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> gmail.com>, 58261 <at> debbugs.gnu.org Subject: [bug#58261] [PATCH v2 10/13] gnu: Add yaehmop-tightbind. Date: Thu, 13 Oct 2022 21:00:55 +0000
Liliana Marie Prikler <liliana.prikler <at> 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?
>> + (license license:bsd-2)))
>
> Cheers
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