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.
View this message in rfc822 format
From: Liliana Marie Prikler <liliana.prikler <at> ist.tugraz.at> To: David Elsing <david.elsing <at> posteo.net>, 58261 <at> debbugs.gnu.org Subject: [bug#58261] [PATCH 11/11] gnu: Add rdkit. Date: Fri, 07 Oct 2022 17:29:26 +0200
Am Freitag, dem 07.10.2022 um 15:12 +0000 schrieb David Elsing:
> 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?
> >
Long package definitions are not inherently bad (unless of course there
is an obviously less verbose way of writing them). I'll take a look at
your v2 at a later time.
Cheers
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