diff options
| author | David Elsing <david.elsing@posteo.net> | 2025-07-29 16:19:32 +0200 |
|---|---|---|
| committer | Sharlatan Hellseher <sharlatanus@gmail.com> | 2025-07-31 23:19:24 +0100 |
| commit | c3e59b2ffa89574e1100f2e260074617b4d2ec7f (patch) | |
| tree | 21401f92033d1c969fcbe7f8966084342fa75c2a | |
| parent | 0d12c3d9ab8cf043ea7c57f18e90f77eee6b6b33 (diff) | |
gnu: gemmi: Update to 0.7.3.
Fixes: guix/guix#1567.
* gnu/packages/chemistry.scm (gemmi): Update to 0.7.3.
[source]: Remove gemmi-fix-sajson-types.patch patch.
[arguments]: Adjust 'patch-includes and 'check phases.
[native-inputs]: Add python-nanobind and zpp-serializer. Remove pybind11 and
tinydir.
Change-Id: Ia1a894226d7d0a9536ed0c6646271d475c397ee7
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
| -rw-r--r-- | gnu/packages/chemistry.scm | 24 |
1 files changed, 14 insertions, 10 deletions
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index d99b817244..f70434b232 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -987,7 +987,7 @@ integrals for Gaussian type functions.") (define-public gemmi (package (name "gemmi") - (version "0.6.4") + (version "0.7.3") (source (origin (method git-fetch) (uri (git-reference @@ -996,10 +996,9 @@ integrals for Gaussian type functions.") (file-name (git-file-name name version)) (sha256 (base32 - "0wciqqswc4p4v4kglfv36gnvyyimqn4lnywdzd0pgrjn443i860y")) + "01fdpb695gqsl5xznrlqjydnrckqbfndzr8fj66pryzv8d0fdfsg")) (patches - (search-patches "gemmi-fix-sajson-types.patch" - "gemmi-fix-pegtl-usage.patch")) + (search-patches "gemmi-fix-pegtl-usage.patch")) (modules '((guix build utils))) (snippet '(begin @@ -1023,24 +1022,28 @@ integrals for Gaussian type functions.") #~(modify-phases %standard-phases (add-after 'unpack 'patch-includes (lambda _ - (substitute* (list "src/sprintf.cpp" + (substitute* (list "src/json.cpp" + "src/sprintf.cpp" "include/gemmi/dirwalk.hpp" "include/gemmi/cif.hpp" "include/gemmi/json.hpp" "python/gemmi.cpp" + "python/serial.h" "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>") + (("\"\\.\\./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>")))) + "<pocketfft_hdronly.h>") + (("\"\\.\\./third_party/serializer.h\"") + "<zpp/serializer.h>")))) (add-after 'unpack 'change-bin-prefix (lambda _ (substitute* "CMakeLists.txt" @@ -1052,7 +1055,7 @@ integrals for Gaussian type functions.") (lambda* (#:key tests? #:allow-other-keys) (when tests? (with-directory-excursion "../source" - (setenv "PYTHONPATH" "../build") + (setenv "PYTHONPATH" "../build/py") (invoke "python3" "-m" "unittest" "discover" "-v" "-s" "tests")))))))) (inputs (list python zlib)) @@ -1061,10 +1064,11 @@ integrals for Gaussian type functions.") optionparser pegtl pocketfft-cpp - pybind11 + python-nanobind sajson-for-gemmi stb-sprintf - tinydir)) + tinydir + zpp-serializer)) (home-page "https://gemmi.readthedocs.io/en/latest/") (synopsis "Macromolecular crystallography library and utilities") (description "GEMMI is a C++ library for macromolecular crystallography. |