Subject: [bug#58261] [PATCH v2 06/13] gnu: Add gemmi.

From: David Elsing <[email-masked]>
Date: Thu, 13 Oct 2022 21:00:07 +0000

Liliana Marie Prikler <[email-masked]> 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
>> <[email-masked]>
>>  ;;; Copyright © 2020 Vincent Legoll <[email-masked]>
>>  ;;; Copyright © 2021 Ricardo Wurmus <[email-masked]>
>> +;;; Copyright © 2022 David Elsing <[email-masked]>
>>  ;;;
>>  ;;; 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);
>> +         }
>> +     }