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 #92 received at 58261 <at> debbugs.gnu.org (full text, mbox):
From: David Elsing <david.elsing <at> posteo.net> To: Liliana Marie Prikler <liliana.prikler <at> ist.tugraz.at>, 58261 <at> debbugs.gnu.org Subject: Re: [PATCH 11/11] gnu: Add rdkit. Date: Fri, 07 Oct 2022 15:12:44 +0000
Liliana Marie Prikler <liliana.prikler <at> ist.tugraz.at> writes:
> 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.
Ok, I unbundled them, but the package definitions became a bit long. :)
Do you think it is ok like that?
>> + (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.
Ok.
>> + (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.
Thanks!
>> + #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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