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build-it
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#
# -*-shell-script-*-
#
# Copyright 2004, 2005, 2006, 2007, 2008 by The University of York
# Copyright 2009, 2010, 2011, 2012 by The University of York
# Copyright 2012 by Paul Emsley
# Copyright 2012, 2013, 2014, 2015, 2016 by Medical Reserch Council
# Copyright 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 by Medical Research Council
# Author: Paul Emsley
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or (at
# your option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
# 02110-1301, USA
#
#
#
# For instructions, read below, starting at :: NOTE ::
#
#
# Prerequisites: sed, GNU make, libtool, wget
#
# libz is optional for the moment
# 1.3 Put RELEASE-NOTES on web site too
# 1.4 Apply both of Ezra's patches of today Wed Mar 2 22:51:36 GMT 2005
# Update clipper version (the one with shelx .fcf ability)
# 1.5 Apply Ezra's gtkglarea patch and GSL patch.
# Update version of FFTW and other updates from MATSUURA Takanori.
# 1.6 Update to mmdb-1.0.8 [# for molrep output]
# 1.7 Fix logic of fftw test
# 1.8 Add the clipper edcalc patch (suggested by Ezra ages ago)
# 1.9 Add Fedora Core 4 support and testing for the need to build mccp4,
# mmdb and clipper.
# 1.10 Tidy up nightly code.
# 1.11 Add code testing the need for guile_gui and goosh.
# 1.12 Tidy nightly code again.
# 1.13 Don't escape the "."s in gsub for new gawk (Ward Smith).
# 1.14 20050628 Test for imlib on the installation, not the system (ignore
# the system).
# 1.15 20050709 Add glib gstrfuncs patch
# 1.16 20050709 Update to guile 1.6.7 and add lt_preloaded_symbols patch
# 1.17 20050721 Added clipper status code to compiling clipper part.
# Redirect stderr output?
# fix build_mccp4 problem.
# 1.18 20050722 Fix guile build (wrong http tar file).
# Added freeglut
# 1.19 20050803 Update version of guile-gtk to 0.41
# 1.20 20050815 Several updates and clean up from MATSUURA Takanori.
# 1.21 20050815 Stop if wget test fails.
# 1.22 20050916 Update build for freeglut to use --disable-warnings and
# CFLAGS
# 1.23 20050916 Move "set" so we don't see confusing default coot_version
# 1.24 20051012 Do pre-release tars for a few days.
# 1.25 20051017 Don't make install if Coot's makes fails. Don't make -k
# 1.26 20051018 Handle clipper nxmap patch.
# 1.27 20051027 [Gif, Paris] Fix tarred directory for nightly pre-release
# tars.
# 1.28 20051101 Fix the md5sum for nxmap.h
# 1.29 20051104 Apply most of MATSUURA Takanori's fixes.
# Use CCP4 libs (mtz, clipper, mmdb).
# 1.30 20051109 Darwin setting of FC for CCP4 libs configure.
# 1.31 20051114 Fix coot tar file problem on building pre-release (or not).
# 1.32 20060205 Add scripting variable debugging (its currently not making
# python tar files)
# 1.33 20060214 Get wget testing tar file from YSBL, not chem.gla
# 1.34 20060219 Correct the install position of libccp4c.la
# 1.35 20060219 create time stamp with current time, not the time of
# the previous ccp4 libs file, now the find ctime test works
# as I wanted.
# 1.36 20060220 Add a libmmdb.la too.
# 1.37 20060222 Add Bob Nolte's proxy settings
# 1.38 20060224 dylib variable for libmmdb.la and libccp4c.la
# 1.39 20060225 Fix sedding of libmmdb.la and libccp4c.la
# 1.40 20060323 copy over coot.py to share/coot/python (if we built with
# python)
# 1.41 20060401 Big changes for ccp4 5.0.2 ccp4c libs.
# 1.42 20060404 Various small build debuggings.
# 1.43 20060405 Fix do_nightlies syntax error and fix up glut_prefix build
# problem.
# 1.44 20060405 Fix the tarred directory name when this is not a pre-release
# 1.45 20060406 Check for missing reference structures and monomer lib and
# install them if needed.
# 1.46 20060418 use install_top_dir variable to copy over coot.py (not
# $coot_prefix!)
# 1.47 20060419 Remove the mmdb binaries
# 1.48 20060420 J. Maclean says no guile. He is right. So check install for
# guile, not system.
# 1.49 20060420 Replace many $AUTOBUILD_INSTALLED with $install_top_dir.
# 1.50 20060421 Replace other $AUTOBUILD_INSTALLED with $install_top_dir for
# tar file creation.
# 1.51 20060425 net-http was installing into the wrong place because it had
# been set to install_top_dir, but this was not set as a shell
# (or configured) variable so it was just blank [James Murray].
# Now we export install_top_dir.
# 1.52 20060427 Don't add unecessary tagging of -pre-release to tar_dir at
# the end.
# 1.53 20060503 Force GSL to be in $install_top_dir rather than anywhere.
# 1.54 20060519 Update to extract the right coot version from the release and
# pre-release directories.
# 1.55 20060621 Shuffle around the test for using pre-release
# 1.56 20060626 Fixes from MATSUURA Takanori. Shuffle around the usage of
# install_top_dir.
# 1.57 20060704 run imlib-config from the installation, not anywhere.
# 1.58 20060705 Fix wrong directory to build libtiff.
# 1.59 20060706 guile-config should run with an argument, otherise it
# returns with exit status 1 (and we test for non-zero).
# 1.60 20060706 Fix (directory for) mmdb include file test.
# 1.61 20060707 Add to coot configure line the option for guile_gtk
# 1.62 20060708 Fix coot_prerelease_exists typo in setting install_top_dir
# (oops).
# 1.63 20060708 Add jpeg dependency for imlib
# 1.64 20060708 Add libungif test to installation, not system (imlib
# dependency).
# 1.65 20060710 Add removal of coot_wrap_guile.cc compilation when python
# scripting.
# 1.66 20060710 Python on a Sunday.
# 1.67 20060711 Try to fix up the Makefile for PNG.
# 1.68 20060723 Add in the updates to ltmain.sh, ltconfig and config.guess/sub
# for Mactel build. Add build for readline.
# Readline version typo fixed.
# 1.69 20060724 ENABLE_PYTHON_COOT variable is tested. Don't display
# a variables if we are using a proxy.
# 1.70 20060728 pass CFLAGS and LDFLAGS to guile's configure
# 1.71 20060730 Add test for 64-bit Linux to update config.xxxs and libtool.
# Installation readline built now, not system.
# 1.72 20060801 Use mmdb-1.0.8-ysbl-2, which installs includes in the include
# dir. This matches clipper cif_data_io.cpp which presumes that
# it is there. (And is a clean thing to do anyway).
# 1.73 20060801 Use the new version of libccp4c, with some of Ralf's patches
# and includes that go into include/ccp4 dir.
# 1.74 20060801 Use CCP4_CXXFLAGS argument to clipper (it does the wrong thing
# with --with-ccp4)
# 1.75 20060801 Use -pre-2 version of SSMlib, that has -Ixxx/include/mmdb to
# find mmdb include files.
# 1.76 20060808 test for libjpeg.$shared_lib_ext not libjpeg.so. LTE bug.
# 1.77 20060818 Force update of libtool and config files for libjpeg. Extend
# the make install proceedure. Lynn Ten Eyck reported problems
# here.
# 1.78 20060823 Add poll fix and getpwuid fix to glib build on Intel Mac.
# 1.79 20060827 Add fix for gtk-canvas from fink for Intel Mac.
# 1.80 20061002 Change freeglut test to test instaltion, not system.
# 1.81 20061012 The path used to find *-config files should be the same one
# that new executables are added (it was $AUTOBUILD_INSTALLED)
# and it should be $AUTOBUILD_INSTALLED-pre-release/bin) when
# we are building a pre-release.
# 1.82 20061012 Change the destination tar file so that there are nightly
# and stable directories for the binary tar files on the web
# server.
# 1.83 20061107 cd to the clipper dir when building clipper. Pirate and
# bucca are not (attempted to be) built then.
# 1.84 20061107 Capture and report error status from make in GSL (intel mac
# build fails).
# 1.85 20061107 Use GSL version 1.8, which includes Charles Ballard's fix for
# fp_regs.h
# 1.86 20061108 Add fink-based args for configure of gtk for Darwin
# 1.87 20061108 Fix ltmain.sh updating for Gtk (oops!).
# 1.88 20061122 Fix coot tar directory now that we have revision numbers in
# tar file name.
# 1.89 20061123 Fix/add test for ssmlib build (now depends on mmdb build) and
# libccp4c build (now depends on xxx/include/ccp4/cmtzlib.h).
# 1.90 20061128 Allow the user to specify if the dependencies should be checked
# on the system or only in the autobuild installed directory.
# Needs more checks to use this. Currently only glib and gtk
# tests.
# 1.91 20061211 Don't make install for guile-gtk if the make fails - or the
# dependency check for guile-gtk in coot's configure passes
# when it should fail (maybe).
# 1.92 20061212 Apply Charles Ballards libtool patch for Macs for imlib and
# guile-gtk.
# 1.93 20061212 Fiddle the env vars to compile gtk+ on Mac.
# 1.94 20070104 Non-pre-release build problems, BINARY_DEST_DIR
# 2.01 20070109 imlib tar gz should be downloaded from the correct directory
# (sigh).
# 2.02 20070117 Try to compile clipper with -fno-strict-aliasing
# 2.03 20070123 Tell us where the gtkglarea include file was found.
# 2.04 20070124 GCC 3.2 on RH8 machine cannot compile new clipper, so add a
# patch if needed.
# 2.05 20070216 Put libtiff after libjpeg and give tiff's configure command
# line args to find jpeg.
# 2.06 20070306 Put in the clipper<->ccp4 new dist patch.
# 2.07 20070319 Remove == comparisons - Lothar Esser.
# 2.08 20070424 --with-jpeg-lib-dir should be a lib dir!
# 2.09 20070501 Fix the setting of coot_version when no pre-release set.
# 2.10 20071002 Post install slim the binaries. Add helper functions.
# 2.11 20071005 Add some debugging to make_tar. It doesn't seem to work
# currently.
# 2.12 20071005 Fix post_install_slim call.
# 2.13 20071005 Fix slim_dir
# 2.14 20071006 Adjust python scripting settings, so that it should try
# to compile with python most of the time now.
# 2.15 20071008 Fix extra fi, uncommented typo.
# 2.16 20071010 ENABLE_PYTHON_COOT=no for now.
# 2.17 20071105 Swap out DL Clipper for York clipper [whoosh, bang, kerpow!]
# enable-cns
# 2.18 20071105 Backpeddle to mmdb 1.08. Baah.
# 2.19 20071108 Version 1.08-ysbl-3 of mmdb.
# 2.20 20071118 No longer make the full fat tar file.
# 2.21 20071120 Sourcefource no longer distributes libungif, now in
# ysbl software/extras
# 2.22 20071121 set the architecture for ubuntu systems.
# 2.23 20071125 Fix typo in recent fixes.
# 2.24 20071126 Fix setting of systype for MacOSX, hopefully.
# 2.25 20071126 Another try to fix setting of systype for MacOSX.
# 2.26 20071130 Try to enable python
# 2.27 20071207 More python tinkering. Upgrade to 2.5.1
# 2.28 20071207 Add greg. If in York, use it to test before installing.
# 2.29 20071208 Setup CCP4 and use it to test coot before making binaries.
# 2.30 20071209 Add dewinter's ccp4 setup in setup_ccp4.
# 2.31 20071212 Redirect testing output to $LOGS/$HOST-testing.log
# 2.32 20071213 Copy over the ChangeLog, README and RELEASE-NOTES on good test
# 2.33 20071215 Pythonize only sometimes, default off.
# 2.34 20071215 Tell us some Python info
# 2.35 20071215 Python settings outside the subshell.
# 2.36 20071219 Set up for testing and tars on biop too.
# 3.00 20080108 Gtk+-2 version
# 3.01 20080118 Add GtkGlExt
# 3.02 20080121 Tinker with guile build settings.
# 3.03 20080124 Build GTK2 from scratch: librsvg, cairo, pango, glitz. glib, gtk+-2
# 3.04 20080128 Add a test for the existance of pygtk
# 3.05 20080129 Add pkg-config and pygobject
# 3.06 20080130 Add test for pycairo
# 3.07 20080130 pycairo needs 1.4.12 - so test for cairo, setting build_gtk=1 on
# failure
# 3.08 20080130 Remove static patch (for sgi). Add test/build for freetype2
# 3.09 20080130 fontconfig added too.
# 3.10 20080131 Change HOSTLOGDIR to include gtk2 to separate it from gtk1 build logs.
# 3.11 20080201 Fix problem in scripting args to coot's configure.
# 3.12 20080207 Add test and build of ATK, needed for gtk+2.10.x
# 3.13 20080208 lib cleaning problems, add debugging.
# 3.14 20080208 Try requiring gtk 2.10
# 4.00 20080208 Remove gtk2 and pkg-config building. Test for Fedora core 5.
# 4.01 20080211 Remove pycairo build and fix up test for build for guile_gtk
# 4.02 20080212 Add in the Neil Jerram guile-gui patch.
# 4.03 20080213 Add Joseph Moran's fix for handling CC when set.
# 4.04 20080213 Allow python to get through rsync filter, for PHENIX usage.
# 4.05 20080226 Fix up build_guile_gtk usage.
# 4.06 20080428 Apply Joseph Moran's fix correctly.
# 4.07 20080518 Update the status reporting system.
# 4.08 20080607 Bump version of python to 2.5.2
# 4.09 20080617 Update to guile-1.8.5
# 4.10 20080618 As per JED request, number the build logs in a more sensible way.
# 4.11 20080620 Don't run the tests if not in biop or york.
# 4.12 20080624 Add guile-lib to build.
# 4.13 20080729 Correctly test for the up to date python version.
# 4.14 20080729 Adjust test for build_guile_gtk.
# 4.15 20080730 Adjust test for up to date python.
# 4.16 20080730 Use old version of pyobject if pkg-config is not new enough
# 4.17 20080730 Test for gtk minor version, use that to apply guile-gtk patches
# if needed.
# 4.18 20080730 Add Diagnosis for applying guile-gtk patch.
# 4.19 20080818 use mmdb version 1.12
# 4.20 20080918 Remove references to glitz, cairo, fontconfig
# 4.21 20080925 Use pygobject 2.4 if needed (e.g on CentOS 4).
# 4.22 20080925 Handle typename in pygobject.h for CentOS4.
# 4.23 20081007 Don't build python if python is not passed as arg.
# 4.24 20081007 Back to version 2.5.1 that compiles on bragg3, 2.5.2 does not
# (port 8080 already in use).
# 4.25 20081008 Migrate to CCP4 version 6.0.2 for testing in York.
# 4.26 20081014 Use Python 2.6
# 4.27 20081105 Adjust clipper configuration. Remove clipper-new-ccp4-install
# usage, it is no longer needed, it seems. Remove configure
# argument --enable-mmdbold
# 4.28 20081110 Upgrade to mmdb-1.19, get it from EBI.
# 4.29 20081118 Use the ccp4 libs underlay.
# 4.30 20081119 Use -O not -O2 to compile coot on 64 bit machine
# 4.31 20081121 Swig 1.3.34 is OK for 32 bit, I think.
# 4.32 20081122 Use clipper-2.1
# 4.33 20081122 Use clipper-2.1, extra tweaks.
# 4.34 20081122 Add a second test, make a holding directory for tar file before
# second test is run.
# 4.35 20081124 test for greg using full path to guile.
# 4.36 20081130 Bump the gmp version to 4.2.4 (Does that fix the gmp.h on
# intrepid problem?)
# 4.37 20090220 Fix up guile-gui, post-neil-jerram patch added.
# 4.38 20090423 Fix up PYTHONPATH when starting greg tests.
# 4.39 20090427 Remove python and its config from bin in slimmed dir
# 4.40 20090506 Upgrade to mmdb 1.21
# 4.41 20090508 add density-score-by-residue to tar ball.
# 4.42 20090517 Remove standard error redirections.
# 4.43 20090522 Update to guile-1.8.6 on the advice of Ed Podharski.
# 4.44 20090523 Add some build info to the mmdb and clipper logs.
# 4.45 20090523 build status results now go to $build_type-build-status
# (not gtk2-build-status)
# 4.46 20090613 Add coot revision info to build status line.
# 4.47 20090617 Make a file (and transfer it if neeeded) type-binary-xxx.txt
# containing the $coot_version of the just-built binary. Used
# in the update-binary mechanism to find if there is a newer
# version than this binary (that we are running).
# 4.48 20090624 Make pre_release_server_dir be biop.ox
# 4.49 20090628 On my_exit, remove the test-status file, not the build-status
# file.
# 4.50 20090628 Change the GSL version to 1.12
# 4.51 20090703 check exit status of wget for coot source tar file.
# 4.52 20090704 mmdb-1.21 from York.
# 4.53 20090706 check build dependencies when on ubuntu
# 4.54 20090722 fix coot_revision typo for build status.
# 4.55 20090724 make compilers_dir depend on build_type (python build logs
# split out)
# 4.56 20090727 Add a date for build-in-progress status
# 4.57 20090728 gtk2 -> $build_type fixups for status
# 4.58 20090730 remove swig from package list tested on ubuntu.
# 4.59 20090913 Add a date to the fail status message
# 4.60 20091001 comment out the deletion of the coot_wrap files.
# 4.61 20091117 update the version of clipper.
# 4.62 20091203 release server is now in oxford.
# 4.63 20091208 Add curl to the build system
# 4.64 20091209 Fix typo in untaring curl tar file.
# 4.65 20091209 Add libidn to build (for curl).
# 4.66 20091209 Test for holding dir in making tar file.
# 4.67 20091209 Add LDFLAGS to args for libcurl configure.
# 4.68 20091210 Add post-process-libcurl logic.
# 4.69 20091216 Don't delete bin/curl, we need it for updates. (20100120 Not any more)
# 4.70 20100120 debugging added to curl build (problems on bragg3).
# 4.71 20100203 Remove goosh.
# 4.72 20100203 Update clipper version.
# 4.73 20100205 only download mmdb once.
# 4.74 20100304 Fix install_top_dir typos.
# 4.75 20101102 Dependency check for gtkglext patch (compatibility with gtk+ version).
# 4.76 20101102 Correct directory for previoius patch.
# 4.77 20110505 switch to new style Refmac library.
# 4.78 20110507 Refmac mon lib to 5.29
# 4.79 20110610 biop -> lmb.bioch
# 4.80 20110707 also make holding directory for stable builds.
# 4.81 20110725 Add goocanvas.
# 4.82 20110725 Add test for gtk and cairo before going ahead with compiling and using
# goocanvas.
# 4.83 20110805 On 64 bit redhat 4, building freeglut, we need to use /usr/X11R6/lib64,
# not /usr/X11R6/lib, edit configure.
# 4.84 20110821 Hack in a solution the the new clipper problem (new clipper with cif
# tools needs new libtools/configure new ccp4 libs (underlay-2).
# 4.85 20111021 Update python to 2.6, guile to 1.8.8, add guile patch.
# 4.86 20111214 Update to mmdb 1.24 (new) which has working LINKRs.
# 4.87 20120108 Use make not MAKE for guile-gtk.
# 4.88 20120120 Don't use -j $nproc for make if we don't have memory.
# 4.89 20120223 Use libccp4c-5.0.2-ysbl-3.tar.gz, that has libccp4c_la_LIBADD.
# 4.90 20120713 debug $coot_dir_name link usage.
# 4.91 20120808 update to handle version of debian in /etc/issue.
# 4.92 20120820 Debian /etc/issue handling for wheezy.
# 4.93 20120921 Update mmdb to version 1.24.2
# 4.94 20130123 Move pre-release and release server-dir to Cambridge.
# 4.95 20130128 Refmac dictionary to 5.39
# 4.96 20130228 New mmdb version - 1.25.0
# 4.97 20130424 Rework (fix typo) for python include directory slimming.
# 4.98 20130424 Remove ssh copying
# 4.99 20130424 swig 1.3.29 is broken no matter what the architecture.
# 5.00 20130425 CXX testing updates (for ubuntu).
# 5.01 20130429 mmdb version bump 1.25.2
# 5.02 20130502 better diagnostic for goocanvas compile
# 5.03 20130503 Remove SWIG version test (now it is not needed to build source)
# 5.04 20130514 Add COOT_BUILD_INFO_STRING.
# 5.05 20130604 For Release 0.7.1, change release vs pre-release logic
# (MRC server).
# 5.06 20130612 More tinkering to get the correct version for release from the server.
# 5.07 20130707 Adjustment to build stable logic.
# 5.08 20130716 Move source server to personal/pemsley.
# 5.09 20130818 Use ssm-1.3
# 5.10 20130824 debugging publish
# 5.11 20130826 Allow build without guile; name directory for building.
# 5.12 20130909 LD_LIBRARY_PATH changes/fixup.
# 5.13 20130910 Force -O usage for guile compilation.
# 5.14 20130920 Publish logs.
# 5.15 20140408 New version of Python.
# 5.16 20140817 Python version to 2.7.8
# 5.17 20140911 SSM updates.
# 5.18 20141128 Add hack bin for debian awk
# 5.19 20141128 Use dist_name for debian (not systype)
# 5.20 20141203 More/better Debian awk hack.
# 5.21 20141203 Unset some build environment variables (including LD_LIBRARY_PATH)
# 5.22 20141210 More LD_LIBRARY_PATH hacking for debian
# 5.23 20141210 libreadline needs to be linked with -lcurses (on Debian)
# 5.25 20141212
# 5.26 20150215 Use /opt/X11 and COOT_CCP4_PACKAGES for dependences on Darwin.
# 5.27 20170925 bump libccp4 version to 6.5.1 - this has libccp4.pc for pkg-config
# 5.28 20170925 Fixes for clipper and guile and gmp version update (gcc-7.2)
# 5.29 20171006 Test for libgnomecanvas devel (now not available in system for Redhat 7.3)
# 5.30 20180109 Update python version.
# 5.31 20180822 gdkshapes.c in gtkglext
# 5.32 20180924 bump the clipper version (pre-Pro)
# 5.33 20181214 bump the mmdb2 version (pdbx_ins_code)
# 5.34 20181215 clipper patch fixes
# 5.35 20190401 clipper configure fftw patch
# 5.36 20200415 Updates for Release 0.9 - a bit delayed
# 5.37 20200514 redirect numpy output
# 5.38 20200921 Add clustalw2
# 5.39 20201203 Add use_system_gnomecanvas_if_possible, default no.
# 5.40 20210109 change the args to boost's build
# 5.41 20210110 change the boost build log output
# 5.42 20210110 Rework the build of numpy, boost and rdkit
# 5.43 20210110 Add unzip to build dependencies
# 5.44 20210110 Bump the python version, rework the readline configure command line
# 5.45 20210110 Bump the python version again - no2 2.7.18
# 5.46 20210110 Add a test for the version of cmake
# 5.47 20210111 Use the correct name for the libtinfo dev package
# 5.48 20210407 Add to the PKG_CONFIG_PATH for 64 bit builds
# 5.49 20210407 find mmdb libs in lib64 maybe for SSM.
# 5.50 20210407 fix previous fix
# 5.51 20210407 adjust LIBS for clipper configure for lib64 usage
# 5.52 20210511 rework the coot configure
# 5.53 20210706 use jfrog.io for boost
# 5.54 20210706 build sqllite3
# 5.55 20210727 shared-static flag --enable-shared - what *was* I thinking? Modern clipper test
# 5.56 20210816 Put libsqlite3 build into the proper log/txt file. Boost 1.72.0
# 5.57 20211019 add another make for guile-lib. Add texinfo to the dependencies for debian
# 5.58 20211019 Add a sort to the awk result when determining the tar file for the stable release
# 5.59 20220708 Use https:: instead of ftp:: for libccp4 and readline
script_version=5.59
# :: NOTE::
# this "strange" construction of variable names: x=${x:=thing} sets the
# variable x only if it has not previously been defined.
#
# So, the idea is that you write a wrapper for this script (defining typically
# AUTOBUILD_INSTALLED, AUTOBUILD_BUILD, LOGS and build_coot_prerelease) then
# source this file. That means that you (probably) don't have to edit your
# version of build-it every time it changes.
# ENABLE_PYTHON_COOT: if ENABLE_PYTHON_COOT is set to 0 or "no" then
# python coot is not enable (guile coot is enabled). if
# ENABLE_PYTHON_COOT is set, but not set to 0 or no then python coot
# is enabled. If ENABLE_PYTHON_COOT is not set, the guile-coot is
# enabled (python coot is not enabled).
# Pythonizing coot makes non-transferable binararies (why?). Let
# the pythonness be controlled on the command line:
#
# At the moment, if you build with Gtk2, you build with python, hence $build_type
# is the same thing.
#
if [ "$1" = "no-python" ] ; then
ENABLE_PYTHON_COOT=no
ENABLE_GUILE_COOT=yes
build_type=gtk2
else
if [ "$1" = "no-guile" ] ; then
ENABLE_PYTHON_COOT=yes
ENABLE_GUILE_COOT=no
build_type=gtk2-noguile
else
ENABLE_PYTHON_COOT=yes
ENABLE_GUILE_COOT=yes
build_type=gtk2-python
fi
fi
# Set the host and the OS.
# Fairly fundamental.
#
OS=$(uname)
HOST=$(hostname)
# Do we need to use a proxy server to get documents from the web? (set
# to 1 if we do)
use_proxy=${use_proxy:=}
# if we do need a proxy then we should give the proxy host and port too:
proxy_host=${proxy_host:=myproxy.com}
proxy_port=${proxy_port:=800}
no_proxy=${no_proxy:=".corp.net.com"}
# set this to true if you want to run the test suite and make binary
# bundles (needs test data and the CCP4 suite):
#
run_tests=${run_tests:=false}
# run the second test? Almost always passes and takes up lots of
# disk space
#
run_second_test=${run_second_test:=true}
# This is where the compiled binaries/libraries/data get installed:
# Note that the directory name must NOT end in a /
#
AUTOBUILD_INSTALLED=${AUTOBUILD_INSTALLED:=${HOME}/autobuild/${OS}-${HOST}}
# or perhaps, for the adventurous:
#AUTOBUILD_INSTALLED=$CCP4_MASTER
# This is where the actual build (compilation) master directory is:
# a temporary or scratch directory would be sensible.
#
# AUTOBUILD_BUILD=${HOME}/autobuild
# I'm putting my build on "scratch space"
AUTOBUILD_BUILD=${AUTOBUILD_BUILD:=$HOME/autobuild/building}
# This is where the build logs go:
# suggested value:
# LOGS=$AUTOBUILD_BUILD/logs
# but I want to put my log file on the web, so I put them here:
LOGS=${LOGS:=$HOME/public_html/build-logs/${OS}-${HOST}}
# set this to "no" if you don't want to compile the pre-release code.
# build_coot_prerelease=
build_coot_prerelease=${build_coot_prerelease:=1}
# get build specials, e.g. change the compiler or the compiler options
# (e.g build for debugging), extra libraries etc setup LD_LIBRARY_PATH
# (or whatever) to include the autobuild library dir so that
# intermediate (configure compile) programs run and the addition to
# the path of GNU make and wget.
#
# use this to specify config_extras
#
# options are: GL_prefix, e.g. SunOS has Mesa Graphics - this is
# where to find them:
# glut_prefix, optionally can use freeglut
#
# Suggested value: comment out this line
specs=${specs:=$HOME/autobuild/build-scripts/${HOST}-specials}
# Make nightly binary tarballs?
# You probably don't want to do this, so recommended is do_nightlies=0
do_nightlies=${do_nightlies:=1}
# if you do want to build them where should they go?
# NIGHTLY_DEST_DIR=$AUTOBUILD_BUILD
NIGHTLY_DEST_DIR=${NIGHTLY_DEST_DIR:=${HOME}/public_html/software/binaries/nightlies/pre-release}
# if we are not building a nightly/pre-release, i.e. this is a binary
# for a stable release, they go somewhere else:
#
STABLE_DEST_DIR=${STABLE_DEST_DIR:=${HOME}/public_html/software/binaries/stable}
# this is given args: arg1(dir) arg2(file-name)
BINARY_INSTALL_CMD=www-placement
# how do we transfer the file on the build host to the web server?
# Some systems we can simply copy the files. For others, we now have
# this "publish" mechanism (to be overwritten as needed)
publish=${publish:=:}
publish_logs=${publish_logs:=:}
# if umask was not set, then use 0022
# umask 0022
if [ -z "$umask" ] ; then
umask 0022
else
umask $umask
fi
# When we fail to extract the correct tar file from the web site, what
# shall we build instead?
#
fallback_coot_version=coot-0.4
# ----------------------------------------------------------------
# End of tinkering with parameters.
# ----------------------------------------------------------------
# First, check that this is bash.
#
if [ "$BASH" = "" ] ; then
echo this shell is not bash\!
echo this script must be run with bash\!
exit
fi
# now the functions:
function mkdir_maybe {
dir=$1
if [ ! -e "$dir" ] ; then
mkdir $dir
fi
}
# Give args: prefix-dir and (based on is-static-flag) either
# "clear-static" or "clear-dynamic"
#
function post_install_slim {
echo we are slimming directory $1
fat_dir="$1"
cleaned_dir="$2"
clear_type="$3"
echo fat_dir is $fat_dir
echo clear_type is $clear_type
echo cleaned_dir is $cleaned_dir
mkdir_maybe $cleaned_dir
mkdir_maybe $cleaned_dir/bin
mkdir_maybe $cleaned_dir/lib
# and this for pyconfig.h
if [ "$ENABLE_PYTHON_COOT" = yes ] ; then
mkdir_maybe $cleaned_dir/include
mkdir_maybe $cleaned_dir/include/$python_version
fi
lib_sos=`cd $fat_dir && ls -1 lib/lib*.so*`
lib_as=`cd $fat_dir && ls -1 lib/lib*.a`
if [ "$clear_type" = "clear-dynamic" ] ; then
keep_lib_archs="$lib_as"
fi
if [ "$clear_type" = "clear-static" ] ; then
keep_lib_archs="$lib_sos"
fi
file_list="etc info man share libexec \
libexec/coot-bin \
libexec/findwaters-bin \
libexec/findligand-bin \
libexec/mini-rsr-bin \
libexec/density-score-by-residue-bin \
bin/coot \
bin/findwaters \
bin/findligand \
bin/guile \
bin/coot-density-score-by-residue \
bin/coot-available-comp-id \
bin/coot-compare-dictionaries \
bin/coot-dictionary-bond-distributions \
bin/coot-make-shelx-restraints \
bin/lidia \
bin/curl \
$keep_lib_archs"
if [ "$ENABLE_PYTHON_COOT" = yes ] ; then
# 20090427 remove python and python config from bin dir (as it
# interfers with system python)
file_list="$file_list html \
lib/$python_version include/$python_version"
fi
echo rsyncing...
for file in $file_list ;
do
dn=$(dirname $file)
if [ -e $fat_dir/$file ] ; then
# echo rsync -axr $fat_dir/$file $cleaned_dir/$dn
rsync -axr $fat_dir/$file $cleaned_dir/$dn
else
echo $fat_dir/$file does not exist
fi
done
echo done rsyncing.
}
function make_tar {
echo in make_tar args: $1 $2
echo in make_tar: in dir: $PWD
tar_dir=$1
tar_file_name=$2
cd $install_top_dir/..
if [ -e $tar_dir ] ; then
echo taring nightly... from $tar_dir to $tar_file_name
tar czf $tar_file_name $tar_dir
status=$?
if [ "$status" != 0 ] ; then
echo ERROR:: tar czf $tar_file_name $tar_dir failed.
echo ERROR:: while in directory $(pwd)
echo ERROR:: tar failed > $tar_file_name.md5sum
rm $tar_file_name
else
md5sum $tar_file_name > $tar_file_name.md5sum
/bin/ls -l $tar_file_name >> $tar_file_name.md5sum
echo done tar successfully.
fi
else
echo ERROR:: tar target directory $tar_dir does not exist.
fi
}
function ssh_copy {
# bin_tar_file=$1
# if [ "$domainname" = "biop" ] ; then
# do_ssh_copy=true
# fi
if [ "$do_ssh_copy" = true ] ; then
dir=public_html/software/binaries/nightlies/pre-release/
echo ssh_copy copying over files using $HOME/bin/sput-with-dir $bin_tar_file $dir
$HOME/bin/sput-with-dir $bin_tar_file $dir
if [ -e $bin_tar_file.md5sum ] ; then
$HOME/bin/sput-with-dir $bin_tar_file.md5sum dir
fi
else
echo Not ssh copying file to York, $domainname
fi
}
function ssh_copy_to_biop {
bin_tar_file=$1
if [ "$do_ssh_biop_copy" = true ] ; then
target_dir=public_html/coot/software/binaries/pre-releases/
echo copying over files to Biop: $HOME/bin/sput-with-dir $bin_tar_file $target_dir
$HOME/bin/sput-with-dir $bin_tar_file $target_dir
if [ -e $bin_tar_file.md5sum ] ; then
echo and also: $HOME/bin/sput-with-dir $bin_tar_file.md5sum $target_dir
$HOME/bin/sput-with-dir $bin_tar_file.md5sum $target_dir
fi
else
echo Not ssh copying file to biop
fi
}
function ssh_copy_logs_to_biop {
local_log_dir=$1
target_dir=$2
if [ "$do_ssh_biop_copy" = true ] ; then
echo copying over log files to Biop...
target_dir=$2
$HOME/bin/sput-with-dir $local_log_dir $target_dir
else
echo Not ssh copying log files to biop
fi
}
function setup_ccp4 {
# we have access to $OS and $arch.
if test "$OS" = Linux ; then
setup_file=/y/programs/xtal/ccp4-6.0.2/ccp4-6.0.2/include/ccp4.setup-sh
if test -e $setup_file ; then
. $setup_file
else
if [ "$systype" = x86_64-centos-6 ] ; then
setup_file=/home/emsley/ccp4/setup-scripts/sh/ccp4.setup
else
if [ "$systype" = x86_64-centos-5 ] ; then
setup_file=/home/emsley/ccp4/ccp4-6.2.0/include/ccp4.setup-sh
else
setup_file=setup-ccp4
fi
fi
if test -e $setup_file ; then
echo evaluating $setup_file
. $setup_file
else
echo WARNING:: ccp4 setup file $setup_file does not exist.
fi
fi
fi
if test "$OS" = Darwin ; then
. /usr/local/ccp4-6.0.2/bin/ccp4.setup-sh
fi
}
# exit
function my_exit {
exit_arg=$1
shift
extra_args=$*
echo fail-build $extra_args > $LOGS/$build-status
if [ -e $LOGS/$test-status ] ; then
rm $LOGS/$test-status
fi
exit $exit_arg
}
# Return 0 on success, 1 on failure (or not tested)
#
#
# This can only be run when the coot tar file and greg tests have been
# untared (in this particular build)
#
# we should be in the directory where coot was untarred for building
# when this function was called.
#
function test_coot {
echo testing with greg
echo testing with greg >&2
echo currently we are here:
pwd
date
if [ "$1" != "" ] ; then
coot_binary=$1
else
coot_binary=$install_top_dir/libexec/coot-bin
fi
if test "$run_tests" = true ; then
# let's test our new coot
# for python build we need to set COOT_PYTHON_DIR and COOT_HOME
# as well as PYTHONPATH things now, because we do a "proper"
# import * from coot, which needs to find coot.py the
# conventional/pythonic way. If pythonic coot doesn't start properly,
# the greg tests fail.
COOT_PYTHON_DIR=$install_top_dir/share/coot/python
PYTHONPATH=$COOT_PYTHON_DIR
PYTHONHOME=$install_top_dir
export COOT_PYTHON_DIR
export PYTHONPATH
export PYTHONHOME
# the greg tests are where the coot source code was untarred.
#
if [ ! -d greg-tests ] ; then
echo greg-tests dir missing in this directory:
pwd
return 1
fi
setup_ccp4
cat <<EOF > command-line-greg.scm
(use-modules (ice-9 greg))
(set! greg-tools (list "greg-tests"))
(set! greg-debug #t)
(set! greg-verbose 5)
(let ((r (greg-test-run)))
(if r
(coot-real-exit 0)
(coot-real-exit 1)))
EOF
echo $install_top_dir/bin/coot --no-graphics --script command-line-greg.scm
$install_top_dir/bin/coot --no-graphics --script command-line-greg.scm
status=$?
if [ $status = 0 ] ; then
echo test_coot: coot test passed
return 0
else
echo test_coot: coot test failed
return 1
fi
else
echo run_tests is not true, not testing.
return 1
fi
}
# Return 0 on success, 1 on failure (or not tested)
#
# we should be in the directory where coot was untarred for building
# when this function was called.
#
function test_coot_python {
echo testing with python unittest
echo testing with python unittest >&2
echo currently we are here:
pwd
if test "$run_tests" = true ; then
# let's test our new coot
# for python build we need to set COOT_PYTHON_DIR and COOT_HOME
# as well as PYTHONPATH things now
COOT_PYTHON_DIR=$install_top_dir/share/coot/python
PYTHONPATH=$COOT_PYTHON_DIR
PYTHONHOME=$install_top_dir
export COOT_PYTHON_DIR
export PYTHONPATH
export PYTHONHOME
echo $install_top_dir/bin/coot --no-graphics --script python-tests/coot_unittest.py
$install_top_dir/bin/coot --no-graphics --script python-tests/coot_unittest.py
status=$?
if [ $status = 0 ] ; then
echo test_coot_python: coot test passed
return 0
else
echo test_coot_python: coot test failed
return 1
fi
else
return 1
fi
}
function fixup_libcurl {
sed s,-L/usr/lib,, curl-config > curl-config.tmp
mv curl-config.tmp curl-config
sed s,-L/usr/lib,, lib/libcurl.la > lib/libcurl.la.tmp
mv lib/libcurl.la.tmp lib/libcurl.la
}
# now on to some code!
if [ "$use_proxy" = 1 ] ; then
# establish proxy settings
printf "Proxy user: "
read proxy_user
printf "Proxy password: "
read -s proxy_pass
printf "\n"
http_proxy="http://${proxy_user}:${proxy_pass}@${proxy_host}:${proxy_port}/"
https_proxy="http://${proxy_user}:${proxy_pass}@${proxy_host}:${proxy_port}/"
ftp_proxy="http://${proxy_user}:${proxy_pass}@${proxy_host}:${proxy_port}/"
ssl_proxy="http://${proxy_user}:${proxy_pass}@${proxy_host}:${proxy_port}/"
export http_proxy https_proxy ftp_proxy ssl_proxy no_proxy
fi
#intltool-update for libgnomecanvas is here /usr/share/intltool-debian/intltool-update on ubuntu
# it's in /usr/bin on RHEL
PATH=/usr/share/intltool-debian:$PATH
# use the right (GNU) tar and provide the path to wget (needed
# for downloads) and to GNU make - (which is necesary for python
# at least).
#
# So that python and the *-configs are found when it is installed:
# A bit of a kludge because we do testing for pre-release later.
# It's a logical mess.
#
if test "$build_coot_prerelease" = 1 ; then
PATH=${AUTOBUILD_INSTALLED}-pre-release-gtk2/bin:$PATH
else
PATH=$AUTOBUILD_INSTALLED-gtk2/bin:$PATH
fi
PATH=$PATH:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin:
PATH=$PATH:/etc:/usr/etc
#
export PATH
echo PATH is now: $PATH
echo AUTOBUILD_BUILD is $AUTOBUILD_BUILD
# This is where the sources downloaded from network go:
AUTOBUILD_SOURCES=${AUTOBUILD_BUILD}/sources
echo AUTOBUILD_SOURCES is $AUTOBUILD_SOURCES
if (! test -d ${AUTOBUILD_SOURCES}) ; then
mkdir -p ${AUTOBUILD_SOURCES}
fi
# now make the build logs directory
mkdir -p $LOGS
shared_static_flag="--disable-shared" # what!? 20210727-PE
shared_static_flag="--enable-shared"
shared_lib_ext=so
systype=unknown
# malloc.h business, Darwin does not have malloc.h
# used in the gtk_canvas build
have_malloc=1
if test "$OS" = "Darwin" ; then
have_malloc=0
fix_ulong=1
update_libtool=1
update_config_guess_sub=1
shared_static_flag="--disable-static"
shared_lib_ext=dylib
need_readline_patch=1
# uname -a gives processor type in last field on Darwin
processor=$(uname -a | awk '{print $(NF)}')
need_gtk_imlib_libtool_fix=1
if test "$processor" = "i386" ; then
need_glib_getpwuid_fix=1
need_glib_poll_fix=1
need_gtk_canvas_patch=1
fi
osversion=$(sw_vers -productVersion)
systype=MacOSX-${osversion}-${processor}
fi
# redirect the output.
#
# exec 2>&1 > $LOGS/$HOST.log
# Try not to redirect standard out so that it goes to
# the sub-shell log? (testing)
echo INFO:: redirecting std output to $LOGS/build.log
exec > $LOGS/build.log
# local tinkering because our sgi runs out of room on /tmp on compiling
if [ $HOST = batman ] ; then
TMPDIR=$HOME/tmp
export TMPDIR
fi