backporting master into devel (devel was behind master)

glicid/packages/glicid.scm

@@ -90,7 +90,7 @@
 ;;  #:use-module (gnu packages glicid)
   #:use-module (gnu packages pretty-print)
   #:use-module (gnu packages virtualization)
-  #:use-module (glicid packages storage)
+;;  #:use-module (glicid packages storage)
   #:use-module (glicid packages mpi)
   #:use-module (glicid packages gcc)
   
@@ -142,23 +142,6 @@
   )  
 )
 
-;(define-public glicid-gromacs-openmpi
-; (package
-;  (inherit gromacs)
-;  (name "glicid-gromacs-openmpi")
-;  (inputs `(("openmpi", openmpi)
-;                    ,@(package-inputs gromacs)))
-;  (build-system cmake-build-system)
-;  (arguments
-;       `(#:configure-flags configure-flags)
-;               (append configure-flags          (list "-DGMX_MPI=on"
-;               "-DCMAKE_C_COMPILER=mpicc"
-;               "-DCMAKE_CXX_COMPILER=mpiicxx"
-;               ))
-;  )
-; )
-;)
-
 
 (define-public glicid-gromacs-openmpi
  (package
@@ -227,39 +210,6 @@
 )
 
 
-
-;; pour futures customisations.
-
-;(define-public glicid-openmpi-gcc-10
-; (package
-;  (inherit openmpi)
-;  (name "glicid-openpmi-gcc-10")
-;  (inputs `(("gcc-10", gcc-10)
-;            ("gfortran-11", gfortran-11)
-;                  ,@(package-inputs openmpi)))
-;  )
-;)
-
-
-(define-public glicid-gromacs-gcc-11
- (package
-  (inherit gromacs)
-  (name "glicid-gromacs-gcc-11")
-  (version "2020.3")
-  (source 
-   (origin
-    (method url-fetch)
-    (uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-" version ".tar.gz"))
-    (sha256 (base32 "1acjrhcfzpqy2dncblhj97602jbg9gdha4q1bgji9nrj25lq6cch"))
-   ))
-
-  (inputs `(("gcc-11", gcc-11)
-            ("gfortran-11", gfortran-11)
-            ("glicid-openmpi-gcc-11", glicid-openmpi-gcc-11)
-                    ,@(package-inputs gromacs)))
-))
-
-
 (define-public glicid-python-nbxmpp
  (package 
   (inherit python-nbxmpp) 
@@ -290,89 +240,6 @@
   )
 )  
 
-(define-public glicid-specific-hdf5-parallel-openmpi
-  (package/inherit glicid-specific-hdf5                      ;use the latest
-    (name "glicid-specific-hdf5-parallel-openmpi")
-    (inputs
-     `(("mpi" ,glicid-specific-openmpi)
-       ,@(package-inputs glicid-specific-hdf5)))
-    (arguments
-     
-;     `(
-;       #:tests? #f
-
-    ( 
-     substitute-keyword-arguments (package-arguments glicid-specific-hdf5)
-       ((#:configure-flags flags)
-        ``("--enable-parallel" "--disable-tests"
-           ,@(delete "--enable-cxx"
-                     (delete "--enable-threadsafe" ,flags))))
-       ((#:phases phases)
-        `(modify-phases ,phases
-           (add-after 'build 'mpi-setup
-             ,%openmpi-setup)
-           (add-before 'check 'patch-tests
-             (lambda _
-               ;; OpenMPI's mpirun will exit with non-zero status if it
-               ;; detects an "abnormal termination", i.e. any process not
-               ;; calling MPI_Finalize().  Since the test is explicitly
-               ;; avoiding MPI_Finalize so as not to have at_exit and thus
-               ;; H5C_flush_cache from being called, mpirun will always
-               ;; complain, so turn this test off.
-               (substitute* "testpar/Makefile"
-                 (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
-                  (string-append front back "\n")))
-               (substitute* "tools/test/h5diff/testph5diff.sh"
-                 (("/bin/sh") (which "sh")))
-               #t))))
-
-))
-  
-
-
-    (synopsis "Management suite for data with parallel IO support")))
-
-
-
-(define-public glicid-specific-openblas
-  (package
-    (inherit openblas)
-    (name "glicid-specific-openblas")
-      (inputs `(
-       ("fortran-lib",gfortran-11 "lib")
-      ,@(package-inputs openblas)))
-      (native-inputs `(
-       ("gcc", gcc-11)
-       ("fortran" ,gfortran-11)
-     ,@(package-native-inputs openblas)))
-  )
-)
-
-(define-public glicid-vspecific-openblas
-  (package
-    (inherit openblas)
-    (name "glicid-vspecific-openblas")
-    (version "0.3.15")
-    (source
-     (origin
-     (method url-fetch)
-     (uri (string-append "https://github.com/xianyi/OpenBLAS/releases/download/v" version "/OpenBLAS-" version ".tar.gz" ))
-;       (file-name (string-append name "-" version ".tar.gz"))
-       (sha256
-        (base32
-         "1gjbkrsh6n28hdp2ciyjigc8vg764d2r0jbzl63v753mjzn9va9h"))))
-
-    (name "glicid-specific-openblas")
-      (inputs `(
-       ("fortran-lib",gfortran-11 "lib")
-      ,@(package-inputs openblas)))
-      (native-inputs `(
-       ("gcc", gcc-11)
-       ("fortran" ,gfortran-11)
-     ,@(package-native-inputs openblas)))
-  )
-)
-
 
 (define-public glicid-motif
   (package
@@ -427,8 +294,9 @@
     (source (origin
               (method git-fetch)
               (uri (git-reference
-              (url "https://oauth2:9i-PgbC2w_JEx6DUUqzf@gitlab.univ-nantes.fr/CCIPL/legacy_code_mirror/grace.git")
+              (url "https://oauth2:glpat-RsX2GjsD2WrzXubiJeou@gitlab.univ-nantes.fr/CCIPL/legacy_code_mirror/grace.git")
               (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256 (base32 "1wb8v0q8xa2akas0swpgdgw1s66i50k7kh1g2f894hnk91fzx56z"))
              )
     )
@@ -537,6 +405,6 @@
 )
 )
 
-
+;; python-glances is now upstreamed as glances in python-xyz
 
 ;;; glicid.scm ends here