[Debichem-devel] Bug#852077: [src:libint2] What about packaging basisset definition files?

Katsuhiko Nishimra ktns.87 at gmail.com
Sat Jan 21 11:50:10 UTC 2017 

Package: src:libint2
Version: 2.3.0~beta3-2
Severity: wishlist
Tags: patch

Dear maintainer,

As you probably know, libint2 has a feature to setup basisset objects by
the basisset name like code below, using bundled basisset definition files.
 libint2::BasisSet obs("cc-pVDZ", atoms);

What do you think about packaging the basisset definition files in
libint2-data package or something like that? I'm believing basisset
definition files can be considered under public domain as they are
scientific data, but I'm not very sure that there is no copyright issue.

I'm attaching a patch for this, and for some additional issues I've
found. I hope this will help you.

By the way, thank you very much for your quick fixing #851546. But it
is still marked as open, just in case you have not noticed. 

Kind regards.
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diff -Nru libint2-2.3.0~beta3/debian/changelog libint2-2.3.0~beta3/debian/changelog
--- libint2-2.3.0~beta3/debian/changelog	2017-01-21 04:40:07.000000000 +0900
+++ libint2-2.3.0~beta3/debian/changelog	2017-01-21 15:31:07.000000000 +0900
@@ -1,3 +1,15 @@
+libint2 (2.3.0~beta3-2+basisset0) UNRELEASED; urgency=medium
+
+  * Non-maintainer upload.
+  * Install basisset definition files via libint2-data package.
+  * Install document files from the upstream.
+  * Respect DEB_BUILD_OPTIONS=parallel.
+  * Avoid using convenience copy from boost.
+  * debian/watch: Scan the upstream github repository.
+  * Fix comma separated file list in the debian/copyright file.
+
+ -- Katsuhiko Nishimra <ktns.87 at gmail.com>  Sat, 21 Jan 2017 15:31:07 +0900
+
 libint2 (2.3.0~beta3-2) unstable; urgency=medium
 
   * Upload to unstable. 
diff -Nru libint2-2.3.0~beta3/debian/control libint2-2.3.0~beta3/debian/control
--- libint2-2.3.0~beta3/debian/control	2016-10-02 06:37:03.000000000 +0900
+++ libint2-2.3.0~beta3/debian/control	2017-01-21 15:31:07.000000000 +0900
@@ -14,6 +14,7 @@
 Section: libs
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
+Recommends: libint2-data (=${binary:Version})
 Description: Computation Chemistry Integral Evaluation Library
  The LIBINT library is used to evaluate the traditional (electron repulsion)
  and certain novel two-body matrix elements (integrals) over Cartesian
@@ -34,7 +35,7 @@
 Package: libint2-dev
 Section: libdevel
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, libint2-2 (= ${binary:Version})
+Depends: ${shlibs:Depends}, ${misc:Depends}, libint2-2 (= ${binary:Version}), libboost-dev
 Description: Computation Chemistry Integral Evaluation Library (development files)
  The Libint2 library is used to evaluate the traditional (electron 
  repulsion) and certain novel two-body matrix elements (integrals) over
@@ -51,3 +52,24 @@
  doubles (CCSD) method, as well as explicitly correlated R12 methods.
  .
  This package contains the static library and header files.
+
+Package: libint2-data
+Architecture: all
+Depends: ${misc:Depends}
+Recommends: libint2-2 (= ${binary:Version})
+Description: Computation Chemistry Integral Evaluation Library (data files)
+ The Libint2 library is used to evaluate the traditional (electron 
+ repulsion) and certain novel two-body matrix elements (integrals) over
+ Cartesian Gaussian functions used in modern atomic and molecular
+ theory.  The idea of the library is to let computer write optimized
+ code for computing such integrals. There are two primary advantages to
+ this: much less human effort is required to write code for computing
+ new integrals, and code can be optimized specifically for a particular
+ computer architecture (e.g., vector processor).
+ .
+ Libint2 has been utilized to implement methods such as Hartree-Fock
+ (HF) and Kohn-Sham density functional theory (KS DFT), second-order
+ Moeller-Plesset perturbation theory (MP2), coupled cluster singles and
+ doubles (CCSD) method, as well as explicitly correlated R12 methods.
+ .
+ This package contains basis set definition files.
diff -Nru libint2-2.3.0~beta3/debian/copyright libint2-2.3.0~beta3/debian/copyright
--- libint2-2.3.0~beta3/debian/copyright	2015-09-02 21:30:13.000000000 +0900
+++ libint2-2.3.0~beta3/debian/copyright	2017-01-21 15:31:07.000000000 +0900
@@ -10,7 +10,7 @@
 Copyright: Curtis Janssen
 License: GPL-2+
 
-Files: include/util_types.h, tests/*
+Files: include/util_types.h tests/*
 Copyright: 2004-2014 Edward F. Valeev
 License: GPL-2+
 
diff -Nru libint2-2.3.0~beta3/debian/libint2-2.docs libint2-2.3.0~beta3/debian/libint2-2.docs
--- libint2-2.3.0~beta3/debian/libint2-2.docs	1970-01-01 09:00:00.000000000 +0900
+++ libint2-2.3.0~beta3/debian/libint2-2.docs	2017-01-21 15:29:11.000000000 +0900
@@ -0,0 +1,2 @@
+CITATION
+README.md
diff -Nru libint2-2.3.0~beta3/debian/libint2-data.install libint2-2.3.0~beta3/debian/libint2-data.install
--- libint2-2.3.0~beta3/debian/libint2-data.install	1970-01-01 09:00:00.000000000 +0900
+++ libint2-2.3.0~beta3/debian/libint2-data.install	2017-01-21 15:29:11.000000000 +0900
@@ -0,0 +1 @@
+usr/share/libint/*/basis/*.g94
diff -Nru libint2-2.3.0~beta3/debian/libint2-data.lintian-overrides libint2-2.3.0~beta3/debian/libint2-data.lintian-overrides
--- libint2-2.3.0~beta3/debian/libint2-data.lintian-overrides	1970-01-01 09:00:00.000000000 +0900
+++ libint2-2.3.0~beta3/debian/libint2-data.lintian-overrides	2017-01-21 15:31:07.000000000 +0900
@@ -0,0 +1,2 @@
+libint2-data: file-name-contains-wildcard-character usr/share/libint/*/basis/*g*.g94
+libint2-data: file-name-contains-wildcard-character usr/share/libint/*/basis/*G*.g94
diff -Nru libint2-2.3.0~beta3/debian/libint2-dev.links libint2-2.3.0~beta3/debian/libint2-dev.links
--- libint2-2.3.0~beta3/debian/libint2-dev.links	1970-01-01 09:00:00.000000000 +0900
+++ libint2-2.3.0~beta3/debian/libint2-dev.links	2017-01-21 15:31:07.000000000 +0900
@@ -0,0 +1,2 @@
+usr/share/doc/libint2-2/CITATION usr/share/doc/libint2-dev/CITATION
+usr/share/doc/libint2-2/README.md usr/share/doc/libint2-dev/README.md
diff -Nru libint2-2.3.0~beta3/debian/patches/no_convenience_copy.patch libint2-2.3.0~beta3/debian/patches/no_convenience_copy.patch
--- libint2-2.3.0~beta3/debian/patches/no_convenience_copy.patch	1970-01-01 09:00:00.000000000 +0900
+++ libint2-2.3.0~beta3/debian/patches/no_convenience_copy.patch	2017-01-21 15:29:11.000000000 +0900
@@ -0,0 +1,75 @@
+--- a/export/MakeRules.export
++++ b/export/MakeRules.export
+@@ -16,7 +16,6 @@
+ 	-$(INSTALL) $(INSTALLLIBOPT) $(SRCTOPDIR)/include/libint2/chemistry/*.h $(DESTDIR)$(includedir)/$(NAME)$(VERSION)/chemistry
+ 	$(INSTALL) $(INSTALLDIROPT) $(DESTDIR)$(includedir)/$(NAME)$(VERSION)/util
+ 	-$(INSTALL) $(INSTALLLIBOPT) $(SRCTOPDIR)/include/libint2/util/*.h $(DESTDIR)$(includedir)/$(NAME)$(VERSION)/util
+-	gunzip -c $(SRCTOPDIR)/external/boost.tar.gz | tar -xf - -C $(DESTDIR)$(includedir)/$(NAME)$(VERSION)
+ 
+ install_pkgconfig::
+ 	$(INSTALL) $(INSTALLDIROPT) $(DESTDIR)$(pkgconfigdir)
+--- a/export/Makefile
++++ b/export/Makefile
+@@ -94,6 +94,5 @@
+ 	-$(INSTALL) $(INSTALLLIBOPT) $(SRCTOPDIR)/doc/Libint_Logo3_alt.eps $(TOPDIR)/$(EXPORTDIR)/doc/Libint_Logo3_alt.eps
+ 	-$(INSTALL) $(INSTALLLIBOPT) $(SRCDIR)/Makefile.doc.export $(TOPDIR)/$(EXPORTDIR)/doc/Makefile.in
+ 	$(INSTALL) $(INSTALLDIROPT) $(TOPDIR)/$(EXPORTDIR)/external
+-	-$(INSTALL) $(INSTALLLIBOPT) $(SRCTOPDIR)/external/boost.tar.gz $(TOPDIR)/$(EXPORTDIR)/external/boost.tar.gz
+ 	$(TOPOBJDIR)/config.status --config > $(TOPDIR)/$(EXPORTDIR)/compiler.config
+ 
+--- a/export/Makefile.tests.export
++++ b/export/Makefile.tests.export
+@@ -46,14 +46,6 @@
+ $(TEST3): $(TEST3).o
+ 	$(LTLINK) $(CXX) $(LDFLAGS) $(COMPUTE_LIB) $(SYSLIBS) -lpthread -o $@ $^
+ 
+-.PHONY: unpack_boost
+-
+-$(TEST2).o :: unpack_boost
+-$(TEST3).o :: unpack_boost
+-
+-unpack_boost::
+-	gunzip -c $(SRCDIR)/external/boost.tar.gz | tar -xf - -C $(TOPDIR)/include/libint2
+-
+ clean:: targetclean
+ 	-rm -f */*.o */*.d
+ 
+--- a/src/lib/MakeRules.in
++++ b/src/lib/MakeRules.in
+@@ -32,7 +32,6 @@
+ 	-$(INSTALL) $(INSTALLLIBOPT) $(SRCTOPDIR)/include/$(NAME)$(VERSION)/chemistry/*.h $(DESTDIR)$(includedir)/$(NAME)$(VERSION)/chemistry
+ 	-$(INSTALL) $(INSTALLLIBOPT) $(SRCTOPDIR)/include/$(NAME)$(VERSION)/util/*.h $(DESTDIR)$(includedir)/$(NAME)$(VERSION)/util
+ 	-$(INSTALL) $(INSTALLLIBOPT) $(SRCDIR)/*.h $(DESTDIR)$(includedir)/$(NAME)$(VERSION)
+-	gunzip -c $(SRCTOPDIR)/external/boost.tar.gz | tar -xf - -C $(DESTDIR)$(includedir)/$(NAME)$(VERSION)
+ 
+ install_target:: $(TOPDIR)/lib/$(TARGET)
+ 	$(INSTALL) $(INSTALLDIROPT) $(DESTDIR)$(libdir)
+--- a/tests/hartree-fock/Makefile
++++ b/tests/hartree-fock/Makefile
+@@ -66,24 +66,20 @@
+ 	-rm -rf $(TEST1) $(TEST2) *.o *.d
+ 
+ distclean:: realclean
+-	-rm -rf $(TOPDIR)/include/libint2/boost
+ 
+ realclean:: clean
+ 
+ targetclean:: clean
+ 
+-$(TOPDIR)/include/libint2/boost/preprocessor.hpp: $(SRCDIR)/$(TOPDIR)/external/boost.tar.gz
+-	gunzip -c $(SRCDIR)/$(TOPDIR)/external/boost.tar.gz | tar -xf - -C $(TOPDIR)/include/libint2
+-
+ depend:: $(CXXTEST1DEP) $(CXXTEST2DEP)
+ 
+ ifneq ($(CXXDEPENDSUF),none)
+-%.d:: %.cc $(TOPDIR)/include/libint2/boost/preprocessor.hpp
++%.d:: %.cc 
+ 	$(CXXDEPEND) $(CXXDEPENDFLAGS) -c $(CPPFLAGS) $(CXXFLAGS) $< > /dev/null
+ 	sed 's/^$*.o/$*.$(OBJSUF) $*.d/g' < $(*F).$(CXXDEPENDSUF) > $(@F)
+ 	/bin/rm -f $(*F).$(CXXDEPENDSUF)
+ else
+-%.d:: %.cc $(TOPDIR)/include/libint2/boost/preprocessor.hpp
++%.d:: %.cc
+ 	$(CXXDEPEND) $(CXXDEPENDFLAGS) -c $(CPPFLAGS) $(CXXFLAGS) $< | sed 's/^$*.o/$*.$(OBJSUF) $*.d/g' > $(@F)
+ endif
+ 
diff -Nru libint2-2.3.0~beta3/debian/patches/series libint2-2.3.0~beta3/debian/patches/series
--- libint2-2.3.0~beta3/debian/patches/series	2017-01-20 03:18:16.000000000 +0900
+++ libint2-2.3.0~beta3/debian/patches/series	2017-01-21 15:29:11.000000000 +0900
@@ -0,0 +1 @@
+no_convenience_copy.patch
diff -Nru libint2-2.3.0~beta3/debian/rules libint2-2.3.0~beta3/debian/rules
--- libint2-2.3.0~beta3/debian/rules	2016-10-02 15:26:53.000000000 +0900
+++ libint2-2.3.0~beta3/debian/rules	2017-01-21 15:29:11.000000000 +0900
@@ -4,7 +4,7 @@
 #export LD_LIBRARY_PATH=$(CURDIR)/lib/.libs 
 
 %:
-	dh $@
+	dh $@ --parallel
 
 override_dh_auto_configure:
 	./autogen.sh
diff -Nru libint2-2.3.0~beta3/debian/watch libint2-2.3.0~beta3/debian/watch
--- libint2-2.3.0~beta3/debian/watch	2015-09-02 21:30:13.000000000 +0900
+++ libint2-2.3.0~beta3/debian/watch	2017-01-21 15:31:07.000000000 +0900
@@ -1,2 +1,4 @@
 version=3
-http://sf.net/libint/libint-([\d.]+)-stable\.tgz
+opts=filenamemangle=s/.+\/v2?(\d\S+)\.tar\.gz/libint2-$1\.tar\.gz/,\
+uversionmangle=s/(\d)-(RC|rc|pre|dev|beta|alpha)\.(\d*)$/$1~$2$3/ \
+  https://github.com/evaleev/libint/tags .*/v2?(\d\S+)\.tar\.gz
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