| Message ID | 616241998ff984b1e7c074c0aa89e7187b3cfc72.1664725832.git.david.elsing@posteo.net |
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| Series | Add rdkit. | expand |
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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?
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.
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 --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)))