Subject: Re: [PATCH v2 10/13] gnu: Add yaehmop-tightbind.

From: David Elsing <[email-masked]>
Date: Thu, 13 Oct 2022 21:00:55 +0000

Liliana Marie Prikler <[email-masked]> 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?
>> +    (license license:bsd-2)))
>
> Cheers