update to tskit 1.0.0b2

omit integrity check in compute_mutation_parents

Author: petrelharp

core/species.cpp

@@ -7414,7 +7414,7 @@ void Species::WriteTreeSequence(std::string &p_recording_tree_path, bool p_simpl
 		// Add in the mutation.parent information; valid tree sequences need parents, but we don't keep them while running
 		ret = tsk_table_collection_build_index(&output_tables, 0);
 		if (ret < 0) handle_error("tsk_table_collection_build_index", ret);
-		ret = tsk_table_collection_compute_mutation_parents(&output_tables, 0);
+		ret = tsk_table_collection_compute_mutation_parents(&output_tables, TSK_NO_CHECK_INTEGRITY);
 		if (ret < 0) handle_error("tsk_table_collection_compute_mutation_parents", ret);
 
 		{
@@ -7801,7 +7801,7 @@ void Species::CrosscheckTreeSeqIntegrity(void)
 				ret = tsk_table_collection_build_index(tables_copy, 0);
 				if (ret < 0) handle_error("tsk_table_collection_build_index", ret);
 
-				ret = tsk_table_collection_compute_mutation_parents(tables_copy, 0);
+				ret = tsk_table_collection_compute_mutation_parents(tables_copy, TSK_NO_CHECK_INTEGRITY);
 				if (ret < 0) handle_error("tsk_table_collection_compute_mutation_parents", ret);
 
 			}

treerec/_README

@@ -8,6 +8,7 @@ The code in `tskit/kastore` is from [kastore/c](https://github.com/tskit-dev/kas
 
 **Changelog:**
 
+- *24 September 2025*: updated to tskit C_1.2.0 (=1.0.0b2) (still kastore C_2.1.1)
 - *15 April 2025*: updated to tskit C_1.1.4 (=0.6.2) (still kastore C_2.1.1)
 - *7 November 2023*: updated to tskit C_1.1.2 (=0.5.5) (still kastore C_2.1.1)
 - *2 June 2022*: updated to tskit C_1.0.0 and kastore C_2.1.1

treerec/tskit/core.c

@@ -168,7 +168,8 @@ 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. "
@@ -346,6 +347,12 @@ tsk_strerror_internal(int err)
                   "(TSK_ERR_DISALLOWED_UNKNOWN_MUTATION_TIME)";
             break;
 
+        case TSK_ERR_BAD_MUTATION_PARENT:
+            ret = "A mutation's parent is not consistent with the topology of the tree. "
+                  "Use compute_mutation_parents to set the parents correctly."
+                  "(TSK_ERR_BAD_MUTATION_PARENT)";
+            break;
+
         /* Migration errors */
         case TSK_ERR_UNSORTED_MIGRATIONS:
             ret = "Migrations must be sorted by time. (TSK_ERR_UNSORTED_MIGRATIONS)";
@@ -519,9 +526,13 @@ tsk_strerror_internal(int err)
                   "(TSK_ERR_BAD_SAMPLE_PAIR_TIMES)";
             break;
         case TSK_ERR_BAD_TIME_WINDOWS:
-            ret = "Time windows must be strictly increasing and end at infinity. "
+            ret = "Time windows must start at zero and be strictly increasing. "
                   "(TSK_ERR_BAD_TIME_WINDOWS)";
             break;
+        case TSK_ERR_BAD_TIME_WINDOWS_END:
+            ret = "Time windows must end at infinity for this method. "
+                  "(TSK_ERR_BAD_TIME_WINDOWS_END)";
+            break;
         case TSK_ERR_BAD_NODE_TIME_WINDOW:
             ret = "Node time does not fall within assigned time window. "
                   "(TSK_ERR_BAD_NODE_TIME_WINDOW)";

treerec/tskit/core.h

@@ -147,12 +147,12 @@ sizes and types of externally visible structs.
 The library minor version. Incremented when non-breaking backward-compatible changes
 to the API or ABI are introduced, i.e., the addition of a new function.
 */
-#define TSK_VERSION_MINOR   1
+#define TSK_VERSION_MINOR   2
 /**
 The library patch version. Incremented when any changes not relevant to the
 to the API or ABI are introduced, i.e., internal refactors of bugfixes.
 */
-#define TSK_VERSION_PATCH   4
+#define TSK_VERSION_PATCH   0
 /** @} */
 
 /*
@@ -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
 /**
@@ -510,6 +510,12 @@ Some mutations have TSK_UNKNOWN_TIME in an algorithm where that's
 disallowed (use compute_mutation_times?).
 */
 #define TSK_ERR_DISALLOWED_UNKNOWN_MUTATION_TIME                    -510
+
+/** 
+A mutation's parent was not consistent with the topology of the tree.
+ */
+#define TSK_ERR_BAD_MUTATION_PARENT                                 -511
+
 /** @} */
 
 /**
@@ -740,13 +746,17 @@ Sample times do not all equal the start of first time window
 */
 #define TSK_ERR_BAD_SAMPLE_PAIR_TIMES                               -923
 /**
-Time windows are not strictly increasing ending at infinity
+Time windows are not strictly increasing
 */
 #define TSK_ERR_BAD_TIME_WINDOWS                                    -924
 /**
+Time windows do not end at infinity
+*/
+#define TSK_ERR_BAD_TIME_WINDOWS_END                                -925
+/**
 Node time does not fall within assigned time window
 */
-#define TSK_ERR_BAD_NODE_TIME_WINDOW                                -925
+#define TSK_ERR_BAD_NODE_TIME_WINDOW                                -926
 /** @} */
 
 /**