Merge pull request #47 from astromatic/develop (08c0ebe3) · Commits · csst-pipeline / msc / sextractor

.github/workflows/doc.yml

0 → 100644

+54 −0

Original line number	Diff line number	Diff line
		name: doc

		on:
		push:
		paths:
		- 'doc/**'
		pull_request:
		paths:
		- 'doc/**'
		workflow_dispatch:

		jobs:

		#############
		# Build doc #
		#############
		build:
		name: Make doc
		continue-on-error: false
		runs-on: ubuntu-latest

		steps:
		- name: Checkout
		uses: actions/checkout@v2

		- name: Install dependencies
		run: \|
		pip3 install -r doc/requirements.txt
		sudo apt-get -y install latexmk texlive-latex-recommended texlive-fonts-recommended texlive-formats-extra

		- name: Build doc
		run: \|
		./autogen.sh
		./configure --disable-model-fitting --disable-cfitsio --disable-threads
		cd doc
		make html
		make latexpdf
		cp build/latex/sextractor.pdf build/html/

		- name: Set destination dir
		if: github.ref_name != 'main'
		run: \|
		echo "DOC_DEST=${{ github.ref_name }}" >> $GITHUB_ENV

		- name: Deploy
		if: success()
		uses: peaceiris/actions-gh-pages@v3
		with:
		publish_branch: doc-pages
		github_token: ${{ secrets.GITHUB_TOKEN }}
		publish_dir: doc/build/html/
		destination_dir: ${{ env.DOC_DEST }}

INSTALL

+11 −11

Original line number	Diff line number	Diff line
		@@ -4,7 +4,7 @@ Installing the software
		Hardware requirements
		=====================

		PSFEx runs in (ANSI) text-mode from a shell. A window system is
		SExtractor runs in (ANSI) text-mode from a shell. A window system is
		not necessary for basic operation.

		When it comes to memory usage, the amount required by SExtractor depends
		@@ -75,18 +75,19 @@ locations:
		$ ./configure

		Compared to "gcc" and the librairies above, the combination of the
		Intel compiler ("icc") and the MKL (Math Kernel Library) libraries
		can give the SExtractor executable a significant boost in performance,
		thanks to better vectorized code, and reduced memory usage. If "icc"
		and the MKL (Math Kernel Library) are installed on your system [4],
		you can take advantage of those using instead
		Intel compiler ("icc" or "icx") and the MKL (Math Kernel Library)
		libraries can give the SExtractor executable a significant boost in
		performance, thanks to better vectorized code, and reduced memory
		usage. If "icc" (or "icx") and the MKL (Math Kernel Library) are
		installed on your system [4], you can take advantage of those using
		instead

		$ ./configure --enable-mkl

		Additionally, if the SExtractor binary is to be run on a different
		machine that does not have "icc" and the MKL (Math Kernel Library)
		installed (e.g., a cluster computing node), you must configure a
		partially statically linked executable using
		machine that does not have "icc" (or "icx") and the MKL installed
		(e.g., a cluster computing node), you must configure a partially
		statically linked executable using

		$ ./configure --enable-mkl --enable-auto-flags --enable-best-link

		@@ -118,6 +119,5 @@ path).
		options "--enable-threads --enable-float".

		[4] The Linux versions of the Intel compiler and MKL (Math
		Kernel Library) are available for free to academic researchers,
		students, educators and open source contributors.
		Kernel Library) are now available for free on Intel's website.

configure.ac

+60 −22

Original line number	Diff line number	Diff line
		@@ -7,7 +7,7 @@
		#
		# This file part of: SExtractor
		#
		# Copyright: (C) 2002-2022 IAP/CNRS/SorbonneU
		# Copyright: (C) 2002-2023 CFHT/IAP/CNRS/SorbonneU
		#
		# License: GNU General Public License
		#
		@@ -22,7 +22,7 @@
		# You should have received a copy of the GNU General Public License
		# along with SExtractor. If not, see <http://www.gnu.org/licenses/>.
		#
		# Last modified: 11/03/2022
		# Last modified: 07/03/2023
		#
		#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

		@@ -31,8 +31,8 @@ define([AC_CACHE_LOAD],)
		define([AC_CACHE_SAVE],)

		# This is your standard AstrOmatic source code...
		AC_INIT(SExtractor, 2.25.3, [astromatic@astromatic.net],
		sextractor, [http://astromatic.net/software/sextractor])
		AC_INIT([SExtractor],[2.28.0],[astromatic@astromatic.iap.fr],
		[sextractor],[http://astromatic.net/software/sextractor])
		AC_CONFIG_MACRO_DIR([m4])
		AC_CONFIG_AUX_DIR(autoconf)
		AC_CONFIG_SRCDIR(src/makeit.c)
		@@ -53,6 +53,7 @@ sinclude(acx_atlas.m4)
		sinclude(acx_openblas.m4)
		sinclude(acx_fftw.m4)
		sinclude(acx_mkl.m4)
		sinclude(acx_cfitsio.m4)
		sinclude(acx_prog_cc_optim.m4)
		sinclude(acx_pthread.m4)
		sinclude(acx_urbi_resolve_dir.m4)
		@@ -79,24 +80,38 @@ AC_ARG_ENABLE(auto-flags,
		AC_MSG_RESULT([yes]),
		AC_MSG_RESULT([no]))

		# Provide special option for the Linux Intel C compiler
		AC_MSG_CHECKING([whether the INTEL compiler is enabled])
		# Provide special option for the Linux Intel C "classic" compiler
		AC_MSG_CHECKING([whether the classic INTEL compiler is enabled])
		AC_ARG_ENABLE(icc,
		[AS_HELP_STRING([--enable-icc],
		[Use the Intel compiler (default = no)])],
		CC="icc"
		enable_iccx="yes"
		AC_MSG_RESULT([yes]),
		AC_MSG_RESULT([no]))

		# Provide special option for the Linux Intel OneAPI C compiler
		AC_MSG_CHECKING([whether the INTEL compiler is enabled])
		AC_ARG_ENABLE(icx,
		[AS_HELP_STRING([--enable-icx],
		[Use the Intel compiler (default = no)])],
		CC="icx"
		enable_iccx="yes"
		AC_MSG_RESULT([yes]),
		AC_MSG_RESULT([no]))

		# Provide special options for INTEL MKL
		# We force the use of icc
		# We use icc if available, if not Intel OneAPI's icx
		# (we don't use AC_PROG_CC as it does not play nice
		# in a conditional block)
		AC_MSG_CHECKING([whether INTEL's MKL is enabled])
		AC_ARG_ENABLE(mkl,
		[AS_HELP_STRING([--enable-mkl],
		[Use INTEL's MKL for solvers and FFTs (default = no)])],
		enable_icc="yes"
		CC="icc"
		AC_MSG_RESULT([yes]),
		AC_MSG_RESULT([yes])
		CC=""
		[AC_CHECK_PROGS(CC, [icc icx cc])]
		enable_iccx="yes",
		AC_MSG_RESULT([no]))

		# Checks for programs.
		@@ -115,11 +130,10 @@ AC_PROG_INSTALL
		AC_CHECK_LIB(m, sin)

		# Checks for header files.
		AC_HEADER_STDC
		AC_CHECK_HEADERS([fcntl.h limits.h malloc.h stdlib.h string.h sys/mman.h \
		sys/types.h unistd.h])
		# Checks for INTEL math header files.
		if test "$enable_icc" = "yes"; then
		if test "$enable_iccx" = "yes"; then
		AC_CHECK_HEADERS(mathimf.h)
		fi

		@@ -135,7 +149,6 @@ AC_TYPE_UID_T
		# Checks for library functions.
		AC_FUNC_ERROR_AT_LINE
		AC_FUNC_MMAP
		AC_TYPE_SIGNAL
		AC_FUNC_STAT
		AC_FUNC_STRFTIME
		AC_CHECK_FUNCS([atexit getenv gettimeofday isinf isnan logf memcpy memmove \
		@@ -180,6 +193,24 @@ AC_ARG_WITH(openblas-incdir,
		[AS_HELP_STRING([--with-openblas-incdir=<OpenBLAS header dir>],
		[Provide an alternative path to the OpenBLAS header directory])])

		# Provide special option for CFITSIO
		AC_MSG_CHECKING([whether CFITSIO support should be disabled (default=enabled)])
		AC_ARG_ENABLE(cfitsio,
		[AS_HELP_STRING([--disable-cfitsio],
		[Disable support for compressed FITS files through the CFITSIO library (default=enabled)])],
		if test "$enable_cfitsio" = "no"; then
		AC_MSG_RESULT([yes])
		else
		AC_MSG_RESULT([no])
		fi,
		AC_MSG_RESULT([no]))
		AC_ARG_WITH(cfitsio-libdir,
		[AS_HELP_STRING([--with-cfitsio-libdir=<CFITSIO library path>],
		[Provide an alternative path to the CFITSIO library])])
		AC_ARG_WITH(cfitsio-incdir,
		[AS_HELP_STRING([--with-cfitsio-incdir=<CFITSIO include dir>],
		[Provide an alternative path to the CFITSIO include directory])])

		# Provide a special option for the default XSLT URL
		with_xsl_url="file://"$(URBI_RESOLVE_DIR([$datadir]))"/$PACKAGE_TARNAME/$PACKAGE_TARNAME.xsl"
		AC_ARG_WITH(xsl_url,
		@@ -222,7 +253,7 @@ use_pthreads="no"
		AC_MSG_CHECKING([for profiler mode])
		AC_ARG_ENABLE(profiling,
		[AS_HELP_STRING([--enable-profiling],
		[Enable special mode for profiling (default = no)])]
		[Enable special mode for profiling (default = no)])],
		AC_MSG_RESULT([yes]),
		AC_MSG_RESULT([no]))

		@@ -256,10 +287,7 @@ if test "$enable_model_fitting" != "no"; then
		if test "$enable_mkl" = "yes"; then
		convlibs="${srcdir}/wcs/libwcs_c.a,${srcdir}/levmar/liblevmar.a"
		ACX_MKL($with_mkl_dir,,$enable_best_link,$convlibs)
		if test "$MKL_WARN" == ""; then
		AC_MSG_RESULT([yes])
		else
		AC_MSG_RESULT([no])
		if test "$MKL_WARN" != ""; then
		AC_MSG_WARN([$MKL_WARN])
		fi
		AM_CFLAGS="$AM_CFLAGS $MKL_CFLAGS "
		@@ -305,11 +333,21 @@ if test "$enable_model_fitting" != "no"; then
		fi
		fi

		########################## handle the CFITSIO library ########################
		if test "$enable_cfitsio" != "no"; then
		ACX_CFITSIO($with_cfitsio_libdir, $with_cfitsio_incdir,
		[LIBS="$CFITSIO_LIBS $LIBS"]
		if test "$CFITSIO_WARN" != ""; then
		AC_MSG_WARN([$CFITSIO_WARN])
		fi,
		AC_MSG_ERROR([$CFITSIO_ERROR Exiting.]))
		fi

		AM_CONDITIONAL(USE_MODEL, [test "$enable_model_fitting" != "no"])

		# Compile with profiling option
		if test "$enable_profiling" = "yes"; then
		if test "$enable_icc" = "yes"; then
		if test "$enable_iccx" = "yes"; then
		AM_CFLAGS="$AM_CFLAGS -pq"
		else
		AM_CFLAGS="$AM_CFLAGS -pg"
		@@ -319,9 +357,9 @@ fi

		# "Best" linking option
		if test "$enable_best_link" = "yes"; then
		if test "$enable_icc" = "yes"; then
		AM_LDFLAGS="-static-intel -qopenmp-link static -shared-libgcc \
		-static-libtool-libs -no-intel-extensions -avoid-version $AM_LDFLAGS"
		if test "$enable_iccx" = "yes"; then
		AM_LDFLAGS="-static-intel -qopenmp-link=static -shared-libgcc \
		-static-libtool-libs -avoid-version $AM_LDFLAGS"
		else
		AM_LDFLAGS="-shared-libgcc -static-libtool-libs -avoid-version $AM_LDFLAGS"
		fi

debian/rules

+1 −1

Original line number	Diff line number	Diff line
		@@ -15,7 +15,7 @@ ifeq ($(USE_BEST),1)
		dh_auto_configure -- --host=$(DEB_HOST_GNU_TYPE) \
		--build=$(DEB_BUILD_GNU_TYPE) \
		--prefix=/usr --mandir=\$${prefix}/share/man \
		--enable-icc --enable-mkl \
		--enable-icx --enable-mkl \
		--enable-auto-flags --enable-best-link \
		--with-release=$(PACKAGE_RELEASE)
		else

doc/requirements.txt

+4 −1

Original line number	Diff line number	Diff line
		sphinxcontrib-bibtex
		sphinx >= 5.0
		sphinx_rtd_theme >= 1.1
		sphinxcontrib-bibtex >= 2.4.0