guix_mirror_bot pushed a commit to branch next-master
in repository guix.
commit 8f3262ad6314777aaa36bc9733cbd352b98bd486
Author: Nicolas Graves <[email protected]>
AuthorDate: Tue Jan 6 16:27:40 2026 +0100
gnu: rdkit: Switch to pyproject.
* gnu/packages/chemistry.scm (rdkit):
[arguments]<#:imported-modules, #:modules, #:phases>: Switch to
pyproject-build-system.
<#:phases>: Take phases 'enable-bytecode-determinism and
'add-install-to-pythonpath from pyproject.
Change-Id: If8b134d38b3e23a6974469c1e68b2834219bd67b
Signed-off-by: Sharlatan Hellseher <[email protected]>
---
gnu/packages/chemistry.scm | 123 ++++++++++++++++++++++-----------------------
1 file changed, 61 insertions(+), 62 deletions(-)
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index e798301430..544209392e 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -1603,11 +1603,10 @@ Tanimoto scoring.")
(arguments
(list
#:imported-modules (append %cmake-build-system-modules
- '((guix build python-build-system)))
+ %pyproject-build-system-modules)
#:modules '((guix build cmake-build-system)
(guix build utils)
- ((guix build python-build-system)
- #:select (add-installed-pythonpath)))
+ ((guix build pyproject-build-system) #:prefix py:))
#:configure-flags
#~(list "-DRDK_BUILD_AVALON_SUPPORT=ON"
"-DRDK_BUILD_CAIRO_SUPPORT=ON"
@@ -1632,67 +1631,67 @@ Tanimoto scoring.")
"-DCMAKE_INCLUDE_PATH="
(search-input-directory %build-inputs
"/include/avalontoolkit")))
#:phases
- #~(modify-phases %standard-phases
- (add-after 'unpack 'copy-external-dependencies
- (lambda _
- (symlink
- (string-append
- (search-input-file
- %build-inputs "/share/fonts/truetype/ComicNeue-Regular.ttf"))
- "Data/Fonts/ComicNeue-Regular.ttf")))
- (add-after 'unpack 'fix-inchi-include
- (lambda _
- (substitute* "Code/cmake/Modules/FindInchi.cmake"
- (("inchi_api.h.*\\)") "inchi/inchi_api.h)")
- (("INCHI_LIBRARY NAMES.*\\)")
- "INCHI_LIBRARY NAMES inchi PATH_SUFFIXES inchi)")
- (("find_library" prev)
+ (with-extensions (list (pyproject-guile-json))
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'copy-external-dependencies
+ (lambda _
+ (symlink
(string-append
- "list(APPEND CMAKE_FIND_LIBRARY_SUFFIXES .so.1)\n"
- prev)))
- (substitute* "External/INCHI-API/inchi.cpp"
- (("<inchi_api.h>") "<inchi/inchi_api.h>"))))
- (add-before 'build 'enable-bytecode-determinism
+ (search-input-file
+ %build-inputs
"/share/fonts/truetype/ComicNeue-Regular.ttf"))
+ "Data/Fonts/ComicNeue-Regular.ttf")))
+ (add-after 'unpack 'fix-inchi-include
(lambda _
- (setenv "PYTHONHASHSEED" "0")
- (setenv "PYTHONDONTWRITEBYTECODE" "1")))
- (add-after 'install 'pre-check
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (with-directory-excursion "../source"
- (invoke "sqlite3" "Data/RDData.sqlt"
- ".read rdkit/Dbase/test_data/RDData.sqlite")
- (invoke "sqlite3" "Data/RDTests.sqlt"
- ".read rdkit/Dbase/test_data/RDTests.sqlite")
- (setenv "RDBASE" (canonicalize-path ".")))
- (add-installed-pythonpath inputs outputs)))
- (delete 'check)
- (add-after 'pre-check 'check
- (lambda* (#:key tests? parallel-tests? #:allow-other-keys)
- (when tests?
- (let ((job-count (number->string
- (if parallel-tests? (parallel-job-count)
1))))
- (invoke
- "ctest" "-j" job-count
- "-E" (string-append
- "("
- (string-join
- '(;; need pickled data
- "pyDiscreteValueVect" "pySparseIntVect"
- "graphmoltestPickler" "pyPartialCharges"
- "substructLibraryTest" "pyFeatures"
- "pythonTestDirML" "pythonTestDirChem"
- "pyRealValueVect" "pyDiscreteValueVect"
- "pickleTestsCatch"
- ;; Catching Python exception fails
- "pyRanker"
- ;; Flaky test depending on floating point rounding
- "testConrec"
- ;; Expensive test which may time out
- "pySynthonSpaceSearch"
- ;; Circular import
- "pythonSourceTests"
- ) "|")
- ")")))))))))
+ (substitute* "Code/cmake/Modules/FindInchi.cmake"
+ (("inchi_api.h.*\\)") "inchi/inchi_api.h)")
+ (("INCHI_LIBRARY NAMES.*\\)")
+ "INCHI_LIBRARY NAMES inchi PATH_SUFFIXES inchi)")
+ (("find_library" prev)
+ (string-append
+ "list(APPEND CMAKE_FIND_LIBRARY_SUFFIXES .so.1)\n"
+ prev)))
+ (substitute* "External/INCHI-API/inchi.cpp"
+ (("<inchi_api.h>") "<inchi/inchi_api.h>"))))
+ (add-before 'build 'enable-bytecode-determinism
+ (assoc-ref py:%standard-phases 'enable-bytecode-determinism))
+ (add-after 'install 'pre-check
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (with-directory-excursion "../source"
+ (invoke "sqlite3" "Data/RDData.sqlt"
+ ".read rdkit/Dbase/test_data/RDData.sqlite")
+ (invoke "sqlite3" "Data/RDTests.sqlt"
+ ".read rdkit/Dbase/test_data/RDTests.sqlite")
+ (setenv "RDBASE" (canonicalize-path ".")))))
+ (add-after 'install 'add-install-to-pythonpath
+ (assoc-ref py:%standard-phases 'add-install-to-pythonpath))
+ (delete 'check)
+ (add-after 'pre-check 'check
+ (lambda* (#:key tests? parallel-tests? #:allow-other-keys)
+ (when tests?
+ (let ((job-count (number->string
+ (if parallel-tests? (parallel-job-count)
1))))
+ (invoke
+ "ctest" "-j" job-count
+ "-E" (string-append
+ "("
+ (string-join
+ '(;; need pickled data
+ "pyDiscreteValueVect" "pySparseIntVect"
+ "graphmoltestPickler" "pyPartialCharges"
+ "substructLibraryTest" "pyFeatures"
+ "pythonTestDirML" "pythonTestDirChem"
+ "pyRealValueVect" "pyDiscreteValueVect"
+ "pickleTestsCatch"
+ ;; Catching Python exception fails
+ "pyRanker"
+ ;; Flaky test depending on floating point
rounding
+ "testConrec"
+ ;; Expensive test which may time out
+ "pySynthonSpaceSearch"
+ ;; Circular import
+ "pythonSourceTests"
+ ) "|")
+ ")"))))))))))
(inputs
(list avalon-toolkit
cairo
