diff mbox series

[bug#58261,10/11] gnu: Add yaehmop-tightbind.

Message ID 616241998ff984b1e7c074c0aa89e7187b3cfc72.1664725832.git.david.elsing@posteo.net
State New
Headers
Series Add rdkit. |

Commit Message

David Elsing Oct. 3, 2022, 12:19 a.m. UTC 
* gnu/packages/chemistry.scm (yaehmop-tightbind): New variable.
---
 gnu/packages/chemistry.scm | 82 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 82 insertions(+)

Comments

Liliana Marie Prikler Oct. 4, 2022, 7:54 a.m. UTC | #1 
Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
> * gnu/packages/chemistry.scm (yaehmop-tightbind): New variable.
> ---
>  gnu/packages/chemistry.scm | 82
> ++++++++++++++++++++++++++++++++++++++
>  1 file changed, 82 insertions(+)
> 
> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
> index cc26aa329a..a39deff4bf 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)
> @@ -817,3 +818,84 @@ (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-tightbind
> +  (package
> +    (name "yaehmop-tightbind")
> +    (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
> +                  (delete-file-recursively "docs")
This one looks suspicious.
> +                  (delete-file-recursively "examples")
As does this.
What gives?
> +                  (delete-file-recursively "viewkel")
> +                  (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")
> +                  #t))))
> +    (build-system cmake-build-system)
> +    (native-inputs (list gfortran))
> +    (inputs (list openblas))
> +    (arguments
> +     (list
> +      #:configure-flags
> +      #~(list
> +         "-DUSE_BLAS_LAPACK=ON"
> +         (string-append "-DPARM_FILE_LOC=" #$output
> +                        "/share/" #$name "-" #$version
> "/eht_parms.dat")
> +         "-DBIND_EXE_NAME=yaehmop-bind")
> +      #:phases
> +      #~(modify-phases %standard-phases
> +          (add-after 'unpack 'chdir
> +            (lambda _
> +              (chdir "tightbind")
> +              #t))
> +          (add-after 'chdir 'patch-fortran-functions
> +            (lambda _
> +              (substitute* '("mov.c" "prototypes.h")
> +                (("lovlap\\(") "lovlap_(")
> +                (("abfns\\(") "abfns_("))
> +              #t))
> +          (add-after 'chdir 'patch-cmake
> +            (lambda _
> +              (substitute* "CMakeLists.txt"
> +                (("project\\(yaehmop C\\)") "project(yaehmop C
> Fortran)")
> +                (("abfns.c") "fortran77/abfns.f")
> +                (("lovlap.c") "fortran77/lovlap.f")
> +                (("(set\\(PARM_FILE_LOC.*)\\)" all init)
> +                 (string-append init " CACHE STRING \"\")"))
> +                (("add_library\\(yaehmop_eht" lib)
> +                 (string-append lib " SHARED "))
> +                (("target_link_libraries\\(test_eht
> \\$\\{LAPACK_LIBRARIES\\}.*"
> +                  all)
> +                 (string-append all
> "\ntarget_link_libraries(yaehmop_eht "
> +                                "${LAPACK_LIBRARIES})\n")))
> +              #t))
> +          (add-after 'install 'install-eht-parms
> +            (lambda _
> +              (install-file "../tightbind/eht_parms.dat"
> +                            (string-append #$output "/share/"
> +                                           #$name "-" #$version))
> +              #t))
> +          (delete 'check)
> +          (add-after 'install-eht-parms 'check
> +            (lambda* (#:key tests? #:allow-other-keys)
> +              (when tests?
> +                (invoke "./test_eht"))
> +              #t)))))
> +    (home-page "https://github.com/greglandrum/yaehmop")
> +    (synopsis "Yet Another extended Hueckel Molecular Orbital
> Package")
> +    (description "@code{YAeHMOP} contains a program and library for
> performing
> +extended Hückel calculations.")
> +    (license license:bsd-2)))
Looking at this it seems unclear whether you are building yaehmop or
tightbind.  What's going on?
David Elsing Oct. 7, 2022, 3:12 p.m. UTC | #2 
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 (yaehmop-tightbind): New variable.
>> ---
>>  gnu/packages/chemistry.scm | 82
>> ++++++++++++++++++++++++++++++++++++++
>>  1 file changed, 82 insertions(+)
>> 
>> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
>> index cc26aa329a..a39deff4bf 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)
>> @@ -817,3 +818,84 @@ (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-tightbind
>> +  (package
>> +    (name "yaehmop-tightbind")
>> +    (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
>> +                  (delete-file-recursively "docs")
> This one looks suspicious.
>> +                  (delete-file-recursively "examples")
> As does this.
> What gives?
I did not want to check the documentation in detail and the examples
contain some corrupted "compress" archives of program outputs. :)
But now I build the documentation instead and remove the archives.
There still is one problem: Even though I set FORCE_SOURCE_DATE=1, the
output of pdflatex is still not reproducible. Do you have an idea why
that could be? There are only 3 bytes different in the pdf.
Alternatively, I could just not build the documentation as it is
independent of the build scripts anyway.
>> +                  (delete-file-recursively "viewkel")
>> +                  (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")
>> +                  #t))))
>> +    (build-system cmake-build-system)
>> +    (native-inputs (list gfortran))
>> +    (inputs (list openblas))
>> +    (arguments
>> +     (list
>> +      #:configure-flags
>> +      #~(list
>> +         "-DUSE_BLAS_LAPACK=ON"
>> +         (string-append "-DPARM_FILE_LOC=" #$output
>> +                        "/share/" #$name "-" #$version
>> "/eht_parms.dat")
>> +         "-DBIND_EXE_NAME=yaehmop-bind")
>> +      #:phases
>> +      #~(modify-phases %standard-phases
>> +          (add-after 'unpack 'chdir
>> +            (lambda _
>> +              (chdir "tightbind")
>> +              #t))
>> +          (add-after 'chdir 'patch-fortran-functions
>> +            (lambda _
>> +              (substitute* '("mov.c" "prototypes.h")
>> +                (("lovlap\\(") "lovlap_(")
>> +                (("abfns\\(") "abfns_("))
>> +              #t))
>> +          (add-after 'chdir 'patch-cmake
>> +            (lambda _
>> +              (substitute* "CMakeLists.txt"
>> +                (("project\\(yaehmop C\\)") "project(yaehmop C
>> Fortran)")
>> +                (("abfns.c") "fortran77/abfns.f")
>> +                (("lovlap.c") "fortran77/lovlap.f")
>> +                (("(set\\(PARM_FILE_LOC.*)\\)" all init)
>> +                 (string-append init " CACHE STRING \"\")"))
>> +                (("add_library\\(yaehmop_eht" lib)
>> +                 (string-append lib " SHARED "))
>> +                (("target_link_libraries\\(test_eht
>> \\$\\{LAPACK_LIBRARIES\\}.*"
>> +                  all)
>> +                 (string-append all
>> "\ntarget_link_libraries(yaehmop_eht "
>> +                                "${LAPACK_LIBRARIES})\n")))
>> +              #t))
>> +          (add-after 'install 'install-eht-parms
>> +            (lambda _
>> +              (install-file "../tightbind/eht_parms.dat"
>> +                            (string-append #$output "/share/"
>> +                                           #$name "-" #$version))
>> +              #t))
>> +          (delete 'check)
>> +          (add-after 'install-eht-parms 'check
>> +            (lambda* (#:key tests? #:allow-other-keys)
>> +              (when tests?
>> +                (invoke "./test_eht"))
>> +              #t)))))
>> +    (home-page "https://github.com/greglandrum/yaehmop")
>> +    (synopsis "Yet Another extended Hueckel Molecular Orbital
>> Package")
>> +    (description "@code{YAeHMOP} contains a program and library for
>> performing
>> +extended Hückel calculations.")
>> +    (license license:bsd-2)))
> Looking at this it seems unclear whether you are building yaehmop or
> tightbind.  What's going on?
I'm building the yaehmop library (with the source code in tightbind/)
and the "bind" program (which I called yaehmop-bind) that uses the library.
Is it better to just call the package "yaehmop" (which I now did)?
The source also includes a separate visualization program "viewkel",
which does not use the library and would belong in another package in my
opinion.
Liliana Marie Prikler Oct. 7, 2022, 3:25 p.m. UTC | #3 
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 (yaehmop-tightbind): New variable.
> > > ---
> > >  gnu/packages/chemistry.scm | 82
> > > ++++++++++++++++++++++++++++++++++++++
> > >  1 file changed, 82 insertions(+)
> > > 
> > > diff --git a/gnu/packages/chemistry.scm
> > > b/gnu/packages/chemistry.scm
> > > index cc26aa329a..a39deff4bf 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)
> > > @@ -817,3 +818,84 @@ (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-tightbind
> > > +  (package
> > > +    (name "yaehmop-tightbind")
> > > +    (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
> > > +                  (delete-file-recursively "docs")
> > This one looks suspicious.
> > > +                  (delete-file-recursively "examples")
> > As does this.
> > What gives?
> I did not want to check the documentation in detail and the examples
> contain some corrupted "compress" archives of program outputs. :)
> But now I build the documentation instead and remove the archives.
> There still is one problem: Even though I set FORCE_SOURCE_DATE=1,
> the
> output of pdflatex is still not reproducible. Do you have an idea why
> that could be? There are only 3 bytes different in the pdf.
> Alternatively, I could just not build the documentation as it is
> independent of the build scripts anyway.
pdflatex has troubles with reproducible builds, but I can't quite
recall what option makes it not so, but rest assured those are likely 3
very well known bytes.

> > > +                  (delete-file-recursively "viewkel")
> > > +                  (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")
> > > +                  #t))))
> > > +    (build-system cmake-build-system)
> > > +    (native-inputs (list gfortran))
> > > +    (inputs (list openblas))
> > > +    (arguments
> > > +     (list
> > > +      #:configure-flags
> > > +      #~(list
> > > +         "-DUSE_BLAS_LAPACK=ON"
> > > +         (string-append "-DPARM_FILE_LOC=" #$output
> > > +                        "/share/" #$name "-" #$version
> > > "/eht_parms.dat")
> > > +         "-DBIND_EXE_NAME=yaehmop-bind")
> > > +      #:phases
> > > +      #~(modify-phases %standard-phases
> > > +          (add-after 'unpack 'chdir
> > > +            (lambda _
> > > +              (chdir "tightbind")
> > > +              #t))
> > > +          (add-after 'chdir 'patch-fortran-functions
> > > +            (lambda _
> > > +              (substitute* '("mov.c" "prototypes.h")
> > > +                (("lovlap\\(") "lovlap_(")
> > > +                (("abfns\\(") "abfns_("))
> > > +              #t))
> > > +          (add-after 'chdir 'patch-cmake
> > > +            (lambda _
> > > +              (substitute* "CMakeLists.txt"
> > > +                (("project\\(yaehmop C\\)") "project(yaehmop C
> > > Fortran)")
> > > +                (("abfns.c") "fortran77/abfns.f")
> > > +                (("lovlap.c") "fortran77/lovlap.f")
> > > +                (("(set\\(PARM_FILE_LOC.*)\\)" all init)
> > > +                 (string-append init " CACHE STRING \"\")"))
> > > +                (("add_library\\(yaehmop_eht" lib)
> > > +                 (string-append lib " SHARED "))
> > > +                (("target_link_libraries\\(test_eht
> > > \\$\\{LAPACK_LIBRARIES\\}.*"
> > > +                  all)
> > > +                 (string-append all
> > > "\ntarget_link_libraries(yaehmop_eht "
> > > +                                "${LAPACK_LIBRARIES})\n")))
> > > +              #t))
> > > +          (add-after 'install 'install-eht-parms
> > > +            (lambda _
> > > +              (install-file "../tightbind/eht_parms.dat"
> > > +                            (string-append #$output "/share/"
> > > +                                           #$name "-"
> > > #$version))
> > > +              #t))
> > > +          (delete 'check)
> > > +          (add-after 'install-eht-parms 'check
> > > +            (lambda* (#:key tests? #:allow-other-keys)
> > > +              (when tests?
> > > +                (invoke "./test_eht"))
> > > +              #t)))))
> > > +    (home-page "https://github.com/greglandrum/yaehmop")
> > > +    (synopsis "Yet Another extended Hueckel Molecular Orbital
> > > Package")
> > > +    (description "@code{YAeHMOP} contains a program and library
> > > for
> > > performing
> > > +extended Hückel calculations.")
> > > +    (license license:bsd-2)))
> > Looking at this it seems unclear whether you are building yaehmop
> > or
> > tightbind.  What's going on?
> I'm building the yaehmop library (with the source code in tightbind/)
> and the "bind" program (which I called yaehmop-bind) that uses the
> library.
> Is it better to just call the package "yaehmop" (which I now did)?
> The source also includes a separate visualization program "viewkel",
> which does not use the library and would belong in another package in
> my opinion.
Taking a cursory glance at the CMakeLists, calling it yaehmop is indeed
the correct thing.  I have no idea what viewkel is supposed to do tbh.
diff mbox series

Patch

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index cc26aa329a..a39deff4bf 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)
@@ -817,3 +818,84 @@  (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-tightbind
+  (package
+    (name "yaehmop-tightbind")
+    (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
+                  (delete-file-recursively "docs")
+                  (delete-file-recursively "examples")
+                  (delete-file-recursively "viewkel")
+                  (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")
+                  #t))))
+    (build-system cmake-build-system)
+    (native-inputs (list gfortran))
+    (inputs (list openblas))
+    (arguments
+     (list
+      #:configure-flags
+      #~(list
+         "-DUSE_BLAS_LAPACK=ON"
+         (string-append "-DPARM_FILE_LOC=" #$output
+                        "/share/" #$name "-" #$version "/eht_parms.dat")
+         "-DBIND_EXE_NAME=yaehmop-bind")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'chdir
+            (lambda _
+              (chdir "tightbind")
+              #t))
+          (add-after 'chdir 'patch-fortran-functions
+            (lambda _
+              (substitute* '("mov.c" "prototypes.h")
+                (("lovlap\\(") "lovlap_(")
+                (("abfns\\(") "abfns_("))
+              #t))
+          (add-after 'chdir 'patch-cmake
+            (lambda _
+              (substitute* "CMakeLists.txt"
+                (("project\\(yaehmop C\\)") "project(yaehmop C Fortran)")
+                (("abfns.c") "fortran77/abfns.f")
+                (("lovlap.c") "fortran77/lovlap.f")
+                (("(set\\(PARM_FILE_LOC.*)\\)" all init)
+                 (string-append init " CACHE STRING \"\")"))
+                (("add_library\\(yaehmop_eht" lib)
+                 (string-append lib " SHARED "))
+                (("target_link_libraries\\(test_eht \\$\\{LAPACK_LIBRARIES\\}.*"
+                  all)
+                 (string-append all "\ntarget_link_libraries(yaehmop_eht "
+                                "${LAPACK_LIBRARIES})\n")))
+              #t))
+          (add-after 'install 'install-eht-parms
+            (lambda _
+              (install-file "../tightbind/eht_parms.dat"
+                            (string-append #$output "/share/"
+                                           #$name "-" #$version))
+              #t))
+          (delete 'check)
+          (add-after 'install-eht-parms 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (invoke "./test_eht"))
+              #t)))))
+    (home-page "https://github.com/greglandrum/yaehmop")
+    (synopsis "Yet Another extended Hueckel Molecular Orbital Package")
+    (description "@code{YAeHMOP} contains a program and library for performing
+extended Hückel calculations.")
+    (license license:bsd-2)))