| Message ID | 20221007152148.32591-7-david.elsing@posteo.net |
|---|---|
| State | Accepted |
| Headers | show |
| Series | None | expand |
Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing: > * gnu/packages/chemistry.scm (gemmi): New variable. > --- > gnu/packages/chemistry.scm | 118 +++++++++++ > .../patches/gemmi-fix-sajson-types.patch | 11 + > .../sajson-for-gemmi-build-with-gcc10.patch | 45 ++++ > .../sajson-for-gemmi-numbers-as-strings.patch | 195 > ++++++++++++++++++ > 4 files changed, 369 insertions(+) > create mode 100644 gnu/packages/patches/gemmi-fix-sajson-types.patch > create mode 100644 gnu/packages/patches/sajson-for-gemmi-build-with- > gcc10.patch > 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..d8f1608a3a 100644 > --- a/gnu/packages/chemistry.scm > +++ b/gnu/packages/chemistry.scm > @@ -6,6 +6,7 @@ > ;;; Copyright © 2020 Björn Höfling > <bjoern.hoefling@bjoernhoefling.de> > ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com> > ;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net> > +;;; Copyright © 2022 David Elsing <david.elsing@posteo.net> > ;;; > ;;; This file is part of GNU Guix. > ;;; > @@ -23,6 +24,7 @@ > ;;; along with GNU Guix. If not, see > <http://www.gnu.org/licenses/>. > > (define-module (gnu packages chemistry) > + #:use-module (guix gexp) > #:use-module (guix packages) > #:use-module (guix utils) > #:use-module ((guix licenses) #:prefix license:) > @@ -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 +571,116 @@ (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 (search-patches > + "sajson-for-gemmi-numbers-as-strings.patch" > + "sajson-for-gemmi-build-with- > gcc10.patch")))) > + (arguments > + (substitute-keyword-arguments (package-arguments sajson) > + ((#:tests? _ #f) #f) Don't forget the comment as to why they're disabled. > + ((#:phases phases) > + #~(modify-phases #$phases > + (delete 'build))))))) Why is the build deleted? Split here. > +(define-public gemmi > + (package > + (name "gemmi") > + (version "0.5.7") > + (source (origin > + (method git-fetch) > + (uri (git-reference > + (url "https://github.com/project-gemmi/gemmi") > + (commit (string-append "v" version)))) > + (file-name (git-file-name name version)) > + (sha256 > + (base32 > + > "00km5q726bslrw7xbfwb3f3mrsk19qbimfnl3hvr4wi1y3z8i18a")) > + (patches > + (search-patches "gemmi-fix-sajson-types.patch")) > + (modules '((guix build utils))) > + (snippet > + '(begin > + (delete-file-recursively > "include/gemmi/third_party") > + (delete-file-recursively "third_party"))))) > + (outputs '("out" "bin" "python")) > + (build-system cmake-build-system) > + (native-inputs > + (list fast-float > + optionparser > + pegtl > + pocketfft-cpp > + pybind11 > + sajson-for-gemmi > + stb-sprintf > + tinydir)) > + (inputs (list python zlib)) > + (arguments > + (list > + #:configure-flags > + #~(let* ((python-lib > + (string-append > + #$output:python "/lib/python" > + #$(version-major+minor (package-version python)) > + "/site-packages"))) Note that python-build-system has a (site-packages) procedure. Writing the boilerplate to include it in the build shouldn't be much worse in terms of lines than what you're doing here. > + (list "-DUSE_PYTHON=ON" > + (string-append "-DPYTHON_INSTALL_DIR=" python-lib))) > + #:phases > + #~(modify-phases %standard-phases > + (add-after 'unpack 'patch-includes > + (lambda _ > + (substitute* "include/gemmi/sprintf.hpp" > + (("<stb/stb_sprintf.h>") "<stb_sprintf.h>")) > + (substitute* "include/gemmi/dirwalk.hpp" > + (("\"third_party/tinydir.h\"") "<tinydir.h>")) > + (substitute* "include/gemmi/cif.hpp" > + (("\"third_party/tao/pegtl.hpp\"") > "<tao/pegtl.hpp>")) > + (substitute* "include/gemmi/json.hpp" > + (("\"third_party/sajson.h\"") "<sajson.h>")) > + (substitute* "python/gemmi.cpp" > + (("\"gemmi/third_party/tao/pegtl/parse_error.hpp\"") > + "<tao/pegtl/parse_error.hpp>")) > + (substitute* '("include/gemmi/atof.hpp" > + "include/gemmi/numb.hpp") > + (("\"third_party/fast_float.h\"") > + "<fast_float/fast_float.h>")) > + (substitute* "include/gemmi/fourier.hpp" > + (("\"third_party/pocketfft_hdronly.h\"") > + "<pocketfft_hdronly.h>")))) I'd collect all the files into a (list ...) and then write out the substitutes. > + (add-after 'patch-includes 'patch-cif > + (lambda _ > + (substitute* "include/gemmi/cif.hpp" > + (((string-append > + "^.*using analyze_t = pegtl::analysis::generic" > + "<pegtl::analysis::rule_type::ANY>;.*$")) "") > + (("TAOCPP_PEGTL_") "TAO_PEGTL_")))) Uhm... I think I'd prefer a patch for this one. > + (add-after 'unpack 'change-bin-prefix > + (lambda _ > + (substitute* "CMakeLists.txt" > + (("install\\(TARGETS program DESTINATION bin\\)") > + (string-append > + "install(TARGETS program DESTINATION " > + #$output:bin "/bin)"))))) > + (replace 'check > + (lambda* (#:key tests? #:allow-other-keys) > + (when tests? > + (with-directory-excursion "../source" > + (setenv "PYTHONPATH" "../build") > + (invoke "python3" "-m" "unittest" "discover" "-v" > + "-s" "tests")))))))) > + (home-page "https://gemmi.readthedocs.io/en/latest/") > + (synopsis "Macromolecular crystallography library and > utilities") > + (description "GEMMI is a C++ library for macromolecular > crystallography. > +It can be used for working with > +@enumerate > +@item macromolecular models (content of PDB, PDBx/mmCIF and mmJSON > files), > +@item refinement restraints (CIF files), > +@item reflection data (MTZ and mmCIF formats), > +@item data on a 3D grid (electron density maps, masks, MRC/CCP4 > format) > +@item crystallographic symmetry. > +@end enumerate") > + (license license:mpl2.0))) > diff --git a/gnu/packages/patches/gemmi-fix-sajson-types.patch > b/gnu/packages/patches/gemmi-fix-sajson-types.patch > new file mode 100644 > index 0000000000..9633ddac8b > --- /dev/null > +++ b/gnu/packages/patches/gemmi-fix-sajson-types.patch > @@ -0,0 +1,11 @@ > +diff -ur a/include/gemmi/json.hpp b/include/gemmi/json.hpp > +--- a/include/gemmi/json.hpp > ++++ b/include/gemmi/json.hpp > +@@ -38,6 +38,7 @@ > + > + inline std::string as_cif_value(const sajson::value& val) { > + switch (val.get_type()) { > ++ case sajson::TYPE_INTEGER: > + case sajson::TYPE_DOUBLE: > + return val.as_string(); > + case sajson::TYPE_NULL: > diff --git a/gnu/packages/patches/sajson-for-gemmi-build-with- > gcc10.patch b/gnu/packages/patches/sajson-for-gemmi-build-with- > gcc10.patch > new file mode 100644 > index 0000000000..878706dc79 > --- /dev/null > +++ b/gnu/packages/patches/sajson-for-gemmi-build-with-gcc10.patch > @@ -0,0 +1,45 @@ > +This patch is from the upstream pull request > +https://github.com/chadaustin/sajson/pull/54. > +It fixes linking with GCC. > + > +diff --git a/include/sajson.h b/include/sajson.h > +index 8b4e05a..1bd045b 100644 > +--- a/include/sajson.h > ++++ b/include/sajson.h > +@@ -138,12 +138,17 @@ constexpr inline size_t make_element(tag t, > size_t value) { > + // header. This trick courtesy of Rich Geldreich's Purple JSON > parser. > + template <typename unused = void> > + struct globals_struct { > ++ static const unsigned char parse_flags[256]; > ++}; > ++typedef globals_struct<> globals; > ++ > + // clang-format off > + > + // bit 0 (1) - set if: plain ASCII string character > + // bit 1 (2) - set if: whitespace > + // bit 4 (0x10) - set if: 0-9 e E . > +- constexpr static const uint8_t parse_flags[256] = { > ++ template <typename unused> > ++ const unsigned char globals_struct<unused>::parse_flags[256] = > { > + // 0 1 2 3 4 5 6 7 8 9 A > B C D E F > + 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, > 0, 0, 2, 0, 0, // 0 > + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, > 0, 0, 0, 0, 0, // 1 > +@@ -162,15 +167,13 @@ struct globals_struct { > + }; > + > + // clang-format on > +-}; > +-typedef globals_struct<> globals; > + > +-constexpr inline bool is_plain_string_character(char c) { > ++inline bool is_plain_string_character(char c) { > + // return c >= 0x20 && c <= 0x7f && c != 0x22 && c != 0x5c; > + return (globals::parse_flags[static_cast<unsigned char>(c)] & > 1) != 0; > + } > + > +-constexpr inline bool is_whitespace(char c) { > ++inline bool is_whitespace(char c) { > + // return c == '\r' || c == '\n' || c == '\t' || c == ' '; > + return (globals::parse_flags[static_cast<unsigned char>(c)] & > 2) != 0; > + } > 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/fccbca4f6040364ba708613e > 1429c2251872240d > + > +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); > + } > + }
Liliana Marie Prikler <liliana.prikler@gmail.com> writes: > Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing: >> * gnu/packages/chemistry.scm (gemmi): New variable. >> --- >> gnu/packages/chemistry.scm | 118 +++++++++++ >> .../patches/gemmi-fix-sajson-types.patch | 11 + >> .../sajson-for-gemmi-build-with-gcc10.patch | 45 ++++ >> .../sajson-for-gemmi-numbers-as-strings.patch | 195 >> ++++++++++++++++++ >> 4 files changed, 369 insertions(+) >> create mode 100644 gnu/packages/patches/gemmi-fix-sajson-types.patch >> create mode 100644 gnu/packages/patches/sajson-for-gemmi-build-with- >> gcc10.patch >> 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..d8f1608a3a 100644 >> --- a/gnu/packages/chemistry.scm >> +++ b/gnu/packages/chemistry.scm >> @@ -6,6 +6,7 @@ >> ;;; Copyright © 2020 Björn Höfling >> <bjoern.hoefling@bjoernhoefling.de> >> ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com> >> ;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net> >> +;;; Copyright © 2022 David Elsing <david.elsing@posteo.net> >> ;;; >> ;;; This file is part of GNU Guix. >> ;;; >> @@ -23,6 +24,7 @@ >> ;;; along with GNU Guix. If not, see >> <http://www.gnu.org/licenses/>. >> >> (define-module (gnu packages chemistry) >> + #:use-module (guix gexp) >> #:use-module (guix packages) >> #:use-module (guix utils) >> #:use-module ((guix licenses) #:prefix license:) >> @@ -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 +571,116 @@ (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 (search-patches >> + "sajson-for-gemmi-numbers-as-strings.patch" >> + "sajson-for-gemmi-build-with- >> gcc10.patch")))) >> + (arguments >> + (substitute-keyword-arguments (package-arguments sajson) >> + ((#:tests? _ #f) #f) > Don't forget the comment as to why they're disabled. >> + ((#:phases phases) >> + #~(modify-phases #$phases >> + (delete 'build))))))) > Why is the build deleted? It fails due to the change and only builds the tests anyway. > > Split here. >> +(define-public gemmi >> + (package >> + (name "gemmi") >> + (version "0.5.7") >> + (source (origin >> + (method git-fetch) >> + (uri (git-reference >> + (url "https://github.com/project-gemmi/gemmi") >> + (commit (string-append "v" version)))) >> + (file-name (git-file-name name version)) >> + (sha256 >> + (base32 >> + >> "00km5q726bslrw7xbfwb3f3mrsk19qbimfnl3hvr4wi1y3z8i18a")) >> + (patches >> + (search-patches "gemmi-fix-sajson-types.patch")) >> + (modules '((guix build utils))) >> + (snippet >> + '(begin >> + (delete-file-recursively >> "include/gemmi/third_party") >> + (delete-file-recursively "third_party"))))) >> + (outputs '("out" "bin" "python")) >> + (build-system cmake-build-system) >> + (native-inputs >> + (list fast-float >> + optionparser >> + pegtl >> + pocketfft-cpp >> + pybind11 >> + sajson-for-gemmi >> + stb-sprintf >> + tinydir)) >> + (inputs (list python zlib)) >> + (arguments >> + (list >> + #:configure-flags >> + #~(let* ((python-lib >> + (string-append >> + #$output:python "/lib/python" >> + #$(version-major+minor (package-version python)) >> + "/site-packages"))) > Note that python-build-system has a (site-packages) procedure. Writing > the boilerplate to include it in the build shouldn't be much worse in > terms of lines than what you're doing here. >> + (list "-DUSE_PYTHON=ON" >> + (string-append "-DPYTHON_INSTALL_DIR=" python-lib))) >> + #:phases >> + #~(modify-phases %standard-phases >> + (add-after 'unpack 'patch-includes >> + (lambda _ >> + (substitute* "include/gemmi/sprintf.hpp" >> + (("<stb/stb_sprintf.h>") "<stb_sprintf.h>")) >> + (substitute* "include/gemmi/dirwalk.hpp" >> + (("\"third_party/tinydir.h\"") "<tinydir.h>")) >> + (substitute* "include/gemmi/cif.hpp" >> + (("\"third_party/tao/pegtl.hpp\"") >> "<tao/pegtl.hpp>")) >> + (substitute* "include/gemmi/json.hpp" >> + (("\"third_party/sajson.h\"") "<sajson.h>")) >> + (substitute* "python/gemmi.cpp" >> + (("\"gemmi/third_party/tao/pegtl/parse_error.hpp\"") >> + "<tao/pegtl/parse_error.hpp>")) >> + (substitute* '("include/gemmi/atof.hpp" >> + "include/gemmi/numb.hpp") >> + (("\"third_party/fast_float.h\"") >> + "<fast_float/fast_float.h>")) >> + (substitute* "include/gemmi/fourier.hpp" >> + (("\"third_party/pocketfft_hdronly.h\"") >> + "<pocketfft_hdronly.h>")))) > I'd collect all the files into a (list ...) and then write out the > substitutes. Is it preferred to put list elements on separate lines (also in inputs)? > >> + (add-after 'patch-includes 'patch-cif >> + (lambda _ >> + (substitute* "include/gemmi/cif.hpp" >> + (((string-append >> + "^.*using analyze_t = pegtl::analysis::generic" >> + "<pegtl::analysis::rule_type::ANY>;.*$")) "") >> + (("TAOCPP_PEGTL_") "TAO_PEGTL_")))) > Uhm... I think I'd prefer a patch for this one. >> + (add-after 'unpack 'change-bin-prefix >> + (lambda _ >> + (substitute* "CMakeLists.txt" >> + (("install\\(TARGETS program DESTINATION bin\\)") >> + (string-append >> + "install(TARGETS program DESTINATION " >> + #$output:bin "/bin)"))))) >> + (replace 'check >> + (lambda* (#:key tests? #:allow-other-keys) >> + (when tests? >> + (with-directory-excursion "../source" >> + (setenv "PYTHONPATH" "../build") >> + (invoke "python3" "-m" "unittest" "discover" "-v" >> + "-s" "tests")))))))) >> + (home-page "https://gemmi.readthedocs.io/en/latest/") >> + (synopsis "Macromolecular crystallography library and >> utilities") >> + (description "GEMMI is a C++ library for macromolecular >> crystallography. >> +It can be used for working with >> +@enumerate >> +@item macromolecular models (content of PDB, PDBx/mmCIF and mmJSON >> files), >> +@item refinement restraints (CIF files), >> +@item reflection data (MTZ and mmCIF formats), >> +@item data on a 3D grid (electron density maps, masks, MRC/CCP4 >> format) >> +@item crystallographic symmetry. >> +@end enumerate") >> + (license license:mpl2.0))) >> diff --git a/gnu/packages/patches/gemmi-fix-sajson-types.patch >> b/gnu/packages/patches/gemmi-fix-sajson-types.patch >> new file mode 100644 >> index 0000000000..9633ddac8b >> --- /dev/null >> +++ b/gnu/packages/patches/gemmi-fix-sajson-types.patch >> @@ -0,0 +1,11 @@ >> +diff -ur a/include/gemmi/json.hpp b/include/gemmi/json.hpp >> +--- a/include/gemmi/json.hpp >> ++++ b/include/gemmi/json.hpp >> +@@ -38,6 +38,7 @@ >> + >> + inline std::string as_cif_value(const sajson::value& val) { >> + switch (val.get_type()) { >> ++ case sajson::TYPE_INTEGER: >> + case sajson::TYPE_DOUBLE: >> + return val.as_string(); >> + case sajson::TYPE_NULL: >> diff --git a/gnu/packages/patches/sajson-for-gemmi-build-with- >> gcc10.patch b/gnu/packages/patches/sajson-for-gemmi-build-with- >> gcc10.patch >> new file mode 100644 >> index 0000000000..878706dc79 >> --- /dev/null >> +++ b/gnu/packages/patches/sajson-for-gemmi-build-with-gcc10.patch >> @@ -0,0 +1,45 @@ >> +This patch is from the upstream pull request >> +https://github.com/chadaustin/sajson/pull/54. >> +It fixes linking with GCC. >> + >> +diff --git a/include/sajson.h b/include/sajson.h >> +index 8b4e05a..1bd045b 100644 >> +--- a/include/sajson.h >> ++++ b/include/sajson.h >> +@@ -138,12 +138,17 @@ constexpr inline size_t make_element(tag t, >> size_t value) { >> + // header. This trick courtesy of Rich Geldreich's Purple JSON >> parser. >> + template <typename unused = void> >> + struct globals_struct { >> ++ static const unsigned char parse_flags[256]; >> ++}; >> ++typedef globals_struct<> globals; >> ++ >> + // clang-format off >> + >> + // bit 0 (1) - set if: plain ASCII string character >> + // bit 1 (2) - set if: whitespace >> + // bit 4 (0x10) - set if: 0-9 e E . >> +- constexpr static const uint8_t parse_flags[256] = { >> ++ template <typename unused> >> ++ const unsigned char globals_struct<unused>::parse_flags[256] = >> { >> + // 0 1 2 3 4 5 6 7 8 9 A >> B C D E F >> + 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, >> 0, 0, 2, 0, 0, // 0 >> + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, >> 0, 0, 0, 0, 0, // 1 >> +@@ -162,15 +167,13 @@ struct globals_struct { >> + }; >> + >> + // clang-format on >> +-}; >> +-typedef globals_struct<> globals; >> + >> +-constexpr inline bool is_plain_string_character(char c) { >> ++inline bool is_plain_string_character(char c) { >> + // return c >= 0x20 && c <= 0x7f && c != 0x22 && c != 0x5c; >> + return (globals::parse_flags[static_cast<unsigned char>(c)] & >> 1) != 0; >> + } >> + >> +-constexpr inline bool is_whitespace(char c) { >> ++inline bool is_whitespace(char c) { >> + // return c == '\r' || c == '\n' || c == '\t' || c == ' '; >> + return (globals::parse_flags[static_cast<unsigned char>(c)] & >> 2) != 0; >> + } >> 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/fccbca4f6040364ba708613e >> 1429c2251872240d >> + >> +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); >> + } >> + }
Am Donnerstag, dem 13.10.2022 um 21:00 +0000 schrieb David Elsing: > Liliana Marie Prikler <liliana.prikler@gmail.com> writes: > > > Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing: > > > * gnu/packages/chemistry.scm (gemmi): New variable. > > > --- > > > gnu/packages/chemistry.scm | 118 +++++++++++ > > > .../patches/gemmi-fix-sajson-types.patch | 11 + > > > .../sajson-for-gemmi-build-with-gcc10.patch | 45 ++++ > > > .../sajson-for-gemmi-numbers-as-strings.patch | 195 > > > ++++++++++++++++++ > > > 4 files changed, 369 insertions(+) > > > create mode 100644 gnu/packages/patches/gemmi-fix-sajson- > > > types.patch > > > create mode 100644 gnu/packages/patches/sajson-for-gemmi-build- > > > with- > > > gcc10.patch > > > 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..d8f1608a3a 100644 > > > --- a/gnu/packages/chemistry.scm > > > +++ b/gnu/packages/chemistry.scm > > > @@ -6,6 +6,7 @@ > > > ;;; Copyright © 2020 Björn Höfling > > > <bjoern.hoefling@bjoernhoefling.de> > > > ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com> > > > ;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net> > > > +;;; Copyright © 2022 David Elsing <david.elsing@posteo.net> > > > ;;; > > > ;;; This file is part of GNU Guix. > > > ;;; > > > @@ -23,6 +24,7 @@ > > > ;;; along with GNU Guix. If not, see > > > <http://www.gnu.org/licenses/>. > > > > > > (define-module (gnu packages chemistry) > > > + #:use-module (guix gexp) > > > #:use-module (guix packages) > > > #:use-module (guix utils) > > > #:use-module ((guix licenses) #:prefix license:) > > > @@ -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 +571,116 @@ (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 (search-patches > > > + "sajson-for-gemmi-numbers-as- > > > strings.patch" > > > + "sajson-for-gemmi-build-with- > > > gcc10.patch")))) > > > + (arguments > > > + (substitute-keyword-arguments (package-arguments sajson) > > > + ((#:tests? _ #f) #f) > > Don't forget the comment as to why they're disabled. > > > + ((#:phases phases) > > > + #~(modify-phases #$phases > > > + (delete 'build))))))) > > Why is the build deleted? > It fails due to the change and only builds the tests anyway. > > > > Split here. > > > +(define-public gemmi > > > + (package > > > + (name "gemmi") > > > + (version "0.5.7") > > > + (source (origin > > > + (method git-fetch) > > > + (uri (git-reference > > > + (url > > > "https://github.com/project-gemmi/gemmi") > > > + (commit (string-append "v" version)))) > > > + (file-name (git-file-name name version)) > > > + (sha256 > > > + (base32 > > > + > > > "00km5q726bslrw7xbfwb3f3mrsk19qbimfnl3hvr4wi1y3z8i18a")) > > > + (patches > > > + (search-patches "gemmi-fix-sajson-types.patch")) > > > + (modules '((guix build utils))) > > > + (snippet > > > + '(begin > > > + (delete-file-recursively > > > "include/gemmi/third_party") > > > + (delete-file-recursively "third_party"))))) > > > + (outputs '("out" "bin" "python")) > > > + (build-system cmake-build-system) > > > + (native-inputs > > > + (list fast-float > > > + optionparser > > > + pegtl > > > + pocketfft-cpp > > > + pybind11 > > > + sajson-for-gemmi > > > + stb-sprintf > > > + tinydir)) > > > + (inputs (list python zlib)) > > > + (arguments > > > + (list > > > + #:configure-flags > > > + #~(let* ((python-lib > > > + (string-append > > > + #$output:python "/lib/python" > > > + #$(version-major+minor (package-version > > > python)) > > > + "/site-packages"))) > > Note that python-build-system has a (site-packages) procedure. > > Writing > > the boilerplate to include it in the build shouldn't be much worse > > in > > terms of lines than what you're doing here. > > > + (list "-DUSE_PYTHON=ON" > > > + (string-append "-DPYTHON_INSTALL_DIR=" python- > > > lib))) > > > + #:phases > > > + #~(modify-phases %standard-phases > > > + (add-after 'unpack 'patch-includes > > > + (lambda _ > > > + (substitute* "include/gemmi/sprintf.hpp" > > > + (("<stb/stb_sprintf.h>") "<stb_sprintf.h>")) > > > + (substitute* "include/gemmi/dirwalk.hpp" > > > + (("\"third_party/tinydir.h\"") "<tinydir.h>")) > > > + (substitute* "include/gemmi/cif.hpp" > > > + (("\"third_party/tao/pegtl.hpp\"") > > > "<tao/pegtl.hpp>")) > > > + (substitute* "include/gemmi/json.hpp" > > > + (("\"third_party/sajson.h\"") "<sajson.h>")) > > > + (substitute* "python/gemmi.cpp" > > > + > > > (("\"gemmi/third_party/tao/pegtl/parse_error.hpp\"") > > > + "<tao/pegtl/parse_error.hpp>")) > > > + (substitute* '("include/gemmi/atof.hpp" > > > + "include/gemmi/numb.hpp") > > > + (("\"third_party/fast_float.h\"") > > > + "<fast_float/fast_float.h>")) > > > + (substitute* "include/gemmi/fourier.hpp" > > > + (("\"third_party/pocketfft_hdronly.h\"") > > > + "<pocketfft_hdronly.h>")))) > > I'd collect all the files into a (list ...) and then write out the > > substitutes. > Is it preferred to put list elements on separate lines (also in > inputs)? > Depends on the length, but in this case I'd say yes. However, if things neatly fit into one line, you don't have to add a new line. Cheers
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index c517610fe8..d8f1608a3a 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com> ;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2022 David Elsing <david.elsing@posteo.net> ;;; ;;; This file is part of GNU Guix. ;;; @@ -23,6 +24,7 @@ ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. (define-module (gnu packages chemistry) + #:use-module (guix gexp) #:use-module (guix packages) #:use-module (guix utils) #:use-module ((guix licenses) #:prefix license:) @@ -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 +571,116 @@ (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 (search-patches + "sajson-for-gemmi-numbers-as-strings.patch" + "sajson-for-gemmi-build-with-gcc10.patch")))) + (arguments + (substitute-keyword-arguments (package-arguments sajson) + ((#:tests? _ #f) #f) + ((#:phases phases) + #~(modify-phases #$phases + (delete 'build))))))) + +(define-public gemmi + (package + (name "gemmi") + (version "0.5.7") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/project-gemmi/gemmi") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "00km5q726bslrw7xbfwb3f3mrsk19qbimfnl3hvr4wi1y3z8i18a")) + (patches + (search-patches "gemmi-fix-sajson-types.patch")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "include/gemmi/third_party") + (delete-file-recursively "third_party"))))) + (outputs '("out" "bin" "python")) + (build-system cmake-build-system) + (native-inputs + (list fast-float + optionparser + pegtl + pocketfft-cpp + pybind11 + sajson-for-gemmi + stb-sprintf + tinydir)) + (inputs (list python zlib)) + (arguments + (list + #:configure-flags + #~(let* ((python-lib + (string-append + #$output:python "/lib/python" + #$(version-major+minor (package-version python)) + "/site-packages"))) + (list "-DUSE_PYTHON=ON" + (string-append "-DPYTHON_INSTALL_DIR=" python-lib))) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-includes + (lambda _ + (substitute* "include/gemmi/sprintf.hpp" + (("<stb/stb_sprintf.h>") "<stb_sprintf.h>")) + (substitute* "include/gemmi/dirwalk.hpp" + (("\"third_party/tinydir.h\"") "<tinydir.h>")) + (substitute* "include/gemmi/cif.hpp" + (("\"third_party/tao/pegtl.hpp\"") "<tao/pegtl.hpp>")) + (substitute* "include/gemmi/json.hpp" + (("\"third_party/sajson.h\"") "<sajson.h>")) + (substitute* "python/gemmi.cpp" + (("\"gemmi/third_party/tao/pegtl/parse_error.hpp\"") + "<tao/pegtl/parse_error.hpp>")) + (substitute* '("include/gemmi/atof.hpp" + "include/gemmi/numb.hpp") + (("\"third_party/fast_float.h\"") + "<fast_float/fast_float.h>")) + (substitute* "include/gemmi/fourier.hpp" + (("\"third_party/pocketfft_hdronly.h\"") + "<pocketfft_hdronly.h>")))) + (add-after 'patch-includes 'patch-cif + (lambda _ + (substitute* "include/gemmi/cif.hpp" + (((string-append + "^.*using analyze_t = pegtl::analysis::generic" + "<pegtl::analysis::rule_type::ANY>;.*$")) "") + (("TAOCPP_PEGTL_") "TAO_PEGTL_")))) + (add-after 'unpack 'change-bin-prefix + (lambda _ + (substitute* "CMakeLists.txt" + (("install\\(TARGETS program DESTINATION bin\\)") + (string-append + "install(TARGETS program DESTINATION " + #$output:bin "/bin)"))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (with-directory-excursion "../source" + (setenv "PYTHONPATH" "../build") + (invoke "python3" "-m" "unittest" "discover" "-v" + "-s" "tests")))))))) + (home-page "https://gemmi.readthedocs.io/en/latest/") + (synopsis "Macromolecular crystallography library and utilities") + (description "GEMMI is a C++ library for macromolecular crystallography. +It can be used for working with +@enumerate +@item macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files), +@item refinement restraints (CIF files), +@item reflection data (MTZ and mmCIF formats), +@item data on a 3D grid (electron density maps, masks, MRC/CCP4 format) +@item crystallographic symmetry. +@end enumerate") + (license license:mpl2.0))) diff --git a/gnu/packages/patches/gemmi-fix-sajson-types.patch b/gnu/packages/patches/gemmi-fix-sajson-types.patch new file mode 100644 index 0000000000..9633ddac8b --- /dev/null +++ b/gnu/packages/patches/gemmi-fix-sajson-types.patch @@ -0,0 +1,11 @@ +diff -ur a/include/gemmi/json.hpp b/include/gemmi/json.hpp +--- a/include/gemmi/json.hpp ++++ b/include/gemmi/json.hpp +@@ -38,6 +38,7 @@ + + inline std::string as_cif_value(const sajson::value& val) { + switch (val.get_type()) { ++ case sajson::TYPE_INTEGER: + case sajson::TYPE_DOUBLE: + return val.as_string(); + case sajson::TYPE_NULL: diff --git a/gnu/packages/patches/sajson-for-gemmi-build-with-gcc10.patch b/gnu/packages/patches/sajson-for-gemmi-build-with-gcc10.patch new file mode 100644 index 0000000000..878706dc79 --- /dev/null +++ b/gnu/packages/patches/sajson-for-gemmi-build-with-gcc10.patch @@ -0,0 +1,45 @@ +This patch is from the upstream pull request +https://github.com/chadaustin/sajson/pull/54. +It fixes linking with GCC. + +diff --git a/include/sajson.h b/include/sajson.h +index 8b4e05a..1bd045b 100644 +--- a/include/sajson.h ++++ b/include/sajson.h +@@ -138,12 +138,17 @@ constexpr inline size_t make_element(tag t, size_t value) { + // header. This trick courtesy of Rich Geldreich's Purple JSON parser. + template <typename unused = void> + struct globals_struct { ++ static const unsigned char parse_flags[256]; ++}; ++typedef globals_struct<> globals; ++ + // clang-format off + + // bit 0 (1) - set if: plain ASCII string character + // bit 1 (2) - set if: whitespace + // bit 4 (0x10) - set if: 0-9 e E . +- constexpr static const uint8_t parse_flags[256] = { ++ template <typename unused> ++ const unsigned char globals_struct<unused>::parse_flags[256] = { + // 0 1 2 3 4 5 6 7 8 9 A B C D E F + 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 0, 0, 2, 0, 0, // 0 + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, // 1 +@@ -162,15 +167,13 @@ struct globals_struct { + }; + + // clang-format on +-}; +-typedef globals_struct<> globals; + +-constexpr inline bool is_plain_string_character(char c) { ++inline bool is_plain_string_character(char c) { + // return c >= 0x20 && c <= 0x7f && c != 0x22 && c != 0x5c; + return (globals::parse_flags[static_cast<unsigned char>(c)] & 1) != 0; + } + +-constexpr inline bool is_whitespace(char c) { ++inline bool is_whitespace(char c) { + // return c == '\r' || c == '\n' || c == '\t' || c == ' '; + return (globals::parse_flags[static_cast<unsigned char>(c)] & 2) != 0; + } 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); + } + }