Package: guix-patches;
Reported by: David Elsing <david.elsing <at> posteo.net>
Date: Mon, 3 Oct 2022 00:06:02 UTC
Severity: normal
Tags: patch
Done: Liliana Marie Prikler <liliana.prikler <at> gmail.com>
Bug is archived. No further changes may be made.
Message #221 received at 58261 <at> debbugs.gnu.org (full text, mbox):
From: David Elsing <david.elsing <at> posteo.net> To: 58261 <at> debbugs.gnu.org Cc: David Elsing <david.elsing <at> posteo.net> Subject: [PATCH v3 07/15] gnu: Add sajson-for-gemmi. Date: Thu, 13 Oct 2022 21:04:16 +0000
* gnu/packages/chemistry.scm (sajson-for-gemmi): New variable.
---
gnu/packages/chemistry.scm | 23 +++
.../sajson-for-gemmi-numbers-as-strings.patch | 195 ++++++++++++++++++
2 files changed, 218 insertions(+)
create mode 100644 gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index c517610fe8..723b7ee8db 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -6,6 +6,7 @@
;;; Copyright © 2020 Björn Höfling <bjoern.hoefling <at> bjoernhoefling.de>
;;; Copyright © 2020 Vincent Legoll <vincent.legoll <at> gmail.com>
;;; Copyright © 2021 Ricardo Wurmus <rekado <at> elephly.net>
+;;; Copyright © 2022 David Elsing <david.elsing <at> posteo.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -27,6 +28,7 @@ (define-module (gnu packages chemistry)
#:use-module (guix utils)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix download)
+ #:use-module (guix gexp)
#:use-module (guix git-download)
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
@@ -35,6 +37,7 @@ (define-module (gnu packages chemistry)
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
+ #:use-module (gnu packages cpp)
#:use-module (gnu packages documentation)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages gl)
@@ -50,8 +53,10 @@ (define-module (gnu packages chemistry)
#:use-module (gnu packages qt)
#:use-module (gnu packages serialization)
#:use-module (gnu packages sphinx)
+ #:use-module (gnu packages stb)
#:use-module (gnu packages xml)
#:use-module (guix build-system cmake)
+ #:use-module (guix build-system copy)
#:use-module (guix build-system gnu)
#:use-module (guix build-system python))
@@ -566,3 +571,21 @@ (define-public python-pymol
used to prepare publication-quality figures, to share interactive results with
your colleagues, or to generate pre-rendered animations.")
(license license:bsd-3)))
+
+(define-public sajson-for-gemmi
+ (package/inherit sajson
+ (name "sajson-for-gemmi")
+ (source (origin
+ (inherit (package-source sajson))
+ (patches (cons
+ (search-patch
+ "sajson-for-gemmi-numbers-as-strings.patch")
+ (origin-patches (package-source sajson))))))
+ (arguments
+ (substitute-keyword-arguments (package-arguments sajson)
+ ;; This is a modified version used in gemmi, in which numbers are kept
+ ;; as strings. Building the tests fails with the modification.
+ ((#:tests? _ #f) #f)
+ ((#:phases phases)
+ #~(modify-phases #$phases
+ (delete 'build)))))))
diff --git a/gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch b/gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch
new file mode 100644
index 0000000000..6f476b8583
--- /dev/null
+++ b/gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch
@@ -0,0 +1,195 @@
+Patch for gemmi: Keep numbers in JSON file as strings.
+
+Adapted from this commit of the bundled fork of sajson in gemmi:
+https://github.com/project-gemmi/gemmi/commit/fccbca4f6040364ba708613e1429c2251872240d
+
+diff -ur a/include/sajson.h b/include/sajson.h
+--- a/include/sajson.h
++++ b/include/sajson.h
+@@ -411,43 +411,6 @@
+ };
+ } // namespace internal
+
+-namespace integer_storage {
+-enum { word_length = 1 };
+-
+-inline int load(const size_t* location) {
+- int value;
+- memcpy(&value, location, sizeof(value));
+- return value;
+-}
+-
+-inline void store(size_t* location, int value) {
+- // NOTE: Most modern compilers optimize away this constant-size
+- // memcpy into a single instruction. If any don't, and treat
+- // punning through a union as legal, they can be special-cased.
+- static_assert(
+- sizeof(value) <= sizeof(*location),
+- "size_t must not be smaller than int");
+- memcpy(location, &value, sizeof(value));
+-}
+-} // namespace integer_storage
+-
+-namespace double_storage {
+-enum { word_length = sizeof(double) / sizeof(size_t) };
+-
+-inline double load(const size_t* location) {
+- double value;
+- memcpy(&value, location, sizeof(double));
+- return value;
+-}
+-
+-inline void store(size_t* location, double value) {
+- // NOTE: Most modern compilers optimize away this constant-size
+- // memcpy into a single instruction. If any don't, and treat
+- // punning through a union as legal, they can be special-cased.
+- memcpy(location, &value, sizeof(double));
+-}
+-} // namespace double_storage
+-
+ /// Represents a JSON value. First, call get_type() to check its type,
+ /// which determines which methods are available.
+ ///
+@@ -585,70 +548,10 @@
+ return length;
+ }
+
+- /// If a numeric value was parsed as a 32-bit integer, returns it.
+- /// Only legal if get_type() is TYPE_INTEGER.
+- int get_integer_value() const {
+- assert_tag(tag::integer);
+- return integer_storage::load(payload);
+- }
+-
+- /// If a numeric value was parsed as a double, returns it.
+- /// Only legal if get_type() is TYPE_DOUBLE.
+- double get_double_value() const {
+- assert_tag(tag::double_);
+- return double_storage::load(payload);
+- }
+-
+- /// Returns a numeric value as a double-precision float.
+- /// Only legal if get_type() is TYPE_INTEGER or TYPE_DOUBLE.
+- double get_number_value() const {
+- assert_tag_2(tag::integer, tag::double_);
+- if (value_tag == tag::integer) {
+- return get_integer_value();
+- } else {
+- return get_double_value();
+- }
+- }
+-
+- /// Returns true and writes to the output argument if the numeric value
+- /// fits in a 53-bit integer. This is useful for timestamps and other
+- /// situations where integral values with greater than 32-bit precision
+- /// are used, as 64-bit values are not understood by all JSON
+- /// implementations or languages.
+- /// Returns false if the value is not an integer or not in range.
+- /// Only legal if get_type() is TYPE_INTEGER or TYPE_DOUBLE.
+- bool get_int53_value(int64_t* out) const {
+- // Make sure the output variable is always defined to avoid any
+- // possible situation like
+- // https://gist.github.com/chadaustin/2c249cb850619ddec05b23ca42cf7a18
+- *out = 0;
+-
+- assert_tag_2(tag::integer, tag::double_);
+- switch (value_tag) {
+- case tag::integer:
+- *out = get_integer_value();
+- return true;
+- case tag::double_: {
+- double v = get_double_value();
+- if (v < -(1LL << 53) || v > (1LL << 53)) {
+- return false;
+- }
+- int64_t as_int = static_cast<int64_t>(v);
+- if (as_int != v) {
+- return false;
+- }
+- *out = as_int;
+- return true;
+- }
+- default:
+- return false;
+- }
+- }
+-
+ /// Returns the length of the string.
+ /// Only legal if get_type() is TYPE_STRING.
+ size_t get_string_length() const {
+- assert_tag(tag::string);
++ assert_tag_3(tag::string, tag::integer, tag::double_);
+ return payload[1] - payload[0];
+ }
+
+@@ -659,7 +562,7 @@
+ /// embedded NULs.
+ /// Only legal if get_type() is TYPE_STRING.
+ const char* as_cstring() const {
+- assert_tag(tag::string);
++ assert_tag_3(tag::string, tag::integer, tag::double_);
+ return text + payload[0];
+ }
+
+@@ -667,7 +570,7 @@
+ /// Returns a string's value as a std::string.
+ /// Only legal if get_type() is TYPE_STRING.
+ std::string as_string() const {
+- assert_tag(tag::string);
++ assert_tag_3(tag::string, tag::integer, tag::double_);
+ return std::string(text + payload[0], text + payload[1]);
+ }
+ #endif
+@@ -690,6 +593,10 @@
+ assert(e1 == value_tag || e2 == value_tag);
+ }
+
++ void assert_tag_3(tag e1, tag e2, tag e3) const {
++ assert(e1 == value_tag || e2 == value_tag || e3 == value_tag);
++ }
++
+ void assert_in_bounds(size_t i) const { assert(i < get_length()); }
+
+ const tag value_tag;
+@@ -2059,6 +1966,8 @@
+ std::pair<char*, internal::tag> parse_number(char* p) {
+ using internal::tag;
+
++ size_t start = p - input.get_data();
++
+ // Assume 32-bit, two's complement integers.
+ static constexpr unsigned RISKY = INT_MAX / 10u;
+ unsigned max_digit_after_risky = INT_MAX % 10u;
+@@ -2235,23 +2144,18 @@
+ u = 0u - u;
+ }
+ }
++
++ bool success;
++ size_t* out = allocator.reserve(2, &success);
++ if (SAJSON_UNLIKELY(!success)) {
++ return std::make_pair(oom(p, "number"), tag::null);
++ }
++ out[0] = start;
++ out[1] = p - input.get_data();
++
+ if (try_double) {
+- bool success;
+- size_t* out
+- = allocator.reserve(double_storage::word_length, &success);
+- if (SAJSON_UNLIKELY(!success)) {
+- return std::make_pair(oom(p, "double"), tag::null);
+- }
+- double_storage::store(out, d);
+ return std::make_pair(p, tag::double_);
+ } else {
+- bool success;
+- size_t* out
+- = allocator.reserve(integer_storage::word_length, &success);
+- if (SAJSON_UNLIKELY(!success)) {
+- return std::make_pair(oom(p, "integer"), tag::null);
+- }
+- integer_storage::store(out, static_cast<int>(u));
+ return std::make_pair(p, tag::integer);
+ }
+ }
--
2.37.0
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1994-97 Ian Jackson.