[bug#58261] [PATCH v2 10/13] gnu: Add yaehmop-tightbind.

[Liliana Marie Prikler <liliana.prikler@gmail.com>]

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