Subject: [bug#58261] [PATCH 11/11] gnu: Add rdkit.

From: David Elsing <[email-masked]>
Date: Fri, 07 Oct 2022 15:12:44 +0000

Liliana Marie Prikler <[email-masked]> 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