diff options
| -rw-r--r-- | gnu/local.mk | 2 | ||||
| -rw-r--r-- | gnu/packages/chemistry.scm | 96 | ||||
| -rw-r--r-- | gnu/packages/patches/gemmi-fix-pegtl-usage.patch | 31 | ||||
| -rw-r--r-- | gnu/packages/patches/gemmi-fix-sajson-types.patch | 11 |
4 files changed, 140 insertions, 0 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index 9313ea81f9..0c77571392 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1180,6 +1180,8 @@ dist_patch_DATA = \ %D%/packages/patches/gdm-wayland-session-wrapper-from-env.patch \ %D%/packages/patches/gdm-pass-gdk-pixbuf-loader-env.patch \ %D%/packages/patches/geeqie-clutter.patch \ + %D%/packages/patches/gemmi-fix-pegtl-usage.patch \ + %D%/packages/patches/gemmi-fix-sajson-types.patch \ %D%/packages/patches/genimage-mke2fs-test.patch \ %D%/packages/patches/geoclue-config.patch \ %D%/packages/patches/ghc-4.patch \ diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 3b06d56711..54d9d9b79b 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. ;;; @@ -36,6 +37,7 @@ #:use-module (gnu packages boost) #:use-module (gnu packages check) #:use-module (gnu packages compression) + #:use-module (gnu packages c) #:use-module (gnu packages cpp) #:use-module (gnu packages documentation) #:use-module (gnu packages fontutils) @@ -570,3 +572,97 @@ symmetries written in C. Spglib can be used to: 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 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" + "gemmi-fix-pegtl-usage.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) + (arguments + (list + #:modules '((guix build cmake-build-system) + (guix build utils) + ((guix build python-build-system) + #:select (site-packages))) + #:imported-modules (append %cmake-build-system-modules + '((guix build python-build-system))) + #:configure-flags + #~(list "-DUSE_PYTHON=ON" + (string-append "-DPYTHON_INSTALL_DIR=" + (site-packages %build-inputs %outputs))) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-includes + (lambda _ + (substitute* (list "include/gemmi/sprintf.hpp" + "include/gemmi/dirwalk.hpp" + "include/gemmi/cif.hpp" + "include/gemmi/json.hpp" + "python/gemmi.cpp" + "include/gemmi/atof.hpp" + "include/gemmi/numb.hpp" + "include/gemmi/fourier.hpp") + (("<stb/stb_sprintf.h>") "<stb_sprintf.h>") + (("\"third_party/tinydir.h\"") "<tinydir.h>") + (("\"third_party/tao/pegtl.hpp\"") "<tao/pegtl.hpp>") + (("\"third_party/sajson.h\"") "<sajson.h>") + (("\"gemmi/third_party/tao/pegtl/parse_error.hpp\"") + "<tao/pegtl/parse_error.hpp>") + (("\"third_party/fast_float.h\"") + "<fast_float/fast_float.h>") + (("\"third_party/pocketfft_hdronly.h\"") + "<pocketfft_hdronly.h>")))) + (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")))))))) + (inputs (list python zlib)) + (native-inputs + (list fast-float + optionparser + pegtl + pocketfft-cpp + pybind11 + sajson-for-gemmi + stb-sprintf + tinydir)) + (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-pegtl-usage.patch b/gnu/packages/patches/gemmi-fix-pegtl-usage.patch new file mode 100644 index 0000000000..3667474847 --- /dev/null +++ b/gnu/packages/patches/gemmi-fix-pegtl-usage.patch @@ -0,0 +1,31 @@ +Use the definitions from (newer) upstream PEGTL. + +diff --git a/include/gemmi/cif.hpp b/include/gemmi/cif.hpp +index c7ffdb44..35d24210 100644 +--- a/include/gemmi/cif.hpp ++++ b/include/gemmi/cif.hpp +@@ -37,7 +37,6 @@ namespace pegtl = tao::pegtl; + namespace rules { + + template<int TableVal> struct lookup_char { +- using analyze_t = pegtl::analysis::generic<pegtl::analysis::rule_type::ANY>; + template<typename Input> static bool match(Input& in) { + if (!in.empty() && cif::char_table(in.peek_char()) == TableVal) { + if (TableVal == 2) // this set includes new-line +@@ -71,11 +70,11 @@ namespace rules { + struct ws_or_eof : pegtl::sor<whitespace, pegtl::eof> {}; + + // (b) Reserved words. +- struct str_data : TAOCPP_PEGTL_ISTRING("data_") {}; +- struct str_loop : TAOCPP_PEGTL_ISTRING("loop_") {}; +- struct str_global : TAOCPP_PEGTL_ISTRING("global_") {}; +- struct str_save : TAOCPP_PEGTL_ISTRING("save_") {}; +- struct str_stop : TAOCPP_PEGTL_ISTRING("stop_") {}; ++ struct str_data : TAO_PEGTL_ISTRING("data_") {}; ++ struct str_loop : TAO_PEGTL_ISTRING("loop_") {}; ++ struct str_global : TAO_PEGTL_ISTRING("global_") {}; ++ struct str_save : TAO_PEGTL_ISTRING("save_") {}; ++ struct str_stop : TAO_PEGTL_ISTRING("stop_") {}; + struct keyword : pegtl::sor<str_data, str_loop, str_global, + str_save, str_stop> {}; + 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: |