Document the famsa_info function and pyfamsa constants

althonos · Aug 28, 2024 · 2f77de0 · 2f77de0
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diff --git a/docs/api/index.rst b/docs/api/index.rst
@@ -9,43 +9,35 @@ API Reference
 
    Aligner <aligner>
    Sequence <sequence>
-   Gapped Sequence <sequence>
+   Gapped Sequence <gapped_sequence>
    Alignment <alignment>
    Guide Tree <guide_tree>
+   Utilities <utilities>
 
-
-Aligner
+Classes
 -------
 
 .. autosummary::
     :nosignatures:
 
     Aligner
-
-
-Sequence
---------
-
-.. autosummary::
-    :nosignatures:
-
     Sequence
     GappedSequence
+    Alignment
+    GuideTree
 
-
-Alignment
+Functions
 ---------
 
 .. autosummary::
     :nosignatures:
 
-    Alignment
-
+    famsa_info
 
-GuideTree
+Constants
 ---------
 
 .. autosummary::
     :nosignatures:
 
-    GuideTree
+    MIQS
diff --git a/docs/api/utilities.rst b/docs/api/utilities.rst
@@ -0,0 +1,24 @@
+Utilities
+=========
+
+.. currentmodule:: pyfamsa
+
+Constants
+---------
+
+.. data:: MIQS
+    :type: scoring_matrices.ScoringMatrix
+
+    The MIQS scoring matrix proposed by Yamada & Tomii (2014), used by 
+    default in FAMSA for scoring alignments.
+
+.. data:: FAMSA_ALPHABET
+    :type: str
+
+    The alphabet used by FAMSA to encode input sequences.
+
+
+Functions
+---------
+
+.. autofunction:: pyfamsa.famsa_info
diff --git a/pyfamsa/__init__.py b/pyfamsa/__init__.py
@@ -21,6 +21,8 @@
     "GuideTree",
     "Sequence",
     "famsa_info",
+    "FAMSA_ALPHABET",
+    "MIQS"
 ]
 
 __author__ = "Martin Larralde <martin.larralde@embl.de>"

diff --git a/pyfamsa/_famsa.pyx b/pyfamsa/_famsa.pyx
@@ -93,6 +93,18 @@ MIQS = _make_miqs()
 
 def famsa_info():
     """Get information about the embedded FAMSA version.
+
+    This function returns an anonymous named tuple with attributes
+    ``version``, ``version_info``, ``date`` and ``authors`` that can
+    be used to get the build information from FAMSA.
+
+    Example:
+        >>> info = famsa_info()
+        >>> info.version
+        '2.2.2'
+        >>> info.date
+        datetime.date(2022, 10, 9)
+
     """
     _VersionInfo = collections.namedtuple("_VersionInfo", ["major", "minor", "micro"])
     _Info = collections.namedtuple("_Info", ["version", "version_info", "date", "authors"])