 @@ if os.getenv("READTHEDOCS", "False") != "True":
 # -- Sphinx Setup ------------------------------------------------------------
 
 def setup(app):
+    pass
     # Add custom stylesheet
-    app.add_css_file("css/main.css")
+    # app.add_css_file("css/main.css")
     # app.add_js_file("js/apitoc.js")
     # app.add_js_file("js/example-admonition.js")
 
@@ -114,60 +115,50 @@ default_role = "py:obj"
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'bootstrap'
-
-# Add any paths that contain custom themes here, relative to this directory.
-html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
+html_theme = 'pydata_sphinx_theme'
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ['_static/js', '_static/bibtex', '_static/css']
+html_js_files = ["custom-icon.js"]
+html_css_files = ["custom.css"]
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 #
 html_theme_options = {
-    # Bootswatch (http://bootswatch.com/) theme.
-    "bootswatch_theme": "flatly",
-    # Choose Bootstrap version.
-    "bootstrap_version": "3",
-    # Tab name for entire site. (Default: "Site")
-    "navbar_site_name": "Documentation",
-    # HTML navbar class (Default: "navbar") to attach to <div> element.
-    # For black navbar, do "navbar navbar-inverse"
-    "navbar_class": "navbar",
-    # Render the next and previous page links in navbar. (Default: true)
-    "navbar_sidebarrel": True,
-    # Render the current pages TOC in the navbar. (Default: true)
-    "navbar_pagenav": False,
-    # A list of tuples containing pages or urls to link to.
-    "navbar_links": [
-        ("GitHub", cfgparser.get("metadata", "url").strip(), True)
-    ] + [
-        (k, v, True)
-        for k, v in project_urls.items()
-        if k in {"Zenodo", "PyPI"}
+    "show_toc_level": 2,
+    "use_edit_page_button": True,
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/pydata/pydata-sphinx-theme",
+            "icon": "fa-brands fa-github",
+        },
+        {
+            "name": "PyPI",
+            "url": "https://pypi.org/project/pydata-sphinx-theme",
+            "icon": "fa-custom fa-pypi",
+        },
     ],
-    "admonition_use_panel": True,
+    "logo": {
+        "text": "PyHMMER",
+        "image_dark": "_images/logo.png",
+    },
+    "navbar_align": "left",
+    "footer_start": ["copyright"],
+    "footer_center": ["sphinx-version"],
 }
 
-# Custom sidebar templates, must be a dictionary that maps document names
-# to template names.
-#
-# The default sidebars (for documents that don't match any pattern) are
-# defined by theme itself.  Builtin themes are using these templates by
-# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
-# 'searchbox.html']``.
-#
-html_sidebars = {
-    "*": ["localtoc.html"],
-    "api/*": ["localtoc.html"],
-    "examples/*": ["localtoc.html"],
+html_context = {
+    "github_user": "althonos",
+    "github_repo": "pyhmmer",
+    "github_version": "master",
+    "doc_path": "docs",
 }
 
-
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.

docs/contributing.md

-../CONTRIBUTING.md
\ No newline at end of file

docs/examples/index.rst

@@ -9,6 +9,7 @@ examples, and running with the latest version of the PyHMMER interface.
 
 .. toctree::
    :maxdepth: 2
+   :caption: Analyses
 
    Build an HMM from an multiple sequence alignment <msa_to_hmm>
    Analyse the active site of an enzymatic domain <active_site>
@@ -24,6 +25,7 @@ PyHMMER API in combination with Python and other Python libraries:
 
 .. toctree::
     :maxdepth: 2
+    :caption: Code & Data
 
     Recipes for extending PyHMMER <recipes>
     Create a Python package with embedded HMMs <embed_hmms>

docs/benchmarks.rst → docs/guide/benchmarks.rst

@@ -16,7 +16,7 @@ the times for pressed HMMs, and dashed-lines the times for HMMs in text format.*
 v0.7.0 - 2022-12-04
 -------------------
 
-.. image:: _images/bench-v0.7.0.svg
+.. image:: /_images/bench-v0.7.0.svg
 
 Collections for storing HMMs and Sequences were updated to allow iterating 
 without the GIL. For `hmmscan`, the `OptimizedProfileBlock` store an array 
@@ -27,7 +27,7 @@ across different threads.
 v0.5.0 - 2022-03-14
 -------------------
 
-.. image:: _images/bench-v0.5.0.svg
+.. image:: /_images/bench-v0.5.0.svg
 
 A new dedicated collection has been added to store the target sequences of a
 `~pyhmmer.plan7.Pipeline`, saving some overhead if the same target sequences
@@ -37,7 +37,7 @@ are reused with multiple queries.
 v0.4.5 - 2021-07-19
 -------------------
 
-.. image:: _images/bench-v0.4.5.svg
+.. image:: /_images/bench-v0.4.5.svg
 
 By adding an extra requirement on the reference sequences passed to a `~pyhmmer.plan7.Pipeline`,
 the Cython code can now evaluate a single HMM against the entirety of the reference
@@ -59,7 +59,7 @@ optimal number of 5+1 threads (42.2s).
 v0.4.0 - 2021-06-05
 -------------------
 
-.. image:: _images/bench-v0.4.0.svg
+.. image:: /_images/bench-v0.4.0.svg
 
 The overhead of PyHMMER has been reduced, and has a much smaller effect when
 using a high number of threads.
@@ -79,7 +79,7 @@ speed up insertions by worker threads.
 v0.3.0 - 2021-03-11
 -------------------
 
-.. image:: _images/bench-v0.3.0.svg
+.. image:: /_images/bench-v0.3.0.svg
 
 The small number of proteins renders the HMMER parallelisation useless for
 any number of worker threads higher than 2 (because of the block size being

docs/guide/changes.md

+../../CHANGELOG.md
\ No newline at end of file

docs/guide/contributing.md

+../../CONTRIBUTING.md
\ No newline at end of file