[bug#58261] [PATCH 07/11] gnu: Add freesasa.

[Liliana Marie Prikler <liliana.prikler@ist.tugraz.at>]

Am Freitag, dem 07.10.2022 um 15:12 +0000 schrieb David Elsing:
> Liliana Marie Prikler <liliana.prikler@ist.tugraz.at> writes:
> 
> > Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
> > > * gnu/packages/chemistry.scm (freesasa): New variable.
> > > ---
> > >  gnu/packages/chemistry.scm | 81
> > > ++++++++++++++++++++++++++++++++++++++
> > >  1 file changed, 81 insertions(+)
> > > 
> > > diff --git a/gnu/packages/chemistry.scm
> > > b/gnu/packages/chemistry.scm
> > > index f8fd85814f..223a27a20d 100644
> > > --- a/gnu/packages/chemistry.scm
> > > +++ b/gnu/packages/chemistry.scm
> > > @@ -34,11 +34,13 @@ (define-module (gnu packages chemistry)
> > >    #:use-module (gnu packages algebra)
> > >    #:use-module (gnu packages autotools)
> > >    #:use-module (gnu packages backup)
> > > +  #:use-module (gnu packages bison)
> > >    #:use-module (gnu packages boost)
> > >    #:use-module (gnu packages check)
> > >    #:use-module (gnu packages compression)
> > >    #:use-module (gnu packages cpp)
> > >    #:use-module (gnu packages documentation)
> > > +  #:use-module (gnu packages flex)
> > >    #:use-module (gnu packages fontutils)
> > >    #:use-module (gnu packages gl)
> > >    #:use-module (gnu packages graphviz)
> > > @@ -54,6 +56,7 @@ (define-module (gnu packages chemistry)
> > >    #:use-module (gnu packages serialization)
> > >    #:use-module (gnu packages sphinx)
> > >    #:use-module (gnu packages stb)
> > > +  #:use-module (gnu packages web)
> > >    #:use-module (gnu packages xml)
> > >    #:use-module (guix build-system cmake)
> > >    #:use-module (guix build-system copy)
> > > @@ -688,3 +691,81 @@ (define-public gemmi
> > >  @item crystallographic symmetry.
> > >  @end enumerate")
> > >      (license license:mpl2.0)))
> > > +
> > > +(define-public freesasa
> > > +  (package
> > > +    (name "freesasa")
> > > +    (version "2.1.2")
> > > +    (source (origin
> > > +              (method git-fetch)
> > > +              (uri (git-reference
> > > +                    (url
> > > "https://github.com/mittinatten/freesasa")
> > > +                    (commit version)))
> > > +              (file-name (git-file-name name version))
> > > +              (sha256
> > > +               (base32
> > > +               
> > > "07wdnahf3g355ryaiqvfxd5f4rl54wv8jwxcbn0nia89fqysbv0f"))
> > > +              (modules '((guix build utils)))
> > > +              (snippet
> > > +               '(begin
> > > +                  ;; Remove C files generated by Flex and Bison
> > > +                  (for-each delete-file
> > > +                            '("src/parser.c" "src/parser.h"
> > > +                              "src/lexer.c" "src/lexer.h"))
> > > +                  #t))))
> > > +    (build-system gnu-build-system)
> > > +    (inputs
> > > +     (list gemmi json-c libxml2))
> > > +    (native-inputs
> > > +     (list bison flex check autoconf automake pkg-config doxygen
> > > perl libtool))
> > > +    (outputs '("out" "doc"))
> > > +    (arguments
> > > +     (list
> > > +      #:configure-flags
> > > +      #~(list "--enable-check"
> > > +              "--enable-parser-generator"
> > > +              "CXXFLAGS=-std=c++17"
> > > +              "--enable-doxygen")
> > > +      #:phases
> > > +      #~(modify-phases %standard-phases
> > > +          (add-after 'unpack 'remove-libc++-linking
> > > +            (lambda _
> > > +              (substitute* "src/Makefile.am"
> > > +                (("-lc\\+\\+") ""))
> > > +              #t))
> > Why?  If it's because you're building a shared library, do this in
> > the
> > next phase.
> This is libc++ from LLVM and the linking against the standard library
> is
> automatic anyway, right?
> > > +          (add-after 'unpack 'build-shared-library
> > > +            (lambda _
> > > +              (substitute* "src/Makefile.am"
> > > +                (("lib_LIBRARIES") "lib_LTLIBRARIES")
> > > +                (("libfreesasa\\.a") "libfreesasa.la")
> > > +                (("freesasa_LDADD \\+= libfreesasa\\.la" prev)
> > > +                 (string-append prev "\nlibfreesasa_la_LIBADD"
> > > +                                " = -ljson-c
> > > ${libxml2_LIBS}\n"))
> > > +                (("_a_SOURCES") "_la_SOURCES"))
> > > +              (substitute* "configure.ac"
> > > +                (("AC_PROG_INSTALL" inst)
> > > +                 (string-append "AM_PROG_LIBTOOL\n" inst)))
> > > +              (substitute* "tests/Makefile.am"
> > > +                (("libfreesasa\\.a") "libfreesasa.la"))
> > > +              #t))
> > > +          (add-before 'build 'build-lexer-and-parser
> > > +            (lambda _
> > > +              (with-directory-excursion "src"
> > > +                (invoke "make" "lexer.h")
> > > +                (invoke "make" "parser.h"))
> > > +              #t))
> > You can do this in one make.
> > > +          (add-after 'install 'install-doc
> > > +            (lambda _
> > > +              (copy-recursively
> > > +               "doc/html"
> > > +               (string-append #$output:doc "/share/doc/" #$name
> > > "-"
> > > #$version))
> > > +              #t)))))
> > > +    (home-page "https://freesasa.github.io/")
> > > +    (synopsis "Library for calculating the solvent accessible
> > > surface area
> > > +(SASA) of molecules")
> > "Calculate the..."
> > > +    (description "FreeSASA is a command line tool and C-library
> > > for
> > > +calculating solvent accessible surface areas (SASA).  By default
> > > Lee
> > > &
> > Use @abbr.
> I get the error "warning: invalid Texinfo markup", do you have an
> idea why?
> > 
Typo'd?  @abbr{SASA, solvent accessible surface areas}