remove upgrade parser. Update documentation

Author: hossam26644

c/tskit/core.c

@@ -168,7 +168,7 @@ tsk_strerror_internal(int err)
             break;
         case TSK_ERR_FILE_VERSION_TOO_OLD:
             ret = "tskit file version too old. Please upgrade using the "
-                  "'tskit upgrade' command. (TSK_ERR_FILE_VERSION_TOO_OLD)";
+                  "'tskit upgrade' command from tskit version<0.6.2. (TSK_ERR_FILE_VERSION_TOO_OLD)";
             break;
         case TSK_ERR_FILE_VERSION_TOO_NEW:
             ret = "tskit file version is too new for this instance. "

c/tskit/core.h

@@ -283,7 +283,7 @@ A file could not be read because it is in the wrong format
 /**
 The file is in tskit format, but the version is too old for the
 library to read. The file should be upgraded to the latest version
-using the ``tskit upgrade`` command line utility.
+using the ``tskit upgrade`` command line utility from tskit version<0.6.2.
 */
 #define TSK_ERR_FILE_VERSION_TOO_OLD                                -101
 /**

docs/file-formats.md

@@ -42,7 +42,7 @@ stored as well as the top-level metadata.
 ### Legacy Versions
 
 Tree sequence files written by older versions of tskit are not readable by
-newer versions of tskit. For major releases of tskit, `tskit upgrade`
+newer versions of tskit. For tskit releases<0.6.2, `tskit upgrade`
 will convert older tree sequence files to the latest version.
 
 

python/_tskitmodule.c

@@ -223,7 +223,7 @@ handle_library_error(int err)
     const char *not_kas_format_msg
         = "File not in kastore format. Either the file is corrupt or it is not a "
           "tskit tree sequence file. It may be a legacy HDF file upgradable with "
-          "`tskit upgrade` or a compressed tree sequence file that can be decompressed "
+          "`tskit upgrade` from tskit version<0.6.2 or a compressed tree sequence file that can be decompressed "
           "with `tszip`.";
     const char *ibd_pairs_not_stored_msg
         = "Sample pairs are not stored by default "

python/tests/test_cli.py

@@ -310,16 +310,6 @@ def test_vcf_allow_position_zero(self, flags, expected):
         assert args.tree_sequence == tree_sequence
         assert args.allow_position_zero == expected
 
-    def test_upgrade_default_values(self):
-        parser = cli.get_tskit_parser()
-        cmd = "upgrade"
-        source = "in.trees"
-        destination = "out.trees"
-        args = parser.parse_args([cmd, source, destination])
-        assert args.source == source
-        assert args.destination == destination
-        assert not args.remove_duplicate_positions
-
     def test_info_default_values(self):
         parser = cli.get_tskit_parser()
         cmd = "info"

python/tskit/cli.py

@@ -170,20 +170,6 @@ def get_tskit_parser():
     )
     parser.set_defaults(runner=run_trees)
 
-    parser = subparsers.add_parser(
-        "upgrade", help="Upgrade legacy tree sequence files."
-    )
-    parser.add_argument(
-        "source", help="The source tskit tree sequence file in legacy format"
-    )
-    parser.add_argument("destination", help="The filename of the upgraded copy.")
-    parser.add_argument(
-        "--remove-duplicate-positions",
-        "-d",
-        action="store_true",
-        default=False,
-        help="Remove any duplicated mutation positions in the source file. ",
-    )
     # suppress fasta visibility until we have a reference sequence
     # See https://github.com/tskit-dev/tskit/issues/1888
     # parser = subparsers.add_parser(

python/tskit/util.py

@@ -867,7 +867,7 @@ def raise_known_file_format_errors(open_file, existing_exception):
             "The specified file appears to be in HDF5 format. This file "
             "may have been generated by msprime < 0.6.0 (June 2018) which "
             "can no longer be read directly. Please convert to the new "
-            "kastore format using the ``tskit upgrade`` command from tskit version 0.6.2"
+            "kastore format using the ``tskit upgrade`` command from tskit version<0.6.2"
         ) from existing_exception
     if header[:2] == b"\x50\x4b":
         raise tskit.FileFormatError(