Package: guix-patches;
Reported by: David Elsing <david.elsing <at> posteo.net>
Date: Mon, 3 Oct 2022 00:06:02 UTC
Severity: normal
Tags: patch
Done: Liliana Marie Prikler <liliana.prikler <at> gmail.com>
Bug is archived. No further changes may be made.
Message #62 received at 58261 <at> debbugs.gnu.org (full text, mbox):
From: Liliana Marie Prikler <liliana.prikler <at> ist.tugraz.at> To: David Elsing <david.elsing <at> posteo.net>, 58261 <at> debbugs.gnu.org Subject: Re: [PATCH 11/11] gnu: Add rdkit. Date: Tue, 04 Oct 2022 10:13:24 +0200
Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
> * gnu/packages/chemistry.scm (rdkit): New variable.
> ---
> gnu/packages/chemistry.scm | 198
> ++++++++++++++++++
> .../rdkit-cmake-external-dependencies.patch | 102 +++++++++
> 2 files changed, 300 insertions(+)
> create mode 100644 gnu/packages/patches/rdkit-cmake-external-
> dependencies.patch
>
> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
> index a39deff4bf..869cf264e3 100644
> --- a/gnu/packages/chemistry.scm
> +++ b/gnu/packages/chemistry.scm
> @@ -34,6 +34,7 @@ (define-module (gnu packages chemistry)
> #:use-module (gnu packages algebra)
> #:use-module (gnu packages autotools)
> #:use-module (gnu packages backup)
> + #:use-module (gnu packages base)
> #:use-module (gnu packages bison)
> #:use-module (gnu packages boost)
> #:use-module (gnu packages check)
> @@ -41,10 +42,12 @@ (define-module (gnu packages chemistry)
> #:use-module (gnu packages cpp)
> #:use-module (gnu packages documentation)
> #:use-module (gnu packages flex)
> + #:use-module (gnu packages fonts)
> #:use-module (gnu packages fontutils)
> #:use-module (gnu packages gcc)
> #:use-module (gnu packages gl)
> #:use-module (gnu packages graphviz)
> + #:use-module (gnu packages gtk)
> #:use-module (gnu packages gv)
> #:use-module (gnu packages image)
> #:use-module (gnu packages maths)
> @@ -56,6 +59,7 @@ (define-module (gnu packages chemistry)
> #:use-module (gnu packages qt)
> #:use-module (gnu packages serialization)
> #:use-module (gnu packages sphinx)
> + #:use-module (gnu packages sqlite)
> #:use-module (gnu packages stb)
> #:use-module (gnu packages web)
> #:use-module (gnu packages xml)
> @@ -899,3 +903,197 @@ (define-public yaehmop-tightbind
> (description "@code{YAeHMOP} contains a program and library for
> performing
> extended Hückel calculations.")
> (license license:bsd-2)))
> +
> +(define-public rdkit
> + (package
> + (name "rdkit")
> + (version "2022.03.5")
> + (source (origin
> + (method git-fetch)
> + (uri (git-reference
> + (url "https://github.com/rdkit/rdkit")
> + (commit
> + (string-append
> + "Release_" (string-replace-substring version
> "." "_")))))
> + (file-name (git-file-name name version))
> + (sha256
> + (base32
> +
> "19idgilabh04cbr1qj6zgrgsfjm248mmfz6fsr0smrd68d0xnml9"))
> + (patches
> + (search-patches "rdkit-cmake-external-
> dependencies.patch"))
> + (modules '((guix build utils)))
> + (snippet
> + #~(begin
> + ;; Remove pickle files (only used in tests),
> + ;; as they are compiled programs
> + (for-each
> + (lambda (name)
> + (display (string-append name "\n"))
> + (delete-file name))
> + (find-files "." "\\.pkl(\\.gz)?$"))
> + ;; Remove SQLite data files (can be generated)
> + (delete-file "Data/RDData.sqlt")
> + (delete-file "Data/RDTests.sqlt")
> + #t))))
> + (build-system cmake-build-system)
> + (native-inputs
> + `(("bison" ,bison)
> + ("boost" ,boost)
> + ("catch2" ,catch2)
> + ("eigen" ,eigen)
> + ("flex" ,flex)
> + ("freesasa" ,freesasa)
> + ("pkg-config" ,pkg-config)
> + ("rapidjson" ,rapidjson)
> + ("tar" ,tar)
> + ("avalontoolkit-src"
> + ,(let ((version "1.2.0"))
> + (origin
> + (method url-fetch)
> + (uri (string-append
> +
> "http://sourceforge.net/projects/avalontoolkit/files/"
> + "AvalonToolkit_" (substring version 0 3)
> "/AvalonToolkit_"
> + version ".source.tar"))
> + (sha256
> + (base32
> +
> "0rnnyy6axs2da7aa4q6l30ldavbk49v6l22llj1adn74h1i67bpv"))
> + (modules '((guix build utils) (ice-9 ftw) (srfi srfi-
> 26)))
> + (snippet
> + #~(begin
> + (chdir "..")
> + (delete-file-recursively "StandardFiles")
> + (delete-file-recursively
> "SourceDistribution/java")
> + #t)))))
> + ("ringdecomposerlib-src"
> + ,(let ((version "1.1.3"))
> + (origin
> + (method git-fetch)
> + (uri (git-reference
> + (url
> "https://github.com/rareylab/RingDecomposerLib")
> + (commit (string-append "v" version "_rdkit"))))
> + (file-name (git-file-name name version))
> + (sha256
> + (base32
> +
> "1rxzs2wpkkdi40wdzxc4sn0brk7dm7ivgqyfh38gf2f5c7pbg0wi")))))))
> + (inputs
> + (list cairo
> + coordgenlibs
> + font-comic-neue
> + freetype
> + inchi
> + maeparser
> + python
> + sqlite
> + yaehmop-tightbind))
> + (propagated-inputs
> + (list python-numpy python-cairocffi python-pillow))
> + (arguments
> + (list
> + #:imported-modules (append %cmake-build-system-modules
> + '((guix build python-build-
> system)))
> + #:modules '((guix build cmake-build-system)
> + (guix build utils)
> + ((guix build python-build-system)
> + #:select (add-installed-pythonpath)))
> + #:configure-flags
> + #~(list
> + "-DRDK_BUILD_AVALON_SUPPORT=ON"
> + "-DRDK_BUILD_CAIRO_SUPPORT=ON"
> + "-DRDK_BUILD_CPP_TESTS=ON"
> + "-DRDK_BUILD_FREESASA_SUPPORT=ON"
> + "-DRDK_BUILD_INCHI_SUPPORT=ON"
> + "-DRDK_BUILD_YAEHMOP_SUPPORT=ON"
> + (string-append "-DCATCH_DIR="
> + #$(this-package-native-input "catch2")
> + "/include/catch2")
> + "-DRDK_INSTALL_DEV_COMPONENT=ON"
> + "-DRDK_INSTALL_INTREE=OFF"
> + "-DRDK_INSTALL_STATIC_LIBS=OFF"
> + (string-append
> + "-DRDK_OPTIMIZE_POPCNT="
> + #$(let ((system (or (%current-target-system)
> + (%current-system))))
> + (cond
> + ((string-prefix? "x86_64" system) "ON")
> + ((string-prefix? "i686" system) "ON")
> + (else "OFF"))))
> + "-DRDK_USE_BOOST_IOSTREAMS=ON"
> + "-DRDK_USE_FLEXBISON=ON")
> + #:phases
> + #~(modify-phases %standard-phases
> + (add-after 'unpack 'copy-external-dependencies
> + (lambda _
> + (symlink
> + (string-append
> + #$(this-package-input "font-comic-neue")
> + "/share/fonts/truetype/ComicNeue-Regular.ttf")
> + "Data/Fonts/ComicNeue-Regular.ttf")
> + (symlink #$(this-package-native-input "rapidjson")
> + "External/rapidjson-1.1.0")
> + (invoke "tar" "xvf"
> + #$(this-package-native-input "avalontoolkit-
> src")
> + "-C" "External/AvalonTools")
> + (symlink #$(this-package-native-input
> "ringdecomposerlib-src")
> + "External/RingFamilies/RingDecomposerLib")
> + #t))
You might want to try unbundling those. Either way, you should find a
solution that doesn't depend on native-input labels.
> + (add-after 'copy-external-dependencies 'patch-source
> + (lambda _
> + (with-directory-excursion "External/AvalonTools"
> + (invoke "patch" "-p0" "-i"
> + "AvalonToolkit_1.2_patch.txt"))
> + (substitute* "External/YAeHMOP/EHTTools.cpp"
> + (("<yaehmop/tightbind/bind.h>") "<yaehmop/bind.h>"))
> + #t))
See my comment on yaehmop.
> + (add-after 'unpack 'create-sqlite-data-files
> + (lambda _
> + (invoke "sqlite3" "Data/RDData.sqlt"
> + ".read rdkit/Dbase/test_data/RDData.sqlite")
> + (invoke "sqlite3" "Data/RDTests.sqlt"
> + ".read rdkit/Dbase/test_data/RDTests.sqlite")
> + #t))
Do you only need this for tests? If so, do this in a pre-check phase.
> + (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>"))
> + #t))
> + (add-before 'build 'enable-bytecode-determinism
> + (lambda _
> + (setenv "PYTHONHASHSEED" "0")
> + (setenv "PYTHONDONTWRITEBYTECODE" "1")
> + #t))
> + (delete 'check)
> + (add-after 'install 'check
> + (lambda* (#:key inputs outputs tests? parallel-tests?
> + #:allow-other-keys)
> + (when tests?
> + (let
> + ((job-count (number->string
> + (or (and parallel-tests?
> + (parallel-job-count))
> + 1))))
> + (setenv "RDBASE" (canonicalize-path "../source"))
> + (add-installed-pythonpath inputs outputs)
This line should also be pre-check, maybe even these two lines.
> + (invoke "ctest"
> + "-j" job-count
> + "-E" (string-append
> + ;; need pickled data
> + "(pyDiscreteValueVect"
> "|pySparseIntVect"
> + "|graphmoltestPickler"
> "|pyPartialCharges"
> + "|substructLibraryTest"
> "|pyFeatures"
> + "|pythonTestDirML"
> "|pythonTestDirChem"
> + ;; Catching Python exception fails
> + "|pyRanker)"))))
Use string-join instead.
> + #t)))))
> + (home-page "https://rdkit.org/")
> + (synopsis "Open-Source Cheminformatics Software")
"Open-Source" is meaningless in Guix.
> + (description "RDKit is a collection of cheminformatics and
> +machine-learning software written in C++ and Python.")
Not particularly descriptive, but then again, neither is rdkit itself.
Cheers
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1997,2003 nCipher Corporation Ltd,
1994-97 Ian Jackson.