From ed8536c940663429ddad38f9232df8547a965457 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Wed, 10 Jul 2024 13:55:00 +0200
Subject: [PATCH] Expand new documentation [ci skip]
---
docs/api/easel/linalg.rst | 6 ------
docs/api/hmmer/index.rst | 2 ++
docs/api/index.rst | 4 ++--
docs/api/plan7/misc.rst | 7 +++++++
pyhmmer/plan7.pyx | 2 +-
5 files changed, 12 insertions(+), 9 deletions(-)
diff --git a/docs/api/easel/linalg.rst b/docs/api/easel/linalg.rst
index 16a414f1..b87b137a 100644
--- a/docs/api/easel/linalg.rst
+++ b/docs/api/easel/linalg.rst
@@ -1,9 +1,6 @@
Linear Algebra
==============
-Vectors
--------
-
.. autoclass:: pyhmmer.easel.Vector
:members:
@@ -16,9 +13,6 @@ Vectors
:members:
-Matrix
-------
-
.. autoclass:: pyhmmer.easel.Matrix
:members:
diff --git a/docs/api/hmmer/index.rst b/docs/api/hmmer/index.rst
index 4fa64195..0e0c8f3e 100644
--- a/docs/api/hmmer/index.rst
+++ b/docs/api/hmmer/index.rst
@@ -3,6 +3,8 @@ HMMER
.. currentmodule:: pyhmmer.hmmer
+.. automodule:: pyhmmer.hmmer
+
Profile Searches
----------------
diff --git a/docs/api/index.rst b/docs/api/index.rst
index 630d1e7d..84dc9b76 100644
--- a/docs/api/index.rst
+++ b/docs/api/index.rst
@@ -3,7 +3,8 @@ API Reference
.. currentmodule:: pyhmmer
-.. automodule:: pyhmmer
+This section contains a complete reference of the API of the different
+``pyhmmer`` modules.
.. toctree::
:maxdepth: 2
@@ -13,4 +14,3 @@ API Reference
Plan7 <plan7/index>
Daemon <daemon/index>
Errors <errors/index>
-
diff --git a/docs/api/plan7/misc.rst b/docs/api/plan7/misc.rst
index 0d8e12e4..ae4a831c 100644
--- a/docs/api/plan7/misc.rst
+++ b/docs/api/plan7/misc.rst
@@ -11,10 +11,17 @@ Miscellaneous
: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/pyhmmer/plan7.pyx b/pyhmmer/plan7.pyx
index 6f8b873e..77049e45 100644
--- a/pyhmmer/plan7.pyx
+++ b/pyhmmer/plan7.pyx
@@ -2755,7 +2755,7 @@ cdef class HMM:
Columns correspond to the following transitions, in order:
:math:`M_n \to M_{n+1}`, :math:`M_n \to I_n`, :math:`M_n \to D_{n+1}`,
:math:`I_n \to I_n`, :math:`I_n \to M_{n+1}`, :math:`D_n \to D_{n+1}`,
- :math:`D_n \to M_{n+1}`. Use the `~pyhmmer.plan7.Transitions` enum
+ :math:`D_n \to M_{n+1}`. Use the `pyhmmer.plan7.Transitions` enum
instead of hardcoded indices to make your code more legible.
Example:
--
GitLab