gnu: Add gemmi.
* gnu/packages/patches/gemmi-fix-pegtl-usage.patch: New file. * gnu/packages/patches/gemmi-fix-sajson-types.patch: New file. * gnu/local.mk (dist_patch_DATA): Register them here. * gnu/packages/chemistry.scm (gemmi): New variable. Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>master
David Elsing
Liliana Marie Prikler
parent
3cbb634a89
commit
696f20f0f6
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@ -1180,6 +1180,8 @@ dist_patch_DATA = \
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%D%/packages/patches/gdm-wayland-session-wrapper-from-env.patch \
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%D%/packages/patches/gdm-pass-gdk-pixbuf-loader-env.patch \
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%D%/packages/patches/geeqie-clutter.patch \
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%D%/packages/patches/gemmi-fix-pegtl-usage.patch \
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%D%/packages/patches/gemmi-fix-sajson-types.patch \
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%D%/packages/patches/genimage-mke2fs-test.patch \
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%D%/packages/patches/geoclue-config.patch \
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%D%/packages/patches/ghc-4.patch \
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@ -6,6 +6,7 @@
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;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
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;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
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;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2022 David Elsing <david.elsing@posteo.net>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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@ -36,6 +37,7 @@
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#:use-module (gnu packages boost)
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#:use-module (gnu packages check)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages c)
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#:use-module (gnu packages cpp)
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#:use-module (gnu packages documentation)
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#:use-module (gnu packages fontutils)
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@ -570,3 +572,97 @@ symmetries written in C. Spglib can be used to:
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used to prepare publication-quality figures, to share interactive results with
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your colleagues, or to generate pre-rendered animations.")
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(license license:bsd-3)))
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(define-public gemmi
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(package
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(name "gemmi")
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(version "0.5.7")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/project-gemmi/gemmi")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"00km5q726bslrw7xbfwb3f3mrsk19qbimfnl3hvr4wi1y3z8i18a"))
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(patches
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(search-patches "gemmi-fix-sajson-types.patch"
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"gemmi-fix-pegtl-usage.patch"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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(delete-file-recursively "include/gemmi/third_party")
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(delete-file-recursively "third_party")))))
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(outputs '("out" "bin" "python"))
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(build-system cmake-build-system)
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(arguments
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(list
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#:modules '((guix build cmake-build-system)
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(guix build utils)
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((guix build python-build-system)
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#:select (site-packages)))
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#:imported-modules (append %cmake-build-system-modules
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'((guix build python-build-system)))
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#:configure-flags
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#~(list "-DUSE_PYTHON=ON"
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(string-append "-DPYTHON_INSTALL_DIR="
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(site-packages %build-inputs %outputs)))
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'patch-includes
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(lambda _
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(substitute* (list "include/gemmi/sprintf.hpp"
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"include/gemmi/dirwalk.hpp"
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"include/gemmi/cif.hpp"
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"include/gemmi/json.hpp"
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"python/gemmi.cpp"
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"include/gemmi/atof.hpp"
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"include/gemmi/numb.hpp"
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"include/gemmi/fourier.hpp")
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(("<stb/stb_sprintf.h>") "<stb_sprintf.h>")
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(("\"third_party/tinydir.h\"") "<tinydir.h>")
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(("\"third_party/tao/pegtl.hpp\"") "<tao/pegtl.hpp>")
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(("\"third_party/sajson.h\"") "<sajson.h>")
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(("\"gemmi/third_party/tao/pegtl/parse_error.hpp\"")
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"<tao/pegtl/parse_error.hpp>")
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(("\"third_party/fast_float.h\"")
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"<fast_float/fast_float.h>")
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(("\"third_party/pocketfft_hdronly.h\"")
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"<pocketfft_hdronly.h>"))))
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(add-after 'unpack 'change-bin-prefix
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(lambda _
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(substitute* "CMakeLists.txt"
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(("install\\(TARGETS program DESTINATION bin\\)")
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(string-append
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"install(TARGETS program DESTINATION "
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#$output:bin "/bin)")))))
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(replace 'check
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(lambda* (#:key tests? #:allow-other-keys)
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(when tests?
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(with-directory-excursion "../source"
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(setenv "PYTHONPATH" "../build")
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(invoke "python3" "-m" "unittest" "discover" "-v"
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"-s" "tests"))))))))
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(inputs (list python zlib))
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(native-inputs
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(list fast-float
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optionparser
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pegtl
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pocketfft-cpp
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pybind11
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sajson-for-gemmi
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stb-sprintf
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tinydir))
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(home-page "https://gemmi.readthedocs.io/en/latest/")
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(synopsis "Macromolecular crystallography library and utilities")
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(description "GEMMI is a C++ library for macromolecular crystallography.
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It can be used for working with
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@enumerate
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@item macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files),
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@item refinement restraints (CIF files),
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@item reflection data (MTZ and mmCIF formats),
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@item data on a 3D grid (electron density maps, masks, MRC/CCP4 format)
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@item crystallographic symmetry.
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@end enumerate")
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(license license:mpl2.0)))
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@ -0,0 +1,31 @@
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Use the definitions from (newer) upstream PEGTL.
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diff --git a/include/gemmi/cif.hpp b/include/gemmi/cif.hpp
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index c7ffdb44..35d24210 100644
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--- a/include/gemmi/cif.hpp
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+++ b/include/gemmi/cif.hpp
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@@ -37,7 +37,6 @@ namespace pegtl = tao::pegtl;
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namespace rules {
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template<int TableVal> struct lookup_char {
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- using analyze_t = pegtl::analysis::generic<pegtl::analysis::rule_type::ANY>;
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template<typename Input> static bool match(Input& in) {
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if (!in.empty() && cif::char_table(in.peek_char()) == TableVal) {
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if (TableVal == 2) // this set includes new-line
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@@ -71,11 +70,11 @@ namespace rules {
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struct ws_or_eof : pegtl::sor<whitespace, pegtl::eof> {};
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// (b) Reserved words.
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- struct str_data : TAOCPP_PEGTL_ISTRING("data_") {};
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- struct str_loop : TAOCPP_PEGTL_ISTRING("loop_") {};
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- struct str_global : TAOCPP_PEGTL_ISTRING("global_") {};
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- struct str_save : TAOCPP_PEGTL_ISTRING("save_") {};
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- struct str_stop : TAOCPP_PEGTL_ISTRING("stop_") {};
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+ struct str_data : TAO_PEGTL_ISTRING("data_") {};
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+ struct str_loop : TAO_PEGTL_ISTRING("loop_") {};
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+ struct str_global : TAO_PEGTL_ISTRING("global_") {};
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+ struct str_save : TAO_PEGTL_ISTRING("save_") {};
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+ struct str_stop : TAO_PEGTL_ISTRING("stop_") {};
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struct keyword : pegtl::sor<str_data, str_loop, str_global,
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str_save, str_stop> {};
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@ -0,0 +1,11 @@
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diff -ur a/include/gemmi/json.hpp b/include/gemmi/json.hpp
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--- a/include/gemmi/json.hpp
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+++ b/include/gemmi/json.hpp
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@@ -38,6 +38,7 @@
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inline std::string as_cif_value(const sajson::value& val) {
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switch (val.get_type()) {
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+ case sajson::TYPE_INTEGER:
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case sajson::TYPE_DOUBLE:
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return val.as_string();
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case sajson::TYPE_NULL:
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