gnu: Add sajson-for-gemmi.
* gnu/packages/cpp.scm (sajson-for-gemmi): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>master
David Elsing
Liliana Marie Prikler
parent
fd4342728d
commit
3cbb634a89
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@ -27,6 +27,7 @@
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#:use-module (guix utils)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (guix download)
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#:use-module (guix gexp)
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#:use-module (guix git-download)
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#:use-module (gnu packages)
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#:use-module (gnu packages algebra)
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@ -35,6 +36,7 @@
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#:use-module (gnu packages boost)
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#:use-module (gnu packages check)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages cpp)
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#:use-module (gnu packages documentation)
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#:use-module (gnu packages fontutils)
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#:use-module (gnu packages gl)
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@ -50,8 +52,10 @@
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#:use-module (gnu packages qt)
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#:use-module (gnu packages serialization)
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#:use-module (gnu packages sphinx)
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#:use-module (gnu packages stb)
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#:use-module (gnu packages xml)
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#:use-module (guix build-system cmake)
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#:use-module (guix build-system copy)
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#:use-module (guix build-system gnu)
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#:use-module (guix build-system python))
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@ -2102,6 +2102,22 @@ different floating point sizes and complex transformations.")
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parsing with only a single memory allocation.")
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(license license:expat))))
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(define-public sajson-for-gemmi
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(package/inherit sajson
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(name "sajson-for-gemmi")
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(source (origin
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(inherit (package-source sajson))
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(patches (cons
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(search-patch
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"sajson-for-gemmi-numbers-as-strings.patch")
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(origin-patches (package-source sajson))))))
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(arguments
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(substitute-keyword-arguments (package-arguments sajson)
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;; This is a modified version used in gemmi, in which numbers are kept
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;; as strings. Building the tests fails with the modification.
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((#:tests? _ #f) #f)))
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(properties '((hidden? . #t)))))
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(define-public optionparser
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(package
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(name "optionparser")
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@ -0,0 +1,195 @@
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Patch for gemmi: Keep numbers in JSON file as strings.
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Adapted from this commit of the bundled fork of sajson in gemmi:
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https://github.com/project-gemmi/gemmi/commit/fccbca4f6040364ba708613e1429c2251872240d
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diff -ur a/include/sajson.h b/include/sajson.h
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--- a/include/sajson.h
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+++ b/include/sajson.h
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@@ -411,43 +411,6 @@
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};
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} // namespace internal
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-namespace integer_storage {
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-enum { word_length = 1 };
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-
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-inline int load(const size_t* location) {
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- int value;
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- memcpy(&value, location, sizeof(value));
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- return value;
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-}
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-
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-inline void store(size_t* location, int value) {
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- // NOTE: Most modern compilers optimize away this constant-size
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- // memcpy into a single instruction. If any don't, and treat
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- // punning through a union as legal, they can be special-cased.
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- static_assert(
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- sizeof(value) <= sizeof(*location),
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- "size_t must not be smaller than int");
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- memcpy(location, &value, sizeof(value));
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-}
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-} // namespace integer_storage
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-
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-namespace double_storage {
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-enum { word_length = sizeof(double) / sizeof(size_t) };
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-
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-inline double load(const size_t* location) {
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- double value;
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- memcpy(&value, location, sizeof(double));
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- return value;
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-}
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-
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-inline void store(size_t* location, double value) {
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- // NOTE: Most modern compilers optimize away this constant-size
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- // memcpy into a single instruction. If any don't, and treat
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- // punning through a union as legal, they can be special-cased.
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- memcpy(location, &value, sizeof(double));
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-}
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-} // namespace double_storage
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-
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/// Represents a JSON value. First, call get_type() to check its type,
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/// which determines which methods are available.
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///
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@@ -585,70 +548,10 @@
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return length;
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}
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- /// If a numeric value was parsed as a 32-bit integer, returns it.
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- /// Only legal if get_type() is TYPE_INTEGER.
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- int get_integer_value() const {
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- assert_tag(tag::integer);
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- return integer_storage::load(payload);
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- }
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-
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- /// If a numeric value was parsed as a double, returns it.
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- /// Only legal if get_type() is TYPE_DOUBLE.
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- double get_double_value() const {
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- assert_tag(tag::double_);
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- return double_storage::load(payload);
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- }
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-
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- /// Returns a numeric value as a double-precision float.
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- /// Only legal if get_type() is TYPE_INTEGER or TYPE_DOUBLE.
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- double get_number_value() const {
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- assert_tag_2(tag::integer, tag::double_);
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- if (value_tag == tag::integer) {
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- return get_integer_value();
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- } else {
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- return get_double_value();
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- }
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- }
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-
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- /// Returns true and writes to the output argument if the numeric value
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- /// fits in a 53-bit integer. This is useful for timestamps and other
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- /// situations where integral values with greater than 32-bit precision
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- /// are used, as 64-bit values are not understood by all JSON
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- /// implementations or languages.
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- /// Returns false if the value is not an integer or not in range.
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- /// Only legal if get_type() is TYPE_INTEGER or TYPE_DOUBLE.
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- bool get_int53_value(int64_t* out) const {
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- // Make sure the output variable is always defined to avoid any
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- // possible situation like
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- // https://gist.github.com/chadaustin/2c249cb850619ddec05b23ca42cf7a18
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- *out = 0;
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-
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- assert_tag_2(tag::integer, tag::double_);
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- switch (value_tag) {
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- case tag::integer:
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- *out = get_integer_value();
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- return true;
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- case tag::double_: {
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- double v = get_double_value();
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- if (v < -(1LL << 53) || v > (1LL << 53)) {
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- return false;
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- }
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- int64_t as_int = static_cast<int64_t>(v);
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- if (as_int != v) {
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- return false;
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- }
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- *out = as_int;
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- return true;
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- }
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- default:
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- return false;
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- }
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- }
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-
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/// Returns the length of the string.
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/// Only legal if get_type() is TYPE_STRING.
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size_t get_string_length() const {
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- assert_tag(tag::string);
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+ assert_tag_3(tag::string, tag::integer, tag::double_);
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return payload[1] - payload[0];
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}
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@@ -659,7 +562,7 @@
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/// embedded NULs.
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/// Only legal if get_type() is TYPE_STRING.
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const char* as_cstring() const {
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- assert_tag(tag::string);
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+ assert_tag_3(tag::string, tag::integer, tag::double_);
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return text + payload[0];
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}
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@@ -667,7 +570,7 @@
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/// Returns a string's value as a std::string.
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/// Only legal if get_type() is TYPE_STRING.
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std::string as_string() const {
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- assert_tag(tag::string);
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+ assert_tag_3(tag::string, tag::integer, tag::double_);
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return std::string(text + payload[0], text + payload[1]);
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}
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#endif
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@@ -690,6 +593,10 @@
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assert(e1 == value_tag || e2 == value_tag);
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}
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+ void assert_tag_3(tag e1, tag e2, tag e3) const {
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+ assert(e1 == value_tag || e2 == value_tag || e3 == value_tag);
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+ }
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+
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void assert_in_bounds(size_t i) const { assert(i < get_length()); }
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const tag value_tag;
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@@ -2059,6 +1966,8 @@
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std::pair<char*, internal::tag> parse_number(char* p) {
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using internal::tag;
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+ size_t start = p - input.get_data();
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+
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// Assume 32-bit, two's complement integers.
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static constexpr unsigned RISKY = INT_MAX / 10u;
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unsigned max_digit_after_risky = INT_MAX % 10u;
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@@ -2235,23 +2144,18 @@
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u = 0u - u;
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}
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}
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+
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+ bool success;
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+ size_t* out = allocator.reserve(2, &success);
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+ if (SAJSON_UNLIKELY(!success)) {
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+ return std::make_pair(oom(p, "number"), tag::null);
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+ }
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+ out[0] = start;
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+ out[1] = p - input.get_data();
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+
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if (try_double) {
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- bool success;
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- size_t* out
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- = allocator.reserve(double_storage::word_length, &success);
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- if (SAJSON_UNLIKELY(!success)) {
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- return std::make_pair(oom(p, "double"), tag::null);
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- }
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- double_storage::store(out, d);
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return std::make_pair(p, tag::double_);
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} else {
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- bool success;
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- size_t* out
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- = allocator.reserve(integer_storage::word_length, &success);
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- if (SAJSON_UNLIKELY(!success)) {
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- return std::make_pair(oom(p, "integer"), tag::null);
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- }
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- integer_storage::store(out, static_cast<int>(u));
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return std::make_pair(p, tag::integer);
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}
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}
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