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Initial definition for TSK_TRACE_ERRORS #3095

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Merged
merged 1 commit into from
Mar 26, 2025
Merged

Initial definition for TSK_TRACE_ERRORS #3095

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4 changes: 4 additions & 0 deletions c/CHANGELOG.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,11 @@
[1.1.4] - 2024-XX-XX
--------------------

**Changes**

- Added the TSK_TRACE_ERRORS macro to enable tracing of errors in the C library.
This is useful for debugging as errors will print to stderr when set.
(:user:`jeromekelleher`, :pr:`3095`).

--------------------
[1.1.3] - 2024-10-16
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7 changes: 6 additions & 1 deletion c/meson.build
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Expand Up @@ -3,6 +3,11 @@ project('tskit', ['c', 'cpp'],
default_options: ['c_std=c99', 'cpp_std=c++11']
)

debug_c_args = []
if get_option('buildtype').startswith('debug')
debug_c_args = ['-DTSK_TRACE_ERRORS']
endif

kastore_proj = subproject('kastore')
kastore_dep = kastore_proj.get_variable('kastore_dep')
kastore_inc = kastore_proj.get_variable('kastore_inc')
Expand All @@ -16,7 +21,7 @@ extra_c_args = [
'-Wmissing-prototypes', '-Wstrict-prototypes',
'-Wconversion', '-Wshadow', '-Wpointer-arith', '-Wcast-align',
'-Wcast-qual', '-Wwrite-strings', '-Wnested-externs',
'-fshort-enums', '-fno-common']
'-fshort-enums', '-fno-common'] + debug_c_args

lib_sources = [
'tskit/core.c', 'tskit/tables.c', 'tskit/trees.c',
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22 changes: 11 additions & 11 deletions c/tskit/convert.c
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
/*
* MIT License
*
* Copyright (c) 2018-2021 Tskit Developers
* Copyright (c) 2018-2025 Tskit Developers
* Copyright (c) 2015-2017 University of Oxford
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
Expand Down Expand Up @@ -68,11 +68,11 @@
const char *label_format = ms_labels ? "%d" : "n%d";

if (root < 0 || root >= (tsk_id_t) self->tree->num_nodes) {
ret = TSK_ERR_NODE_OUT_OF_BOUNDS;
ret = tsk_trace_error(TSK_ERR_NODE_OUT_OF_BOUNDS);
goto out;
}
if (buffer == NULL) {
ret = TSK_ERR_BAD_PARAM_VALUE;
ret = tsk_trace_error(TSK_ERR_BAD_PARAM_VALUE);
goto out;
}
root_parent = tree->parent[root];
Expand All @@ -82,7 +82,7 @@
v = stack[stack_top];
if (tree->left_child[v] != TSK_NULL && v != u) {
if (s >= buffer_size) {
ret = TSK_ERR_BUFFER_OVERFLOW;
ret = tsk_trace_error(TSK_ERR_BUFFER_OVERFLOW);
goto out;
}
buffer[s] = '(';
Expand All @@ -104,17 +104,17 @@
}
if (label != -1) {
if (s >= buffer_size) {
ret = TSK_ERR_BUFFER_OVERFLOW;
ret = tsk_trace_error(TSK_ERR_BUFFER_OVERFLOW);
goto out;
}
r = snprintf(buffer + s, buffer_size - s, label_format, label);
if (r < 0) {
ret = TSK_ERR_IO;
ret = tsk_trace_error(TSK_ERR_IO);

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}
s += (size_t) r;
if (s >= buffer_size) {
ret = TSK_ERR_BUFFER_OVERFLOW;
ret = tsk_trace_error(TSK_ERR_BUFFER_OVERFLOW);
goto out;
}
}
Expand All @@ -123,12 +123,12 @@
r = snprintf(buffer + s, buffer_size - s, ":%.*f", (int) self->precision,
branch_length);
if (r < 0) {
ret = TSK_ERR_IO;
ret = tsk_trace_error(TSK_ERR_IO);

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}
s += (size_t) r;
if (s >= buffer_size) {
ret = TSK_ERR_BUFFER_OVERFLOW;
ret = tsk_trace_error(TSK_ERR_BUFFER_OVERFLOW);
goto out;
}
if (v == tree->right_child[u]) {
Expand All @@ -141,7 +141,7 @@
}
}
if ((s + 1) >= buffer_size) {
ret = TSK_ERR_BUFFER_OVERFLOW;
ret = tsk_trace_error(TSK_ERR_BUFFER_OVERFLOW);
goto out;
}
buffer[s] = ';';
Expand All @@ -164,7 +164,7 @@
self->traversal_stack
= tsk_malloc(tsk_tree_get_size_bound(tree) * sizeof(*self->traversal_stack));
if (self->traversal_stack == NULL) {
ret = TSK_ERR_NO_MEMORY;
ret = tsk_trace_error(TSK_ERR_NO_MEMORY);

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}
out:
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24 changes: 14 additions & 10 deletions c/tskit/core.c
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@@ -1,7 +1,7 @@
/*
* MIT License
*
* Copyright (c) 2019-2024 Tskit Developers
* Copyright (c) 2019-2025 Tskit Developers
* Copyright (c) 2015-2018 University of Oxford
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
Expand Down Expand Up @@ -43,22 +43,24 @@
get_random_bytes(uint8_t *buf)
{
/* Based on CPython's code in bootstrap_hash.c */
int ret = TSK_ERR_GENERATE_UUID;
int ret = 0;
HCRYPTPROV hCryptProv = (HCRYPTPROV) NULL;

if (!CryptAcquireContext(
&hCryptProv, NULL, NULL, PROV_RSA_FULL, CRYPT_VERIFYCONTEXT)) {
ret = tsk_trace_error(TSK_ERR_GENERATE_UUID);
goto out;
}
if (!CryptGenRandom(hCryptProv, (DWORD) UUID_NUM_BYTES, buf)) {
ret = tsk_trace_error(TSK_ERR_GENERATE_UUID);
goto out;
}
if (!CryptReleaseContext(hCryptProv, 0)) {
hCryptProv = (HCRYPTPROV) NULL;
ret = tsk_trace_error(TSK_ERR_GENERATE_UUID);
goto out;
}
hCryptProv = (HCRYPTPROV) NULL;
ret = 0;
out:
if (hCryptProv != (HCRYPTPROV) NULL) {
CryptReleaseContext(hCryptProv, 0);
Expand All @@ -72,19 +74,21 @@
static int TSK_WARN_UNUSED
get_random_bytes(uint8_t *buf)
{
int ret = TSK_ERR_GENERATE_UUID;
int ret = 0;
FILE *f = fopen("/dev/urandom", "r");

if (f == NULL) {
ret = tsk_trace_error(TSK_ERR_GENERATE_UUID);

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}
if (fread(buf, UUID_NUM_BYTES, 1, f) != 1) {
ret = tsk_trace_error(TSK_ERR_GENERATE_UUID);

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}
if (fclose(f) != 0) {
ret = tsk_trace_error(TSK_ERR_GENERATE_UUID);

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}
ret = 0;
out:
return ret;
}
Expand All @@ -111,7 +115,7 @@
buf[4], buf[5], buf[6], buf[7], buf[8], buf[9], buf[10], buf[11], buf[12],
buf[13], buf[14], buf[15])
< 0) {
ret = TSK_ERR_GENERATE_UUID;
ret = tsk_trace_error(TSK_ERR_GENERATE_UUID);

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}
out:
Expand Down Expand Up @@ -764,7 +768,7 @@

tsk_memset(self, 0, sizeof(tsk_blkalloc_t));
if (chunk_size < 1) {
ret = TSK_ERR_BAD_PARAM_VALUE;
ret = tsk_trace_error(TSK_ERR_BAD_PARAM_VALUE);
goto out;
}
self->chunk_size = chunk_size;
Expand All @@ -775,12 +779,12 @@
self->num_chunks = 0;
self->mem_chunks = malloc(sizeof(char *));
if (self->mem_chunks == NULL) {
ret = TSK_ERR_NO_MEMORY;
ret = tsk_trace_error(TSK_ERR_NO_MEMORY);

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}
self->mem_chunks[0] = malloc(chunk_size);
if (self->mem_chunks[0] == NULL) {
ret = TSK_ERR_NO_MEMORY;
ret = tsk_trace_error(TSK_ERR_NO_MEMORY);

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}
self->num_chunks = 1;
Expand Down Expand Up @@ -1256,7 +1260,7 @@
+ (num_bits % TSK_BIT_ARRAY_NUM_BITS ? 1 : 0);
self->data = tsk_calloc(self->size * length, sizeof(*self->data));
if (self->data == NULL) {
ret = TSK_ERR_NO_MEMORY;
ret = tsk_trace_error(TSK_ERR_NO_MEMORY);

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goto out;
}
out:
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17 changes: 16 additions & 1 deletion c/tskit/core.h
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@@ -1,7 +1,7 @@
/*
* MIT License
*
* Copyright (c) 2019-2024 Tskit Developers
* Copyright (c) 2019-2025 Tskit Developers
* Copyright (c) 2015-2018 University of Oxford
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
Expand Down Expand Up @@ -953,6 +953,21 @@ not be freed by client code.
*/
const char *tsk_strerror(int err);

#ifdef TSK_TRACE_ERRORS

static inline int
_tsk_trace_error(int err, int line, const char *file)
{
fprintf(stderr, "tskit-trace-error: %d='%s' at line %d in %s\n", err,
tsk_strerror(err), line, file);
return err;
}

#define tsk_trace_error(err) (_tsk_trace_error(err, __LINE__, __FILE__))
#else
#define tsk_trace_error(err) (err)
#endif

#ifndef TSK_BUG_ASSERT_MESSAGE
#define TSK_BUG_ASSERT_MESSAGE \
"If you are using tskit directly please open an issue on" \
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