Clarify docs on allowing mixed node types

Author: benjeffery

python/CHANGELOG.rst

@@ -2,6 +2,15 @@
 [0.6.4] - 2025-XX-XX
 --------------------
 
+**Changes**
+
+- Allow mixed sample and non-sample nodes to be output by ``write_vcf``.
+  and for individuals without nodes to be specified for output, although
+  they will not appear in the VCF. Individuals without nodes no longer
+  raise an error and are instead ignored, except in the case where they
+  are explicitly specified in the ``individuals`` argument.
+  (:user:`benjeffery`, :pr:`3157`)
+
 **Features**
 
 - Add ``TreeSequence.sample_nodes_by_ploidy`` method to return the sample nodes

python/tskit/trees.py

@@ -6432,14 +6432,9 @@ def write_vcf(
         with sample nodes are included in increasing order of individual ID.
 
         Subsets or permutations of the sample individuals may be specified
-        using the ``individuals`` argument. It is an error to specify any
-        individuals that are not associated with any nodes, or whose
-        nodes are not all samples.
-
-        Mixed-sample individuals (e.g., those associated with one node
-        that is a sample and another that is not) in the data model will
-        result in an error by default. However, such individuals can be
-        excluded using the ``individuals`` argument.
+        using the ``individuals`` argument. An individual specified that
+        is not associated with any nodes will be ignored and not included in the
+        output.
 
         If there are no individuals in the tree sequence,
         synthetic individuals are created by combining adjacent samples, and