update changelog and remove upgrade

Author: hossam26644

python/CHANGELOG.rst

@@ -8,7 +8,8 @@
   the original schema instead (:user:`benjeffery`, :issue:`3129`, :pr:`3130`)
 
 **Breaking Changes**
-- HDF5 support is dropped (:user:`hossam26644`, :issue:`2812`, :pr:`3138`)
+- Legacy formats from msprime<0.6 (HDF5 formats) support is dropped. This includes the support for
+  ``tskit upgrade``  (:user:`hossam26644`, :issue:`2812`, :pr:`3138`)
 
 --------------------
 [0.6.1] - 2025-03-31

python/tskit/cli.py

@@ -1,7 +1,7 @@
 #
 # MIT License
 #
-# Copyright (c) 2018-2024 Tskit Developers
+# Copyright (c) 2018-2025 Tskit Developers
 # Copyright (c) 2015-2018 University of Oxford
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -68,19 +68,6 @@ def run_trees(args):
             print(tree.draw(format="unicode"))
 
 
-def run_upgrade(args):
-    try:
-        tree_sequence = tskit.load_legacy(args.source, args.remove_duplicate_positions)
-        tree_sequence.dump(args.destination)
-    except tskit.DuplicatePositionsError:
-        sys_exit(
-            "Error: Duplicate mutation positions in the source file detected.\n\n"
-            'This is not supported in the current file format. Running "upgrade -d" '
-            "will remove these duplicate positions. However, this will result in loss "
-            "of data from the original file!"
-        )
-
-
 def run_individuals(args):
     tree_sequence = load_tree_sequence(args.tree_sequence)
     tree_sequence.dump_text(individuals=sys.stdout, precision=args.precision)
@@ -197,7 +184,6 @@ def get_tskit_parser():
         default=False,
         help="Remove any duplicated mutation positions in the source file. ",
     )
-    parser.set_defaults(runner=run_upgrade)
     # suppress fasta visibility until we have a reference sequence
     # See https://github.com/tskit-dev/tskit/issues/1888
     # parser = subparsers.add_parser(