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

From: Liliana Marie Prikler <[email-masked]>
Date: Sun, 09 Oct 2022 13:54:07 +0200

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?

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);
> +         }
> +     }