prepare release v1.3.1 and update lphy doc #223

LinguaPhylo · Aug 9, 2022 · c533300 · c533300
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Showing 5 changed files with 18 additions and 4 deletions.
diff --git a/build.gradle.kts b/build.gradle.kts
@@ -37,7 +37,7 @@ allprojects {
 // Configures the sub-projects of this project.
 subprojects {
     group = "io.github.linguaphylo"
-    version = "1.3.1-SNAPSHOT"
+    version = "1.3.1"//-SNAPSHOT
     val webSteam = "github.com/LinguaPhylo/linguaPhylo"
     val web = "https://${webSteam}"
     val homepage = "https://linguaphylo.github.io/"

diff --git a/lphy/doc/index.md b/lphy/doc/index.md
@@ -1,4 +1,4 @@
-LPhy Language Reference (version 1.3.0)
+LPhy Language Reference (version 1.3.1)
 =======================================
 This an automatically generated language reference of the LinguaPhylo (LPhy) statistical phylogenetic modeling language.
 

diff --git a/lphy/doc/types/Alignment.md b/lphy/doc/types/Alignment.md
@@ -5,6 +5,10 @@ Methods
 
 - **ages**
   - gets the ages of these taxa as an array of doubles.
+- **canonicalStateCount**
+  - the number of canonical states excluding ambiguous states in the alignment.
+- **canonicalStates**
+  - the canonical states excluding ambiguous states.
 - **dataType**
   - get the data type of this alignment.
 - **length**
@@ -14,7 +18,9 @@ Methods
 - **nodeCount**
   - the total number of nodes (left + internal) in a binary tree with these taxa.
 - **stateCount**
-  - the number of possible states in the alignment.
+  - the number of possible states including ambiguous states in the alignment.
+- **states**
+  - the possible states including ambiguous states.
 - **taxa**
   - the taxa of the alignment.
 - **taxaNames**

diff --git a/lphy/doc/types/MetaDataAlignment.md b/lphy/doc/types/MetaDataAlignment.md
@@ -5,6 +5,10 @@ Methods
 
 - **ages**
   - gets the ages of these taxa as an array of doubles.
+- **canonicalStateCount**
+  - the number of canonical states excluding ambiguous states in the alignment.
+- **canonicalStates**
+  - the canonical states excluding ambiguous states.
 - **charset**
   - return a partition alignment. If the string doesn't match charset's syntax, then check if the string matches a defined name in the nexus file. Otherwise it is an error. The string is referred to one partition at a call, but can be multiple blocks, such as d.charset("2-457\3 660-896\3").
 - **dataType**
@@ -18,7 +22,9 @@ Methods
 - **nodeCount**
   - the total number of nodes (left + internal) in a binary tree with these taxa.
 - **stateCount**
-  - the number of possible states in the alignment.
+  - the number of possible states including ambiguous states in the alignment.
+- **states**
+  - the possible states including ambiguous states.
 - **taxa**
   - the taxa of the alignment.
 - **taxaNames**

diff --git a/lphy/doc/types/TimeTree.md b/lphy/doc/types/TimeTree.md
@@ -3,6 +3,8 @@ TimeTree
 Methods
 -------
 
+- **branchCount**
+  - the total number of branches in the tree (returns nodeCount() - 1)
 - **directAncestorCount**
   - the total number of nodes in the tree that are direct ancestors (i.e. have a single parent and a single child, or have one child that is a zero-branch-length leaf).
 - **extantCount**