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: David Elsing <david.elsing <at> posteo.net> To: Liliana Marie Prikler <liliana.prikler <at> ist.tugraz.at>, 58261 <at> debbugs.gnu.org Subject: [bug#58261] [PATCH 10/11] gnu: Add yaehmop-tightbind. Date: Fri, 07 Oct 2022 15:12:25 +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 (yaehmop-tightbind): New variable.
>> ---
>> gnu/packages/chemistry.scm | 82
>> ++++++++++++++++++++++++++++++++++++++
>> 1 file changed, 82 insertions(+)
>>
>> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
>> index cc26aa329a..a39deff4bf 100644
>> --- a/gnu/packages/chemistry.scm
>> +++ b/gnu/packages/chemistry.scm
>> @@ -42,6 +42,7 @@ (define-module (gnu packages chemistry)
>> #:use-module (gnu packages documentation)
>> #:use-module (gnu packages flex)
>> #:use-module (gnu packages fontutils)
>> + #:use-module (gnu packages gcc)
>> #:use-module (gnu packages gl)
>> #:use-module (gnu packages graphviz)
>> #:use-module (gnu packages gv)
>> @@ -817,3 +818,84 @@ (define-public coordgenlibs
>> (description "@code{coordgenlibs} contains algorithms to
>> generate 2D
>> coordinates. It has an emphasis on quality rather than speed.")
>> (license license:bsd-3)))
>> +
>> +(define-public yaehmop-tightbind
>> + (package
>> + (name "yaehmop-tightbind")
>> + (version "2022.09.1")
>> + (source (origin
>> + (method git-fetch)
>> + (uri (git-reference
>> + (url "https://github.com/greglandrum/yaehmop")
>> + (commit (string-append "v" version))))
>> + (file-name (git-file-name name version))
>> + (sha256
>> + (base32
>> +
>> "1x0d75m1hgdb411fiv7c5bwq1n4y0swrll0gigh8v5c73kjxrja0"))
>> + (modules '((guix build utils)))
>> + (snippet
>> + '(begin
>> + (delete-file-recursively "docs")
> This one looks suspicious.
>> + (delete-file-recursively "examples")
> As does this.
> What gives?
I did not want to check the documentation in detail and the examples
contain some corrupted "compress" archives of program outputs. :)
But now I build the documentation instead and remove the archives.
There still is one problem: Even though I set FORCE_SOURCE_DATE=1, the
output of pdflatex is still not reproducible. Do you have an idea why
that could be? There are only 3 bytes different in the pdf.
Alternatively, I could just not build the documentation as it is
independent of the build scripts anyway.
>> + (delete-file-recursively "viewkel")
>> + (delete-file-recursively "tightbind/f2c_files")
>> + (delete-file "tightbind/diag.c")
>> + (delete-file "tightbind/cboris.c")
>> + (delete-file "tightbind/abfns.c")
>> + (delete-file "tightbind/lovlap.c")
>> + #t))))
>> + (build-system cmake-build-system)
>> + (native-inputs (list gfortran))
>> + (inputs (list openblas))
>> + (arguments
>> + (list
>> + #:configure-flags
>> + #~(list
>> + "-DUSE_BLAS_LAPACK=ON"
>> + (string-append "-DPARM_FILE_LOC=" #$output
>> + "/share/" #$name "-" #$version
>> "/eht_parms.dat")
>> + "-DBIND_EXE_NAME=yaehmop-bind")
>> + #:phases
>> + #~(modify-phases %standard-phases
>> + (add-after 'unpack 'chdir
>> + (lambda _
>> + (chdir "tightbind")
>> + #t))
>> + (add-after 'chdir 'patch-fortran-functions
>> + (lambda _
>> + (substitute* '("mov.c" "prototypes.h")
>> + (("lovlap\\(") "lovlap_(")
>> + (("abfns\\(") "abfns_("))
>> + #t))
>> + (add-after 'chdir 'patch-cmake
>> + (lambda _
>> + (substitute* "CMakeLists.txt"
>> + (("project\\(yaehmop C\\)") "project(yaehmop C
>> Fortran)")
>> + (("abfns.c") "fortran77/abfns.f")
>> + (("lovlap.c") "fortran77/lovlap.f")
>> + (("(set\\(PARM_FILE_LOC.*)\\)" all init)
>> + (string-append init " CACHE STRING \"\")"))
>> + (("add_library\\(yaehmop_eht" lib)
>> + (string-append lib " SHARED "))
>> + (("target_link_libraries\\(test_eht
>> \\$\\{LAPACK_LIBRARIES\\}.*"
>> + all)
>> + (string-append all
>> "\ntarget_link_libraries(yaehmop_eht "
>> + "${LAPACK_LIBRARIES})\n")))
>> + #t))
>> + (add-after 'install 'install-eht-parms
>> + (lambda _
>> + (install-file "../tightbind/eht_parms.dat"
>> + (string-append #$output "/share/"
>> + #$name "-" #$version))
>> + #t))
>> + (delete 'check)
>> + (add-after 'install-eht-parms 'check
>> + (lambda* (#:key tests? #:allow-other-keys)
>> + (when tests?
>> + (invoke "./test_eht"))
>> + #t)))))
>> + (home-page "https://github.com/greglandrum/yaehmop")
>> + (synopsis "Yet Another extended Hueckel Molecular Orbital
>> Package")
>> + (description "@code{YAeHMOP} contains a program and library for
>> performing
>> +extended Hückel calculations.")
>> + (license license:bsd-2)))
> Looking at this it seems unclear whether you are building yaehmop or
> tightbind. What's going on?
I'm building the yaehmop library (with the source code in tightbind/)
and the "bind" program (which I called yaehmop-bind) that uses the library.
Is it better to just call the package "yaehmop" (which I now did)?
The source also includes a separate visualization program "viewkel",
which does not use the library and would belong in another package in my
opinion.
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