Commit f746446b authored by Nicholas Breen's avatar Nicholas Breen

New build and install process for documentation

parent cc6d07eb
usr/share/doc/gromacs
usr/share/doc/gromacs-data
usr/share/doc/gromacs-dev
usr/share/doc/libgromacs-dev
usr/share/doc/libgromacs1
usr/share/gromacs
usr/share/gromacs/shell-specific
......@@ -7,5 +7,8 @@ Abstract: This manual describes the configuration and use of gromacs,
Section: Science/Chemistry
Format: HTML
Index: /usr/share/doc/gromacs/html/online/getting_started.html
Files: /usr/share/doc/gromacs/html/online/*.html
Index: /usr/share/doc/gromacs/html/index.html
Files: /usr/share/doc/gromacs/html/*.html /usr/share/doc/gromacs/html/user-guide/*.html
Format: PDF
Files: /usr/share/doc/gromacs/html/manual-5.1.pdf
build/documentation/docs/html usr/share/doc/gromacs/
# This override is the worst solution, except for all the other ones.
# For background, see #736360, #736432, and a number of threads over the years,
# such as https://lists.debian.org/debian-devel/2014/10/msg00774.html
gromacs-data: embedded-javascript-library
# Adaptive Resolution Molecular Dynamics Simulation
gromacs-mpich: spelling-error-in-binary usr/bin/mdrun_mpi.mpich AdresS Address
gromacs-mpich: spelling-error-in-binary usr/bin/mdrun_mpi_d.mpich AdresS Address
# Seems to be a version-specific, platform-specific false positive; not in source
gromacs-mpich [amd64]: spelling-error-in-binary usr/bin/mdrun_mpi.mpich tEH the
gromacs-mpich [amd64]: spelling-error-in-binary usr/bin/mdrun_mpi_d.mpich tEH the
gromacs-mpich: spelling-error-in-binary usr/bin/mdrun_mpi.mpich AdResS Address
gromacs-mpich: spelling-error-in-binary usr/bin/mdrun_mpi_d.mpich AdResS Address
# Adaptive Resolution Molecular Dynamics Simulation
gromacs-openmpi: spelling-error-in-binary usr/bin/mdrun_mpi.openmpi AdresS Address
gromacs-openmpi: spelling-error-in-binary usr/bin/mdrun_mpi_d.openmpi AdresS Address
# Seems to be a version-specific, platform-specific false positive; not in source
gromacs-openmpi [amd64]: spelling-error-in-binary usr/bin/mdrun_mpi.openmpi tEH the
gromacs-openmpi [amd64]: spelling-error-in-binary usr/bin/mdrun_mpi_d.openmpi tEH the
gromacs-openmpi: spelling-error-in-binary usr/bin/mdrun_mpi.openmpi AdResS Address
gromacs-openmpi: spelling-error-in-binary usr/bin/mdrun_mpi_d.openmpi AdResS Address
This diff is collapsed.
usr/lib
usr/share/gromacs
usr/share/doc/gromacs-dev
gromacs: no-symbols-control-file
no-symbols-control-file
# Adaptive Resolution Molecular Dynamics Simulation
gromacs: spelling-error-in-binary usr/lib/*/libgromacs.so.0.0.0 AdResS Address
gromacs: spelling-error-in-binary usr/lib/*/libgromacs_d.so.0.0.0 AdResS Address
spelling-error-in-binary usr/lib/*/libgromacs.so.* AdResS Address
spelling-error-in-binary usr/lib/*/libgromacs_d.so.* AdResS Address
Description: Do not create empty man/man7 directory
Author: Nicholas Breen
Origin: vendor
Last-Update: 2015-09-27
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Index: gromacs-5.1/docs/CMakeLists.txt
===================================================================
--- gromacs-5.1.orig/docs/CMakeLists.txt
+++ gromacs-5.1/docs/CMakeLists.txt
@@ -268,10 +268,6 @@ if (MAN_PAGE_DIR)
DESTINATION ${MAN_INSTALL_DIR}/man1
COMPONENT man OPTIONAL
FILES_MATCHING PATTERN "*.1")
- install(DIRECTORY ${MAN_PAGE_DIR}/
- DESTINATION ${MAN_INSTALL_DIR}/man7
- COMPONENT man OPTIONAL
- FILES_MATCHING PATTERN "*.7")
endif()
gmx_cpack_add_generated_source_directory(man)
This source diff could not be displayed because it is too large. You can view the blob instead.
readme.patch
copyright-file.patch
# manpage_hyphenation.patch
spelling.patch
empty-man7-directory.patch
......@@ -83,3 +83,42 @@ Index: gromacs-5.1/src/gromacs/gmxana/gmx_wham.cpp
"during smoothing"},
{ "-nBootstrap", FALSE, etINT, {&opt.nBootStrap},
"nr of bootstraps to estimate statistical uncertainty (e.g., 200)" },
Index: gromacs-5.1/src/gromacs/gmxana/dlist.c
===================================================================
--- gromacs-5.1.orig/src/gromacs/gmxana/dlist.c
+++ gromacs-5.1/src/gromacs/gmxana/dlist.c
@@ -318,7 +318,7 @@ gmx_bool has_dihedral(int Dih, t_dlist *
break;
default:
pr_dlist(stdout, 1, dl, 1, 0, TRUE, TRUE, TRUE, TRUE, MAXCHI);
- gmx_fatal(FARGS, "Non existant dihedral %d in file %s, line %d",
+ gmx_fatal(FARGS, "Non existent dihedral %d in file %s, line %d",
Dih, __FILE__, __LINE__);
}
return b;
Index: gromacs-5.1/src/gromacs/pbcutil/mshift.cpp
===================================================================
--- gromacs-5.1.orig/src/gromacs/pbcutil/mshift.cpp
+++ gromacs-5.1/src/gromacs/pbcutil/mshift.cpp
@@ -146,7 +146,7 @@ static void mk_igraph(t_graph *g, int ft
gmx_noreturn static void g_error(int line, const char *file)
{
- gmx_fatal(FARGS, "Tring to print non existant graph (file %s, line %d)",
+ gmx_fatal(FARGS, "Tring to print non existent graph (file %s, line %d)",
file, line);
}
#define GCHECK(g) if (g == NULL) g_error(__LINE__, __FILE__)
Index: gromacs-5.1/docs/man/gmx-mdrun.1
===================================================================
--- gromacs-5.1.orig/docs/man/gmx-mdrun.1
+++ gromacs-5.1/docs/man/gmx-mdrun.1
@@ -200,7 +200,7 @@ is sufficient, this signal should not be
the \fBmdrun\fP process that is the parent of the others.
.sp
Interactive molecular dynamics (IMD) can be activated by using at least one
-of the three IMD switches: The \fB\-imdterm\fP switch allows to terminate the
+of the three IMD switches: The \fB\-imdterm\fP switch allows one to terminate the
simulation from the molecular viewer (e.g. VMD). With \fB\-imdwait\fP,
\fBmdrun\fP pauses whenever no IMD client is connected. Pulling from the
IMD remote can be turned on by \fB\-imdpull\fP\&.
......@@ -55,6 +55,11 @@ endif
# You must have the pacakges "nvidia-cuda-toolkit" and "nvidia-cuda-dev"
# installed. Those are not official build dependencies to keep the package in
# Debian main!
#
# If you use this option, it is strongly recommended that you also set
# DEB_BUILD_OPTIONS=cpuopt, assuming you are compiling and running on the same
# machine.
#
# Further details at http://www.gromacs.org/GPU_acceleration
GPU_CONFIG_PARAMS =
ifneq (,$(findstring gpu,$(DEB_BUILD_OPTIONS)))
......@@ -109,12 +114,12 @@ build-basic: configure-stamp
$(MAKE) -C build/basic-dp
touch $@
build-manual: configure-stamp build-basic
build-manual:
dh_testdir
# Build speedy, stripped-down version just for documentation generation.
# Derived from admin/build-docs.sh
(mkdir -p build/documentation ; cd build/documentation; \
cmake $(CURDIR) -DCMAKE_BUILD_TYPE=Debug -DGMX_OPENMP=OFF -DGMX_SIMD=None -DGMX_GPU=OFF -DCMAKE_VERBOSE_MAKEFILE=ON)
cmake $(CURDIR) -DCMAKE_BUILD_TYPE=Debug -DGMX_OPENMP=OFF -DGMX_SIMD=None -DGMX_GPU=OFF -DCMAKE_VERBOSE_MAKEFILE=ON -DGMX_BUILD_MANUAL=ON)
$(MAKE) gmx -C build/documentation
# Generate PDF
$(MAKE) manual -C build/documentation
......@@ -145,12 +150,12 @@ endif
clean:
dh_testdir
dh_testroot
rm -rf build
dh_clean build-basic build-mpich build-openmpi configure-stamp \
rm -rf build docs/doxygen/*.pyc
dh_clean build-basic build-mpich build-openmpi build-manual configure-stamp \
debian/gromacs-mpich.README.Debian debian/gromacs-openmpi.README.Debian
install: build install-basic install-mpich install-openmpi
install: build-arch install-basic install-mpich install-openmpi
dh_testdir
dh_testroot
dh_prep -pgromacs-data -plibgromacs-dev
......@@ -158,9 +163,6 @@ install: build install-basic install-mpich install-openmpi
dh_installdirs -pgromacs-data
mv $(CURDIR)/debian/gromacs/usr/share/gromacs/top \
$(CURDIR)/debian/gromacs-data/usr/share/gromacs
# XXX CHECK
# mv $(CURDIR)/debian/gromacs/usr/share/gromacs/html \
# $(CURDIR)/debian/gromacs-data/usr/share/doc/gromacs
mv $(CURDIR)/debian/gromacs/usr/share/man \
$(CURDIR)/debian/gromacs-data/usr/share/man
# some of the default installation directories for documentation and
......@@ -171,6 +173,7 @@ install: build install-basic install-mpich install-openmpi
chmod 644 $(CURDIR)/debian/gromacs-data/usr/share/gromacs/shell-specific/*
dh_link -pgromacs-data usr/share/doc/gromacs/html usr/share/doc/gromacs-data/html
dh_link -pgromacs-data usr/share/doc/gromacs/html usr/share/doc/libgromacs-dev/html
dh_link -pgromacs-data usr/share/doc/gromacs/html usr/share/doc/libgromacs1/html
# this name is also given in documentation
dh_link -pgromacs-data usr/share/doc/gromacs-data/copyright usr/share/doc/gromacs-data/COPYING
# rename a pair of Perl scripts to drop the .pl extension (Policy 10.4)
......@@ -187,13 +190,20 @@ install: build install-basic install-mpich install-openmpi
mv $(CURDIR)/debian/gromacs/usr/lib/$(DEB_HOST_MULTIARCH)/*.so \
$(CURDIR)/debian/gromacs/usr/lib/$(DEB_HOST_MULTIARCH)/pkgconfig \
$(CURDIR)/debian/libgromacs-dev/usr/lib/$(DEB_HOST_MULTIARCH)/
rmdir $(CURDIR)/debian/gromacs/usr/lib/$(DEB_HOST_MULTIARCH) $(CURDIR)/debian/gromacs/usr/lib
mv $(CURDIR)/debian/gromacs/usr/share/gromacs/template $(CURDIR)/debian/libgromacs-dev/usr/share/gromacs/template
# remaining documentation catch-all
mv $(CURDIR)/debian/gromacs/usr/share/gromacs/* $(CURDIR)/debian/gromacs-data/usr/share/doc/gromacs
-rmdir $(CURDIR)/debian/gromacs/usr/share/gromacs
install-manual: build-manual
dh_testdir
dh_testroot
dh_prep -pgromacs-data
dh_installdirs -pgromacs-data
dh_install -pgromacs-data
install-basic: build
install-basic: build-arch
dh_testdir
dh_testroot
dh_prep -pgromacs
......@@ -201,14 +211,11 @@ install-basic: build
$(MAKE) -C build/basic install DESTDIR=$(CURDIR)/debian/gromacs
$(MAKE) -C build/basic-dp install DESTDIR=$(CURDIR)/debian/gromacs
dh_installman -pgromacs debian/man/demux.1 debian/man/xplor2gmx.1
# Here's a fun part. In 5.0, "gmx command" replaced nearly all of the
# "g_command" names, but the mapping is not 1:1 and some commands were
# renamed, added, deleted, etc. So now we generate the man page symlinks
# from a fixed list instead, including _d suffixes.
# gmx(1) -> gmx_d(1)
dh_link -pgromacs
dh_lintian -pgromacs
install-mpich: build
install-mpich: build-mpich
dh_testdir
dh_testroot
dh_prep -pgromacs-mpich
......@@ -221,7 +228,7 @@ install-mpich: build
dh_link -pgromacs-mpich usr/share/man/man1/mdrun_mpi.mpich.1.gz usr/share/man/man1/mdrun_mpi_d.mpich.1.gz
dh_lintian -pgromacs-mpich
install-openmpi: build
install-openmpi: build-openmpi
dh_testdir
dh_testroot
dh_prep -pgromacs-openmpi
......@@ -236,7 +243,7 @@ ifneq (,$(findstring $(DEB_HOST_ARCH),$(OPENMPI_ARCH)))
dh_lintian -pgromacs-openmpi
endif
binary-indep: build install
binary-indep: build-arch build-indep install install-manual
dh_testdir
dh_testroot
dh_installchangelogs -i
......@@ -248,7 +255,7 @@ binary-indep: build install
dh_md5sums -i
dh_builddeb -i
binary-arch: build install
binary-arch: build-arch install
dh_testdir -s
dh_testroot -s
dh_installchangelogs -s
......@@ -270,7 +277,7 @@ endif
binary: binary-indep binary-arch
.PHONY: binary binary-arch binary-indep build clean install install-basic install-mpich install-openmpi
.PHONY: binary binary-arch binary-indep build clean install install-basic install-mpich install-openmpi install-manual
# Because multiple versions of the same programs are created using the same source tree,
# the various build-* targets can't be compiled simultaneously.
......
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