Update from scikit-bio/scikit-bio@a8d4426

scikit-bio · Dec 31, 2024 · 4a25b1d · 4a25b1d
1 parent 0b8bc11
commit 4a25b1d
Show file tree

Hide file tree

Showing 555 changed files with 14,161 additions and 13,492 deletions.
diff --git a/docs/dev/_images/diversity-1.png b/docs/dev/_images/diversity-1.png
diff --git a/docs/dev/_images/diversity-2_00.png b/docs/dev/_images/diversity-2_00.png
diff --git a/docs/dev/_images/diversity-2_01.png b/docs/dev/_images/diversity-2_01.png
diff --git a/docs/dev/_images/diversity-3_00.png b/docs/dev/_images/diversity-3_00.png
diff --git a/docs/dev/_images/diversity-3_01.png b/docs/dev/_images/diversity-3_01.png
diff --git a/docs/dev/_images/diversity-3_02.png b/docs/dev/_images/diversity-3_02.png
diff --git a/docs/dev/_images/skbio-stats-distance-DissimilarityMatrix-plot-1.png b/docs/dev/_images/skbio-stats-distance-DissimilarityMatrix-plot-1.png
diff --git a/docs/dev/_images/skbio-stats-ordination-OrdinationResults-plot-1.png b/docs/dev/_images/skbio-stats-ordination-OrdinationResults-plot-1.png
diff --git a/docs/dev/_sources/generated/skbio.diversity.alpha.observed_otus.rst.txt b/docs/dev/_sources/generated/skbio.diversity.alpha.observed_otus.rst.txt
diff --git a/...v/_sources/generated/skbio.stats.composition.multiplicative_replacement.rst.txt b/...v/_sources/generated/skbio.stats.composition.multiplicative_replacement.rst.txt
diff --git a/docs/dev/_sources/generated/skbio.tree.TreeNode.accumulate_to_ancestor.rst.txt b/docs/dev/_sources/generated/skbio.tree.TreeNode.accumulate_to_ancestor.rst.txt
diff --git a/docs/dev/_sources/generated/skbio.tree.TreeNode.compare_tip_distances.rst.txt b/docs/dev/_sources/generated/skbio.tree.TreeNode.compare_tip_distances.rst.txt
diff --git a/docs/dev/_sources/generated/skbio.tree.TreeNode.descending_branch_length.rst.txt b/docs/dev/_sources/generated/skbio.tree.TreeNode.descending_branch_length.rst.txt
diff --git a/docs/dev/_sources/generated/skbio.tree.TreeNode.get_max_distance.rst.txt b/docs/dev/_sources/generated/skbio.tree.TreeNode.get_max_distance.rst.txt
diff --git a/docs/dev/_sources/generated/skbio.tree.TreeNode.invalidate_caches.rst.txt b/docs/dev/_sources/generated/skbio.tree.TreeNode.invalidate_caches.rst.txt
diff --git a/docs/dev/_sources/generated/skbio.tree.TreeNode.lowest_common_ancestor.rst.txt b/docs/dev/_sources/generated/skbio.tree.TreeNode.lowest_common_ancestor.rst.txt
diff --git a/docs/dev/_sources/generated/skbio.tree.TreeNode.rst.txt b/docs/dev/_sources/generated/skbio.tree.TreeNode.rst.txt
@@ -254,22 +254,6 @@ skbio.tree.TreeNode
 
 
 
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
 
 
 
@@ -737,54 +721,6 @@ skbio.tree.TreeNode
 
 
 
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
 
 
 
@@ -890,7 +826,6 @@ skbio.tree.TreeNode
       ~TreeNode.ancestors
       ~TreeNode.siblings
       ~TreeNode.neighbors
-      ~TreeNode.lowest_common_ancestor
       ~TreeNode.lca
       ~TreeNode.path
 
@@ -955,7 +890,6 @@ skbio.tree.TreeNode
 
       ~TreeNode.has_caches
       ~TreeNode.clear_caches
-      ~TreeNode.invalidate_caches
       ~TreeNode.cache_attr
       ~TreeNode.assign_ids
       ~TreeNode.index_tree
@@ -979,21 +913,22 @@ skbio.tree.TreeNode
       ~TreeNode.is_bifurcating
       ~TreeNode.observed_node_counts
       ~TreeNode.depth
-      ~TreeNode.accumulate_to_ancestor
       ~TreeNode.height
       ~TreeNode.total_length
-      ~TreeNode.descending_branch_length
       ~TreeNode.distance
       ~TreeNode.maxdist
-      ~TreeNode.get_max_distance
       ~TreeNode.cophenet
-      ~TreeNode.tip_tip_distances
+
+   .. rubric:: Tree comparison
+
+   .. autosummary::
+      :toctree:
+
       ~TreeNode.compare_rfd
       ~TreeNode.compare_wrfd
       ~TreeNode.compare_subsets
       ~TreeNode.compare_biparts
       ~TreeNode.compare_cophenet
-      ~TreeNode.compare_tip_distances
 
    .. rubric:: Tree visualization
 

diff --git a/docs/dev/_sources/generated/skbio.tree.TreeNode.tip_tip_distances.rst.txt b/docs/dev/_sources/generated/skbio.tree.TreeNode.tip_tip_distances.rst.txt
diff --git a/docs/dev/_sources/generated/skbio.util.aliased.rst.txt b/docs/dev/_sources/generated/skbio.util.aliased.rst.txt
@@ -0,0 +1,6 @@
+skbio.util.aliased
+==================
+
+.. currentmodule:: skbio.util
+
+.. autofunction:: aliased