guix_mirror_bot pushed a commit to branch master
in repository guix.
commit c3e59b2ffa89574e1100f2e260074617b4d2ec7f
Author: David Elsing <[email protected]>
AuthorDate: Tue Jul 29 16:19:32 2025 +0200
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 <[email protected]>
---
gnu/packages/chemistry.scm | 24 ++++++++++++++----------
1 file 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.
