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.
Message #173 received at 58261 <at> debbugs.gnu.org (full text, mbox):
From: Liliana Marie Prikler <liliana.prikler <at> gmail.com> To: David Elsing <david.elsing <at> posteo.net>, 58261 <at> debbugs.gnu.org Subject: Re: [PATCH v2 10/13] gnu: Add yaehmop-tightbind. Date: Sun, 09 Oct 2022 14:02:58 +0200
Am Freitag, dem 07.10.2022 um 15:21 +0000 schrieb David Elsing:
> * gnu/packages/chemistry.scm (yaehmop-tightbind): New variable.
Don't forget to update the ChangeLog.
> ---
> gnu/packages/chemistry.scm | 110
> +++++++++++++++++++++++++++++++++++++
> 1 file changed, 110 insertions(+)
>
> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
> index 1510cbab41..68d28a52c3 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)
> @@ -56,6 +57,7 @@ (define-module (gnu packages chemistry)
> #:use-module (gnu packages serialization)
> #:use-module (gnu packages sphinx)
> #:use-module (gnu packages stb)
> + #:use-module (gnu packages tex)
> #:use-module (gnu packages web)
> #:use-module (gnu packages xml)
> #:use-module (guix build-system cmake)
> @@ -818,3 +820,111 @@ (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
> + (package
> + (name "yaehmop")
> + (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
> + ;; Separate program
> + (delete-file-recursively "viewkel")
> + ;; Remove example output (some are corrupted)
> + (for-each delete-file (find-files "examples"
> "\\.Z$"))
> + ;; Documentation outputs
> + (for-each delete-file (find-files "docs"
> "\\.(ps|pdf)$"))
> + ;; These are transpiled from Fortran to C, but we
> build the
> + ;; Fortran code instead
> + (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")))))
> + (build-system cmake-build-system)
> + (arguments
> + (list
> + #:configure-flags
> + #~(list
> + "-DUSE_BLAS_LAPACK=ON"
> + (string-append "-DPARM_FILE_LOC=" #$output
> + "/share/" #$name "-" #$version
> "/eht_parms.dat")
> + "-DBIND_EXE_NAME=yaehmop-bind")
> + #:phases
> + #~(modify-phases %standard-phases
> + (add-after 'unpack 'chdir
> + (lambda _
> + (chdir "tightbind")))
> + (add-after 'chdir 'patch-fortran-functions
> + (lambda _
> + (substitute* '("mov.c" "prototypes.h")
> + (("lovlap\\(") "lovlap_(")
> + (("abfns\\(") "abfns_("))))
> + (add-after 'chdir 'patch-cmake
> + (lambda _
> + (substitute* "CMakeLists.txt"
> + (("project\\(yaehmop C\\)") "project(yaehmop C
> Fortran)")
> + (("abfns.c") "fortran77/abfns.f")
> + (("lovlap.c") "fortran77/lovlap.f")
> + (("(set\\(PARM_FILE_LOC.*)\\)" all init)
> + (string-append init " CACHE STRING \"\")"))
> + (("add_library\\(yaehmop_eht" lib)
> + (string-append lib " SHARED "))
> + (("target_link_libraries\\(test_eht
> \\$\\{LAPACK_LIBRARIES\\}.*"
> + all)
> + (string-append all
> "\ntarget_link_libraries(yaehmop_eht "
> + "${LAPACK_LIBRARIES})\n")))))
> + (add-after 'build 'fix-latex
> + (lambda _
> + (chdir "../docs")
> + (substitute* "bind_manual.tex"
> + (("\\\\usepackage\\{bindpage\\}")
> + (string-append
> +
> "\\usepackage[left=2cm,right=2cm,top=4cm,bottom=2cm]"
> + "{geometry}")))
> + (substitute* "Zmat_appendix.tex"
> + (("file=dihedral\\.eps")
> + "file=figs/dihedral.eps"))))
> + (add-after 'fix-latex 'build-doc
> + (lambda _
> + ;; TODO: not reproducible
> + (setenv "FORCE_SOURCE_DATE" "1")
> + ;; Needs to run twice to compile completely
> + (invoke "pdflatex" "bind_manual.tex")
> + (invoke "pdflatex" "bind_manual.tex")
> + (chdir "../build")))
Note that we have rubber to automate building PDFs. Also prefer "with-
directory-excursion" over chdir where possible.
> + (add-after 'install 'install-eht-parms
> + (lambda _
> + (install-file "../tightbind/eht_parms.dat"
> + (string-append #$output "/share/"
> + #$name "-" #$version))))
> + (add-after 'install-eht-parms 'install-doc
> + (lambda _
> + (install-file "../docs/bind_manual.pdf"
> + (string-append #$output "/share/doc/"
> + #$name "-" #$version))))
> + (delete 'check)
> + (add-after 'install-doc 'check
> + (lambda* (#:key tests? #:allow-other-keys)
> + (when tests?
> + (invoke "./test_eht")))))))
> + (native-inputs
> + `(("gfortran" ,gfortran)
> + ("texlive" ,(texlive-updmap.cfg (list texlive-fonts-ec
> + texlive-latex-graphics
> + texlive-latex-
> geometry)))))
I think you can do without labels here (see my comment regarding
rubber).
> + (inputs (list openblas))
> + (home-page "https://github.com/greglandrum/yaehmop")
> + (synopsis "Yet Another extended Hueckel Molecular Orbital
> Package")
You can use this as an @acronym in the description. For the synopsis,
I'd use something else, e.g. "Perform Hückel calculations".
> + (description "@code{YAeHMOP} contains a program and library for
> performing
> +extended Hückel calculations.")
I recommend adding "and analyzing and visualizing the results." (see
plug_it.tex)
> + (license license:bsd-2)))
Cheers
GNU bug tracking system
Copyright (C) 1999 Darren O. Benham,
1997,2003 nCipher Corporation Ltd,
1994-97 Ian Jackson.