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Merge branch 'main' of gitlab.univ-nantes.fr:glicid-public/guix-glicid into main

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Yann Dupont 2022-05-02 12:30:08 +02:00
commit 6a8ef44101
2 changed files with 151 additions and 125 deletions
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260
glicid/packages/glicid.scm
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@ -4,10 +4,11 @@
#:use-module (guix git-download) #:use-module (guix git-download)
#:use-module (guix build-system gnu) #:use-module (guix build-system gnu)
#:use-module (guix build-system cmake) #:use-module (guix build-system cmake)
#:use-module (guix build-system python) ; #:use-module (guix licenses)
#:use-module (gnu packages gawk) #:use-module (gnu packages gawk)
#:use-module (gnu packages gcc) #:use-module (gnu packages gcc)
#:use-module (gnu packages commencement) #:use-module (gnu packages commencement)
#:use-module (guix build-system python)
#:use-module ((guix licenses) #:prefix license:) #:use-module ((guix licenses) #:prefix license:)
#:use-module ((guix utils) #:select (target-64bit?)) #:use-module ((guix utils) #:select (target-64bit?))
#:use-module (gnu packages) #:use-module (gnu packages)
@ -56,7 +57,7 @@
#:use-module (gnu packages maths) #:use-module (gnu packages maths)
#:use-module (guix utils) #:use-module (guix utils)
#:use-module (gnu packages cmake) #:use-module (gnu packages cmake)
#:use-module (gnu packages pretty-print) #:use-module (gnu packages pretty-print)
#:use-module (gnu packages boost) #:use-module (gnu packages boost)
#:use-module (gnu packages curl) #:use-module (gnu packages curl)
#:use-module (gnu packages cryptsetup) #:use-module (gnu packages cryptsetup)
@ -86,145 +87,156 @@
#:use-module (gnu packages sphinx) #:use-module (gnu packages sphinx)
#:use-module (gnu packages tls) #:use-module (gnu packages tls)
#:use-module (gnu packages web) #:use-module (gnu packages web)
;; #:use-module (gnu packages glicid)
#:use-module (gnu packages pretty-print) #:use-module (gnu packages pretty-print)
#:use-module (gnu packages virtualization) #:use-module (gnu packages virtualization)
;; #:use-module (glicid packages storage)
#:use-module (glicid packages mpi) #:use-module (glicid packages mpi)
#:use-module (glicid packages gcc) #:use-module (glicid packages gcc)
) )
;;;;;;;;
(define-public glicid-librdkafka-09 (define-public glicid-librdkafka-09
(package (package
(inherit librdkafka) (inherit librdkafka)
(name "glicid-librdkafka-09") (name "glicid-librdkafka-09")
(version "0.9.2") (version "0.9.2")
(source (source
(origin (origin
(method url-fetch) (method url-fetch)
(uri (string-append "https://github.com/edenhill/librdkafka/archive/v" version ".tar.gz")) (uri (string-append "https://github.com/edenhill/librdkafka/archive/v" version ".tar.gz"))
(sha256 (base32 "0938yn1msaq8xcj5z7b3jcdy6rslh9kxmvz01r8rdcgbarlvchy2")) (sha256 (base32 "0938yn1msaq8xcj5z7b3jcdy6rslh9kxmvz01r8rdcgbarlvchy2"))
) ))
) ))
)
)
(define-public glicid-x2go (define-public glicid-x2go
(package (package
(name "glicid-x2go") (name "glicid-x2go")
(version "4.1.0.3") (version "4.1.0.3")
(source (source
(origin (origin
(method url-fetch) (method url-fetch)
(uri (string-append "https://code.x2go.org/releases/source/x2goserver/x2goserver-" version ".tar.gz")) (uri (string-append "https://code.x2go.org/releases/source/x2goserver/x2goserver-" version ".tar.gz"))
(sha256 (base32 "1l6wd708kbipib4ldprfiihqmj4895nifg0bkws4x97majislxk7")) (sha256 (base32 "1l6wd708kbipib4ldprfiihqmj4895nifg0bkws4x97majislxk7"))
) ))
)
(native-inputs (native-inputs
(autoconf automake libtool) `(("autoconf" ,autoconf)
) ("automake" ,automake)
(inputs ("libtool" ,libtool)))
(perl)
) (inputs
(build-system gnu-build-system) `(("perl" , perl)))
(synopsis "X2go")
(description "X2go") (build-system gnu-build-system)
(license "not checked") (synopsis "X2go")
(home-page "https://wiki.x2go.org") (description "X2go")
(license "not checked")
(home-page "https://wiki.x2go.org")
) )
) )
(define-public glicid-gromacs-openmpi (define-public glicid-gromacs-openmpi
(package (package
(inherit gromacs) (inherit gromacs)
(name "glicid-gromacs-openmpi") (name "glicid-gromacs-openmpi")
(inputs (inputs `(("openmpi", openmpi)
`( ;; ("openssh", openssh) ;; only for tests... disabled now
("openmpi", openmpi) ,@(package-inputs gromacs)))
,@(package-inputs gromacs)
)
)
)
(build-system cmake-build-system) (build-system cmake-build-system)
(arguments
`(#:configure-flags (arguments
(list `(#:configure-flags
"-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests (list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests
;; Unbundling ;; Unbundling
"-DGMX_USE_LMFIT=EXTERNAL" "-DGMX_USE_LMFIT=EXTERNAL"
"-DGMX_BUILD_OWN_FFTW=off" "-DGMX_BUILD_OWN_FFTW=off"
"-DGMX_EXTERNAL_BLAS=on" "-DGMX_EXTERNAL_BLAS=on"
"-DGMX_EXTERNAL_LAPACK=on" "-DGMX_EXTERNAL_LAPACK=on"
"-DGMX_EXTERNAL_TNG=on" "-DGMX_EXTERNAL_TNG=on"
"-DGMX_EXTERNAL_ZLIB=on" "-DGMX_EXTERNAL_ZLIB=on"
"-DGMX_EXTERNAL_TINYXML2=on" "-DGMX_EXTERNAL_TINYXML2=on"
;; special glicid ;; special glicid
"-DGMX_MPI=on" "-DGMX_MPI=on"
"-DCMAKE_C_COMPILER=mpicc" "-DCMAKE_C_COMPILER=mpicc"
"-DCMAKE_CXX_COMPILER=mpicxx" "-DCMAKE_CXX_COMPILER=mpicxx"
"-DGMX_DOUBLE=off" "-DGMX_DOUBLE=off"
"-DGMX_OPENMP=on" "-DGMX_OPENMP=on"
"-DGMX_SIMD=AVX2_256" "-DGMX_SIMD=AVX2_256"
(string-append "-DTinyXML2_DIR=" (assoc-ref %build-inputs "tinyxml2")) (string-append "-DTinyXML2_DIR="
;; Workaround for cmake/FindSphinx.cmake version parsing that does (assoc-ref %build-inputs "tinyxml2"))
;; not understand the guix-wrapped `sphinx-build --version' answer ;; Workaround for cmake/FindSphinx.cmake version parsing that does
(string-append "-DSPHINX_EXECUTABLE_VERSION=",(package-version python-sphinx)) ;; not understand the guix-wrapped `sphinx-build --version' answer
) (string-append "-DSPHINX_EXECUTABLE_VERSION="
#:tests? #f ,(package-version python-sphinx)))
#:phases #:tests? #f
(modify-phases %standard-phases #:phases
(add-after 'unpack 'fixes (modify-phases %standard-phases
(lambda* (#:key inputs #:allow-other-keys) (add-after 'unpack 'fixes
;; Still bundled: part of gromacs, source behind registration (lambda* (#:key inputs #:allow-other-keys)
;; but free software anyways ;; Still bundled: part of gromacs, source behind registration
;;(delete-file-recursively "src/external/vmd_molfile") ;; but free software anyways
;; Still bundled: threads-based OpenMPI-compatible fallback ;;(delete-file-recursively "src/external/vmd_molfile")
;; designed to be bundled like that ;; Still bundled: threads-based OpenMPI-compatible fallback
;;(delete-file-recursively "src/external/thread_mpi") ;; designed to be bundled like that
;; Unbundling ;;(delete-file-recursively "src/external/thread_mpi")
(delete-file-recursively "src/external/lmfit") ;; Unbundling
(delete-file-recursively "src/external/clFFT") (delete-file-recursively "src/external/lmfit")
(delete-file-recursively "src/external/fftpack") (delete-file-recursively "src/external/clFFT")
(delete-file-recursively "src/external/build-fftw") (delete-file-recursively "src/external/fftpack")
(delete-file-recursively "src/external/tng_io") (delete-file-recursively "src/external/build-fftw")
(delete-file-recursively "src/external/tinyxml2") (delete-file-recursively "src/external/tng_io")
(delete-file-recursively "src/external/googletest") (delete-file-recursively "src/external/tinyxml2")
(copy-recursively (assoc-ref inputs "googletest-source") "src/external/googletest") (delete-file-recursively "src/external/googletest")
;; This test warns about the build host hardware, disable (copy-recursively (assoc-ref inputs "googletest-source")
(substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp" (("TEST\\(HardwareTopologyTest, HwlocExecute\\)") "void __guix_disabled()")) "src/external/googletest")
#t ;; This test warns about the build host hardware, disable
) (substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp"
) (("TEST\\(HardwareTopologyTest, HwlocExecute\\)")
) "void __guix_disabled()"))
) #t)))))
) )
) )
(define-public glicid-python-nbxmpp (define-public glicid-python-nbxmpp
(package (package
(inherit python-nbxmpp) (inherit python-nbxmpp)
(name "glicid-python-nbxmpp") (name "glicid-python-nbxmpp")
(version "1.0.2") (version "1.0.2")
(source (source
(origin (origin
(method url-fetch) (method url-fetch)
(uri (pypi-uri "nbxmpp" version)) (uri (pypi-uri "nbxmpp" version))
(sha256 (base32 "0vw5drr077w9ks4crnw6pwa4735ycyjdcm54knc3w4in4x5027wr")) (sha256
) (base32
) "0vw5drr077w9ks4crnw6pwa4735ycyjdcm54knc3w4in4x5027wr"))))
)
) ))
(define-public glicid-specific-hdf5 (define-public glicid-specific-hdf5
(package (package
(inherit hdf5-1.12) (inherit hdf5-1.12)
(name "glicid-specific-hdf5") (name "glicid-specific-hdf5")
(native-inputs ; (arguments
`( ; `(#:tests? #f)
("gcc",gcc-11) ; )
("gfortran",gfortran-11) (native-inputs `(
,@(package-native-inputs hdf5-1.12) ("gcc",gcc-11)
) ("gfortran",gfortran-11)
) ,@(package-native-inputs hdf5-1.12)))
) )
) )
@ -244,7 +256,9 @@
(arguments (arguments
`(#:make-flags `(#:make-flags
;; #:make-flags
(list (string-append "PREFIX=" %output) (list (string-append "PREFIX=" %output)
; (string-append "CC=" ,(cc-for-target))
;; Xft.h #includes <ft2build.h> without ‘freetype2/’. The Makefile ;; Xft.h #includes <ft2build.h> without ‘freetype2/’. The Makefile
;; works around this by hard-coding /usr/include & $PREFIX. ;; works around this by hard-coding /usr/include & $PREFIX.
(string-append "CPPFLAGS=-I" (string-append "CPPFLAGS=-I"
@ -264,10 +278,12 @@
("flex" ,flex) ("flex" ,flex)
("bison" ,bison) ("bison" ,bison)
("libxt" ,libxt))) ("libxt" ,libxt)))
(synopsis "Motif") (synopsis "Motif")
(description "Motif ") (description "Motif ")
(home-page "https://sourceforge.net/untested") (home-page "https://sourceforge.net/untested")
(license " ") (license " ")
) )
) )
@ -313,12 +329,16 @@
("fontconfig", fontconfig) ("fontconfig", fontconfig)
("gfortran", gfortran) ("gfortran", gfortran)
("libjpeg-turbo", libjpeg-turbo) ("libjpeg-turbo", libjpeg-turbo)
;; ("libxmhtml", libxmhtml)
) )
) )
(synopsis "Xmgrace") (synopsis "Xmgrace")
(description "xmgrace") (description "xmgrace")
(home-page "https://sourceforge.net/untested") (home-page "https://sourceforge.net/untested")
(license " ") (license " ")
) )
) )
@ -326,6 +346,9 @@
(use-modules (guix download)) (use-modules (guix download))
(use-modules (gnu packages ruby)) (use-modules (gnu packages ruby))
(use-modules (guix build-system ruby)) (use-modules (guix build-system ruby))
;(use-modules (guix licenses))
(define-public ruby-asciidoctor-revealjs (define-public ruby-asciidoctor-revealjs
(package (package
@ -343,6 +366,7 @@
'(#:tests? #f)) '(#:tests? #f))
(propagated-inputs (propagated-inputs
`(("ruby-asciidoctor" ,ruby-asciidoctor) `(("ruby-asciidoctor" ,ruby-asciidoctor)
; ("ruby-concurrent-ruby" ,ruby-concurrent-ruby)
("ruby-concurrent" ,ruby-concurrent) ("ruby-concurrent" ,ruby-concurrent)
("ruby-asciidoctor-kroki", ruby-asciidoctor-kroki) ("ruby-asciidoctor-kroki", ruby-asciidoctor-kroki)
("ruby-thread-safe" ,ruby-thread-safe))) ("ruby-thread-safe" ,ruby-thread-safe)))
@ -380,3 +404,7 @@
(license license:expat) (license license:expat)
) )
) )
;; python-glances is now upstreamed as glances in python-xyz
;;; glicid.scm ends here

16
glicid/packages/vpn.scm
View file

@ -8,15 +8,13 @@
(package (package
(inherit gnu:openconnect) (inherit gnu:openconnect)
(version "8.20") (version "8.20")
(source (origin (source
(method url-fetch) (origin
(uri (string-append "http://www.infradead.org/pub/openconnect/download" (method url-fetch)
"openconnect-" version ".tar.gz")) (uri (string-append "https://www.infradead.org/openconnect/download/openconnect-" version ".tar.gz"))
(sha256 (sha256 (base32 "1cdsx4nsrwawbsisfkldfc9i4qn60g03vxb13nzppr2br9p4rrih"))
(base32 "1cdsx4nsrwawbsisfkldfc9i4qn60g03vxb13nzppr2br9p4rrih")))) )
)
(name "openconnect-upstream") (name "openconnect-upstream")
; )
) )
) )