From: David Elsing <david.elsing@posteo.net>
To: Liliana Marie Prikler <liliana.prikler@gmail.com>, 58261@debbugs.gnu.org
Subject: [bug#58261] [PATCH v2 10/13] gnu: Add yaehmop-tightbind.
Date: Thu, 13 Oct 2022 21:00:55 +0000 [thread overview]
Message-ID: <86zgdza16g.fsf@posteo.net> (raw)
In-Reply-To: <c275f851ee13b2e14c44263ac63eaca8b3dc7769.camel@gmail.com>
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?
>> + (license license:bsd-2)))
>
> Cheers
next prev parent reply other threads:[~2022-10-13 21:02 UTC|newest]
Thread overview: 87+ messages / expand[flat|nested] mbox.gz Atom feed top
2022-10-02 22:55 [bug#58261] [PATCH 00/11] Add rdkit David Elsing
2022-10-03 0:19 ` [bug#58261] [PATCH 01/11] gnu: Add fast-float David Elsing
2022-10-04 6:57 ` Liliana Marie Prikler via Guix-patches via
2022-10-07 15:08 ` David Elsing
2022-10-03 0:19 ` [bug#58261] [PATCH 02/11] gnu: Add pocketfft David Elsing
2022-10-04 7:09 ` Liliana Marie Prikler
2022-10-07 15:10 ` David Elsing
2022-10-03 0:19 ` [bug#58261] [PATCH 03/11] gnu: Add sajson David Elsing
2022-10-04 7:22 ` Liliana Marie Prikler
2022-10-07 15:10 ` David Elsing
2022-10-03 0:19 ` [bug#58261] [PATCH 04/11] gnu: Add tinydir David Elsing
2022-10-04 7:27 ` Liliana Marie Prikler
2022-10-07 15:11 ` David Elsing
2022-10-07 15:13 ` Liliana Marie Prikler
2022-10-03 0:19 ` [bug#58261] [PATCH 05/11] gnu: Add optionparser David Elsing
2022-10-04 7:42 ` Liliana Marie Prikler
2022-10-07 15:11 ` David Elsing
2022-10-03 0:19 ` [bug#58261] [PATCH 06/11] gnu: Add gemmi David Elsing
2022-10-04 7:49 ` Liliana Marie Prikler
2022-10-07 15:11 ` David Elsing
2022-10-07 15:17 ` Liliana Marie Prikler
2022-10-03 0:19 ` [bug#58261] [PATCH 07/11] gnu: Add freesasa David Elsing
2022-10-04 8:02 ` Liliana Marie Prikler
2022-10-07 15:12 ` David Elsing
2022-10-07 15:19 ` Liliana Marie Prikler
2022-10-03 0:19 ` [bug#58261] [PATCH 08/11] gnu: Add maeparser David Elsing
2022-10-03 0:19 ` [bug#58261] [PATCH 09/11] gnu: Add coordgenlibs David Elsing
2022-10-03 0:19 ` [bug#58261] [PATCH 10/11] gnu: Add yaehmop-tightbind David Elsing
2022-10-04 7:54 ` Liliana Marie Prikler
2022-10-07 15:12 ` David Elsing
2022-10-07 15:25 ` Liliana Marie Prikler
2022-10-03 0:19 ` [bug#58261] [PATCH 11/11] gnu: Add rdkit David Elsing
2022-10-04 8:13 ` Liliana Marie Prikler
2022-10-07 15:12 ` David Elsing
2022-10-07 15:29 ` Liliana Marie Prikler
2022-10-07 15:21 ` [bug#58261] [PATCH v2 00/13] Add rdkit v2 David Elsing
2022-10-09 10:02 ` Liliana Marie Prikler
2022-10-13 20:58 ` David Elsing
2022-10-13 21:04 ` [bug#58261] [PATCH v3 00/15] Add rdkit v3 David Elsing
2022-10-15 14:37 ` bug#58261: " Liliana Marie Prikler
2022-10-17 9:55 ` [bug#58261] " David Elsing
2022-10-13 21:04 ` [bug#58261] [PATCH v3 01/15] gnu: Add fast-float David Elsing
2022-10-13 21:04 ` [bug#58261] [PATCH v3 02/15] gnu: Add pocketfft-cpp David Elsing
2022-10-13 21:04 ` [bug#58261] [PATCH v3 03/15] gnu: Add sajson David Elsing
2022-10-13 21:04 ` [bug#58261] [PATCH v3 04/15] gnu: Add cbehave David Elsing
2022-10-13 21:04 ` [bug#58261] [PATCH v3 05/15] gnu: Add tinydir David Elsing
2022-10-13 21:04 ` [bug#58261] [PATCH v3 06/15] gnu: Add optionparser David Elsing
2022-10-13 21:04 ` [bug#58261] [PATCH v3 07/15] gnu: Add sajson-for-gemmi David Elsing
2022-10-13 21:04 ` [bug#58261] [PATCH v3 08/15] gnu: Add gemmi David Elsing
2022-10-13 21:04 ` [bug#58261] [PATCH v3 09/15] gnu: Add freesasa David Elsing
2022-10-13 21:04 ` [bug#58261] [PATCH v3 10/15] gnu: Add maeparser David Elsing
2022-10-13 21:04 ` [bug#58261] [PATCH v3 11/15] gnu: Add coordgenlibs David Elsing
2022-10-13 21:04 ` [bug#58261] [PATCH v3 12/15] gnu: Add yaehmop David Elsing
2022-10-13 21:04 ` [bug#58261] [PATCH v3 13/15] gnu: Add avalon-toolkit David Elsing
2022-10-13 21:04 ` [bug#58261] [PATCH v3 14/15] gnu: Add ringdecomposerlib David Elsing
2022-10-13 21:04 ` [bug#58261] [PATCH v3 15/15] gnu: Add rdkit David Elsing
2022-10-07 15:21 ` [bug#58261] [PATCH v2 01/13] gnu: Add fast-float David Elsing
2022-10-09 10:04 ` Liliana Marie Prikler
2022-10-07 15:21 ` [bug#58261] [PATCH v2 02/13] gnu: Add pocketfft David Elsing
2022-10-09 11:42 ` Liliana Marie Prikler
2022-10-07 15:21 ` [bug#58261] [PATCH v2 03/13] gnu: Add sajson David Elsing
2022-10-09 11:46 ` Liliana Marie Prikler
2022-10-13 20:59 ` David Elsing
2022-10-14 21:30 ` Liliana Marie Prikler
2022-10-07 15:21 ` [bug#58261] [PATCH v2 04/13] gnu: Add tinydir David Elsing
2022-10-09 11:48 ` Liliana Marie Prikler
2022-10-07 15:21 ` [bug#58261] [PATCH v2 05/13] gnu: Add optionparser David Elsing
2022-10-07 15:21 ` [bug#58261] [PATCH v2 06/13] gnu: Add gemmi David Elsing
2022-10-09 11:54 ` Liliana Marie Prikler
2022-10-13 21:00 ` David Elsing
2022-10-14 21:32 ` Liliana Marie Prikler
2022-10-07 15:21 ` [bug#58261] [PATCH v2 07/13] gnu: Add freesasa David Elsing
2022-10-07 15:21 ` [bug#58261] [PATCH v2 08/13] gnu: Add maeparser David Elsing
2022-10-07 15:21 ` [bug#58261] [PATCH v2 09/13] gnu: Add coordgenlibs David Elsing
2022-10-09 11:56 ` Liliana Marie Prikler
2022-10-13 21:00 ` David Elsing
2022-10-07 15:21 ` [bug#58261] [PATCH v2 10/13] gnu: Add yaehmop-tightbind David Elsing
2022-10-09 12:02 ` Liliana Marie Prikler
2022-10-13 21:00 ` David Elsing [this message]
2022-10-14 21:33 ` Liliana Marie Prikler
2022-10-07 15:21 ` [bug#58261] [PATCH v2 11/13] gnu: Add avalontoolkit David Elsing
2022-10-09 12:06 ` Liliana Marie Prikler
2022-10-13 21:01 ` David Elsing
2022-10-07 15:22 ` [bug#58261] [PATCH v2 12/13] gnu: Add ringdecomposerlib David Elsing
2022-10-07 15:22 ` [bug#58261] [PATCH v2 13/13] gnu: Add rdkit David Elsing
2022-10-09 12:12 ` Liliana Marie Prikler
2022-10-13 21:01 ` David Elsing
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