From e9b8d526ca0e8df584ee4caa3dc6491fb02c1326 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Wed, 10 Jul 2024 13:34:27 +0200
Subject: [PATCH] Reorganize documentation to use the PyData theme
---
docs/_static/css/custom.css | 3 +
docs/_static/js/custom-icon.js | 16 ++
docs/api/{daemon.rst => daemon/client.rst} | 18 +-
docs/api/daemon/index.rst | 21 ++
docs/api/easel.rst | 193 -----------------
docs/api/easel/block.rst | 13 ++
docs/api/easel/data.rst | 10 +
docs/api/easel/index.rst | 130 ++++++++++++
docs/api/easel/linalg.rst | 31 +++
docs/api/easel/misc.rst | 21 ++
docs/api/easel/msa.rst | 13 ++
docs/api/easel/parsers.rst | 11 +
docs/api/easel/seq.rst | 13 ++
docs/api/errors.rst | 70 -------
docs/api/errors/index.rst | 53 +++++
docs/api/errors/mem.rst | 6 +
docs/api/errors/runtime.rst | 14 ++
docs/api/errors/value.rst | 19 ++
docs/api/hmmer.rst | 49 -----
docs/api/hmmer/index.rst | 70 +++++++
docs/api/hmmer/jackhmmer.rst | 4 +
docs/api/hmmer/profile.rst | 6 +
docs/api/hmmer/seq.rst | 6 +
docs/api/hmmer/utils.rst | 6 +
docs/api/index.rst | 230 +--------------------
docs/api/plan7.rst | 219 --------------------
docs/api/plan7/hmms.rst | 18 ++
docs/api/plan7/index.rst | 128 ++++++++++++
docs/api/plan7/iter.rst | 10 +
docs/api/plan7/misc.rst | 20 ++
docs/api/plan7/parsers.rst | 10 +
docs/api/plan7/pli.rst | 18 ++
docs/api/plan7/results.rst | 22 ++
docs/api/plan7/traces.rst | 14 ++
docs/changes.md | 1 -
docs/conf.py | 71 +++----
docs/contributing.md | 1 -
docs/examples/index.rst | 2 +
docs/{ => guide}/benchmarks.rst | 10 +-
docs/guide/changes.md | 1 +
docs/guide/contributing.md | 1 +
docs/guide/index.rst | 20 ++
docs/{ => guide}/install.rst | 18 +-
docs/{ => guide}/performance.rst | 2 +-
docs/{ => guide}/publications.rst | 4 +-
docs/index.rst | 12 +-
docs/requirements.txt | 4 +-
47 files changed, 791 insertions(+), 841 deletions(-)
create mode 100644 docs/_static/css/custom.css
create mode 100644 docs/_static/js/custom-icon.js
rename docs/api/{daemon.rst => daemon/client.rst} (56%)
create mode 100644 docs/api/daemon/index.rst
delete mode 100644 docs/api/easel.rst
create mode 100644 docs/api/easel/block.rst
create mode 100644 docs/api/easel/data.rst
create mode 100644 docs/api/easel/index.rst
create mode 100644 docs/api/easel/linalg.rst
create mode 100644 docs/api/easel/misc.rst
create mode 100644 docs/api/easel/msa.rst
create mode 100644 docs/api/easel/parsers.rst
create mode 100644 docs/api/easel/seq.rst
delete mode 100644 docs/api/errors.rst
create mode 100644 docs/api/errors/index.rst
create mode 100644 docs/api/errors/mem.rst
create mode 100644 docs/api/errors/runtime.rst
create mode 100644 docs/api/errors/value.rst
delete mode 100644 docs/api/hmmer.rst
create mode 100644 docs/api/hmmer/index.rst
create mode 100644 docs/api/hmmer/jackhmmer.rst
create mode 100644 docs/api/hmmer/profile.rst
create mode 100644 docs/api/hmmer/seq.rst
create mode 100644 docs/api/hmmer/utils.rst
delete mode 100644 docs/api/plan7.rst
create mode 100644 docs/api/plan7/hmms.rst
create mode 100644 docs/api/plan7/index.rst
create mode 100644 docs/api/plan7/iter.rst
create mode 100644 docs/api/plan7/misc.rst
create mode 100644 docs/api/plan7/parsers.rst
create mode 100644 docs/api/plan7/pli.rst
create mode 100644 docs/api/plan7/results.rst
create mode 100644 docs/api/plan7/traces.rst
delete mode 120000 docs/changes.md
delete mode 120000 docs/contributing.md
rename docs/{ => guide}/benchmarks.rst (95%)
create mode 120000 docs/guide/changes.md
create mode 120000 docs/guide/contributing.md
create mode 100644 docs/guide/index.rst
rename docs/{ => guide}/install.rst (99%)
rename docs/{ => guide}/performance.rst (99%)
rename docs/{ => guide}/publications.rst (97%)
diff --git a/docs/_static/css/custom.css b/docs/_static/css/custom.css
new file mode 100644
index 00000000..e1fb2599
--- /dev/null
+++ b/docs/_static/css/custom.css
@@ -0,0 +1,3 @@
+code-data#setup span.caption-text {
+ display: none;
+}
\ No newline at end of file
diff --git a/docs/_static/js/custom-icon.js b/docs/_static/js/custom-icon.js
new file mode 100644
index 00000000..bc64dd6b
--- /dev/null
+++ b/docs/_static/js/custom-icon.js
@@ -0,0 +1,16 @@
+/*******************************************************************************
+ * 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)
+ ],
+ }),
+);
diff --git a/docs/api/daemon.rst b/docs/api/daemon/client.rst
similarity index 56%
rename from docs/api/daemon.rst
rename to docs/api/daemon/client.rst
index 1bc46f20..f934cc6f 100644
--- a/docs/api/daemon.rst
+++ b/docs/api/daemon/client.rst
@@ -1,24 +1,10 @@
-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
diff --git a/docs/api/daemon/index.rst b/docs/api/daemon/index.rst
new file mode 100644
index 00000000..cc096a25
--- /dev/null
+++ b/docs/api/daemon/index.rst
@@ -0,0 +1,21 @@
+Daemon
+======
+
+.. currentmodule:: pyhmmer.daemon
+
+.. automodule:: pyhmmer.daemon
+
+
+Client
+------
+
+.. autosummary::
+
+ Client
+ IterativeSearch
+
+.. toctree::
+ :hidden:
+ :caption: Client
+
+ Client <client>
\ No newline at end of file
diff --git a/docs/api/easel.rst b/docs/api/easel.rst
deleted file mode 100644
index c2907391..00000000
--- a/docs/api/easel.rst
+++ /dev/null
@@ -1,193 +0,0 @@
-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:
diff --git a/docs/api/easel/block.rst b/docs/api/easel/block.rst
new file mode 100644
index 00000000..1b869472
--- /dev/null
+++ b/docs/api/easel/block.rst
@@ -0,0 +1,13 @@
+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
diff --git a/docs/api/easel/data.rst b/docs/api/easel/data.rst
new file mode 100644
index 00000000..a4837795
--- /dev/null
+++ b/docs/api/easel/data.rst
@@ -0,0 +1,10 @@
+Data Structures
+===============
+
+.. autoclass:: pyhmmer.easel.Bitfield
+ :special-members: __init__
+ :members:
+
+.. autoclass:: pyhmmer.easel.KeyHash
+ :special-members: __init__
+ :members:
\ No newline at end of file
diff --git a/docs/api/easel/index.rst b/docs/api/easel/index.rst
new file mode 100644
index 00000000..ad43314a
--- /dev/null
+++ b/docs/api/easel/index.rst
@@ -0,0 +1,130 @@
+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>
+
diff --git a/docs/api/easel/linalg.rst b/docs/api/easel/linalg.rst
new file mode 100644
index 00000000..16a414f1
--- /dev/null
+++ b/docs/api/easel/linalg.rst
@@ -0,0 +1,31 @@
+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
diff --git a/docs/api/easel/misc.rst b/docs/api/easel/misc.rst
new file mode 100644
index 00000000..79147463
--- /dev/null
+++ b/docs/api/easel/misc.rst
@@ -0,0 +1,21 @@
+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:
diff --git a/docs/api/easel/msa.rst b/docs/api/easel/msa.rst
new file mode 100644
index 00000000..c566bfbe
--- /dev/null
+++ b/docs/api/easel/msa.rst
@@ -0,0 +1,13 @@
+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
diff --git a/docs/api/easel/parsers.rst b/docs/api/easel/parsers.rst
new file mode 100644
index 00000000..32a8f66a
--- /dev/null
+++ b/docs/api/easel/parsers.rst
@@ -0,0 +1,11 @@
+MSAFile
+=======
+
+.. autoclass:: pyhmmer.easel.SequenceFile
+ :special-members: __init__
+ :members:
+
+.. autoclass:: pyhmmer.easel.MSAFile
+ :special-members: __init__
+ :members:
+
diff --git a/docs/api/easel/seq.rst b/docs/api/easel/seq.rst
new file mode 100644
index 00000000..80979a19
--- /dev/null
+++ b/docs/api/easel/seq.rst
@@ -0,0 +1,13 @@
+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
diff --git a/docs/api/errors.rst b/docs/api/errors.rst
deleted file mode 100644
index 77d0cd37..00000000
--- a/docs/api/errors.rst
+++ /dev/null
@@ -1,70 +0,0 @@
-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)
- :special-members: __init__
- :members:
-
-
-InvalidHMM
-----------
-
-.. autoexception:: InvalidHMM(ValueError)
- :special-members: __init__
- :members:
diff --git a/docs/api/errors/index.rst b/docs/api/errors/index.rst
new file mode 100644
index 00000000..3c7c7cd1
--- /dev/null
+++ b/docs/api/errors/index.rst
@@ -0,0 +1,53 @@
+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
diff --git a/docs/api/errors/mem.rst b/docs/api/errors/mem.rst
new file mode 100644
index 00000000..8fc7c42d
--- /dev/null
+++ b/docs/api/errors/mem.rst
@@ -0,0 +1,6 @@
+Memory Errors
+-------------
+
+.. autoexception:: AllocationError(MemoryError)
+ :special-members: __init__
+ :members:
diff --git a/docs/api/errors/runtime.rst b/docs/api/errors/runtime.rst
new file mode 100644
index 00000000..bc5b07b4
--- /dev/null
+++ b/docs/api/errors/runtime.rst
@@ -0,0 +1,14 @@
+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
diff --git a/docs/api/errors/value.rst b/docs/api/errors/value.rst
new file mode 100644
index 00000000..443bdcd9
--- /dev/null
+++ b/docs/api/errors/value.rst
@@ -0,0 +1,19 @@
+Value Errors
+------------
+
+
+.. autoexception:: AlphabetMismatch(ValueError)
+ :special-members: __init__
+ :members:
+
+.. autoexception:: MissingCutoffs(ValueError)
+ :special-members: __init__
+ :members:
+
+.. autoexception:: InvalidHMM(ValueError)
+ :special-members: __init__
+ :members:
+
+.. autoexception:: InvalidParameter(ValueError)
+ :special-members: __init__
+ :members:
\ No newline at end of file
diff --git a/docs/api/hmmer.rst b/docs/api/hmmer.rst
deleted file mode 100644
index 66883083..00000000
--- a/docs/api/hmmer.rst
+++ /dev/null
@@ -1,49 +0,0 @@
-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)
diff --git a/docs/api/hmmer/index.rst b/docs/api/hmmer/index.rst
new file mode 100644
index 00000000..4fa64195
--- /dev/null
+++ b/docs/api/hmmer/index.rst
@@ -0,0 +1,70 @@
+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
+
+
+
+
+
+
+
diff --git a/docs/api/hmmer/jackhmmer.rst b/docs/api/hmmer/jackhmmer.rst
new file mode 100644
index 00000000..97517e81
--- /dev/null
+++ b/docs/api/hmmer/jackhmmer.rst
@@ -0,0 +1,4 @@
+Iterative Searches
+==================
+
+.. autofunction:: pyhmmer.hmmer.jackhmmer(queries, sequences, cpus=0, allback=None, builder=None, max_iterations=5, select_hits=None, checkpoints=False, **options)
diff --git a/docs/api/hmmer/profile.rst b/docs/api/hmmer/profile.rst
new file mode 100644
index 00000000..32de1c37
--- /dev/null
+++ b/docs/api/hmmer/profile.rst
@@ -0,0 +1,6 @@
+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)
diff --git a/docs/api/hmmer/seq.rst b/docs/api/hmmer/seq.rst
new file mode 100644
index 00000000..f40131fa
--- /dev/null
+++ b/docs/api/hmmer/seq.rst
@@ -0,0 +1,6 @@
+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)
diff --git a/docs/api/hmmer/utils.rst b/docs/api/hmmer/utils.rst
new file mode 100644
index 00000000..ff3d79ae
--- /dev/null
+++ b/docs/api/hmmer/utils.rst
@@ -0,0 +1,6 @@
+Utilities
+=========
+
+.. autofunction:: pyhmmer.hmmer.hmmpress(hmms, output)
+
+.. autofunction:: pyhmmer.hmmer.hmmalign(hmm, sequences, trim=False, digitize=False, all_consensus_cols=True)
diff --git a/docs/api/index.rst b/docs/api/index.rst
index b7a35cba..630d1e7d 100644
--- a/docs/api/index.rst
+++ b/docs/api/index.rst
@@ -1,232 +1,16 @@
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
diff --git a/docs/api/plan7.rst b/docs/api/plan7.rst
deleted file mode 100644
index cf73b546..00000000
--- a/docs/api/plan7.rst
+++ /dev/null
@@ -1,219 +0,0 @@
-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
-
diff --git a/docs/api/plan7/hmms.rst b/docs/api/plan7/hmms.rst
new file mode 100644
index 00000000..9f8aac62
--- /dev/null
+++ b/docs/api/plan7/hmms.rst
@@ -0,0 +1,18 @@
+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
diff --git a/docs/api/plan7/index.rst b/docs/api/plan7/index.rst
new file mode 100644
index 00000000..1fcee76a
--- /dev/null
+++ b/docs/api/plan7/index.rst
@@ -0,0 +1,128 @@
+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>
diff --git a/docs/api/plan7/iter.rst b/docs/api/plan7/iter.rst
new file mode 100644
index 00000000..9963777f
--- /dev/null
+++ b/docs/api/plan7/iter.rst
@@ -0,0 +1,10 @@
+Iterative Searches
+==================
+
+.. autoclass:: pyhmmer.plan7.IterativeSearch
+ :special-members: __init__
+ :members:
+
+.. autoclass:: pyhmmer.plan7.IterationResult
+ :special-members: __init__
+ :members:
\ No newline at end of file
diff --git a/docs/api/plan7/misc.rst b/docs/api/plan7/misc.rst
new file mode 100644
index 00000000..0d8e12e4
--- /dev/null
+++ b/docs/api/plan7/misc.rst
@@ -0,0 +1,20 @@
+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
diff --git a/docs/api/plan7/parsers.rst b/docs/api/plan7/parsers.rst
new file mode 100644
index 00000000..9fdbbb1d
--- /dev/null
+++ b/docs/api/plan7/parsers.rst
@@ -0,0 +1,10 @@
+Parsers
+=======
+
+.. autoclass:: pyhmmer.plan7.HMMFile
+ :special-members: __init__
+ :members:
+
+.. autoclass:: pyhmmer.plan7.HMMPressedFile
+ :special-members: __init__
+ :members:
\ No newline at end of file
diff --git a/docs/api/plan7/pli.rst b/docs/api/plan7/pli.rst
new file mode 100644
index 00000000..cf1c75d6
--- /dev/null
+++ b/docs/api/plan7/pli.rst
@@ -0,0 +1,18 @@
+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
diff --git a/docs/api/plan7/results.rst b/docs/api/plan7/results.rst
new file mode 100644
index 00000000..6d6c7c11
--- /dev/null
+++ b/docs/api/plan7/results.rst
@@ -0,0 +1,22 @@
+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
diff --git a/docs/api/plan7/traces.rst b/docs/api/plan7/traces.rst
new file mode 100644
index 00000000..6bdb50d9
--- /dev/null
+++ b/docs/api/plan7/traces.rst
@@ -0,0 +1,14 @@
+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
diff --git a/docs/changes.md b/docs/changes.md
deleted file mode 120000
index 04c99a55..00000000
--- a/docs/changes.md
+++ /dev/null
@@ -1 +0,0 @@
-../CHANGELOG.md
\ No newline at end of file
diff --git a/docs/conf.py b/docs/conf.py
index 96a05088..daa4a5f4 100644
--- a/docs/conf.py
+++ b/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.
diff --git a/docs/contributing.md b/docs/contributing.md
deleted file mode 120000
index 44fcc634..00000000
--- a/docs/contributing.md
+++ /dev/null
@@ -1 +0,0 @@
-../CONTRIBUTING.md
\ No newline at end of file
diff --git a/docs/examples/index.rst b/docs/examples/index.rst
index e143547d..590b2f59 100644
--- a/docs/examples/index.rst
+++ b/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>
diff --git a/docs/benchmarks.rst b/docs/guide/benchmarks.rst
similarity index 95%
rename from docs/benchmarks.rst
rename to docs/guide/benchmarks.rst
index f974ae06..f0e2c67c 100644
--- a/docs/benchmarks.rst
+++ b/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
diff --git a/docs/guide/changes.md b/docs/guide/changes.md
new file mode 120000
index 00000000..699cc9e7
--- /dev/null
+++ b/docs/guide/changes.md
@@ -0,0 +1 @@
+../../CHANGELOG.md
\ No newline at end of file
diff --git a/docs/guide/contributing.md b/docs/guide/contributing.md
new file mode 120000
index 00000000..f939e75f
--- /dev/null
+++ b/docs/guide/contributing.md
@@ -0,0 +1 @@
+../../CONTRIBUTING.md
\ No newline at end of file
diff --git a/docs/guide/index.rst b/docs/guide/index.rst
new file mode 100644
index 00000000..b320ff7e
--- /dev/null
+++ b/docs/guide/index.rst
@@ -0,0 +1,20 @@
+User Guide
+==========
+
+.. toctree::
+ :maxdepth: 1
+ :caption: Getting Started
+
+ Installation <install>
+ Publications <publications>
+ Performance <performance>
+
+
+.. toctree::
+ :maxdepth: 1
+ :caption: Resources
+
+ Contribution Guide <contributing>
+ Changelog <changes>
+ Benchmarks <benchmarks>
+
diff --git a/docs/install.rst b/docs/guide/install.rst
similarity index 99%
rename from docs/install.rst
rename to docs/guide/install.rst
index b11ddbc2..5d70cedd 100644
--- a/docs/install.rst
+++ b/docs/guide/install.rst
@@ -1,14 +1,7 @@
Installation
============
-.. note::
-
- Wheels are provided for Linux and MacOS on x86-64 and NEON-enabled Arm platforms,
- but other machines will have to build the wheel from the source distribution.
- Building ``pyhmmer`` involves compiling HMMER3 and Easel, which requires a
- C compiler to be available.
-
-.. hint::
+.. caution::
Windows is not supported by HMMER, so it is not possible to build PyHMMER
on Windows as the moment. Consider using a Python install inside the
@@ -27,7 +20,14 @@ one is available, or from source after compiling the Cython code :
.. code:: console
$ pip install --user pyhmmer
-
+
+.. note::
+
+ Wheels are provided for Linux and MacOS on x86-64 and NEON-enabled Arm platforms,
+ but other machines will have to build the wheel from the source distribution.
+ Building ``pyhmmer`` involves compiling HMMER3 and Easel, which requires a
+ C compiler to be available.
+
Conda
^^^^^
diff --git a/docs/performance.rst b/docs/guide/performance.rst
similarity index 99%
rename from docs/performance.rst
rename to docs/guide/performance.rst
index c9de8f85..2e8968f5 100644
--- a/docs/performance.rst
+++ b/docs/guide/performance.rst
@@ -77,7 +77,7 @@ we annotated proteins from representative genomes of the
`Pfam <http://pfam.xfam.org/>`_ collection of HMMs. ``hmmsearch`` runs
are shown in green, ``pyhmmer`` runs in blue.
-.. image:: _images/progenomes-v0.4.5.svg
+.. image:: /_images/progenomes-v0.4.5.svg
*The proteins of each genomes were extracted into one FASTA file per genome,
and we measured the runtime of either the* ``hmmsearch`` *binary or the*
diff --git a/docs/publications.rst b/docs/guide/publications.rst
similarity index 97%
rename from docs/publications.rst
rename to docs/guide/publications.rst
index 0f80b57d..89980acc 100644
--- a/docs/publications.rst
+++ b/docs/guide/publications.rst
@@ -23,8 +23,8 @@ PyHMMER has been used in the following research works:
- Bhandari, B.K., Goldman, N. *A generalised protein identification method for novel and diverse sequencing technologies* (preprint). bioRxiv. :doi:`10.1101/2024.02.29.582769`.
- Carroll, L.M., M. Larralde, J.S. Fleck, R. Ponnudurai, A. Milanese, E. Cappio, G. Zeller, 2021. *Accurate de novo identification of biosynthetic gene clusters with GECCO* (preprint). bioRxiv. :doi:`10.1101/2021.05.03.442509`.
- Ducarmon, Q.R., N. Karcher, H.L.P. Tytgat, O. Delannoy-Bruno, S. Pekel, F. Springer, C. Schudoma, G. Zeller. *Large-scale computational analyses of gut microbial CAZyme repertoires enabled by Cayman* (preprint). bioRxiv. :doi:`10.1101/2024.01.08.574624`.
-- Erdrich, S.H., Luthe, T., Kever, L., Roigé, B.B., Arsova, B., Davoudi, E., Frunzke, J. *Expanding the phage galaxy: Isolation and characterization of five novel Streptomyces siphoviruses Ankus, Byblos, DekoNeimoidia, Mandalore, and Naboo* (preprint). bioRxiv. :doi:`10.1101/2024.02.16.580700 `.
-- Erdrich, S.H., Schurr, U., Frunzke, J., Arsova, B. *Seed coating with phages for sustainable plant biocontrol of plant pathogens and influence of the seed coat mucilage* (preprint). bioRxiv. :doi:`10.1101/2024.01.12.575253 `.
+- Erdrich, S.H., Luthe, T., Kever, L., Roigé, B.B., Arsova, B., Davoudi, E., Frunzke, J. *Expanding the phage galaxy: Isolation and characterization of five novel Streptomyces siphoviruses Ankus, Byblos, DekoNeimoidia, Mandalore, and Naboo* (preprint). bioRxiv. :doi:`10.1101/2024.02.16.580700`.
+- Erdrich, S.H., Schurr, U., Frunzke, J., Arsova, B. *Seed coating with phages for sustainable plant biocontrol of plant pathogens and influence of the seed coat mucilage* (preprint). bioRxiv. :doi:`10.1101/2024.01.12.575253`.
- Gaschignard, G., Millet, M., Bruley, A., Benzerara, K., Dezi, M., Skouri-Panet, F., Duprat, E., Callebaut, I. *AlphaFold2-guided description of CoBaHMA, a novel family of bacterial domains within the heavy-metal-associated superfamily*. Proteins. 2024 Jan 22. :doi:`10.1002/prot.26668`. :pmid:`38258321`.
- Jamali, K., L. Käll, R. Zhang, A. Brown, D. Kimanius, S.H.W. Scheres, 2023. *Automated model building and protein identification in cryo-EM maps* (preprint). bioRxiv. :doi:`10.1101/2023.05.16.541002`.
- Kautsar, S.A., J.J.J van der Hooft, D. de Ridder, M.H. Medema, 2021. *BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters*. GigaScience 10, giaa154. :doi:`10.1093/gigascience/giaa154`.
diff --git a/docs/index.rst b/docs/index.rst
index 62b7c0e4..54142a1c 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -110,7 +110,7 @@ Setup
Run ``pip install pyhmmer`` in a shell to download the latest release and all
its dependencies from PyPi, or have a look at the
-:doc:`Installation page <install>` to find other ways to install ``pyhmmer``.
+:doc:`Installation page <guide/install>` to find other ways to install ``pyhmmer``.
Citation
@@ -119,7 +119,7 @@ Citation
PyHMMER is scientific software, with a
`published paper <https://doi.org/10.1093/bioinformatics/btad214>`_
in the `Bioinformatics <https://academic.oup.com/bioinformatics>`_. Check the
-:doc:`Publications page <publications>` to see how to cite PyHMMER.
+:doc:`Publications page <guide/publications>` to see how to cite PyHMMER.
Library
@@ -128,15 +128,9 @@ Library
.. toctree::
:maxdepth: 2
- Installation <install>
+ User Guide <guide/index>
Examples <examples/index>
- Performance <performance>
- Contributing <contributing>
- Publications <publications>
- Benchmarks <benchmarks>
API Reference <api/index>
- Changelog <changes>
-
Related Projects
----------------
diff --git a/docs/requirements.txt b/docs/requirements.txt
index 2769e34e..c593b273 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -11,9 +11,7 @@ ipython ~=7.19
pygments ~=2.4
nbsphinx ~=0.5
sphinxcontrib-jquery ~=4.1
-
-# sphinx-bootstrap-theme ~=0.7 with patched admonition
-https://github.com/althonos/sphinx-bootstrap-theme/archive/master.zip
+pydata-sphinx-theme
# dependencies to run the example notebook(s)
biopython ==1.79
--
GitLab