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gnu: rdkit: Switch to pyproject.

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* 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 <sharlatanus@gmail.com>
Signed-off-by: Rutherther <rutherther@ditigal.xyz>
This commit is contained in:
Nicolas Graves
2026-01-06 16:27:40 +01:00
committed by Rutherther
parent 4acb4ce02e
commit 733ec52b07
1 changed files with 62 additions and 63 deletions
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gnu/packages/chemistry.scm
+62 -63
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@@ -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)
(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
(with-extensions (list (pyproject-guile-json))
#~(modify-phases %standard-phases
(add-after 'unpack 'copy-external-dependencies
(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"
) "|")
")")))))))))
(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)
(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