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May 17, 2022
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Doc err macros #2260

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5 changes: 5 additions & 0 deletions c/CHANGELOG.rst
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Expand Up @@ -27,6 +27,11 @@

(:user:`benjeffery`, :issue:`1720`, :pr:`2226`, :pr:`2229`, :pr:`2224`)

- Remove the generic ``TSK_ERR_OUT_OF_BOUNDS`` - replacing with specific errors.
Remove ``TSK_ERR_NON_SINGLE_CHAR_MUTATION`` which was unused.
(:user:`benjeffery`, :pr:`2260`)


**Features**

- Make dumping of tables and tree sequences to disk a zero-copy operation.
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6 changes: 3 additions & 3 deletions c/tests/test_genotypes.c
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Expand Up @@ -575,12 +575,12 @@ test_single_tree_errors(void)

samples[0] = -1;
ret = tsk_vargen_init(&vargen, &ts, samples, 2, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_OUT_OF_BOUNDS);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_NODE_OUT_OF_BOUNDS);
tsk_vargen_free(&vargen);

samples[0] = 7;
ret = tsk_vargen_init(&vargen, &ts, samples, 2, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_OUT_OF_BOUNDS);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_NODE_OUT_OF_BOUNDS);
tsk_vargen_free(&vargen);

samples[0] = 3;
Expand Down Expand Up @@ -945,7 +945,7 @@ test_variant_decode_errors(void)

/* Bad samples */
ret = tsk_variant_init(&var, &ts, bad_samples, 3, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_OUT_OF_BOUNDS);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_NODE_OUT_OF_BOUNDS);
tsk_variant_free(&var);

/* Site out of bounds */
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4 changes: 2 additions & 2 deletions c/tests/test_haplotype_matching.c
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Expand Up @@ -271,9 +271,9 @@ test_single_tree_errors(void)
forward.tree_sequence = &ts;

ret = tsk_compressed_matrix_store_site(&forward, 3, 0, 0, NULL);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_OUT_OF_BOUNDS);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_SITE_OUT_OF_BOUNDS);
ret = tsk_compressed_matrix_store_site(&forward, 4, 0, 0, NULL);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_OUT_OF_BOUNDS);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_SITE_OUT_OF_BOUNDS);

T[0].tree_node = -1;
T[0].value = 0;
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29 changes: 14 additions & 15 deletions c/tskit/core.c
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Expand Up @@ -183,9 +183,6 @@ tsk_strerror_internal(int err)
case TSK_ERR_BAD_OFFSET:
ret = "Bad offset provided in input array";
break;
case TSK_ERR_OUT_OF_BOUNDS:
ret = "Object reference out of bounds";
break;
case TSK_ERR_NODE_OUT_OF_BOUNDS:
ret = "Node out of bounds";
break;
Expand Down Expand Up @@ -338,7 +335,7 @@ tsk_strerror_internal(int err)
ret = "Table too large; cannot allocate more than 2**31 rows.";
break;
case TSK_ERR_COLUMN_OVERFLOW:
ret = "Table column too large; cannot be more than 2**32 bytes.";
ret = "Table column too large; cannot be more than 2**64 bytes.";
break;
case TSK_ERR_TREE_OVERFLOW:
ret = "Too many trees; cannot be more than 2**31.";
Expand All @@ -349,17 +346,15 @@ tsk_strerror_internal(int err)

/* Limitations */
case TSK_ERR_ONLY_INFINITE_SITES:
ret = "Only infinite sites mutations are supported for this operation";
ret = "Only infinite sites mutations are supported for this operation, "
"i.e. at most a single mutation per site.";
break;
case TSK_ERR_SIMPLIFY_MIGRATIONS_NOT_SUPPORTED:
ret = "Migrations not currently supported by simplify";
break;
case TSK_ERR_SORT_MIGRATIONS_NOT_SUPPORTED:
ret = "Migrations not currently supported by sort";
break;
case TSK_ERR_MIGRATIONS_NOT_SUPPORTED:
ret = "Migrations not currently supported by this operation";
break;
case TSK_ERR_SORT_OFFSET_NOT_SUPPORTED:
ret = "Sort offsets for sites and mutations must be either 0 "
"or the length of the respective tables. Intermediate values "
Expand All @@ -368,6 +363,9 @@ tsk_strerror_internal(int err)
case TSK_ERR_NONBINARY_MUTATIONS_UNSUPPORTED:
ret = "Only binary mutations are supported for this operation";
break;
case TSK_ERR_MIGRATIONS_NOT_SUPPORTED:
ret = "Migrations not currently supported by this operation";
break;
case TSK_ERR_CANNOT_EXTEND_FROM_SELF:
ret = "Tables can only be extended using rows from a different table";
break;
Expand Down Expand Up @@ -430,19 +428,19 @@ tsk_strerror_internal(int err)
break;

/* Genotype decoding errors */
case TSK_ERR_TOO_MANY_ALLELES:
ret = "Cannot have more than 127 alleles";
break;
case TSK_ERR_ZERO_ALLELES:
ret = "Must have at least one allele when specifying an allele map";
break;
case TSK_ERR_MUST_IMPUTE_NON_SAMPLES:
ret = "Cannot generate genotypes for non-samples when isolated nodes are "
"considered as missing";
break;
case TSK_ERR_ALLELE_NOT_FOUND:
ret = "An allele was not found in the user-specified allele map";
break;
case TSK_ERR_TOO_MANY_ALLELES:
ret = "Cannot have more than 2147483647 alleles";
break;
case TSK_ERR_ZERO_ALLELES:
ret = "Must have at least one allele when specifying an allele map";
break;

/* Distance metric errors */
case TSK_ERR_SAMPLE_SIZE_MISMATCH:
Expand Down Expand Up @@ -508,7 +506,8 @@ tsk_strerror_internal(int err)

/* Simplify errors */
case TSK_ERR_KEEP_UNARY_MUTUALLY_EXCLUSIVE:
ret = "You cannot specify both KEEP_UNARY and KEEP_UNARY_IN_INDIVDUALS.";
ret = "You cannot specify both TSK_SIMPLIFY_KEEP_UNARY and "
"TSK_SIMPLIFY_KEEP_UNARY_IN_INDIVDUALS.";
break;

/* Individual errors */
Expand Down
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