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

[Liliana Marie Prikler]

Am Donnerstag, dem 13.10.2022 um 21:00 +0000 schrieb David Elsing:
> Liliana Marie Prikler <liliana.prikler@gmail.com> writes:
> 
> > 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.
> Ah thanks. :)
> > > ---
> > >  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 "
> > > +                                "${LAPACK_LIBRARIES})\n")))))
> > > +          (add-after 'build 'fix-latex
> > > +            (lambda _
> > > +              (chdir "../docs")
> > > +              (substitute* "bind_manual.tex"
> > > +                (("\\\\usepackage\\{bindpage\\}")
> > > +                 (string-append
> > > +                 
> > > "\\usepackage[left=2cm,right=2cm,top=4cm,bottom=2cm]"
> > > +                  "{geometry}")))
> > > +              (substitute* "Zmat_appendix.tex"
> > > +                (("file=dihedral\\.eps")
> > > +                 "file=figs/dihedral.eps"))))
> > > +          (add-after 'fix-latex 'build-doc
> > > +            (lambda _
> > > +              ;; TODO: not reproducible
> > > +              (setenv "FORCE_SOURCE_DATE" "1")
> > > +              ;; Needs to run twice to compile completely
> > > +              (invoke "pdflatex" "bind_manual.tex")
> > > +              (invoke "pdflatex" "bind_manual.tex")
> > > +              (chdir "../build")))
> > Note that we have rubber to automate building PDFs.  Also prefer
> > "with-
> > directory-excursion" over chdir where possible.
> I used latexmk as it's already included in texlive-bin
> (it is also reproducible with \pdfsuppressptexinfo=-1).
> > > +          (add-after 'install 'install-eht-parms
> > > +            (lambda _
> > > +              (install-file "../tightbind/eht_parms.dat"
> > > +                            (string-append #$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)
> The visualization program is not built, so maybe without visualizing?
SGTM