#!/bin/bash
# 
# -*-shell-script-*-
# Local Variables:
# mode: shell-script
# sh-shell: bash
# End:
#  ----------------- this is now the python-3 version ----------------
#
# 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 by Medical Reserch Council
# Copyright 2019, 2020, 2021, 2022, 2023, 2024 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.
# 6.00 20200812 include glm
# 6.01 20210430 pkg-config tweak and no remove rdkit libs for coot configure
# 6.02 20220417 add ffi into Python setup.py
# 6.03 20220704 work on GLIB and python modules
# 6.04 20220705 Python still doesn't build (on cluster) - add debugging
# 6.05 20220706 Use https:: instead of ftp::
# 6.06 20220707 try export LD_LIBRARY_PATH=$install_top_dir/lib in Coot section
# 6.07 20220710 libffi fixes for python
# 6.08 20220803-PE pygobject cleanups
# 6.09 20220907-PE meson adjustment for compiling glib (what a pain)
# 6.10 20230603-PE remove goocanvas
# 6.11 20231113-PE print out the script_version
# 6.12 20240105-PE link $HOME/data/greg-data for the testing step
# 6.13 20240216-PE Install Darwin OpenSSL in $install_top_dir
# 6.14 20240220-PE Set the C++ flags for Catch2 (needed for macOS/clang) and build with CMake
# 6.15 20240220-PE OpenSSL and python apiflags and boost bjam updates
# 6.16 20240228-PE Add status of FFTW building
# 6.17 20240229-PE Portentious day. Adding in gettext for libintl for python and rdkit
# 6.18 20240304-PE Remove the --pydebug from Python's configuration
# 6.19 20240306-PE Don't build gettext on anything other than Darwin
# 6.20 20240326-PE Add cairo
# 6.21 20240327-PE Reposition the cairo build (after ninja)
# 6.22 20240427-PE Fix-ups for building on fedora (partial)
# 6.23 20250214-PE Remove build_type (gtk4) from directory names
script_version=6.22



echo ==================================================== add test for SWIG version
echo ==================================================== add test for CMake version
echo this is script version $script_version


# :: 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.
#

# Set the host and the OS.
# Fairly fundamental.
#

# arch needs inetutils for hostname
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}}

if test x$GITHUB_ENV = x ; then
    : # we are not in a hithub actions build
else
    if [ "$CHAPI_ONLY" = true ] ; then
        if [ $OS = Darwin ]  ; then
            AUTOBUILD_INSTALLED=$HOME/install/chapi-Darwin-macos
        else
            AUTOBUILD_INSTALLED=$HOME/install/chapi-Linux-ubuntu
        fi
    else
        AUTOBUILD_INSTALLED=$HOME/install/coot-Linux-ubuntu
    fi
fi

# 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}

# if we are not in chapi mode, we ask
# where has gtk been installed if this is Mac OS?
# (this was from when gtk3 could be installed on macOS).
# I should add /usr/local of course these days
if test "$CHAPI_ONLY" = true ; then
    :
else
   if test "$OS" = "Darwin" ; then
      if test -n "$gtk" ; then
         if test -d "$gtk" ; then
            : # pass, good
         else
            echo gtk variable must point to the directory where gtk has been installed
         fi
      else
         # gtk was not set, let's try to guess
         testdir=$HOME/gtk/inst
         if test -d $testdir ; then
            gtk=$HOME/gtk/inst
         else
            echo this build script needs to know where gtk has been installed
            echo \(at the moment\)
            echo set gtk to point to the directory where gtk has been installed
            exit 2
         fi
      fi
   fi
fi


# 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)


# 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-make-shelx-restraints     \
	bin/coot-dictionary-bond-distributions \
	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 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 it's not there, then let's link it.
   if [ ! -d greg-tests ] ; then
      echo greg-tests dir missing in this directory:
      pwd
      echo trying to link
      if [ -d ~/data/greg-data ] ; then
          ln -s ~/data/greg-data .
      else
          echo $HOME/data/greg-data data files are not in place
      fi
      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 we can set the gtk version
gtk_version=${gtk_version:=4}
build_type="" # python and gtk4 are implicit - we will do guile when we can


# 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



# 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/bin:$PATH
else
   PATH=$AUTOBUILD_INSTALLED/bin:$PATH
fi
   
PATH=$PATH:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin:
PATH=$PATH:/etc:/usr/etc
#

# This is where the sources downloaded from network go:
AUTOBUILD_SOURCES=${AUTOBUILD_BUILD}/sources
if (! test -d ${AUTOBUILD_SOURCES}) ; then
   mkdir -p ${AUTOBUILD_SOURCES}
fi

export PATH
echo PATH is now: $PATH
echo LOGS is $LOGS
echo AUTOBUILD_SOURCES is $AUTOBUILD_SOURCES
echo AUTOBUILD_BUILD is $AUTOBUILD_BUILD
echo AUTOBUILD_INSTALLED is $AUTOBUILD_INSTALLED
echo GITHUB_ENV $GITHUB_ENV
echo GITHUB_WORKSPACE $GITHUB_WORKSPACE

# now make the build logs directory
mkdir -p $LOGS

shared_static_flag="--disable-shared" # huh?
shared_static_flag="--disable-static"
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 "$OS" = "Darwin" ; then
   have_malloc=0
   fix_ulong=1
   update_libtool=1
   update_config_guess_sub=1
   shared_static_flag="--disable-static"
   shared_lib_ext=dylib
   # what happens if I do this?
   # need_readline_patch=1
   # uname -a gives processor type in last field on Darwin
   processor=$(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
   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)

if [ -n "$TEE_STDOUT" ]; then
   echo INFO:: std output will be both printed here and written to $LOGS/build-gtk4.log
   exec > >(tee $LOGS/build-gtk4.log)
else
    if test "$CHAPI_ONLY" = true ; then
	echo INFO:: redirecting std output to $LOGS/build-chapi.log
	exec > $LOGS/build-chapi.log
    else
	echo INFO:: redirecting std output to $LOGS/build-gtk4.log
	exec > $LOGS/build-gtk4.log
    fi
fi

date
#
if [ -n "$specs" ] ; then
   if [ -e "$specs" ] ; then
	echo running these extras:
	echo . --------------------------------
	cat "$specs"
	. "$specs"
	echo . --------------------------------
   fi
fi

#initially unset:
if test $OS = Linux ; then
  architecture=$(uname -i)
  # uname -i and uname -p (strangely) return unknown on my ubuntu
  if test $architecture = unknown ; then
     architecture=$(uname -m)
  fi
fi
# now architecture is something like i386 or x86_64

# now test for 64 bit Linux:
if test "$OS" = "Linux" ; then
   processor=$(uname -a | awk '{print $NF}')
   # on my Redhat i386, uname returns:
   # Linux kalypso 2.6.12-1.1398_FC4 #1 Fri Jul 15 00:52:32 EDT 2005 i686 athlon i386 GNU/Linux
   # 64 bit Ubuntu:
   # Linux kalypso 2.6.22-14-generic #1 SMP Sun Oct 14 21:45:15 GMT 2007 x86_64 GNU/Linux
   # from that I presume we need $(NF-2) to get the arch (not NF-1).  Eh?
   # arch=`uname -a | awk '{print $(NF-1)}'`
   arch=$(uname -a | awk '{print $(NF-1)}')
   echo currently architecture is $architecture
   if test "$architecture" = x86_64 -o "$architecture" = ia64 -o "$architecture" = aarch64 ; then
      update_libtool=1
      update_config_guess_sub=1
   else
       echo this is not a 64 bit machine
   fi
fi


if test $OS = Linux ; then

   if [ -e /bin/rpm ] ; then
      if rpm -a ; then
         if test -e /etc/os-release ; then
             # 20240914 strip quote marks also now
             dist_name=$(grep ^ID= /etc/os-release | sed -e 's/ID=//' -e 's/"//g')
             dist_ver=$(grep ^VERSION_ID /etc/os-release | sed -e 's/VERSION_ID=//')
         else
             for i in fedora-release redhat-release redhat-release-workstation centos-release sl-release openSUSE-release ; do
                 rpm -q --qf '%{name}' ${i}
                 dist=`rpm -q --qf '%{name}' ${i}`
                 echo  dist is $dist
                 dist=`rpm -q --qf '%{name}' ${i}`
                 if test $? = 0 ; then
                     echo passes with dist $dist
                     dist_name=$(echo ${dist} | sed -e 's/\-release//g' -e 's/\-workstation//g')
                     dist_ver=$(rpm -q --qf '%{version}' ${i})
                     break
                 else
                   echo does not pass
                   dist_name='unknown'
               fi
            done
        fi
      else
         dist_name='unknown'
      fi
   else
     if test -e /etc/os-release ; then
         # 20240914 strip quote marks also now
         dist_name=$(grep ^ID= /etc/os-release | sed -e 's/ID=//' -e 's/"//g')
         dist_ver=$(grep ^VERSION_ID /etc/os-release | sed -e 's/VERSION_ID=//')
         if grep BUILD_ID=rolling /etc/os-release ; then
             dist_ver=rolling
         fi
     fi
   fi

   echo here 2222 with dist_name $dist_name
   echo here 2222 with dist_ver $dist_ver

  case ${dist_name} in

    redhat* )
    case ${dist_ver} in
      [0-9] | [0-9].[0-9]* )
        systype=${architecture}-redhat-${dist_ver}
      ;;
      * )
        systype=${architecture}-rhel-$(echo ${dist_ver} | sed s/[A-Za-z]//g)
        if [ $arch = x86_64 ] ; then
	   if [ $dist_ver = 4WS ] ; then
	      echo RedHat 4 Linux x86_64 detected. need to update libtool
              update_libtool=1
              # stupid la file of libcur puts /usr/lib in the link path (early).  This causes link
              # problems on 64 bit RHEL4.  So lets fix curl-config and libcurl.la
              post_process_libcurl=1
	   fi
        fi
      ;;
    esac
    ;;

    fedora | centos | openSUSE | rocky | almalinux)
      systype=${architecture}-${dist_name}-${dist_ver}
    ;;


    sl )
      systype=${architecture}-scientific-linux-${dist_ver}
      ;;

    arch )
      systype=${architecture}-arch
      ;;


    * )
      if test -r /etc/issue; then
          echo this fallback case............
          dist_name=$(awk 'NR==1{print tolower($1)}' /etc/issue)
          if [ "$dist_name" = "debian" ] ; then
              dist_ver=$(awk  'NR==1{x=tolower($2); y=tolower($3); gsub("/","-",x); gsub("/","-",y); print x "-" y}' /etc/issue)
          else
              dist_ver=$(awk  'NR==1{x=tolower($2); gsub("/","-",x); print x}' /etc/issue)
          fi
          systype=${architecture}-${dist_name}-${dist_ver}
      else
          systype=${architecture}-unknown-Linux
      fi
    ;;
  esac
fi

echo dist_name $dist_name
echo systype $systype

if test $OS = IRIX64 ; then
   osversion=`uname -r`
   systype=${osversion}-sgi
fi

if test $OS = IRIX ; then
   osversion=`uname -r`
   systype=${osversion}-sgi
fi

if test $OS = OSF1 ; then
   osversion=`uname -r | sed s/V//g`
   systype=${osversion}-OSF1
fi

echo systype: $systype

echo update_libtool: $update_libtool
echo update_config_guess_sub: $update_config_guess_sub


# we need these dependencies:
# - libgtk-3-dev
# - git
# - libsqlite3-dev  # needed for python compilation by jupyterlab

# check dependencies for Ubuntu.
case $dist_name in
   *ubuntu*)

      dep_list='
       patch
       pkg-config
       m4
       g++
       git
       libtool
       cmake
       flex
       bison
       gfortran
       autoconf
       automake
       libssl-dev
       libblas-dev
       liblapack-dev
       libc6-dev
       libncurses-dev
       libjpeg-dev
       libgtk-4-dev'
       # gfortran is for numpy
      if test "$CHAPI_ONLY" = true ; then
          dep_list='
          patch
          pkg-config
          m4
          g++
          git
          libtool
          cmake
          flex
          bison
          gfortran
          autoconf
          automake
          libssl-dev
          libblas-dev
          liblapack-dev
          libc6-dev
          libncurses-dev
          libjpeg-dev'
      fi

      for dep in $dep_list
      do
         echo $dep
         if dpkg-query --status $dep > /dev/null ; then
            echo system has $dep
         else
            echo ======== $dep is missing ======
            missing_list="$missing_list $dep"
         fi
      done
      if [ "$missing_list" != '' ] ; then
         echo " "
         echo " "
         echo install these packages: $missing_list
         echo then re-run
         echo " "
         echo " "
         my_exit 2
      fi
      # swig is special.  On 6.06 it is not new enough.  So Kevin compiled his own.
      # swig is tested for later separately.

      ;;

    debian)
      # python is needed to configure ninja. Sigh. flex and bison are needed for gobject-introspection
      # libbz2-dev is for building python so that torchvision can be installed.
      # libsqlite3-dev is needed for ipython (so that Python is compiled "correctly")
      dep_list='wget pkg-config libgtk-4-dev build-essential libdw-dev libvorbis-dev libncurses5-dev libssl-dev g++ git libxext-dev libglu1-mesa-dev mesa-common-dev flex bison m4 cmake autoconf gfortran rsync libbz2-dev'
      # converted from dep_list='libncurses5-dev g++ libxext-dev libglu1-mesa-dev mesa-common-dev libgtk2.0-dev'
      # not tested

      for dep in $dep_list
      do
         echo $dep
         if dpkg-query --status $dep > /dev/null ; then
            echo system has $dep
         else
            echo ======== $dep is missing ======
            missing_list="$missing_list $dep"
         fi
      done
      if [ "$missing_list" != '' ] ; then
         echo " "
         echo " "
         echo install these packages: $missing_list
         echo then re-run
         echo " "
         echo " "
         my_exit 2
      fi

      ;;

   # centos7 needs package gtk3-devel to be installed(!)

   # fedora needs automake

esac

# 20240305 too noisy
# give us some diagnostic shell information:
# (what extra things did $specs give us?)
#
# if [ "$use_proxy" = 1 ] ; then
#  echo no diagnostic variables, we are using a proxy.
# else
#  set
# fi

# On 64 bit redhat 4, we (might) need to add X11 to the path for freeglut configure.
#
echo \n\n ============================================ start ============================
echo INFO:: MACHTYPE is $MACHTYPE
echo INFO:: systype is $systype
if [ "$systype" = x86_64-rhel-4 ] ; then
    PATH=$PATH:/usr/X11R6/bin
    export PATH
fi

# Do we link with sqlite (for the ligands database)?
# We allow the calling script to set use_sqlite=yes
use_sqlite=${use_sqlite:=no}

if [ "$use_sqlite" = "yes" ] ; then
    sqlite_config_args=--with-sqlite3
else
    sqlite_config_args=
fi

# We want to add some compiler info in the directory name.
# If CC is set, use that,
# If not, try gcc,
# if not, try cc
#
# Similarly for the c++ compiler info
# If CXX is set, use that
# if not, try g++
# if not, try c++

if [ -n "$CC" ] ; then

        # CC was set
        echo \$HOST is $HOST
        echo \$OS is is $OS
        gcctest=`$CC --version | awk 'NR==1 {print $2}'`
        echo debugging \$CC was $CC
        echo debugging gcctest is $gcctest and "(GCC)" is "(GCC)"
        if [ "$gcctest" != '(GCC)' ] ; then
           # but not gcc
           v=$CC-`$CC -v`
              if [ $? -ne 0 ] ; then
                 v="missing_version"
              fi
        else
              # gcc
              v=$CC-`$CC --version | awk 'NR==1 {print $3}'`
        fi

else
	# CC not set
	v=gcc-`gcc -dumpversion | head -1`
        if [ $? -ne 0 ] ; then
		# not gcc
	        # try cc
		v=cc-`cc -v`
		if [ $? -ne 0 ] ; then
		   v="missing_version"
		fi
	fi
fi


if [ -n "$CXX" ] ; then

	# CXX was set
	gxxtest=$($CXX --version | awk 'NR==1 {print $2}')
        # typically gxxtest is set to "(GCC)", but not on Ubuntu, where the line is:
	# g++ (Ubuntu 4.4.3-4ubuntu5.1) 4.4.3
        # Scientific Linux:
        # g++ (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4)
        # RHEL 6:
        # g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3)
        echo gxxtest: $gxxtest
	if [ "$gxxtest" != "(GCC)" ] ; then

             # but not g++ (?).  Maybe it was Ubuntu...

             case "$gxxtest" in
                *[Uu]buntu*)
                   w=$($CXX --version | head -1 | awk '{print $3}' | tr -d ')')
                   ;;

                *)
                   w=$CXX-$($CXX -v | head -1 | sed 's/ / /g')
   	           if [ $? -ne 0 ] ; then
	    	      w="missing_cxx_version"
	           fi
                   ;;
             esac
	else
           # g++
           w=$CXX-$($CXX --version | awk 'NR==1 {print $3}')
	fi
else
	# CXX not set
	w=g++-`g++ -dumpversion | head -1`
        if [ $? -ne 0 ] ; then
		# not g++
	        # try c++
		w=c++-`c++ -v`
		if [ $? -ne 0 ] ; then
		   # try CC
		   w=CC-`CC -v`
		   if [ $? -ne 0 ] ; then
		      w="missing_c++_version"
		   fi
		fi
	fi
        # note that g++ 3.2 cannot compile clipper's test_contrib.cpp.
        # So, if we have g++ 3.2 or less, then we need to get and apply
        # test_contrib.cpp.patch
        # add a space before argument setting
	awk -v version=$w 'BEGIN{ exit (version+0 >= 3.3)}'
        wvers=$?
        if [ $wvers = 0 ] ; then
	   need_clipper_contrib_patch=true
        fi
fi

# do we actually have g++ (or c++?)
if ! g++ --version ; then
   if ! c++ --version ; then
      echo no c++/g++ compiler.  Exit now
      my_exit 2
   fi
fi




# so now we have v and w set to something.  We
# need to sanitize that something.
v_fid=`echo $v | sed 's/ /_/g'`
w_fid=`echo $w | sed 's/ /_/g'`

compilers_dir=gtk4-coot-${v_fid}_and_${w_fid}
if test "$CHAPI_ONLY" = true ; then
    compilers_dir=chapi-${v_fid}_and_${w_fid}
fi
HOSTLOGDIR=$LOGS/$compilers_dir
if [ ! -e $HOSTLOGDIR ] ; then
  mkdir -p $HOSTLOGDIR
  if [ $? -ne 0 ] ; then
    #
    echo DISASTER: could not make directory $HOSTLOGDIR
    echo exiting.
    my_exit 2
  fi
fi

# 20120223 Whether or not we need to patch guile depends on the
# version of the compiler (or so I currently believe).  So here we do
# a string comparison vs "4.5".  If greater than this (e.g. "4.5.1") then
# we do need the patch.
#
if awk -v v_fid=$v_fid 'BEGIN{if (v_fid > "gcc-4.5") exit 1 ; else exit 0}' ; then
  echo gcc version: $v_fid
else
  need_guile_unused_values_patch=true
  echo new version path
fi

echo need_guile_unused_values_patch is $need_guile_unused_values_patch



# need to add test that make is GNU make, and set number of processor if we have
# enough memory and cpus...
#
echo "Testing version of make"
MAKE=make
if make --version ; then
   # let's try to set some args
   if [ -e /proc/meminfo ] ; then
      memory_kb=$(awk '/MemTotal:/ {print $2} ' /proc/meminfo)
      if [ "$memory_kb" -gt 2000512 ] ; then
         if [ -e /proc/cpuinfo ] ; then
            if np=$(grep processor /proc/cpuinfo | wc -l) ; then
               # limit to 8 processors
               if [ "$np" -gt 8 ] ; then
                  np=8
               fi
               if [ "$HOST" = hal.lmb.internal ] ; then
                  np=64
               fi
               echo using $np processors in compilation
               MAKE="make -j$np"
               echo MAKE set to $MAKE
            fi
         fi
      fi
   fi
   if [ $OS = Darwin ] ; then
      np=$(system_profiler SPHardwareDataType | awk '/Total Number/ { print $5 }')
      MAKE="make -j$np"
   fi
else
   # definately not GNU make
   # Try gmake then....
   gmake --version
   if [ $? -ne 0 ] ; then
      nomake=1
   else
      MAKE=gmake
      nomake=0
   fi
   if [ $nomake -eq 1 ] ; then
      echo Ooops.  Your make '(' `which make` ')' is not GNU make and gmake not found.
      echo Exiting now.
      my_exit 2
   fi
fi

echo number of processors for compiling: $np

echo testing for patch
patch --version > /dev/null
if [ $? -ne 0 ] ; then
   echo no patch - exit now
   my_exit 2
fi

echo testing awk type \(prefer GNU awk\)
if awk --version ; then
   echo good, you have an awk from GNU.
else
   echo WARNING:: awk is not a GNU awk, trouble ahead possibly.
fi



########################################################################
# cmake
########################################################################

r=$(cmake --version)
echo $r

case $r in

cmake\ version\ 3.1[0-9]*)
    echo found recent cmake
    cmake_is_good=true
    ;;

cmake\ version\ 3.[2-9]*)
    echo found recent cmake
    cmake_is_good=true
    ;;

cmake\ version\ 4*)
    echo found recent cmake
    cmake_is_good=true
    ;;

esac

echo cmake_is_good: $cmake_is_good
if [ "$cmake_is_good" = true  ] ; then
    echo cmake passes
else
    echo $r
    echo cmake too old - Version 3.2 or later is needed. Ending now.
    exit 2
fi



# create $AUTOBUILD_BUILD directory

if [ ! -d "$AUTOBUILD_BUILD" ] ; then
   mkdir "$AUTOBUILD_BUILD"
   if [ $? -ne 0 ] ; then

        prev_dir=$(dirname $AUTOBUILD_BUILD)
        echo $prev_dir
        if [ ! -d "$prev_dir" ] ; then
           mkdir $prev_dir
           mkdir "$AUTOBUILD_BUILD"
        fi
   fi

   if [ ! -d "$AUTOBUILD_BUILD" ] ; then
      # echo mkdir of the AUTOBUILD_BUILD \(i.e. "$AUTOBUILD_BUILD"\) failed.
      my_exit 2
   fi

fi


start_dir=$PWD
echo start_dir $start_dir
cd $AUTOBUILD_BUILD
if [ $? -ne 0 ] ; then
	echo $AUTOBUILD_BUILD failed for some reason. Now in `pwd`
fi
# for ccp4 (20051104) compatibility, we can't use colons in the date string
date=$(date -u +'%Y-%m-%d__T%H_%M_%S')
echo Date: $date

# now in $AUTOBUILD_BUILD
BUILDING_DIR=${BUILDING_DIR:=${HOST}_$date}
mkdir $BUILDING_DIR
if [ $? -ne 0 ] ; then
	echo mkdir  $BUILDING_DIR failed for some reason. Now in `pwd`
fi
cd $BUILDING_DIR
if [ $? -ne 0 ] ; then
	echo cd $BUILDING_DIR failed for some reason. Now in `pwd`
fi
build_dir=`pwd`


# test for pkg-config
if type pkg-config ; then
   if pkg-config --atleast-pkgconfig-version 0.16 ; then
      build_pkg_config=
      echo pkg-config is new enough `pkg-config --version`
   else
      build_pkg_config=1
      echo pkg-config should be built \(but won\'t be\).
   fi
else
   echo pkg-config doesn\'t exist.
fi

echo checking wget
echo which wget
which wget
# use -P for timestamping
# Note that now wget depends on libhogweed and that depends on libgmp
# but we are compiling an old version of gmp (not sure that we need
# an old version) and libhogweed refers to a (now) non-existant
# functions and the dynamic loading fails.
# This setting of the alias fails.  It works on the command line.
# -nv is means not-verbose (but not quiet)
# WGET="LD_LIBRARY_PATH=/usr/lib wget -N -P ${AUTOBUILD_SOURCES}"
# WGETO="LD_LIBRARY_PATH=/usr/lib wget   -P ${AUTOBUILD_SOURCES}"
WGET="wget -nv -N -P ${AUTOBUILD_SOURCES}"
WGETO="wget -nv  -P ${AUTOBUILD_SOURCES}"

# latest version (without .tar.gz extension)
coot_version=$fallback_coot_version

pre_release_server_dir=http://www.ysbl.york.ac.uk/~emsley/software/pre-release/
pre_release_server_dir=http://lmb.bioch.ox.ac.uk/coot/software/source/pre-releases/
pre_release_server_dir=http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/coot/source/pre-releases/
pre_release_server_dir=http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/pre-releases
#
release_server_dir=http://www.ysbl.york.ac.uk/~emsley/software
release_server_dir=http://lmb.bioch.ox.ac.uk/coot/software/source/releases
release_server_dir=http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/coot/source/releases/
release_server_dir=http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases
#
extras_place=http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies


${WGETO} -O ${AUTOBUILD_SOURCES}/index.html -o ${AUTOBUILD_SOURCES}/wget-e.s.p.log $release_server_dir/
${WGETO} -O ${AUTOBUILD_SOURCES}/index-pre-release.html -o ${AUTOBUILD_SOURCES}/wget-e.s.p.log $pre_release_server_dir/
pre_release_files_html="none"
if [ $build_coot_prerelease = 1 ]  ; then
   pre_release_files_html=${AUTOBUILD_SOURCES}/index-pre-release.html
fi
if [ $build_coot_prerelease = yes ]  ; then
   pre_release_files_html=${AUTOBUILD_SOURCES}/index-pre-release.html
fi

coot_version_tmp=$(awk  ' /a href=.*.tar.gz/ {f=$6; split($6, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); print file}' \
$pre_release_files_html | tail -1)

echo pre_release_files_html $pre_release_files_html
echo coot_version_tmp : $coot_version_tmp :

if [ -z "$coot_version_tmp" ] ; then
    echo clever coot_version extraction failed, using default.
else
    coot_version=$coot_version_tmp
    echo clever coot_version succeeded, setting coot_version to $coot_version from extraction
fi


# override the switch which turns off the building of the pre-release here:
# build_coot_prerelease=1

# Let's initially set coot_prerelease_exists to not-exist, then we
# try to download it from the Coot web site, and if it exists we set
# coot_prerelease_exists to 1.  If it doesn't exist, we don't do that
# of course and we also don't make the install_top_dir to be the pre-release
# directory later on.
coot_prerelease_exists=

# coot_version_pre no longer has .tar.gz extension

if test "$build_coot_prerelease" = 1 ; then

   echo debug:: ${WGETO} -O ${AUTOBUILD_SOURCES}/index.html -o ${AUTOBUILD_SOURCES}/wget-e.s.p.log $pre_release_server_dir/
   ${WGETO} -O ${AUTOBUILD_SOURCES}/index.html -o ${AUTOBUILD_SOURCES}/wget-e.s.p.log $pre_release_server_dir/
   coot_version_pre=$(awk  ' /a href=.*.tar.gz/ {f=$6; split($6, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); print file}' \
       ${AUTOBUILD_SOURCES}/index.html | tail -1)

   echo INFO:: building pre-release and coot_version_pre is $coot_version_pre
   if [ -z "$coot_version_pre" ] ; then
      # this path when there are no pre-releases to be built, i.e. build the latest release.
      echo trying to build pre-release coot, but failed to find pre-release version
      echo make a stable release then
      build_coot_prerelease=
      BINARY_TAR_DEST_DIR=$STABLE_DEST_DIR
      mkdir -p ${BINARY_TAR_DEST_DIR}/holding

      ${WGETO} -O ${AUTOBUILD_SOURCES}/index.html -o ${AUTOBUILD_SOURCES}/wget-e.s.p.log $release_server_dir/
      echo examining release server files ${AUTOBUILD_SOURCES}/index.html
      # coot_version=$(awk  ' /compressed.*a href=/ {f=$6; split($6, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); files[file]=1; } END { for (file in files) { final=file } ; print final } '
      # have another go at latest version extraction.
      coot_version=$(awk '/compressed.*a href=/ {f=$6; split($6, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); files[++n]=file; } END {  for (file in files) print files[file]}'  \
          ${AUTOBUILD_SOURCES}/index.html | sort | tail -1)
      echo coot_version $coot_version

   else
      build_coot_prerelease=1  # belt and braces
      coot_prerelease_exists=1
      # tinker with coot_prefix, it is generic_prefix with pre-release added to prefix dir
      coot_prefix="--prefix=${AUTOBUILD_INSTALLED}-pre-release ${config_extras:-}"
      coot_source_tar_file=${pre_release_server_dir}/$coot_version_pre.tar.gz
      echo DEBUG:: set coot_source_tar_file to $coot_source_tar_file
      coot_version=`echo $coot_version_pre | sed s/\.tar.gz//`
      BINARY_TAR_DEST_DIR=$NIGHTLY_DEST_DIR
      mkdir -p ${NIGHTLY_DEST_DIR}
      mkdir -p ${BINARY_TAR_DEST_DIR}/holding
      echo INFO:: set the target destination for binary tar file \(BINARY_TAR_DEST_DIR\) to $NIGHTLY_DEST_DIR
   fi
else
    # this is a stable release

    echo ============= This is a stable build ==============

    ${WGETO} -O ${AUTOBUILD_SOURCES}/index.html -o ${AUTOBUILD_SOURCES}/wget-e.s.p.log $release_server_dir/
    echo examining release server files ${AUTOBUILD_SOURCES}/index.html
    coot_version=$(awk  ' /compressed.*a href=/ {f=$6; split($6, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); files[file]=1; } END { asort(files, indices) ; for (file in files) { final=file } ; print final } ' \
        ${AUTOBUILD_SOURCES}/index.html | tail -1)
    if test -z "$coot_version" ; then
       # maybe it wasn't GNU awk (we can't sort the associative array), this will pick a "random" arry key -> coot_version
       coot_version=$(awk  ' /compressed.*a href=/ {f=$6; split($6, arr, "\""); file=arr[2]; gsub(".tar.gz", "", file); files[file]=1; } END { for (file in files) { final=file } ; print final } ' \
        ${AUTOBUILD_SOURCES}/index.html | tail -1)
    fi
    echo coot_version $coot_version

    BINARY_TAR_DEST_DIR=$STABLE_DEST_DIR
    mkdir -p ${BINARY_TAR_DEST_DIR}
    mkdir -p ${BINARY_TAR_DEST_DIR}/holding
fi

echo INFO:: binary tar destination dir: BINARY_TAR_DEST_DIR is $BINARY_TAR_DEST_DIR



echo INFO:: coot_version_pre is $coot_version_pre
echo INFO:: build_coot_prerelease is $build_coot_prerelease
echo INFO:: release_server_dir is $release_server_dir
echo INFO:: coot_version is $coot_version
echo INFO:: build_type is $build_type



# set the build prefix for installed stuff.  Put everything in the
# pre-release directory if we are building a pre-release.
# (Perhaps this bit of code should go down lower, where we test
# build_coot_prerelease again
#
# we need install_top_dir because we use it to copy over coot.py
# to the install python directory.

# Notes for SSL with python:
# after configure, run this sed:
# real_ssl_prefix=/usr  # for mac, for PC, libs go in /usr/lib64 and
# sed -i -e "s?#SSL=.*?SSL=$real_ssl_prefix?" -e 's/^#_ssl/_ssl/' -e's/^#.*-DUSE_SSL/    -DUSE_SSL/' -e 's?^#.*-L$(SSL)/lib?    -L$(SSL)/lib?' Modules/Setup
# also add --with-ensurepip=install
# For ubuntu, you need system OpenSSL:
# sudo apt-get install openssl-dev
#
if [ "$build_coot_prerelease" = 1 ] ; then
    if [ "$coot_prerelease_exists" = 1 ] ; then
      generic_prefix="--prefix=${AUTOBUILD_INSTALLED}-pre-release ${config_extras:-}"
      coot_prefix="$generic_prefix"
      install_top_dir=${AUTOBUILD_INSTALLED}-pre-release
      # python seems to link OK on Darwin, so no need for this jiggery pokery
      if [ $(uname) != Darwin ] ; then
         # 20220228-PE also -L$install_top_dir/lib64
         python_lib_flags=LDFLAGS="-L$install_top_dir/lib64 -Wl,--rpath=${AUTOBUILD_INSTALLED}-pre-release/lib"
         python_ldflags="LDFLAGS=-Wl,--rpath=${AUTOBUILD_INSTALLED}-pre-release/lib"
         python_libs="LIBS=\"-L$install_top_dir/lib64 -lffi\""
         python_libs="LIBS='""-L$install_top_dir/lib64 -lffi""'"
         python_libs="LIBS=-L$install_top_dir/lib64"  # finds libffi
         python_rpath="LDFLAGS=-Wl,--rpath=${AUTOBUILD_INSTALLED}-pre-release/lib"
      else
         pv=$(sw_vers -productVersion)
         # e.g. 10.10
         os_minor_version="${pv%.*}"
         python_spec_flags="MACOSX_DEPLOYMENT_TARGET=$os_minor_version"
      fi
    else
      # don't use pre-release
      generic_prefix="--prefix=$AUTOBUILD_INSTALLED ${config_extras:-}"
      coot_prefix="$generic_prefix"
      install_top_dir=${AUTOBUILD_INSTALLED}
      if [ $(uname) != Darwin ] ; then
         python_lib_flags=LDFLAGS="-L$install_top_dir/lib64 -Wl,--rpath=${AUTOBUILD_INSTALLED}-pre-release/lib"
      fi
    fi
else
   # not pre-release
   generic_prefix="--prefix=$AUTOBUILD_INSTALLED ${config_extras:-}"
   install_top_dir=${AUTOBUILD_INSTALLED}
   coot_prefix="$generic_prefix"
   if [ $(uname) != Darwin ] ; then
      python_lib_flags=LDFLAGS="-L$install_top_dir/lib64 -Wl,--rpath=${AUTOBUILD_INSTALLED}/lib"
      python_ldflags="LDFLAGS=-Wl,--rpath=${AUTOBUILD_INSTALLED}/lib"
      python_libs="LIBS=\"-L$install_top_dir/lib64 -lffi\""
      python_libs="LIBS='""-L$install_top_dir/lib64 -lffi""'"
      python_libs="LIBS=-L$install_top_dir/lib64"  # finds libffi
      python_rpath="LDFLAGS=-Wl,--rpath=${AUTOBUILD_INSTALLED}/lib"
      echo python_libs is $python_libs

   else
      pv=$(sw_vers -productVersion)
      # e.g. 10.10
      os_minor_version="${pv%.*}"
      python_spec_flags="MACOSX_DEPLOYMENT_TARGET=$os_minor_version"
   fi
fi

echo install_top_dir $install_top_dir


# this should not be needed
export PATH=$install_top_dir/bin:$PATH

# Hmmm... I am not sure that I want to mess with pkg-config in the
# simple version.  But we do...
#
# This allows standard pkg-config to find gtkglext and several other
# things.
#
# override STD_PKGCONFIG_DIR to lib64 dir if we are in 64 bit.
#

os_arch=x86_64-linux-gnu # for now

STD_PKGCONFIG_DIR=/usr/lib/pkgconfig
case "$architecture" in
   x86_64*)
     STD_PKGCONFIG_DIR=/usr/lib64/pkgconfig
     ;;
esac


echo HERE A ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH
echo HERE A ppppppppppppppp with gtk $gtk
echo HERE A ppppppppppppppp with os_arch $os_arch

if [ -z "$PKG_CONFIG_PATH" ] ; then
  # I think that the standard dir is not needed.
  # PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig:$STD_PKGCONFIG_DIR
  # FYI packages that go into $install_top_dir/lib/$os_arch/pkgconfig:
  #   gobject-introspection-1.0.pc
  #   pygobject-3.0.pc
  #   py3cairo.pc
  #   glm.pc
  if test -n "$gtk" ; then
     PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig:$install_top_dir/lib/$os_arch/pkgconfig
  else
     PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig:$install_top_dir/lib/$os_arch/pkgconfig:$gtk/lib/pkgconfig
     # glib-2.0.pc is found in $install_top_dir/lib64
     PKG_CONFIG_PATH=$install_top_dir/lib64/pkgconfig:$install_top_dir/lib/pkgconfig:$install_top_dir/lib/$os_arch/pkgconfig:$gtk/lib/pkgconfig
  fi
else
   echo HERE B ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH
   echo setting PKG_CONFIG_PATH: testing dir $install_top_dir/lib/$os_arch/pkgconfig
   if [ -d $install_top_dir/lib/$os_arch/pkgconfig ] ; then
      echo HERE C ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH
      if test -z "$gtk" ; then
         PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig:$install_top_dir/lib/$os_arch/pkgconfig:$PKG_CONFIG_PATH:$STD_PKGCONFIG_DIR
      else
         PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig:$install_top_dir/lib/$os_arch/pkgconfig:$gtk/lib/pkgconfig:$PKG_CONFIG_PATH:$STD_PKGCONFIG_DIR
      fi
      echo HERE D ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH
   else
      echo HERE E ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH
      if test -z "$gtk" ; then
         echo HERE F ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH
         PKG_CONFIG_PATH=$install_top_dir/lib64/pkgconfig:$install_top_dir/lib/pkgconfig:$PKG_CONFIG_PATH:$STD_PKGCONFIG_DIR
      else
         echo HERE G ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH
         #PKG_CONFIG_PATH=$install_top_dir/lib/pkgconfig:$gtk/lib/pkgconfig:$PKG_CONFIG_PATH:$STD_PKGCONFIG_DIR
         # glib-2.0.pc is found in $install_top_dir/lib64
         PKG_CONFIG_PATH=$install_top_dir/lib64/pkgconfig:$install_top_dir/lib/pkgconfig:$gtk/lib/pkgconfig:$PKG_CONFIG_PATH:$STD_PKGCONFIG_DIR
      fi
   fi
fi

if [ -e /opt/X11/lib/pkgconfig ] ; then
    PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:$PKG_CONFIG_PATH
fi

echo HERE Z ppppppppppppppp with PKG_CONFIG_PATH $PKG_CONFIG_PATH

echo "COOT_CCP4_PACKAGES" "$COOT_CCP4_PACKAGES"
if [ -n "$COOT_CCP4_PACKAGES" ] ; then
    # PKG_CONFIG_PATH=$COOT_CCP4_PACKAGES/lib/pkgconfig:$PKG_CONFIG_PATH
    PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$COOT_CCP4_PACKAGES/lib/pkgconfig
fi

export PKG_CONFIG_PATH
echo  PKG_CONFIG_PATH is now $PKG_CONFIG_PATH


# Do we have freetype2?  cairo depends on it.
if pkg-config freetype2 ; then
   build_freetype2=
   echo system/installation has freetype2
else
   echo freetype2 should be built
   build_freetype2=1
fi

if command -v swig -version ; then
    echo swig found
else
    if [ "$CHAPI_ONLY" = true ] ; then
        :
    else
        echo swig is needed
        exit 2
    fi
fi


# we need to export this for net-http, because it doesn't set
# variables from configure, we rely on a shell (environment) variable.
export install_top_dir

echo testing for install_top_dir: "$install_top_dir"
if [ ! -e "$install_top_dir" ] ; then
	echo $install_top_dir does not exist
	echo making directory $install_top_dir
	mkdir -p $install_top_dir
	if [ $? -ne 0 ] ; then
		echo DISASTER: $install_top_dir does not exist and no way
		echo to make it.
	        my_exit 2
	fi
else
	echo INFO:: $install_top_dir exists already.
fi
echo done testing for $install_top_dir

if [ ! -e "$install_top_dir/lib" ] ; then
	echo making "$install_top_dir/lib"
	mkdir -p "$install_top_dir/lib"
        if [ $? -ne 0 ] ; then
                echo DISASTER: $install_top_dir/lib cannot be created
                echo to make it.
                my_exit 2
        fi
fi
#
# append or set LD_LIBRARY_PATH.
#
# this can be problematic for a distributable tar build because this can cause linkage
# against ccp4's libxml2! Hmm!
#
#
if [ -z "$LD_LIBRARY_PATH" ] ; then
    LD_LIBRARY_PATH=$install_top_dir/lib
    export LD_LIBRARY_PATH
else
    LD_LIBRARY_PATH=$install_top_dir/lib:$LD_LIBRARY_PATH
    export LD_LIBRARY_PATH
fi



#for Macs:
if test "$OS" = "Darwin" ; then
   if [ -z "$DYLD_LIBRARY_PATH" ] ; then
      # DYLD_LIBRARY_PATH=$install_top_dir/lib
      # export DYLD_LIBRARY_PATH
      :
   else
      #DYLD_LIBRARY_PATH=$install_top_dir/lib:$DYLD_LIBRARY_PATH
      #export DYLD_LIBRARY_PATH
      :
   fi
fi

#
# IRIX64 (on batman at least) does not seem to use LD_LIBRARY_PATH,
# it uses, instead, LD_LIBRARYN32_PATH.  So we set that for all
# systems, hoping that it won't do any harm on other systems.
#
# This surely is no longer used - PE 20130909
# LD_LIBRARYN32_PATH=$LD_LIBRARY_PATH
# export LD_LIBRARYN32_PATH



# ccp4_system_type can be one of the following
# irix irix64 sunos sunos64 aix hpux osf1 linux freebsd
# linux_compaq_compilers linux_intel_compilers generic Darwin
# ia64_linux_intel Darwin_ibm_compilers linux_ibm_compilers

ccp4_system_type="$OS"
if test "$OS" = Linux ; then
   ccp4_system_type=linux
else
   if test "$OS" = IRIX64 ; then
       ccp4_system_type=irix64
   else
      if test "$OS" = IRIX ; then
          ccp4_system_type=irix
      else
         if test "$OS" = Darwin ; then
            ccp4_system_type=Darwin
         fi
      fi
   fi
fi
echo ccp4_system_type $ccp4_system_type



# clean up old test status:
# echo build-in-progress @`date +"%a_%d_%b_%H:%M"` > $LOGS/build-status
# echo waiting > $LOGS/test-status



# ----------------------------------------------------------------------------
# ----------------------------------------------------------------------------
#                                which components?
# ----------------------------------------------------------------------------
# ----------------------------------------------------------------------------
#
# Often there are components provided by the operating system or optional
# installs thereof.
#
build_mmdb=0
build_ssmlib=0
build_fftw=0
build_clipper=
build_guile=0
build_guile_www=0
build_guile_gui=0
build_libtool=1
build_net_http=0
build_gsl=0
# build_libungif=0
# build_libtiff=0
# build_libjpeg=0
# build_libpng=0
# build_imlib=0
build_python=
build_pygobject=
build_guile_gtk=
# build_readline=
build_curl=
build_libidn=



# In Gtk2, we presume that glib, gtk2 and gnomecanvas are available.
# We shall test for these, but not build them.

# Where might the "system" components be?
#
non_standard_dir_list="/usr/freeware /sw /opt/gnome $install_top_dir"
dir_list="/usr /usr/X11R6 /usr/local $non_standard_dir_list"

# fftw
# We can eventually get fancy on this... but then clipper configure
# needs changing.
# The test is -n, i.e. a non-zero string length to build things.
#
# We need to test the $AUTOBUILD_INSTALLED directory for fftw because any
# other place could quite well have the fftw that is compiled with doubles.
#
if test -e $install_top_dir/include/fftw.h ; then
   echo installation has fftw
   build_fftw=
fi

if test -n "$build_fftw" ; then
   echo fftw should be built
   build_fftw=1
fi


if [ -e $install_top_dir/include/curl/curl.h ] ; then
   echo installation has curl/libcurl
else
   echo curl should be built
   build_curl=1
fi

# ---------- test installation libidn ------------------
#
if [ -e $install_top_dir/include/idn2.h ] ; then
   echo installation has libidn2 devel
   build_libidn=
else
   echo installation does not have libidn2, libcurl should be built also
   build_libidn=1
   build_curl=1
fi



# Test the output of pkg-config gtk+-2.0 for recent enough gtk.
# If not, then build it yourself.
#
# Experiment, to force bragg3 to compile gtk+2
#
# was 2.8
needed_gtk_version=3.94

# what a mess. Needs cleaning
pkg-config --atleast-version=$needed_gtk_version gtk+-2.0
gtk_pkg_config_status=$?
if [ "$gtk_pkg_config_status" = 0 ] ; then
   echo :::::::: gtk version is at least $needed_gtk_version
   echo :::::::: gtk version is `pkg-config --modversion gtk+-2.0`
fi


echo libtool test: looking for ${install_top_dir}/include/ltdl.h
if test -e ${install_top_dir}/include/ltdl.h ; then
    echo installation has libtool
    build_libtool=
else
    echo libtool should be built
fi


# ============= python ================
#
# python_version is the filename of the python executable.  For python
# 2.5.1 it is python2.5, not python2.5.1
#
python_version=python3.13
pver=3.13.5
python_version_extension=3.13 # extract this
# I think that for python to be compatible with Blender, we don't want the debug version
# python_abiflags=d # because we use --with-pydebug on the command line for Python configure
python_version_squish=313

# for Blender 4 in 2024, we want Python 3.10.13, so uncomment the 3 lines below:
# for Blender 4.1 in June 2025, we want Python 3.11.x
# But the CMakeLists file here rqures 3.12.4 - so let's use that
if [ "$CHAPI_ONLY" = true ] ; then

    # blender
    python_version=python3.11
    pver=3.11.11
    python_version_extension=3.11
    python_version_squish=311

    # chapi
    python_version=python3.12
    pver=3.12.11
    python_version_extension=3.12
    python_version_squish=312

fi


# for compatibility with gtk build system
# use_python_version_3_8 is not yet set anywhere.
# future self: set use_python_version_3_8 when needed so that this block gets executed
if [ "$use_python_version_3_8" = true ] ;then
   python_version=3.9
   pvers=3.9.12
   python_version_extension=3.8
fi


# 20240203-PE I don't want version 3.8.
# but more modern pythons do not compile (at least on my mac)
# 20201225-PE this needs checking
# if [ $OS = Darwin ] ; then
#    pver=3.6.5
#    pver=3.8.12
# fi


# set build_pygobject here
if [ ! -e $install_top_dir/include/pygobject-3.0/pygobject.h ] ; then
    build_pygobject=true
fi



# force the GSL config to be in $install_top_dir, rather than
# potenially getting it from the system
# but does this compile cleanly on Mac OS X?  I've forgotten.
# Perhaps we will need to be more clever and potentially use
# the fink GSL if it is available.
# 20240302-PE "fink"? Blimey.
if test -e $install_top_dir/bin/gsl-config ; then
    if test "$dist_name" = arch ; then
        unset LD_LIBRARY_PATH
    fi
    echo $install_top_dir/bin/gsl-config --prefix
    $install_top_dir/bin/gsl-config --prefix 2>&1
    $install_top_dir/bin/gsl-config --prefix
    if test $? != 0 ; then
       echo gsl should be built
       build_gsl=1
    else
        gsl_version=`gsl-config --version`

        # if you change this, change also gsl_version below.
        needed_gsl_version=1.11
        needed_gsl_version=1.12
        needed_gsl_version=1.15
        needed_gsl_version=1.16
        needed_gsl_version=2.7

        if [ -e $install_top_dir/include/gsl/gsl_version.h ] ; then
            build_gsl=
        fi

        echo installation has the GSL version $gsl_version
        if [ "$build_gsl" = 1 ] ; then
             echo need to build GSL
        else
             echo GSL is up to date
        fi
    fi
else
    build_gsl=1
fi



# test for mmdb: Does mmdb_model.h exist, and if it does, does it
# contain MMDBF_IgnoreHash.  If not, then build mmdb.
#
# CCP4 mmdb installs in the include/mmdb2 directory,
#
if test -e "${install_top_dir}/include/mmdb2/mmdb_model.h" ; then
    build_mmdb=
else
    echo installation has no mmdb, build mmdb.
    build_mmdb=1
fi



ssm_include_dir=ssm
if [ -e $install_top_dir/include/$ssm_include_dir/ssm_align.h ] ; then
   if [ "$build_mmdb" = 1 ] ; then
      build_ssmlib=1
   else

      # do we have SSM version 1.4 or later?
      if grep --silent "MINOR_VERSION = [4-9]" $install_top_dir/include/$ssm_include_dir/ssm_defs.h ; then
         echo SSM is found.
         build_ssmlib=
      else
         echo we need a newer SSM.
         build_ssmlib=1
      fi
   fi
else
   echo SSM not found - needs to be built
   build_ssmlib=1
fi


# clipper depends on mmdb, so if mmdb was built, the so must clipper be.
# likewise for fftw.
#
build_clipper=1
if [ -z "$build_mmdb" ] ; then
    # we potentially can pass the building of clipper:
    echo INFO:: shall we build clipper: mmdb not to be built
    if [ -z "$build_fftw" ] ; then
       echo INFO:: shall we build clipper: fftw not to be built
       # test for new ccp4-based clipper (for mtz and maps)
       if [ -e $install_top_dir/include/clipper/ccp4/ccp4_mtz_io.h ] ; then
          # echo $install_top_dir/include/clipper/ccp4/ccp4_mtz_io.h exist
          if [ -e $install_top_dir/include/clipper/contrib/sfscale.h ] ; then
             # echo $install_top_dir/include/clipper/contrib/sfscale.h exist
             build_clipper=
          else
             echo $install_top_dir/include/clipper/contrib/sfscale.h not exist, building clipper
             build_clipper=1
          fi
       else
          echo $install_top_dir/include/clipper/ccp4/ccp4_mtz_io.h not exist, building clipper
       fi
    fi
else
   echo mmdb needs to be built, so clipper needs building.
fi

# shall we build libccp4c?
if [ -e $install_top_dir/lib/libccp4c.la ] ; then
    # 20170925 test for the pkg-config file
    if [ -e $install_top_dir/lib/pkgconfig/libccp4c.pc ] ; then
        # no need to rebuild
        build_ccp4c=
    else
        build_ccp4c=1
    fi
else
    build_ccp4c=1
fi

if [ -e $install_top_dir/bin/$python_version ] ; then
   if ${install_top_dir}/bin/$python_version -V ; then
      # test for ctypes - was it installed correctly?
      ld_lib_path_backup=$LD_LIBRARY_PATH
      unset LD_LIBRARY_PATH
      if [ "$(${install_top_dir}/bin/$python_version -V)" = "Python $pver" ] ; then
         echo found version of Python `${install_top_dir}/bin/$python_version -V` 2>&1
         if ${install_top_dir}/bin/$python_version -c 'import ctypes' ; then
            echo we have $python_version with working ctypes
         else
            echo $python_version ctypes failure
            build_python=1
         fi
      else
         echo wrong version of Python - needs rebuild
         ${install_top_dir}/bin/$python_version -V
      fi
      export LD_LIBRARY_PATH=$ld_lib_path_backup
   else
      build_python=1
   fi
else
   build_python=1
fi
# -----------------------------------------------------------------------------
# -----------------------------------------------------------------------------
# hack!
# build_python=1
# -----------------------------------------------------------------------------
# -----------------------------------------------------------------------------



# -----------------------------------------------------------------------------
# -----------------------------------------------------------------------------
#                                build components
# -----------------------------------------------------------------------------
# -----------------------------------------------------------------------------
#

#
# libccp4: (not fortran)
if test -n "$build_ccp4c" ; then
    libccp4_version=6.5.1
    libccp4_version=8.0.0
    echo BUILDING libccp4: $libccp4_version
    # ${WGET} http://www.ysbl.york.ac.uk/~emsley/software/extras/libccp4c-5.0.2-ysbl-2.tar.gz
    # ${WGET} http://www.ysbl.york.ac.uk/~emsley/software/extras/libccp4c-5.0.2-ysbl-3.tar.gz
    #${WGET} http://www.ysbl.york.ac.uk/~emsley/software/extras/martyn-extras.tar.gz
    #${WGET} http://lmb.bioch.ox.ac.uk/coot/software/extras/libccp4c-5.0.2-ysbl-3.tar.gz
    #${WGET} http://lmb.bioch.ox.ac.uk/coot/software/extras/martyn-extras.tar.gz
    #${WGET} http://lmb.bioch.ox.ac.uk/coot/software/extras/ccp4-libs-underlay-2.tar.gz
    # ${WGET} $extras_place/libccp4c-5.0.2-ysbl-3.tar.gz
    # ${WGET} $extras_place/martyn-extras.tar.gz
    # ${WGET} $extras_place/ccp4-libs-underlay-2.tar.gz
    # ${WGET} $extras_place/libccp4-6.4.0.tar.gz
    # ${WGET} ftp://ftp.ccp4.ac.uk/opensource/libccp4-$libccp4_version.tar.gz
    ${WGET} $extras_place/libccp4-$libccp4_version.tar.gz
    echo BUILDING libccp4 $libccp4_version >&2
    (
    unset LD_LIBRARY_PATH
    date
    echo gunzip/untar ${AUTOBUILD_SOURCES}/libccp4-$libccp4_version.tar.gz
    gzip -dc ${AUTOBUILD_SOURCES}/libccp4-$libccp4_version.tar.gz | tar xf -
    cd libccp4-$libccp4_version
    if ./configure $generic_prefix --enable-shared --disable-static --disable-fortran ; then
       if $MAKE ; then
           $MAKE install
           # 20250621-PE
           # libccp4 installs $install_top_dir/lib/pkgconfig/ccp4c.pc
           # lib libclipper needs libccp4c! How have I not run into this before!?
           cp $install_top_dir/lib/pkgconfig/ccp4c.pc $install_top_dir/lib/pkgconfig/libccp4c.pc
       fi
    fi
    ) > $HOSTLOGDIR/01-libccp4.txt 2>&1
    echo done libccp4 $libccp4_version >&2
else
    echo not building libccp4:
fi

#
# mmdb
#
#
# mmdb
#
if test -n "$build_mmdb" ; then
   echo BUILDING mmdb:
#
# mmdb_version=1.0.10.  Not yet.
# mmdb_version=1.0.8-ysbl-3
mmdb_version=1.11
mmdb_version=1.12
mmdb_version=1.19
mmdb_version=1.21
mmdb_version=1.22
mmdb_version=1.23
mmdb_version=1.23.2
mmdb_version=1.24
mmdb_version=1.24.2
mmdb_version=1.25.0
mmdb_version=1.25.2
mmdb_version=1.25.3
mmdb_version=2.0.1
mmdb_version=2.0.2
mmdb_version=2.0.5
mmdb_version=2.0.11
mmdb_version=2.0.16
mmdb_version=2.0.19
mmdb_version=2.0.20
mmdb_version=2.0.22
    # mmdb_server_dir=ftp://ftp.ccp4.ac.uk/opensource
    mmdb_server_dir=$extras_place
    ${WGET} $mmdb_server_dir/mmdb2-$mmdb_version.tar.gz
    echo BUILDING mmdb $mmdb_version >&2
    (
    date
    gzip -dc ${AUTOBUILD_SOURCES}/mmdb2-$mmdb_version.tar.gz | tar xf -
    echo gzip -dc ${AUTOBUILD_SOURCES}/mmdb2-$mmdb_version.tar.gz
    cd  mmdb2-$mmdb_version
    pwd
    # patch to read long lines in a cif file
    # 20091110 this patch is not available, above says that it is badly formed.
    #   Needs fixing.
    # add the following 2 touches because centos 4.6 jackal gives LIBTOOL
    # problems on `make'.
    # if configure.in newer than aclocal.m4 -> rebuild aclocal.m4
    # if aclocal.m4 newer than Makefile.in -> rebuild Makfile.in
    # mmdb 1.21 has configure.in newer than aclocal.m4 for some reason.
    # must make sure that next version does not.
    # touch aclocal.m4
    # sleep 2
    # touch Makefile.in
    ./configure $generic_prefix --enable-shared --disable-static
    if $MAKE ; then
       make install
    fi
    ) > $HOSTLOGDIR/02-mmdb.txt 2>&1
    echo done mmdb $mmdb_version >&2
else
    echo not building mmdb:
fi

if test -n "$build_ssmlib" ; then

    echo BUILDING SSM $ssm_version
    echo BUILDING SSM $ssm_version >&2
    #
    # ssm_version=0.0-pre-2-ysbl
    ssm_version=1.4
    #${WGET} http://lmb.bioch.ox.ac.uk/coot/software/extras/SSMlib-$ssmlib_version.tar.gz
    #${WGET} http://lmb.bioch.ox.ac.uk/coot/software/extras/SSMlib-$ssmlib_version.tar.gz
    # ${WGET} $extras_place/SSMlib-$ssmlib_version.tar.gz
    # ${WGET} ftp://ftp.ccp4.ac.uk/opensource/ssm-1.3.tar.bz2
    # ${WGET} ftp://ftp.ccp4.ac.uk/opensource/ssm-1.3.tar.bz2
    ${WGET} $extras_place/ssm-$ssm_version.tar.gz
    (
    date
    # gzip -dc ${AUTOBUILD_SOURCES}/ssm-1.3.tar.bz2 | tar xf -
    tar xf ${AUTOBUILD_SOURCES}/ssm-$ssm_version.tar.gz
    cd ssm-$ssm_version
    ./configure $generic_prefix --enable-shared --disable-static CPPFLAGS=-I$install_top_dir/include LDFLAGS=-L$install_top_dir/lib
    if $MAKE ; then
       $MAKE install
    fi
    ) >  $HOSTLOGDIR/02-ssm.txt 2>&1
    echo done SSM $ssm_version >&2
else
    echo not building ssm:
fi


# fftw
if test -n "$build_fftw" ; then
    echo BUILDING fftw:
    echo BUILDING fftw 2.1.5: >&2
#
# ${WGET} http://www.ysbl.york.ac.uk/~emsley/software/fftw-2.1.5.tar.gz
# ${WGET} http://www.ysbl.york.ac.uk/~emsley/software/extras/fftw-configure-stuff.tar.gz
#${WGET} http://lmb.bioch.ox.ac.uk/coot/software/extras/fftw-2.1.5.tar.gz
#${WGET} http://lmb.bioch.ox.ac.uk/coot/software/extras/fftw-configure-stuff.tar.gz
${WGET} $extras_place/fftw-2.1.5.tar.gz
# ${WGET} $extras_place/fftw-configure-stuff.tar.gz # Don't need

    (
    date
    pwd
    gzip -dc ${AUTOBUILD_SOURCES}/fftw-2.1.5.tar.gz | tar xf -
    # gzip -dc ${AUTOBUILD_SOURCES}/fftw-configure-stuff.tar.gz | tar xf - # don't need.
    cd fftw-2.1.5
    fftw_configure_extras=
    if test $architecture = aarch64 ; then
        fftw_configure_extras=--build=aarch64-unknown-linux-gnu
    fi
    if ./configure $generic_prefix $fftw_configure_extras --enable-shared --enable-float ; then
       if $MAKE ; then
          $MAKE install
       fi
    fi
    )  > $HOSTLOGDIR/03-fftw.txt 2>&1
    echo "done fftw" >&2
else
    echo not building fftw:
fi

# # clipper
# #
# #
if test -n "$build_clipper" ; then

    # clipper: we use the ccp4 version of clipper now.
    # (it uses configure, not scons)
    #
    echo BUILDING clipper:
    # clipper_version is for the file name on the server, clipper_dir_version is the directory
    # that files untars into (20160713 with Marcin in control of the tar dist now they are the
    # same, it seems?).
    clipper_version=20ac
    clipper_version=2.1-081118-ac
    clipper_version=2.1-081201-ac
    clipper_version=2.1-090210-ac
    clipper_version=2.1-090522-ac
    clipper_version=2.1-090826-ac
    clipper_version=2.1-091215-ac
    clipper_version=2.1-100511-ac
    clipper_version=2.1
    clipper_version=2.1.20160708
    clipper_dir_version=2.1
    clipper_dir_version=$clipper_version
    # ${WGET} http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper-$clipper_version.tar.gz

    # 20110921 hack in a temporary solution, while Kevin's new clipper
    # is not available yet from his site.
    clipper_hack_version=2.1-110915-fixup-2
    clipper_hack_version=2.1-140110-fixup
    clipper_hack_version=2.1-20170202.tar.gz
    # ${WGET} $extras_place/clipper-$clipper_hack_version.tar.gz

    # now clipper has all the bits.
    # ${WGET} $extras_place/clipper-$clipper_version.tar.gz
    # ${WGET} ftp://ftp.ccp4.ac.uk/opensource/clipper-$clipper_version.tar.gz

    # Bernie made this tarball
    clipper_version=2.1.20180802
    clipper_version_dir=2.1
    ${WGET} $extras_place/clipper-$clipper_version.tar.gz
    ${WGET} $extras_place/clipper-configure-2.patch
    echo BUILDING clipper $clipper_version >&2
    (
    gzip -dc ${AUTOBUILD_SOURCES}/clipper-$clipper_version.tar.gz | tar xf -

    cd clipper-$clipper_version_dir
    pwd
    date

    # patch the hkl_data.h header
    # sed -ibackup -e 's/int i = 0; i < list.size(); i++/unsigned int i = 0; i < list.size(); i++/' clipper/core/hkl_data.h

    # --- make clipper

    # patch clipper

    # fix the linking to the wrong libfftw
    echo patching clipper with ${AUTOBUILD_SOURCES}/clipper-configure-2.patch
    patch -p0 < ${AUTOBUILD_SOURCES}/clipper-configure-2.patch

    echo . ------------------------------------------------------------------------------
    echo . "         clipper                                                            "
    echo . ------------------------------------------------------------------------------
    export     CPPFLAGS=-I$install_top_dir/include
    export      LDFLAGS=-L$install_top_dir/lib
    echo CPPFLAGS $CPPFLAGS
    echo LDFLAGS  $LDFLAGS
    echo PKG_CONFIG_PATH  $PKG_CONFIG_PATH

    # if /usr/lib64/lib(r)fftw.so exists, clipper will link to them
    # despite our having build fftw for ourselves - I need to stop
    # that (because of clipper's m4/fftw.m4)

    save_libs="$LIBS"
    export LIBS="-L$install_top_dir/lib:$LIBS"
    if [ -z "$LIBS" ] ; then
      save_libs=
      export LIBS=-L$install_top_dir/lib
    else
      save_libs="$LIBS"
      export LIBS=-L$install_top_dir/lib:$LIBS
    fi
    echo now we have LIBS $LIBS

    echo ./configure --prefix=$install_top_dir \
	--enable-mmdb=$install_top_dir \
	--enable-ccp4=$install_top_dir \
	--enable-shared  \
	--enable-mmdb    \
	--enable-cif     \
	--enable-ccp4    \
	--enable-minimol \
	--enable-cns     \
       CXXFLAGS="-g -O2 -fno-strict-aliasing"

    ./configure --prefix=$install_top_dir \
	--enable-mmdb=$install_top_dir \
	--enable-ccp4=$install_top_dir \
	--enable-shared  \
	--enable-mmdb    \
	--enable-cif     \
	--enable-ccp4    \
	--enable-minimol \
	--enable-cns     \
       CXXFLAGS="-g -O2 -fno-strict-aliasing -Wno-narrowing"
    export LIBS="$save_libs"
    # 20110921 I don't think we need these flags any longer
    #        CCP4_CXXFLAGS=-I$install_top_dir/include CCP4_LIBS=$install_top_dir/lib/libccp4c.la
    # we don't want to make the clipper executables, so let's cd in to the clipper libs and
    # make (just) those.
    if $MAKE ; then
       $MAKE install
    fi

    ) > $HOSTLOGDIR/04-clipper.txt 2>&1

    clipper_build_status=$?
    if [ $clipper_build_status != 0 ] ; then
        echo clipper build failed, exiting
        my_exit 2
    fi
    echo done clipper >&2

else
    echo not building clipper:
fi



###############################################################################
# GEMMI is frequently updated and uses git not releases - so always install it.
###############################################################################

if true ; then
    echo BUILDING gemmi from git repo \(and installing GEMMI\)
    echo BUILDING gemmi from git repo \(and installing GEMMI\) >&2
    pwd >&2
    echo gemmi build start_dir is $start_dir
    echo gemmi build start_dir is $start_dir >&2
    (
          save_dir=$(pwd)
          cd "$start_dir"
          needs_rebuild=false
          ls -l
          if [ -e gemmi ] ; then
              pwd
              echo path A
              cd gemmi
              git remote update
              git status -uno
              needs_rebuild=false
              if git status -uno | grep -q "branch is behind" ; then
                  needs_rebuild=true
                  git fetch
                  git merge
              fi
              echo needs rebuild: $needs_rebuild
              cd -
          else
              pwd
              echo path B
              git clone https://github.com/project-gemmi/gemmi.git
              needs_rebuild=true
          fi
          # cd gemmi/include
          # note to self: fix this for Darwin - which has a crippled cp
          # cp -a -r gemmi $install_top_dir/include
          # cd -
          # cd $save_dir
          needs_rebuild=true; # hack to see what happens
          echo gemmi needs rebuild: $needs_rebuild
          echo gemmi needs rebuild: $needs_rebuild > $start_dir/gemmi-rebuild.txt
          if test "$needs_rebuild" = true ; then
              if [ -d build-gemmi ] ; then
                  :
              else
                  mkdir build-gemmi
              fi
              cd build-gemmi
              pwd
              # add -DUSE_PYTHON=1 here at some stage.
              cmake -DCMAKE_INSTALL_PREFIX=$install_top_dir -DBUILD_SHARED_LIBS=ON ../gemmi
              if $MAKE ; then
                  make install
              else
                  echo gemmi make failed
              fi
          fi
    ) > $HOSTLOGDIR/05-gemmi.txt 2>&1
    cat $start_dir/gemmi-rebuild.txt 2>&1
    echo BUILDING: "done gemmi"
    echo BUILDING: "done gemmi" >&2
fi



#######################################################################
# readline is a dependency of python and guile
#######################################################################

build_readline=true
if [ -e $install_top_dir/include/readline/readline.h ] ; then
   build_readline=false
fi

if test "$build_readline" = true ; then
    echo BUILDING readline:
    echo BUILDING readline: >&2
    readline_version=6.2
    readline_version=6.3
    readline_version=8.2
    ${WGET} https://ftp.gnu.org/gnu/readline/readline-$readline_version.tar.gz
    ${WGET} $extras_place/readline-5.1.patch
    (
    unset LD_LIBRARY_PATH
    date
    pwd
    gzip -dc ${AUTOBUILD_SOURCES}/readline-$readline_version.tar.gz | tar xf -
    cd readline-$readline_version
    if test -n "$need_readline_patch" ; then
       ls -l
       echo patching readline...
       # need a patch (for debian only) to add curses to the additional libs line
       echo patch -p0 input-from ${AUTOBUILD_SOURCES}/readline-5.1.patch
       ls -l ${AUTOBUILD_SOURCES}/readline-5.1.patch
       patch -p0 < ${AUTOBUILD_SOURCES}/readline-5.1.patch
    fi
    if [ "$dist_name" = debian ] ; then
       echo applying debian sed patch for shared-lib libreadline
       # thanks for the quoting help tony duan @ stackoverflow
       sed  -i '125,135 s/SHOBJ_LDFLAGS=.*/&\n        SHLIB_LIBS='"'"'$(TERMCAP_LIB)'"'"'/' support/shobj-conf
       extra_args_for_debian="--with-curses --enable-shared"
    fi
    if [ "$dist_name" = arch ] ; then
       echo in arch block, applying debian sed patch for shared-lib libreadline
       # thanks for the quoting help tony duan @ stackoverflow
       sed  -i '125,135 s/SHOBJ_LDFLAGS=.*/&\n        SHLIB_LIBS='"'"'$(TERMCAP_LIB)'"'"'/' support/shobj-conf
       extra_args_for_debian="--with-curses --enable-shared"
    fi
    echo ./configure $generic_prefix --enable-shared --with-curses $extra_args_for_debian
    ./configure $generic_prefix --enable-shared --with-curses $extra_args_for_debian
    cp shlib/Makefile shlib/Makefile.orig
    sed -ibackup -e 's/SHLIB_LIBS = /SHLIB_LIBS = -lcurses/' shlib/Makefile
    # single thread
    if make ; then
       make install
    else
       echo make of readline failed
    fi
    ) > $HOSTLOGDIR/08-readline.txt 2>&1
else
    echo not building readline:
fi


###############################################################################
##########         build python and friends                       #############
###############################################################################


test_for_already_installed_dependencies=true
    unset LD_LIBRARY_PATH

# So that python3 is found when it is installed:
#
#this should not be needed
export PATH=$install_top_dir/bin:$PATH


# gobject-introspection needs libffi
# meson needs libffi to be intalled before python, so that meson can find ctypes modules

libffi_version=3.2.1
# libffi_version=3.4.3 is available now 20231021-PE
libffi_version=3.4.6

skip_build=false
if [ $test_for_already_installed_dependencies = true ] ; then
      if [ -e $install_top_dir/include/ffi.h ] ; then
         skip_build=true
         echo installation has libffi
      else
         echo $install_top_dir/include/ffi.h does not exist
      fi
fi

if [ $skip_build = false ] ; then
    echo BUILDING libffi from libffi-master.zip
    echo BUILDING libffi from libffi-master.zip >&2
    (
    unset LD_LIBRARY_PATH

    pwd
    echo ${WGET} https://github.com/libffi/libffi/archive/refs/heads/master.zip
    ${WGET} https://github.com/libffi/libffi/archive/refs/heads/master.zip
    ls -l
    mv ${AUTOBUILD_SOURCES}/master.zip ${AUTOBUILD_SOURCES}/libffi-master.zip
    unzip ${AUTOBUILD_SOURCES}/libffi-master.zip
    cd libffi-master
    bash autogen.sh
    # this was from the other build:
    # ./configure --prefix=$install_top_dir --disable-multi-os-directory --enable-portable-binary --enable-shared --disable-static
    # where --disable-multi-os-directory was commented out
    ./configure --prefix="$install_top_dir"
    make -j 4
    make install
    cd -
    ) > $HOSTLOGDIR/09-libffi.txt 2>&1
else
    echo not building libffi >&2
fi

echo post libffi with LD_LIBRARY_PATH $LD_LIBRARY_PATH
echo post libffi with LD_LIBRARY_PATH $LD_LIBRARY_PATH >&2

############## 09b-libffi #####################

build_libffi=true
echo ================= here with build_libffi $build_libffi
#
if [ "$build_libffi" = true ] ; then
   skip_this=false
   if [ "$test_for_already_installed_dependencies" = true ] ; then
      if [ -e $install_top_dir/lib/pkgconfig/libffi.pc ] ; then
         skip_this=true
      fi
   fi

   if [ $skip_this = false ] ; then
      echo ========================= build 09b-libffi =================================
      (
      unset LD_LIBRARY_PATH # or otherwise UP in libreadline problems
      echo ========================= build 09b-libffi =================================
      echo BUILDING libffi $libffi_version >&2
      ${WGET} https://github.com/libffi/libffi/releases/download/v$libffi_version/libffi-$libffi_version.tar.gz
      if [ -e ${AUTOBUILD_SOURCES}/libffi-$libffi_version.tar.gz ] ; then
         tar xf ${AUTOBUILD_SOURCES}/libffi-$libffi_version.tar.gz
      else
         exit
      fi
      cd libffi-$libffi_version
      # if ./configure --prefix=$install_top_dir --disable-multi-os-directory --enable-portable-binary --enable-shared --disable-static ; then
      if ./configure --prefix=$install_top_dir --enable-portable-binary --enable-shared --disable-static ; then
         if $MAKE ; then
            make install
         fi
      fi
      cd -
      ) > $HOSTLOGDIR/09b-libffi.txt 2>&1
   fi
fi
build_openssl=false
if [ $OS = Darwin ] ; then
   if [ -e $install_top_dir/include/openssl ] ; then
      echo OpenSSL is installed
      build_openssl=false
   else
      build_openssl=true
   fi
else
   # what about rocky here also?
   if test "$dist_name" = fedora ; then
       if [ -e $install_top_dir/include/openssl ] ; then
           build_openssl=false
       else
           build_openssl=true
       fi
   fi
fi

if [ $build_openssl = true ] ; then
    echo BUILDING OpenSSL
    echo BUILDING OpenSSL >&2
    (
    openssl_version=3.2.1
    ${WGET} https://github.com/openssl/openssl/releases/download/openssl-$openssl_version/openssl-$openssl_version.tar.gz
    ls -alt ${AUTOBUILD_SOURCES}
    tar xf ${AUTOBUILD_SOURCES}/openssl-$openssl_version.tar.gz
    ls -alt
    cd openssl-$openssl_version
    ./Configure --prefix=$install_top_dir --openssldir=$install_top_dir  '-Wl,-rpath,$(LIBRPATH)'
    $MAKE && make install
    cd -
    ) > $HOSTLOGDIR/10-openssl.txt 2>&1
    echo done OpenSSL
    echo done OpenSSL >&2
fi

# gettext provides -lintl - which is needed for python on macOS
build_gettext=true
if test $OS = Darwin ; then
    if test -e $install_top_dir/include/libintl.h ; then
        build_gettext=false
    else
        echo where is libintl.h in $install_top_dir/include question-mark
        ls -l $install_top_dir/include
        echo $install_top_dir/include/libintl.h does not exist - hence build_gettext $build_gettext
    fi
else
    echo gettext: this is $OS, not Darwin
    build_gettext=false
fi

if $build_gettext = true ; then
    gettext_version=0.22.5
    echo BUILDING gettext
    echo BUILDING gettext $gettext_version >&2
    (
     unset LD_LIBRARY_PATH # or otherwise UP in libreadline problems
     ${WGET} http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/gettext/gettext-$gettext_version.tar.gz
       tar xf $AUTOBUILD_SOURCES/gettext-$gettext_version.tar.gz
       cd gettext-$gettext_version
       ./configure --prefix=$install_top_dir --disable-java
       $MAKE && make install
       cd -
    ) > $HOSTLOGDIR/11-gettext.txt 2>&1
    echo done gettext >&2
else
    echo not building gettext >&2
fi

# python
#
if test -n "$build_python" ; then
   echo BUILDING Python ${pver}:
   echo BUILDING Python ${pver}: >&2

   echo ${WGET} http://www.python.org/ftp/python/$pver/Python-$pver.tgz
   # hacking in --no-check-certificate is not the right way to do it.
   # This is a problem with old(?) wgets.  In future, we should remove this.
   if ${WGET} --no-check-certificate http://www.python.org/ftp/python/$pver/Python-$pver.tgz ; then
      echo got Python-$pver.tgz
   else
      echo problem getting Python-$pver.tgz
   fi
   (
   date
   echo building in: $PWD

   unset LD_LIBRARY_PATH
   # test raw awk
   which awk
   awk --version

   env
   gzip -dc ${AUTOBUILD_SOURCES}/Python-$pver.tgz | tar xf -

   cd Python-$pver

   # stuff ffi into setup.py
   sed -ibackup -e 's/def detect_decimal/    ext.libraries.append("ffi")\n\n    &/' setup.py
   ffilibdir=$install_top_dir/lib64
   sed -ibackup2 -e "s?add_dir_to_list(self.compiler.library_dirs, ./usr/local/lib.)?add_dir_to_list(self.compiler.library_dirs, '$ffilibdir')?" setup.py


   # --with-ensurepip=install
   # echo INFO:: ./configure $generic_prefix --with-ensurepip=install --enable-shared $python_lib_flags $python_spec_flags
   # /Users/pemsley/ccp4/devtools/install
   # this should be configured
   # note to self: We need ffi.h (and lib presumably) to build the ctypes module (libffi-devel)
   # (or I could include it in this build script) (I don't know if ctypes is important)
   # 20220227-PE ctypes is crucial for meson
   # remove --with-pydebug for now because __PyNegativeRefcount problem on trying to load this into Blender
   #
   # do we also need to use --with-threads=dir?
   if test "$dist_name" = fedora ; then
       python_install_top_dir=$HOME/building-python
       python_install_top_dir=$HOME/building-python-tt
       python_install_top_dir=$install_top_dir
       ssl_top_dir=$HOME/building-python
       ffi_top_dir=$HOME/building-python
       ssl_top_dir=$install_top_dir
       ffi_top_dir=$install_top_dir
       # INFO:: ./configure --prefix=/home/pemsley/autobuild/Linux-emsley-vm-fedora-2.lmb.internal-gtk4 \
       #                    --with-ensurepip=install --enable-shared --with-openssl=/usr \
       #                    CFLAGS=-I/home/pemsley/autobuild/Linux-emsley-vm-fedora-2.lmb.internal-gtk4/lib/libffi-3.2.1/include \
       #                    LIBS=-L/home/pemsley/autobuild/Linux-emsley-vm-fedora-2.lmb.internal-gtk4/lib64 \
       #                    LDFLAGS=-Wl,--rpath=/home/pemsley/autobuild/Linux-emsley-vm-fedora-2.lmb.internal-gtk4/lib
       echo ./configure --prefix="$python_install_top_dir" --with-ensurepip=install --enable-shared \
                --with-openssl="$ssl_top_dir" \
                LIBS=-L$install_top_dir/lib64 LDFLAGS="-Wl,--rpath=$install_top_dir/lib"
       if ./configure --prefix="$python_install_top_dir" --with-ensurepip=install --enable-shared \
                --with-openssl="$ssl_top_dir" \
                LIBS=-L$install_top_dir/lib64 LDFLAGS="-Wl,--rpath=$install_top_dir/lib" ; then
           echo INFO:: make for python
           if $MAKE ; then
              echo INFO:: make install for python
              $MAKE install
           fi
       fi
   else
       openssl_prefix=/usr
       if [ $OS = Darwin ] ; then
           openssl_prefix=$install_top_dir
       fi
       echo PKG_CONFIG_PATH is $PKG_CONFIG_PATH - does that mean that libffi config is discoverable\?
       echo INFO:: ./configure $generic_prefix --with-ensurepip=install --enable-shared --with-openssl=$openssl_prefix \
            CXXFLAGS=-I$install_top_dir/lib/libffi-3.2.1/include $python_libs $python_ldflags $python_spec_flags
       if ./configure $generic_prefix --with-ensurepip=install --enable-shared --with-openssl=$openssl_prefix \
                      CPPFLAGS=-I$install_top_dir/lib/libffi-3.2.1/include $python_libs $python_ldflags $python_spec_flags ; then
           echo INFO:: make for python
           if $MAKE ; then
              echo INFO:: make install for python
              $MAKE install
           fi
       fi
   fi
   # test it
   echo test cypes in the new python
   # or use this test: if $install_top_dir/bin/python3 -c 'import ctypes' ; then ...
   $install_top_dir/bin/$python_version <<EOF
import ctypes
print(dir(ctypes))
print('post ctypes test')
EOF
   ) >  $HOSTLOGDIR/12-python.txt 2>&1

   # we need this because boost configuration runs "python" - at least on my Mac
   # (finding the correct python(3) doesn't seem to be a problem on the PC).
   # The better way is to use cmd-or-prefix, it seems:
   # https://www.phind.com/search?cache=z8ao21y6rh5grg4wezeybr06
   # try this:
   # add
   # echo "using python : 3.10 : $install_top_dir/bin/python3 ;" > user-config.jam
   if test -e $install_top_dir/bin/$python_version ; then
      if test -e $install_top_dir/bin/python3 ; then
         rm $install_top_dir/bin/python3
      fi
      echo linking python3 to $python_version
      ln -s $install_top_dir/bin/$python_version $install_top_dir/bin/python3
   fi
   if [ -e $install_top_dir/bin/python3 ] ; then
      echo linking python to python3
      if [ -e $install_top_dir/bin/python ] ; then
          rm $install_top_dir/bin/python
      fi
      ln -s $install_top_dir/bin/python3 $install_top_dir/bin/python
   fi

   echo BUILDING: Python $pver done >&2

   echo Upgrading pip
   (
   which pip3
   $python_version -m pip install --upgrade pip
   $python_version -m pip install setuptools
   # pip3 install pycairo
   # pip3 install pygobject
   ) >  $HOSTLOGDIR/13-pip-upgrade.txt 2>&1

   echo Pip update done >&2
else
    echo not building python
    echo not building python >&2
fi

############ test python, exit on failure ##################

$install_top_dir/bin/$python_version <<EOF
import ctypes
print(dir(ctypes))
EOF
if [ $? = 0 ] ; then
   echo Good Python
else
   echo Python not working
   exit 2
fi


###############################################################################
##########         meson before gobject-introspection             #############
###############################################################################
# this needs to be reconsidered because gobject-intropsection needs python3
# to build.

build_gobject_introspection=true

if [ -e $install_top_dir/include/gobject-introspection-1.0/giversionmacros.h ] ; then
   build_gobject_introspection=false
   echo installation has gobject-introspection
fi

# 200918-PE install meson before using it.
#
## --------------- meson ---------------------------------
##
# this version of meson is too old to compile gobject-introspection (20220221)
# pip3 install meson

# we should have meson for pygobject, need version 0.46 or later
# however, is this the way to install pygobject? Or is done with pip3?
#

# we need python3 to have setuptools for meson - sigh
python3 -m pip install setuptools

build_meson=true
if command -v meson --version ; then

    echo meson --version
    which meson >&2
    echo meson --version >&2
    meson --version >&2
    if meson --version ; then
        echo we have meson
        v=$(meson --version)
       if [[ $v < 1.2.3 ]] ; then
          echo meson is too old, current version is $v
          build_meson=true
       else
          build_meson=false
       fi
    else
       build_meson=true
    fi
fi

if $build_meson = true ; then
   meson_version=1.2.3
   meson_version=1.7.0
   meson_version=1.8.1
   echo BUILDING: meson $meson_version:
   echo BUILDING: meson $meson_version: >&2
   (
   ${WGET} https://github.com/mesonbuild/meson/releases/download/$meson_version/meson-$meson_version.tar.gz
   tar xf ${AUTOBUILD_SOURCES}/meson-$meson_version.tar.gz
   cd meson-$meson_version
   python3 setup.py build
   python3 setup.py install
   cd -
   echo which meson
   which meson
   echo meson --version
   meson --version
   ) > $HOSTLOGDIR/14-meson.txt 2>&1
else
   echo not building meson:
fi



###############################################################################
##########         ninja before glib                              #############
###############################################################################

build_ninja=true
if [ -e $install_top_dir/bin/ninja ] ; then
   build_ninja=false
fi

if [ $build_ninja = true ] ; then
   echo BUILDING ninja
   (
   # see https://github.com/ninja-build/ninja/releases
   unset LD_LIBRARY_PATH
   ninja_version=1.10.2
   ${WGET} https://github.com/ninja-build/ninja/archive/refs/tags/v$ninja_version.tar.gz
   tar xf ${AUTOBUILD_SOURCES}/v$ninja_version.tar.gz
   cd ninja-$ninja_version
   python3 ./configure.py --bootstrap # builds ninja, requires python
   if [ -e ninja ] ; then
      cp ninja $install_top_dir/bin
   else
      echo configure/boostrap of ninja failed - what a surprise.
   fi
   cd -
   ) > $HOSTLOGDIR/15-ninja.txt 2>&1
fi



#######################################################################
# Pixman
#######################################################################
# cairo depends on pixman. So let's install that too.
if test -e $install_top_dir/include/pixman-1/pixman.h ; then
    echo installation has pixman
else
    unset LD_LIBRARY_PATH
    pixman_version=0.43.4
    echo BUILDING: pixman $pixman_version
    echo BUILDING: pixman $pixman_version >&2
    (
    ${WGET} https://www.cairographics.org/releases/pixman-$pixman_version.tar.gz
    tar xf $AUTOBUILD_SOURCES/pixman-$pixman_version.tar.gz
    cd pixman-$pixman_version
    pwd
    mkdir build
    cd build
    # put /usr/lib64 at the front of PKG_CONFIG_PATH so that meson
    # picks up the correct version of libpng
    export PKG_CONFIG_PATH=/usr/lib64/pkgconfig:$PKG_CONFIG_PATH
    echo PKG_CONFIG_PATH is $PKG_CONFIG_PATH
    echo meson setup -Dprefix=$install_top_dir ..
    meson setup -Dprefix=$install_top_dir ..
    ninja
    ninja install
    ) > $HOSTLOGDIR/16-a-pixman.txt
fi


#######################################################################
# Cairo - needed for RKit molecule drawing - which can be used by chapi
#######################################################################
# 20240326-PE
if [ -e $install_top_dir/include/cairo/cairo.h ] ; then
    echo installation has cairo
else
    # we need modern cairo - because that is what is used by GTK4.
    # in fact, perhaps we should build cairo at all on arch...
    use_new_cairo=false
    if test "$dist_name" = arch ; then
        use_new_cairo=true
    fi
    if test "$dist_name" = ubuntu ; then
        use_new_cairo=true
    fi
    if $use_new_cairo = true ; then
        (
        cairo_version=1.18.2
        echo BUILDING: cairo $cairo_version
        echo BUILDING: cairo $cairo_version >&2
        ${WGET} https://www.cairographics.org/releases/cairo-$cairo_version.tar.xz
        tar xf $AUTOBUILD_SOURCES/cairo-$cairo_version.tar.xz
        cd cairo-$cairo_version
        meson setup -Dprefix=$install_top_dir build
        cd build
        ninja
        # ninja install
        echo no install of cairo in this path at the moment.
        cd ..
        cd ..
        ) > $HOSTLOGDIR/16-b-cairo-by-ninja.txt 2>&1
    else
       cairo_version=1.16.0 # not meson/ninja
        echo BUILDING: cairo $cairo_version
        echo BUILDING: cairo $cairo_version >&2
        (
            unset LD_LIBRARY_PATH
            ${WGET} https://www.cairographics.org/releases/cairo-$cairo_version.tar.xz
            tar xf $AUTOBUILD_SOURCES/cairo-$cairo_version.tar.xz
            cd cairo-$cairo_version
            pwd
            # meson/ninja
            # mkdir build
            # cd build
            # meson -Dprefix=$install_top_dir ..
            # ninja
            # ninja install
            # cd ..
            # cd ..
            # standard
            ./configure --prefix=$install_top_dir
            if $MAKE ; then
                make install
            fi
        ) > $HOSTLOGDIR/16-b-cairo.txt 2>&1
    fi
fi


###############################################################################
##########         build guile and friends                        #############
###############################################################################


if test -n "$build_libtool" ; then
    echo BUILDING libtool:
    # libtool_version=1.5.24
    libtool_version=2.4.6
    ${WGET} http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/libtool/libtool-$libtool_version.tar.gz
    (date
     pwd
     gzip -dc ${AUTOBUILD_SOURCES}/libtool-$libtool_version.tar.gz | tar xf -
     unset LD_LIBRARY_PATH
     cd libtool-$libtool_version
     ./configure $generic_prefix
     $MAKE
    status=$?
    if [ "$status" != 0 ] ; then
       echo make of libtool failed
    else
       $MAKE install
    fi
    ) > $HOSTLOGDIR/17-libtool.txt 2>&1
else
    echo not building libtool:
fi


###############################################################################
##########         build idn                                      #############
###############################################################################

# we build libidn for libcurl.  libcurl needs it on RHEL4 because
# there is no /usr/lib/libidn.so.  There is a rpm devel package, of
# course, but that is more pain to install than compiling it from
# scratch for coot install.

if test -n "$build_libidn" ; then
    echo BUILDING: libidn:
    echo BUILDING: libidn: >&2
    (
    unset LD_LIBRARY_PATH
    libidn_version=1.15
    libidn_version=2.2.0
    # ${WGET} http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/libidn/libidn-$libidn_version.tar.gz
    ${WGET} https://www.mirrorservice.org/sites/ftp.gnu.org/gnu/libidn/libidn2-$libidn_version.tar.gz

    gzip -dc ${AUTOBUILD_SOURCES}/libidn2-$libidn_version.tar.gz | tar xf -
    cd libidn2-$libidn_version

    ./configure  $generic_prefix
    if $MAKE ; then
       $MAKE install
    fi
    ) > $HOSTLOGDIR/18-libidn2.txt 2>&1
else
    echo not building libidn2:
fi

# note: libpsl depends on libunistring. If I compile on the command line
# libpsl#s configure finds a library for u8_tolower. From this script
# it does (did) not. Hence move this build up before libpsl
###############################################################################
##########       build unistring                                  #############
###############################################################################

build_unistring=true
unistring_version=0.9.6
unistring_version=0.9.10

if [ "$build_unistring" = true ] ; then
   skip_this=false
   if [ "$test_for_already_installed_dependencies" = true ] ; then
      if [ -e $install_top_dir/include/unistr.h ] ; then
         skip_this=true
      fi
   fi

   echo libunistring skip_this $skip_this

   if [ $skip_this = false ] ; then
      echo BUILDING libunistring $unistring_version >&2
      echo BUILDING libunistring:
      (
      unset LD_LIBRARY_PATH
      echo ========================= build unistring =================================
      if [ -e $AUTOBUILD_SOURCES/libunistring-$unistring_version.tar.gz ] ; then
         tar xf $AUTOBUILD_SOURCES/libunistring-$unistring_version.tar.gz
      else
         echo missing file $AUTOBUILD_SOURCES/libunistring-$unistring_version.tar.gz
         ${WGET} http://mirrorservice.org/sites/ftp.gnu.org/gnu/libunistring/libunistring-$unistring_version.tar.gz
         tar xf $AUTOBUILD_SOURCES/libunistring-$unistring_version.tar.gz
      fi
      cd libunistring-$unistring_version
      echo ./configure --prefix=$install_top_dir
      if ./configure --prefix=$install_top_dir  ; then
         if $MAKE ; then
            make install
         fi
      fi
      cd -
      ) > $HOSTLOGDIR/18-libubunistring.txt 2>&1
      echo done libunistring $unistring_version >&2
   else
      echo not building libunistring
   fi
fi



#
###############################################################################
##########         build libpsl                                   #############
###############################################################################
#

# curl depends on libpsl - should we build that?
# https://github.com/rockdaboot/libpsl/releases/download/0.21.5/libpsl-0.21.5.tar.gz
# seems straightforward...

build_libpsl=true
if test -e $install_top_dir/include/libpsl.h ; then
    build_libpsl=false
fi

if test $build_libpsl = true ; then
   libpsl_version=0.21.5
   echo BUILDING: libpsl $libpsl_version
   echo BUILDING: libpsl $libpsl_version >&2
   (
   pwd
   unset LD_LIBRARY_PATH
   ${WGET} https://github.com/rockdaboot/libpsl/releases/download/0.21.5/libpsl-0.21.5.tar.gz
   tar xf ${AUTOBUILD_SOURCES}/libpsl-0.21.5.tar.gz
   cd libpsl-$libpsl_version
   ./configure --prefix=$install_top_dir
   $MAKE && make install
   ) > $HOSTLOGDIR/18-libpsl.txt
fi

#
###############################################################################
##########         build curl                                     #############
###############################################################################
#

if test -n "$build_curl" ; then
   # curl version 8.10.1 has a build problem on Alma 9.4 (at least). Let's
   # try the latest version: 8.11.1
   libcurl_version=7.65.3
   libcurl_version=8.10.1
   libcurl_version=8.11.1
   libcurl_version_directory=7_65_3
   libcurl_version_directory=8_10_1
   libcurl_version_directory=8_11_1
   echo BUILDING: curl $libcurl_version
   echo BUILDING: curl $libcurl_version >&2
   (
   # get libcurl from here:
   # libcurl_version=7.19.7
   # libcurl_version=7.25.0
   # libcurl_version=7.27.0
   # libcurl_version=7.32.0
   # ${WGET} http://curl.haxx.se/download/curl-$libcurl_version.tar.gz
   ${WGET} https://github.com/curl/curl/releases/download/curl-$libcurl_version_directory/curl-$libcurl_version.tar.gz

   gzip -dc ${AUTOBUILD_SOURCES}/curl-$libcurl_version.tar.gz | tar xf -
   cd curl-$libcurl_version

   echo from tar file ${AUTOBUILD_SOURCES}/curl-$libcurl_version.tar.gz
   echo building in: $PWD

   unset LD_LIBRARY_PATH

   # libcurl has problems with putting the libraries ine right order when we specify
   # --with-libidn (it puts the libidn prefix libs at the end of its LDFLAGS and that
   # is bad because /usr/lib gets in front, and /usr/lib/libidn.so is missing). So here
   # we force the libidn libs at the front of LDFLAGS.  Problem found on RHEL4-64bit
   # (lemur).
   #
   # this implicitly uses OpenSSL if it can be configured via pkg-config
   #
   # 20191211-PE on modern ubuntu: apt install libssl-dev, so that curl's configure finds it
   #             It's OK to depend on system libssl rather than build it myself.

   # Make sure (here) that system has OpenSSL
   # on Ubuntu: install it like this:
   # apt-get install libssl-dev
   #
   echo ./configure  $generic_prefix --enable-versioned-symbols --with-libidn2=$install_top_dir LDFLAGS=-L$install_top_dir/lib --with-openssl
   ./configure  $generic_prefix --enable-versioned-symbols --with-libidn2=$install_top_dir LDFLAGS=-L$install_top_dir/lib --with-openssl
   if $MAKE ; then
      if [ -n $post_process_libcurl ] ; then
         fixup_libcurl
      fi
      $MAKE install
      # argh! This is such a hack! `make install' installs a broken (see post_process_libcurl
      # comments) even though it is fixed by the sed in fixup_libcurl.  So *after* the install
      # let's install the corrected libcurl.la.  Wonderful stuff.
      #
      if [ -n "$post_process_libcurl" ] ; then
         /usr/bin/install -c 'libcurl.la' $install_top_dir/lib/libcurl.la
      fi
   fi

   ) > $HOSTLOGDIR/19-curl.txt 2>&1
   echo BUILDING: done curl: >&2

else
    echo not building curl:
fi




###############################################################################
##########         build gsl                                      #############
###############################################################################
#

if test -n "$build_gsl" ; then
    # wget http://www.mirror.ac.uk/sites/ftp.gnu.org/gnu/gsl/gsl-1.5.tar.gz
    # wget http://ftp.gnu.org/gnu/gsl/gsl-1.6.tar.gz
    # if you change this, change needed_gsl_version above
    gsl_version=1.12
    gsl_version=1.15
    gsl_version=1.16
    gsl_version=2.7
    echo BUILDING: gsl $gsl_version
    echo BUILDING: gsl $gsl_version >&2
    #
    # ${WGET} http://ftp.gnu.org/gnu/gsl/gsl-$gsl_version.tar.gz
    # ${WGET} http://ftp.gnu.org/gnu/gsl/gsl-$gsl_version.tar.gz
    ${WGET} http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/gsl/gsl-$gsl_version.tar.gz
    (
    date
    pwd
    unset LD_LIBRARY_PATH
    gzip -dc ${AUTOBUILD_SOURCES}/gsl-$gsl_version.tar.gz | tar xf -
    cd gsl-$gsl_version
    ./configure $generic_prefix
    $MAKE
    status=$?
    if [ "$status" != 0 ] ; then
        echo ERROR:: GSL make failed.
        exit 2
    else
       echo 1 --------------------------------------------------------------- 
       echo '                                ' make install
       echo 1 ----------------------------------------------------------------
       $MAKE install
    fi
    ) > $HOSTLOGDIR/20-gsl.txt 2>&1
    echo BUILDING: done gsl >&2
else
    echo not building gsl:
fi


###############################################################################
##########         GLM                                            #############
###############################################################################
if [ -e $install_top_dir/include/glm/glm.hpp ] ; then
    echo not building glm
else
    echo where is glm/include question-mark
    ls $install_top_dir/include
    # The glm version is 0.9.9.5 because glm.pc was deleted after that.
    # thanks sayurlinux.
    # ${WGET} $extras_place/glm-$glm_version.tar.gz
    # However, that fails to compile:
    # In file included from /Users/runner/autobuild/building/Mac-1710037648402.local_2024-03-10__T03_03_05/glm-0.9.9.5/glm/gtc/random.hpp:82:
    # /Users/runner/autobuild/building/Mac-1710037648402.local_2024-03-10__T03_03_05/glm-0.9.9.5/glm/gtc/random.inl:25:17: error: implicit conversion loses integer precision: 'int' to 'unsigned char' [-Werror,-Wimplicit-int-conversion]
    # so let's try 0.9.8
    glm_version=0.9.9.2
    glm_version=1.0.0
    glm_version=0.9.9.5
    glm_version=0.9.9.8
    glm_version=1.0.0
    echo BUILDING glm $glm_version:
    echo BUILDING glm $glm_version: >&2
    # echo fetching https://github.com/g-truc/glm/archive/refs/tags/$glm_version.tar.gz >&2
    ${WGET} https://github.com/g-truc/glm/archive/refs/tags/$glm_version.tar.gz
    echo cp ${AUTOBUILD_SOURCES}/$glm_version.tar.gz ${AUTOBUILD_SOURCES}/glm-$glm_version.tar.gz
    cp ${AUTOBUILD_SOURCES}/$glm_version.tar.gz ${AUTOBUILD_SOURCES}/glm-$glm_version.tar.gz
    echo ${WGET} $extras_place/glm-CMakeLists-for-glm.pc.patch
    ${WGET} $extras_place/glm-CMakeLists-for-glm.pc.patch
    (
    date
    pwd
    gzip -dc ${AUTOBUILD_SOURCES}/glm-$glm_version.tar.gz | tar xf -
    cd glm-$glm_version
    # restore glm.pc
    echo 'prefix=@CMAKE_INSTALL_PREFIX@
includedir=${prefix}/include

Name: GLM
Description: OpenGL Mathematics
Version: @GLM_VERSION@
Cflags: -I${includedir}' > cmake/glm.pc.in
    cat cmake/glm.pc.in
    echo patch from ${AUTOBUILD_SOURCES}/glm-CMakeLists-for-glm.pc.patch
    patch < ${AUTOBUILD_SOURCES}/glm-CMakeLists-for-glm.pc.patch
    echo cmake . -DCMAKE_INSTALL_PREFIX=$install_top_dir
    cmake . -DCMAKE_INSTALL_PREFIX=$install_top_dir
    if $MAKE ; then
       make install
    fi
    ) > $HOSTLOGDIR/22-glm.txt 2>&1
   echo INFO:: glm-build-sub-shell-status $? >&2
   echo done glm: >&2
fi


###############################################################################
##########         build numpy                                    #############
###############################################################################

# Let's stop if we need a fortran compiler and don't have it.
#
if [ "$build_numpy" = true ] ; then
    if gfortran --version > /dev/null ; then
        echo found fortran compiler
    else
        echo fortran compiler not found.
        exit 2
    fi
else
   echo debug:: build_numpy was $build_numpy
fi

# numpy needs system libblas (and liblapack?) - it's not clear to
# me how to build them otherwise.
# sudo apt-get install libblas-dev liblapack-dev

echo command -v pip3
command -v pip3
# cython
echo pip3 install --upgrade pip
pip3 install --upgrade pip
echo pip3 install cython
pip3 install cython
if test -d $install_top_dir/lib/$python_version/site-packages/nanobind ; then
    :
else
    echo pip3 install nanobind
    echo pip3 install nanobind >&2
    pip3 install nanobind
    echo pip3 install nanobind done >&2
fi

if [ true = true ] ; then
   skip_this=false
   # ls -alt $install_top_dir/lib/$python_version/site-packages/numpy/lib/_version.py
   if [ -e $install_top_dir/lib/$python_version/site-packages/numpy/lib/_version.py ] ;  then
         echo numpy is found, skip
         skip_this=true
   else
         echo numpy test file not found: $install_top_dir/lib/$python_version/site-packages/numpy/lib/_version.py
         echo numpy was not found - needs building
   fi
   if [ $skip_this = false ] ;  then
      # numpy_version=1.19.4
      # 20240127-PE Using 1.19.4 I am getting an error installing with Python 3.10 [errno #1].
      # So let's try the latest numpy - 1.26.3
      numpy_version=1.26.3
      # still compilation errors:
      # numpy-1.26.3/numpy/core/src/npysort/simd_qsort.dispatch.cpp:11:14: fatal error: x86 -simd-sort/src/avx512-32bit-qsort.hpp: No such file or directory
      # 11 |     #include "x86-simd-sort/src/avx512-32bit-qsort.hpp"
      #    |              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      # compilation terminated.
      # numpy_version=2.2.2 # hellish build complexity
      numpy_version=1.26.4
      echo BUILDING numpy $numpy_version
      echo BUILDING numpy $numpy_version >&2
      (
      echo this gfortran:
      command -v gfortran
      echo $PATH
      # this needs fortran compiler gfortran

      # maybe get numpy from github?
      # https://github.com/numpy/numpy/releases/download/v1.14.1/numpy-1.14.1.tar.gz
      # numpy needset setuptools
      # https://github.com/pypa/setuptools/archive/v41.5.1.tar.gz
      # numpy source is now zip
      # ${WGET} https://pypi.python.org/packages/source/n/numpy/numpy-$numpy_version.tar.gz
      # ${WGET} https://pypi.python.org/packages/source/n/numpy/numpy-$numpy_version.zip
      # echo Fetching https://github.com/numpy/numpy/archive/refs/tags/v$numpy_version.tar.gz >&2
      # ${WGET} https://github.com/numpy/numpy/archive/refs/tags/v$numpy_version.tar.gz
      echo ${WGET} https://github.com/numpy/numpy/releases/download/v$numpy_version/numpy-$numpy_version.tar.gz
      ${WGET} https://github.com/numpy/numpy/releases/download/v$numpy_version/numpy-$numpy_version.tar.gz
      #
      tar xf ${AUTOBUILD_SOURCES}/numpy-$numpy_version.tar.gz
      cd numpy-$numpy_version/
      # we need to check that we have a fortran compiler, in this case gnu95
      #
      if gfortran --version ; then
        echo found fortran compiler
      else
        echo fortran compiler not found.
        exit 2
      fi
      which python3
      # OK, back to compiling...
      $python_version setup.py build --fcompiler=gfortran
      $python_version setup.py install
      if [ ! $? ] ; then
         echo something bad about numpy.
         exit 2
      fi
      cd -
      # let's just try to install it using pip! Maybe that will do good things?
      $python_version -m pip install numpy==$numpy_version --force-reinstall
      ) > $HOSTLOGDIR/23-numpy.txt 2>&1
      echo BUILDING numpy $numpy_version finished >&2
   fi
fi

###############################################################################
##########         build boost  - after numpy                     #############
###############################################################################
# which messes up the log numbering

# there is something wrong here - boost needs to come after numpy
# rdkit needs boost-numpy

build_boost=true
test_for_already_installed_dependencies=true

if [ "$build_boost" = true ] ; then
   skip_this=false
   if [ "$test_for_already_installed_dependencies" = true ] ; then
      if [ -e $install_top_dir/include/boost/functional/hash.hpp ] ;  then
         echo not building boost
         skip_this=true
      fi
   fi

   if [ $skip_this = false ] ;  then

      # 20241002-PE
      # try 1.86.0 becausee 1.83 doesn't compile - like this:
      # https://github.com/bambulab/BambuStudio/issues/3957
      # They fixed the problem by udating the boost - let's try that
      boost_version=1_71_0
      boost_version=1_72_0
      boost_version=1_74_0
      boost_version=1_83_0
      boost_version=1_86_0
      boost_version=1_87_0
      boost_server_dir=1.72.0
      boost_server_dir=1.72.0
      boost_server_dir=1.74.0
      boost_server_dir=1.82.0
      boost_server_dir=1.83.0
      boost_server_dir=1.86.0
      boost_server_dir=1.87.0
      echo BUILDING boost $boost_version :
      echo BUILDING boost $boost_version >&2

      boost_home_url=https://dl.bintray.com/boostorg/release/$boost_server_dir/source # old
      boost_home_url=https://boostorg.jfrog.io/artifactory/main/release/$boost_server_dir/source
      boost_home_url=https://archives.boost.io/release/$boost_server_dir/source/
      echo wgetting $boost_home_url/boost_$boost_version.tar.gz
      echo ${WGET} $boost_home_url/boost_$boost_version.tar.gz 2>&1
      ${WGET} $boost_home_url/boost_$boost_version.tar.gz
      echo done ${WGET} $boost_home_url/boost_$boost_version.tar.gz 2>&1
      echo fetch of $boost_home_url/boost_$boost_version.tar.gz complete.. compiling...

      (
      echo building ========================= boost $boost_version =========================

      gzip -dc ${AUTOBUILD_SOURCES}/boost_$boost_version.tar.gz | tar xf -
      cd boost_$boost_version

      # compilation falls over

      # cc.compile.c++ bin.v2/libs/python/build/gcc-9/release/address-model-/python-3.6/threading-multi/visibility-hidden/long.o
      # In file included from ./boost/python/detail/prefix.hpp:13,
      #           from ./boost/python/long.hpp:8,
      #           from libs/python/src/long.cpp:5:
      # ./boost/python/detail/wrap_python.hpp:57:11: fatal error: pyconfig.h: No such file or directory
      #    57 | # include <pyconfig.h>
      #       |           ^~~~~~~~~~~~
      # compilation terminated.

      # But pyconfig.h is here:
      # $HOME/autobuild/Linux-penelope-pre-release-gtk3-python/include/python3.6m/pyconfig.h

      address_model=64
      pwd
      # echo "using python : 3.10 : $install_top_dir/bin/python3 ;" > user-config.jam
      echo "using python : $python_version_extension : $install_top_dir/bin/python3 ;" > user-config.jam
      echo ./bootstrap.sh --prefix=$install_top_dir --with-python=$install_top_dir/bin/python3 --with-python-root=$install_top_dir --with-libraries=system,python,regex,thread,serialization,iostreams,program_options --without-icu
      echo ./bootstrap.sh --prefix=$install_top_dir --with-python=$install_top_dir/bin/python3 --with-python-root=$install_top_dir --with-libraries=system,python,regex,thread,serialization,iostreams,program_options --without-icu > bootstrap-command-save
      ./bootstrap.sh --prefix=$install_top_dir --with-python=$install_top_dir/bin/python3 --with-python-root=$install_top_dir --with-libraries=system,python,regex,thread,serialization,iostreams,program_options --without-icu
      echo boostrap.sh done

      # now edit the project-config.jam file using python line

      cp project-config.jam project-config.jam-orig
      # awk -v itd=$install_top_dir '
      #    /using python : 3.6/ { print "   ",$1,$2,$3,$4,$5,"python3 :", itd "/include/python3.6m :", itd "/lib/libpython3.6m.so ;" }
      #   $0 !~ "using python : 3.6 "
      # ' project-config.jam-orig > project-config.jam
      # that was flipping hard work.
      # 20201215-PE and now I've commented it out.

      # bjam no longer exists
      # use -Wno-deprecated-declarations
      echo ./b2 address-model=$address_model --debug-configuration cflags=-fPIC -j$np cxxflags="-fPIC -I$install_top_dir/include/python$python_version_extension$python_abiflags -Wno-maybe-uninitialized -Wno-deprecated-declarations" install > b2-command-save
           ./b2 address-model=$address_model --debug-configuration cflags=-fPIC -j$np cxxflags="-fPIC -I$install_top_dir/include/python$python_version_extension$python_abiflags -Wno-maybe-uninitialized -Wno-deprecated-declarations" install
      cd -
      ) > $HOSTLOGDIR/23-boost.txt
      echo BUILDING: "done boost" $boost_version >&2
   fi
else
    echo boost $boost_version was installed >&2
fi


################## python diagnostics #########################################

if [ -e $install_top_dir/lib/libboost_python$python_version_squish.a ] ; then
   echo libboost_python $install_top_dir/lib/libboost_python$python_version_squish.a was installed
   echo libboost_python $install_top_dir/lib/libboost_python$python_version_squish.a was installed >&2
else
   echo libboost_python $install_top_dir/lib/libboost_python$python_version_squish.a was not installed
   echo libboost_python $install_top_dir/lib/libboost_python$python_version_squish.a was not installed >&2
   exit
fi


# this is a hack for charybdis   - we need cmake version 3.1 or later
# export PATH=$HOME/cmake/bin:$PATH

############################### eigen ##########################################

eigen_version=3.3.9
if [ -e $install_top_dir/include/eigen3 ] ; then
   echo eigen3 is installed
   echo eigen3 is installed >&2
else
   echo BUILDING eigen $eigen_version
   echo BUILDING eigen $eigen_version >&2
   (
   ${WGET} https://gitlab.com/libeigen/eigen/-/archive/$eigen_version/eigen-$eigen_version.tar.gz
   tar xf $AUTOBUILD_SOURCES/eigen-$eigen_version.tar.gz

   mkdir -p build-eigen
   cd build-eigen
   cmake -DCMAKE_INSTALL_PREFIX=$install_top_dir ../eigen-$eigen_version
   make install
   cd -
   ) > $HOSTLOGDIR/24-eigen.txt 2>&1
   echo BUILDING eigen finished >&2
fi

############################### catch2 ##########################################
# rdkit needs catch2 (C++ testing framework).

if [ -e $install_top_dir/include/catch2/catch_config.hpp ] ; then
    echo Catch2 is installed
    echo Catch2 is installed >&2
else
   catch2_version=3.5.2
   echo BUILDING catch2 $catch2_version
   ${WGET} https://github.com/catchorg/Catch2/archive/refs/tags/v$catch2_version.tar.gz
   (
       unset LD_LIBRARY_PATH
       tar xf $AUTOBUILD_SOURCES/v$catch2_version.tar.gz
       echo cd Catch2-$catch2_version
       cd Catch2-$catch2_version
       # meson setup -Dcpp_std=c++17 -Dprefix=$install_top_dir build
       # cd build
       # ninja
       # ninja install
       # cd ..
       mkdir build
       cd build
       cmake -DCMAKE_INSTALL_PREFIX=$install_top_dir ..
       echo $MAKE && make install
       $MAKE && make install
       cd ..
       cd ..
   ) > $HOSTLOGDIR/25-catch2.txt 2>&1
fi

if [ -d $install_top_dir/include/catch2 ] ; then
    echo OK, Catch2 is installed
else
    echo FAIL BUILDING Catch2
    echo FAIL BUILDING Catch2 >&2
    exit
fi

############################### rdkit ##########################################

# we need to set rdkit_tar_size because the WGET doesn't skip the download if the
# file exists. Amazon.
#
build_rdkit=true
rdkit_version=2017_09_3
rdkit_version=2019_09_1 # python 3
rdkit_version=2018_09_2 # Atom pointer wrappers gone, needs coot Dec 2020 patch
rdkit_version=2020_09_3
rdkit_version=2023_03_1
rdkit_version=2023_09_4
rdkit_version=2024_09_4
rdkit_version=2024_09_5
# see https://github.com/rdkit/rdkit/releases
rdkit_home=https://github.com/rdkit/rdkit/archive
rdkit_tar_host_file_name=Release_$rdkit_version.tar.gz
rdkit_tar_download_file_name=rdkit-Release_$rdkit_version.tar.gz
rdkit_tar_size=54644792
rdkit_tar_size=58598385 # 2020_09_3
rdkit_tar_size=79454133 # 2023_03_1
rdkit_tar_size=80212603 # 2023_09_4
rdkit_tar_size=82055856 # 2024_09_4
rdkit_tar_size=82181626 # 2024_09_5

if [ "$build_rdkit" = true ] ; then
   skip_this=false
   if [ "$test_for_already_installed_dependencies" = true ] ; then
      # this file is in 2018_09 but not in 2017_09
      if [ -e $install_top_dir/include/rdkit/GraphMol/StereoGroup.h ] ;  then
         echo not building rdkit:
         echo not building rdkit: >&2
         skip_this=true
      fi
   fi

   # hack
   # skip_this=false

   if [ $skip_this = false ] ;  then

      echo BUILDING: RDKit $rdkit_version
      echo BUILDING: RDKit $rdkit_version >&2
      (
      echo building ========================= rdkit ==============================

      # at last we get to actually compile rdkit
      export CC=gcc
      export CXX=g++
      RDKIT=$install_top_dir
      RDBASE=$install_top_dir
      CMAKE_INSTALL_PREFIX=$install_top_dir
      export RDKIT
      export RDBASE
      export CMAKE_INSTALL_PREFIX

      # shall we build from github rdkit?
      github_rdkit=false

      if [ $(uname) = Darwin ] ; then
         echo LD_LIBRARY_FALLBACK_PATH  $LD_LIBRARY_FALLBACK_PATH
	 # what is unexport in bash?
         export LD_LIBRARY_PATH=
      fi

      echo ==================== LD_LIBRARY_PATH is $LD_LIBRARY_PATH

      if [ "$github_rdkit" = true ] ; then
         echo PATH A - pull
         if [ ! -d rdkit-github/build ] ; then
            mkdir -p rdkit-github/build
         fi
         echo pulling...
         # cd rdkit-github/rdkit && git pull && cd -
         cd rdkit-github/build
         pwd
         tree_from_build=../rdkit
      else

         # old wget $rdkit_home/$rdkit_tar_host_file_name -P ${AUTOBUILD_SOURCES} -O ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
         echo PATH B

         # OK, So, AFAICS, -N doesn't work with this file. So check the size
         get_the_rdkit_tar_file=true
         echo testing for existance of ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
         if [ -e ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name ] ; then
            which stat
            echo   found the file   ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
            if [ $OS = Darwin ] ; then
                echo stat -f%z   ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
                stat -f%z ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
                size=$(stat -f%z ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name)
                echo rdkit tar ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name size from stat: $size
            else
                echo stat --format=%s   ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
                stat --format=%s        ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
                size=$(stat --format=%s ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name)
                echo rdkit tar ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name size from stat: $size
            fi
            if [ "$size" = $rdkit_tar_size ] ; then
                get_the_rdkit_tar_file=false
            fi
         fi
         echo here C with get_the_rdkit_tar_file $get_the_rdkit_tar_file

         if [ $get_the_rdkit_tar_file = true ] ; then
            echo $WGET $rdkit_home/$rdkit_tar_host_file_name -O ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
            $WGET $rdkit_home/$rdkit_tar_host_file_name -O ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
            do_rdkit_download=true
            if [ -e ${AUTOBUILD_SOURCES}/$rdkit_tar_host_file_name ] ; then
                echo here D
                if [ $OS = Darwin ] ; then
                    s=$(stat -f%z ${AUTOBUILD_SOURCES}/$rdkit_tar_host_file_name)
                else
                    s=$(stat --format=%s ${AUTOBUILD_SOURCES}/$rdkit_tar_host_file_name)
                fi
                if [ "$s" = $rdkit_tar_size ] ; then
                   do_rdkit_download=false
                fi
            fi
            if [ $do_rdkit_download = true ] ; then
               echo here E
               echo $WGET $rdkit_home/$rdkit_tar_host_file_name
               if ${WGET} $rdkit_home/$rdkit_tar_host_file_name ; then
                  if [ -e ${AUTOBUILD_SOURCES}/$rdkit_tar_host_file_name ] ; then
                     cp ${AUTOBUILD_SOURCES}/$rdkit_tar_host_file_name ${AUTOBUILD_SOURCES}/rdkit-$rdkit_tar_host_file_name
                  else
                     echo $rdkit_tar_host_file_name does not exist after download
                  fi
               fi
            fi
         fi

         pwd
         echo tar xf ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
         tar xf ${AUTOBUILD_SOURCES}/$rdkit_tar_download_file_name
         ls
         if [ ! -e rdkit-Release_$rdkit_version ] ; then
             echo RDKit untar dir not found: rdkit-Release_$rdkit_version
             exit 2
         fi
         cd rdkit-Release_$rdkit_version
         ${WGET} $extras_place/rdkit-maeparser.patch
         pwd
         echo patch -p0 < ${AUTOBUILD_SOURCES}/rdkit-maeparser.patch
         patch -p0 < ${AUTOBUILD_SOURCES}/rdkit-maeparser.patch

         # now fix for modern boost:
         # Code/RDGeneral/RDValue-taggedunion.h needs numeric_cast.hpp


         mkdir -p build
         cd build
         pwd
         tree_from_build=..
      fi

      # New (1.60) boost uses BOOST_PYTHON not Boost_PYTHON
      #
      echo which cmake
      which cmake

      # No help:  -DBoost_INCLUDE_DIR=$install_top_dir/include
      # Cmake policy:	 -DMACOSX_RPATH=ON

      # old verisons of boost (before 1.60?) can't find boost python
      # with new (github Feb 2016) rdkit

      # -DPYTHON_LIBRARY=$install_top_dir/lib/libpython2.7.$extension_type

      # no help apparently
      # -DBoost_EXTERNAL_OBJECTS=$install_top_dir/lib/libboost_python.$extension_type
      # -DBoost_INCLUDE_DIR=$install_top_dir/include
      #
      #  -DBOOST_ROOT=$install_top_dir
      # -DBoost_INCLUDE_DIR=$install_top_dir/include
      #  -DBoost_LIBRARY_DIRS=$install_top_dir/lib
      #  -DBoost_PYTHON_LIBRARY=$install_top_dir/lib/libboost_python.$extension_type
      #  -DBoost_REGEX_LIBRARY=$install_top_dir/lib/libboost_regex.$extension_type


      # catches correctly (no need to specify)
      # 	 -DPYTHON_INCLUDE_DIR=$install_top_dir/include/python2.7

      if [ $(uname) = Darwin ] ; then
         cmake_macosx_rpath=-DCMAKE_MACOSX_RPATH=ON
      fi

      # last time I looked, the include files of RDKit MolDraw2D were wrong.
      # I had to hack in GraphMol/MolDraw2D into include/rdkit and copy the files
      # there.

      # -- Could NOT find InChI in system locations (missing:  INCHI_LIBRARY INCHI_INCLUDE_DIR)
      # CMake Warning at External/INCHI-API/CMakeLists.txt:43 (message):
      #   ** NO INCHI SOFTWARE FOUND
      #
      #   InChI support will be turned off.  If you want to add InChI support, please
      #   follow the instructions inside $RDBASE/External/INCHI-API/README to
      #   download a copy of InChI software and then rerun cmake.
      #
      # http://www.inchi-trust.org/download/105/INCHI-1-SRC.zip

      # now libboost_python comes with an extended name: libboost_python27

      libboost_python_ext=$python_version_extension
      libboost_python_ext=
      extension_type=so
      python_arch=x86_64-linux-gnu

      if [ $(uname) = Darwin ] ; then
         extension_type=dylib
         python_arch=darwin
      fi

      if test "$dist_name" = debian ; then
          echo don.t mess with LDFLAGS here on debian
      else
          if test "$dist_name" = ubuntu ; then
              echo don.t mess with LDFLAGS here on ubuntu
          else
              if test "$dist_name" = almalinux ; then
                  echo don.t mess with LDFLAGS on almalinux
              else
		  if test "$dist_name" = arch ; then
		      echo don.t mess with LDFLAGS here on arch
                  else
                      export LDFLAGS="-L$install_top_dir/lib -lintl"
                  fi
              fi
          fi
      fi

      echo AAAAAAAAAAAAAAAAAAAAAAAA LDFLAGS is $LDFLAGS

      # echo will configure with cmake like this:
      # DBoost_PYTHON39_LIBRARY_RELEASE needs to be extracted?
      # probblem: $install_top_dir/include/boost/python/detail/wrap_python.hpp:57:23: fatal error: pyconfig.h: No such file or directory
      # solution: https://github.com/rdkit/rdkit/issues/3884
      # -DPYTHON_INCLUDE_DIR=$PYROOT/include/python3.8
      # -DBoost_PYTHON39_LIBRARY_RELEASE=$install_top_dir/lib/libpython3.so

               # -DCMAKE_CXX_STANDARD_LIBRARIES="-lintl -dl"
               # -DCMAKE_SHARED_LINKER_FLAGS="-lintl -dl"
               # libpython is linking with /usr/local/opt/gettext/lib:
               # otool -L ~/autobuild/build-chapi-gtk4/lib/libpython3.10d.dylib | grep libint
               # /usr/local/opt/gettext/lib/libintl.8.dylib (compatibility version 13.0.0, current version 13.0.0)

               # no help
               # -DCMAKE_C_STANDARD_LIBRARIES="-lintl -ldl -framework CoreFoundation" \

               # remove to see if this fixes the non-Darwin build.
               # -DCMAKE_STATIC_LINKER_FLAGS="$install_top_dir/lib/libintl.a"

      echo cmake \
               -DCMAKE_PREFIX_PATH=$install_top_dir \
               -DCatch2_DIR=$install_top_dir \
               -DPYTHON_INCLUDE_DIR=$install_top_dir/include/python$python_version_extension$python_abiflags \
               $cmake_macosx_rpath \
               -DPYTHON_EXECUTABLE=$install_top_dir/bin/python3 \
               -DPYTHON_LIBRARY=$install_top_dir/lib/python$python_version_extension/config-${python_version_extension}$python_abiflags-$python_arch/libpython$python_version_extension$python_abiflags.a \
               -DCMAKE_INSTALL_PREFIX=$install_top_dir \
               -DRDK_BUILD_MAEPARSER_SUPPORT=OFF \
               -DRDK_BUILD_CAIRO_SUPPORT=ON \
               -DRDK_INSTALL_INTREE=OFF \
               -DRDK_INSTALL_COMIC_FONTS=OFF \
               -DCatch2_DIR=$install_top_dir \
                $tree_from_build

      if cmake  \
               -DCMAKE_PREFIX_PATH=$install_top_dir \
               -DCatch2_DIR=$install_top_dir \
               -DPYTHON_INCLUDE_DIR=$install_top_dir/include/python$python_version_extension$python_abiflags \
               $cmake_macosx_rpath \
               -DPYTHON_EXECUTABLE=$install_top_dir/bin/python3 \
               -DPYTHON_LIBRARY=$install_top_dir/lib/python$python_version_extension/config-${python_version_extension}$python_abiflags-$python_arch/libpython$python_version_extension$python_abiflags.a \
               -DCMAKE_INSTALL_PREFIX=$install_top_dir \
               -DRDK_BUILD_MAEPARSER_SUPPORT=OFF \
               -DRDK_BUILD_CAIRO_SUPPORT=ON \
               -DRDK_INSTALL_INTREE=OFF \
               -DRDK_INSTALL_COMIC_FONTS=OFF \
               -DCatch2_DIR=$install_top_dir \
                $tree_from_build ; then


         # now patch rapidjson document.h
         sed -i.backup -e 's/const SizeType length/SizeType length/' ../External/rapidjson-1.1.0/include/rapidjson/document.h

         # it seems that make -j n fails to compile (race condition?)
         # so use just plain make? (currently not fixed)
         if $MAKE ; then
            make install
         else
            echo problem making the RDKit.
            exit 1
         fi
      else
         echo problem configuring the RDKit.
         exit 1
      fi
      cd ..
      cd ..
      ) > $HOSTLOGDIR/26-rdkit.txt 2>&1
      echo BUILDING rdkit finished
      echo BUILDING rdkit finished >&2
      wc $HOSTLOGDIR/26-rdkit.txt >&2
   fi
fi


###############################################################################
# exit here for the chapi-dependencies build
###############################################################################

if [ "$CHAPI_ONLY" = true ] ; then
   echo done CHAPI_ONLY
   exit
fi

###############################################################################
##########         gmp                                            #############
###############################################################################


if [ -e $install_top_dir/include/gmp.h ] ; then
    build_gmp=false
else
    build_gmp=true
fi

if "$build_gmp" = true ; then
    # gmp_version=4.2.4
    # gmp_version=5.1.2
    # gmp_version=6.0.0a # it doesn't untar into this directory
    # gmp_version=5.1.3
    gmp_version=6.1.2
    echo BUILDING gmp $gmp_version
    echo BUILDING gmp $gmp_version >&2
    ${WGET} http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/gmp/gmp-$gmp_version.tar.bz2
    (date
     pwd
     unset LD_LIBRARY_PATH
     tar xf ${AUTOBUILD_SOURCES}/gmp-$gmp_version.tar.bz2
     cd gmp-$gmp_version
     ./configure $generic_prefix
     $MAKE
    status=$?
    if [ "$status" != 0 ] ; then
       echo make of gmp failed
    else
       $MAKE install
    fi
    ) > $HOSTLOGDIR/27-gmp.txt 2>&1
    echo done gmp $gmp_version >&2
else
    echo not building gmp:
fi



# glib was removed because glib is a dependency of gtk-4 and we don't build gtk-4,
# so if we want to use glib for other packages, we need to use the same glib that
# gtk-4 used.

# we need python3 to have packaging
python3 -m pip install packaging

###### pcre2 is needed for glib. glib is compiled by gobject-introspection
###### (that doesn't seem good). Let's install pcre2 and see what happens

if test -e $install_top_dir/include/pcre2.h ; then
    echo installation has pcre2
    echo installation has pcre2 >&2
else
   pcre2_version=10.43
   echo BUILDING: pcre2 $pcre2_version
   echo BUILDING: pcre2 $pcre2_version >&2
   (
   unset LD_LIBRARY_PATH
   d=https://github.com/PCRE2Project/pcre2/releases/download/pcre2-$pcre2_version
   ${WGET} $d/pcre2-$pcre2_version.tar.gz
   tar xf $AUTOBUILD_SOURCES/pcre2-$pcre2_version.tar.gz
   cd pcre2-$pcre2_version
   ./configure --prefix=$install_top_dir
   if $MAKE ; then
       make install
   fi
   cd -
   ) > $HOSTLOGDIR/28-pcre2.txt 2>&1
fi

###############################################################################
##########         gobject-introspection                          #############
###############################################################################

# hack to use system library:
build_gobject_introspection=false
if test "$build_gobject_introspection" = true ; then
   echo BUILDING gobject-introspection:
   echo BUILDING gobject-introspection: >&2
   (
   # just for gobject-introspection - depends on our glib installation
   export PKG_CONFIG_PATH=$install_top_dir/lib64/pkgconfig:$install_top_dir/lib/pkgconfig
   export LD_LIBRARY_PATH=$install_top_dir/lib64:$install_top_dir/lib
   date
   echo BUILDING gobject-introspection:

   # or else very annoying:
   # symbol lookup error: /home/paule/autobuild/Linux-penelope-arch-gtk4/lib/libreadline.so.8: undefined symbol: UP
   if test $dist_name = arch ; then
       unset LD_LIBRARY_PATH
   fi
   echo environment variables
   echo PATH @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
   echo $PATH
   echo PKG_CONFIG_PATH @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
   echo $PKG_CONFIG_PATH
   echo LD_LIBRARY_PATH @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
   echo $LD_LIBRARY_PATH
   which gcc
   which g++
   gcc --version

   gobject_introspection_version=1.50.0
   gobject_introspection_version=1.68.0
   gobject_introspection_version=1.71.0
   gobject_introspection_version=1.72.0
   gobject_introspection_version=1.80.0
   gobject_introspection_version_stub=1.80
   # 20220820-PE note to self: 1.73.0 is now avaliable
   # https://download.gnome.org/sources/gobject-introspection/1.73/
   d=http://ftp.acc.umu.se/pub/GNOME/sources/gobject-introspection/1.50
   d=http://ftp.acc.umu.se/pub/GNOME/sources/gobject-introspection/1.68
   d=http://ftp.acc.umu.se/pub/GNOME/sources/gobject-introspection/1.71
   d=http://ftp.acc.umu.se/pub/GNOME/sources/gobject-introspection/1.72
   d=http://ftp.acc.umu.se/pub/GNOME/sources/gobject-introspection/1.72
   d=http://ftp.acc.umu.se/pub/GNOME/sources/gobject-introspection/$gobject_introspection_version_stub

   ${WGET} $d/gobject-introspection-$gobject_introspection_version.tar.xz
   tar xf ${AUTOBUILD_SOURCES}/gobject-introspection-$gobject_introspection_version.tar.xz
   cd gobject-introspection-$gobject_introspection_version
   # 1.68 (probably earlier) has moved on from configure. meson baby
   # echo ./configure --prefix=$install_top_dir PYTHON=python3
   # ./configure --prefix=$install_top_dir PYTHON=python3
   # if $MAKE ; then
   #   $MAKE install
   # fi
   echo PKG_CONFIG_PATH is...
   echo $PKG_CONFIG_PATH

   echo this is the result of /bin/pkg-config glib-2.0
   /bin/pkg-config --modversion glib-2.0
   /bin/pkg-config --cflags glib-2.0
   /bin/pkg-config --libs glib-2.0

   echo building in:
   pwd

   echo which meson
   which meson
   meson --version

   export CC=gcc
   # $install_top_dir/bin/meson is important, otherwise the wrong meson
   # is used.
   #
   # if $install_top_dir/bin/meson -Dprefix=$install_top_dir build ; then
   #
   # BUT... if we don't build meson because we have a new enough meson
   # in the path then $install_top_dir/bin/meson does not exist!

   # how about setting --libdir?
   # if meson setup -Dprefix=$install_top_dir --libdir=$install_top_dir/lib64 build ; then
   if meson setup -Dprefix=$install_top_dir build ; then
      echo meson passed
      cd build
      ninja
      ninja install
      cd -
   else
      echo meson failed
   fi
   export -n CC
   cd ..
   ) > $HOSTLOGDIR/29-gobject-introspection.txt 2>&1
   echo done gobject-introspection: >&2
fi


sources_dir=${AUTOBUILD_SOURCES}


# pycairo is a dependency of pygobject.  Is this gtk2 stuff?
pycairo_version=1.17.0 #  check for a more recent version.
skip_build=true
if [ $test_for_already_installed_dependencies = true ] ; then
   # check this file name.
   #  $install_top_dir/lib/python$python_version_extension/site-packages/pycairo-1.17.0-py3.6-linux-x86_64.egg/cairo/_cairo.py
   if [ -e $install_top_dir/lib/include/pycairo/py3cairo.h ] ; then
      skip_build=true
   fi
fi

if [ true ] ; then
   if [ $skip_build = false ] ; then
      ${WGET} https://github.com/pygobject/pycairo/releases/download/v1.17.0/pycairo-$pycairo_version.tar.gz
      (
      if [ -e ${AUTOBUILD_SOURCES}/pycairo-$pycairo_version.tar.gz ] ; then
         date
         echo BUILDING pycairo
         echo BUILDING pycairo >&2
         tar xf ${AUTOBUILD_SOURCES}/pycairo-$pycairo_version.tar.gz
         cd pycairo-$pycairo_version
         python3 setup.py build
         python3 setup.py install
         cd -
      fi
      ) > $HOSTLOGDIR/30-pycairo.txt 2>&1
   else
      echo installation has pycairo
   fi
fi

# https://pypi.org/project/PyGObject/#files
# https://download.gnome.org/sources/pygobject
pygobject_major_minor_version=3.29
pygobject_major_minor_version=3.30
pygobject_major_minor_version=3.36
pygobject_major_minor_version=3.42
pygobject_major_minor_version=3.52 # 20250621-PE
pygobject_version=3.29.1
pygobject_version=3.30.5
pygobject_version=3.42.1
pygobject_version=3.52.3
# pygobject_version=3.42.2 add me to the extras place!
# https://download.gnome.org/sources/pygobject/3.42/pygobject-3.42.2.tar.xz
# https://download.gnome.org/sources/pygobject/3.52/pygobject-3.52.3.tar.gz

date
pwd
skip_build=false
if [ $test_for_already_installed_dependencies = true ] ; then
   if [ -e $install_top_dir/include/pygobject-3.0/pygobject.h ] ; then
      skip_build=true
   fi
fi
if [ -e /usr/include/pygobject-3.0 ] ; then
    skip_build=true
fi

echo $install_top_dir/bin/glib-compile-schemas --targetdir tests ../tests
$install_top_dir/bin/glib-compile-schemas --targetdir tests ../tests

if [ $skip_build = false ] ; then

      echo BUILDING pygobject $pygobject_version:
      echo BUILDING pygobject $pygobject_version: >&2
      (
      echo :::: PKG_CONFIG_PATH is $PKG_CONFIG_PATH
      unset LD_LIBRARY_PATH
      echo glib-compile-schemas --targetdir tests ../tests
      glib-compile-schemas --targetdir tests ../tests
      # ${WGET} $extras_place/PyGObject-$pygobject_version.tar.gz
      ${WGET} https://download.gnome.org/sources/pygobject/$pygobject_major_minor_version/pygobject-$pygobject_version.tar.gz
      # echo ::: trying to untar ${AUTOBUILD_SOURCES}/PyGObject-$pygobject_version.tar.gz
      echo ::: trying to untar ${AUTOBUILD_SOURCES}/pygobject-$pygobject_version.tar.gz
      if [ -e ${AUTOBUILD_SOURCES}/pygobject-$pygobject_version.tar.gz ] ; then
         gzip -dc ${AUTOBUILD_SOURCES}/pygobject-$pygobject_version.tar.gz | tar xf -
         cd pygobject-$pygobject_version
         ### python setup.py build
         ### python setup.py install
         echo ::: which python3
         which python3
         echo ld_library_path $LD_LIBRARY_PATH
         x=$LD_LIBRARY_PATH
         # unset LD_LIBRARY_PATH # I want LD_LIBRARY_PATH so that libffi.so is found
         unset LD_LIBRARY_PATH # 20250621-PE just a guess
         echo :::: in directory "$(pwd)"
         echo :::: building using meson -Dprefix=$install_top_dir build
         if meson setup -Dprefix=$install_top_dir build ; then
            echo :::: meson passed
            cd build
            echo :::: ninja
            if ninja ; then
                echo :::: ninja install
                ninja install
            else
                echo ninja failed
            fi
            cd -
         else
            echo :::: meson failed
         fi
         export LD_LIBRARY_PATH=$x
      else
         echo ERROR:: ${AUTOBUILD_SOURCES}/pygobject-$pygobject_version.tar.gz file not found.
      fi ) > $HOSTLOGDIR/31-pygobject.txt 2>&1
      echo BUILDING: "done" pygobject $pygobject_version: >&2
else
   echo not building pygobject:
   echo not building pygobject: 2>&1
fi

# restore Raster3D here at some stage
# When you do, make it work with transparent density and ribbons/surfaces
# (look up how to send the triangles)

###############################################################################
# pygobject
###############################################################################
# this needs to find gobject-introspection-1.0 >= 1.46.0 (now 1.56.0 apparently)
# and it does if PKG_CONFIG_PATH is set correctly
if [ -e $install_top_dir/include/pygobject-3.0/pygobject.h ] ; then
    echo installation has pygobject
else
    echo installing pygobject with pip3
    echo installing pygobject with pip3 >&2
    (
    echo installing pygobject
    echo PKG_CONFIG_PATH $PKG_CONFIG_PATH
    which pip3
    pip3 install wheel
    pip3 install pygobject
    ) > $HOSTLOGDIR/34-pip-wheel-pygobject.txt 2>&1
    echo BUILDING: "done" install pygobject with pip3 >&2
fi

# silicos-it's biscu-it (QED) is now part of RDKit main.

###############################################################################
##################### guile and friends #######################################
###############################################################################

# libffi_version=3.2.1 built above (for python)
guile_version=3.0.5 # no g-wrap for this
guile_version=2.2.7
g_wrap_version=1.9.15
libtool_version=2.4.6
gmp_version=6.1.1
gmp_version=6.2.1
guile_gnome_platform_version=2.16.5
readline_version=6.3
gc_version=8.0.4
guile_cairo_version=1.9.91

# wget http://ftp.gnu.org/pub/gnu/guile-gnome/guile-gnome-platform/guile-gnome-platform-$guile_gnome_platform_version.tar.gz
# wget http://savannah.nongnu.org/download/g-wrap/g-wrap-$g_wrap_version.tar.gz
# wget sourceware.org:/pub/libffi/libffi-$libffi_version.tar.gz
# wget ftp://ftp.gnu.org/pub/gnu/guile/guile-2.0.12.tar.gz
# wget ftp://www.mirrorservice.org/sites/ftp.gnu.org/gnu/guile/guile-2.0.12.tar.gz
# wget http://ftp.heanet.ie/mirrors/gnu/libtool/libtool-$libtool_version.tar.gz
# wget http://mirrorservice.org/sites/ftp.gnu.org/gnu/gmp/gmp-$gmp_version.tar.xz
# wget http://mirrorservice.org/sites/ftp.gnu.org/gnu/libunistring/libunistring-$unistring_version.tar.gz
# wget http://www.hboehm.info/gc/gc_source/gc-7.2g.tar.gz
# wget http://mirrorservice.org/sites/ftp.gnu.org/gnu/readline/readline-6.3.tar.gz
# wget http://download.savannah.gnu.org/releases/guile-cairo/guile-cairo-$guile_cairo_version.tar.gz

build_guile=true
build_g_wrap=true
build_gmp=true
build_guile_gnome_platform=true
# build_readline=true
build_guile_cairo=true
build_guile_lib=true



build_gc=true

if [ "$build_gc" = true ] ; then
   skip_this=false
   if [ "$test_for_already_installed_dependencies" = true ] ; then
      if [ -e $install_top_dir/include/gc.h ] ; then # use the right file
         skip_this=true
      fi
   fi

   if [ $skip_this = false ] ; then
      echo BUILDING libatomic-ops:
      echo BUILDING libatomic-ops: >&2
      (
      unset LD_LIBRARY_PATH
      if [ ! -e $AUTOBUILD_SOURCES/libatomic_ops-7.6.12.tar.gz ] ; then
         ${WGET} https://github.com/ivmai/libatomic_ops/releases/download/v7.6.12/libatomic_ops-7.6.12.tar.gz
      fi
      tar xf $AUTOBUILD_SOURCES/libatomic_ops-7.6.12.tar.gz
      cd libatomic_ops-7.6.12
      ./configure --prefix=$install_top_dir
      $MAKE
      make install
      cd -
      ) > $HOSTLOGDIR/37-libatomic-ops.txt 2>&1
      echo BUILDING: done libatomic-ops: >&2
   fi

   # echo gc skip_this $skip_this

   if [ $skip_this = false ] ; then
      gc_version=7.2g
      gc_version_dir=7.2
      gc_version=7.6.12     # needs libatomic_ops. can we find a version that doesn't need that?
      gc_version_dir=7.6.12 # I guess not.
      gc_version=8.2.4
      gc_version_dir=8.2.4
      echo BUILDING: gc $gc_version
      echo BUILDING: gc $gc_version >&2
      (
      echo ========================= build gc =================================
      unset LD_LIBRARY_PATH
      echo PKG_CONFIG_PATH is $PKG_CONFIG_PATH
      echo testing for presence of tar file $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz
      if [ -e $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz ] ; then
         echo Here build-gc A
         echo found gc source file $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz
         echo Here build-gc B
         echo tar xf $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz
         tar xf $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz
         echo Here build-gc B2
      else
         echo no file $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz
         echo ${WGET} http://www.hboehm.info/gc/gc_source/gc-$gc_version.tar.gz
         ${WGET} http://www.hboehm.info/gc/gc_source/gc-$gc_version.tar.gz
         # this file is double-gzipped!
         # 2024-08-23 no more. It's been fixed
         # mv $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz.gz
         # gunzip $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz.gz
         if [ -e $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz ] ; then
            tar xf $AUTOBUILD_SOURCES/gc-$gc_version.tar.gz
         else
            echo download failed for http://www.hboehm.info/gc/gc_source/gc-$gc_version.tar.gz
         fi
      fi
      echo Here build-gc C
      cd gc-$gc_version_dir
      pwd
      echo ./configure --prefix=$install_top_dir
      echo Here D
      if ./configure --prefix=$install_top_dir ; then
         if $MAKE ; then
            make install
         fi
      fi
      cd -
      ) > $HOSTLOGDIR/38-gc.txt 2>&1
      echo BUILDING: done gc $gc_version >&2
   else
      echo not building gc
   fi
fi

if [ "$build_gmp" = true ] ; then
   skip_this=false
   if [ "$test_for_already_installed_dependencies" = true ] ; then
      if [ -e $install_top_dir/include/gmp.h ] ; then # use the right file
         skip_this=true
      fi
   fi

fi

if [ "$build_guile" = true ] ; then
   skip_this=false
   if [ "$test_for_already_installed_dependencies" = true ] ; then
      if [ -e $install_top_dir/include/guile/2.2/libguile.h ] ; then # use the right file
         skip_this=true
      fi
   fi

   # echo guile skip_this $skip_this

   if [ $skip_this = false ] ; then
      echo BUILDING guile:
      echo BUILDING guile $guile_version >&2
      (
      unset LD_LIBRARY_PATH
      echo ========================= build guile =================================
      if [ -e   $AUTOBUILD_SOURCES/guile-$guile_version.tar.xz ] ; then
         tar xf $AUTOBUILD_SOURCES/guile-$guile_version.tar.xz
      else
         echo no file $AUTOBUILD_SOURCES/guile-$guile_version.tar.xz
         ${WGET} https://ftp.gnu.org/pub/gnu/guile/guile-$guile_version.tar.xz
         tar xf ${AUTOBUILD_SOURCES}/guile-$guile_version.tar.xz
      fi
      cd guile-$guile_version
      # LIBFFI_LIBS=-L$install_top_dir/lib
      # LIBFFI_CFLAGS=-I$install_top_dir/include
      if ./configure --prefix=$install_top_dir      \
         --with-libltdl-prefix=$install_top_dir     \
         --with-libreadline-prefix=$install_top_dir \
         LIBS=-L$install_top_dir/lib CFLAGS=-I$install_top_dir/include ; then
         if $MAKE ; then
            make install
            # this file causes problems on linking coot
            if [ -e $install_top_dir/lib/libguile-2.2.so.1.4.2-gdb.scm ] ; then
               mv $install_top_dir/lib/libguile-2.2.so.1.4.2-gdb.scm $install_top_dir/lib/script-libguile-2.2.so.1.4.2-gdb.scm
            fi
         fi
      fi
      cd -
      ) > $HOSTLOGDIR/39-guile.txt 2>&1
      echo "done guile:"
   fi
else
   echo not building guile:
   echo not building guile: >&2
fi

# ------------------------------------  template -------------------------------------
if [ "$build_template_thing" = true ] ; then
   skip_this=false
   if [ "$test_for_already_installed_dependencies" = true ] ; then
      if [ -e $install_top_dir/include/template.h ] ; then # use the right file
         skip_this=true
      fi
   fi

   # echo template skip_this $skip_this

   template_version=1.2.3
   server_for_template=https://thing

   if [ $skip_this = false ] ; then
      echo ========================= build template =================================
      if [ -e $AUTOBUILD_SOURCES/template-$template_version.tar.gz ] ; then
         tar xf $AUTOBUILD_SOURCES/template-$template_version.tar.gz
      else
         ${WGET} $server_for_template/template-$template_version.tar.gz
         tar xf $AUTOBUILD_SOURCES/template-$template_version.tar.gz
      fi
      (
      cd template-$template_version
      if ./configure --prefix=$install_top_dir ; then
         if $MAKE ; then
            make install
         fi
      fi
      cd -
      ) > $HOSTLOGDIR/2x-xx.txt 2>&1
   fi
fi
# ------------------------------------  template end ----------------------------------


if [ "$build_g_wrap" = true ] ; then
   skip_this=false
   if [ "$test_for_already_installed_dependencies" = true ] ; then
      if [ -e $install_top_dir/include/g-wrap/guile-runtime.h ] ; then # use the right file
         skip_this=true
      fi
   fi

   # echo g-wrap skip_this $skip_this

   if [ $skip_this = false ] ; then
      echo BUILDING: g-wrap $g_wrap_version
      echo BUILDING: g-wrap $g_wrap_version >&2
      (
      unset LD_LIBRARY_PATH
      echo ========================= build g-wrap =================================
      if [ -e $AUTOBUILD_SOURCES/g-wrap-$g_wrap_version.tar.gz ] ; then
         tar xf $AUTOBUILD_SOURCES/g-wrap-$g_wrap_version.tar.gz
      else
         g_wrap_version=1.9.15
         ${WGET} http://savannah.nongnu.org/download/g-wrap/g-wrap-$g_wrap_version.tar.gz
         tar xf $AUTOBUILD_SOURCES/g-wrap-$g_wrap_version.tar.gz
      fi
      if [ ! -e $install_top_dir/bin/guile ] ; then
         echo no guile
         exit
      fi
      cd g-wrap-$g_wrap_version
      # if ./configure --prefix=$install_top_dir
      # LIBFFI_LIBS=-L$install_top_dir/lib
      # LIBFFI_CFLAGS=-I$install_top_dir/include; then
      if ./configure --prefix=$install_top_dir --disable-Werror ; then
         if $MAKE ; then
            make install
         fi
      fi
      ) > $HOSTLOGDIR/40-g-wrap.txt 2>&1
      echo BUILDING: g-wrap done >&2
   fi
else
   echo not building g_wrap
fi

if [ "$build_guile_cairo" = true ] ; then
   skip_this=false
   if [ "$test_for_already_installed_dependencies" = true ] ; then
      if [ -e $install_top_dir/include/guile-cairo/guile-cairo.h ] ; then
         skip_this=true
      fi
   fi

   if [ $skip_this = false ] ; then
      echo BUILDING guile-cairo:
      echo BUILDING guile-cairo $guile_cairo_version >&2
      (
      unset LD_LIBRARY_PATH
      echo ========================= build guile-cairo =================================
      if [ -e $AUTOBUILD_SOURCES/guile-cairo-$guile_cairo_version.tar.gz ] ; then
         tar xf $AUTOBUILD_SOURCES/guile-cairo-$guile_cairo_version.tar.gz
      else
         echo fetching file $AUTOBUILD_SOURCES/guile-cairo-$guile_cairo_version.tar.gz
         ${WGET} http://download.savannah.gnu.org/releases/guile-cairo/guile-cairo-$guile_cairo_version.tar.gz
         tar xf $AUTOBUILD_SOURCES/guile-cairo-$guile_cairo_version.tar.gz
      fi
      if [ ! -e $install_top_dir/bin/guile ] ; then
         echo no guile
         exit
      fi
      cd guile-cairo-$guile_cairo_version
      if ./configure --prefix=$install_top_dir ; then
         if $MAKE ; then
            make install
         fi
      fi
      cd -
      ) > $HOSTLOGDIR/41-guile-cairo.txt 2>&1
      echo BUILDING: "guile-cairo done" >&2
   fi
else
   echo not building guile-cairo:
   echo not building guile-cairo: >&2
fi

# guile-lib
if test -f $install_top_dir/share/guile/site/sxml/simple.scm ; then
    echo installation has guile-lib
    build_guile_lib=
else
    build_guile_lib=1
    echo guile-lib needs to be installed
fi

echo some test here " "
if guile-config --version ; then
  echo guile-config found
else
  echo no guile-config
fi
guile_version=$(guile-config --version |& cut -f5 -d" ") # 2.2.7
guile_major_minor=2.2
guile_lib_version=0.2.7

if [ "$build_guile_lib" = true ] ; then
   skip_this=false
   if [ "$test_for_already_installed_dependencies" = true ] ; then
      if [ -e $install_top_dir/share/guile/site/os/process.scm ] ; then
         skip_this=true
      fi
   fi

   if [ $skip_this = false ] ; then
      echo ========================= build guile-lib =================================
      if [ -e $AUTOBUILD_SOURCES/guile-lib-$guile_lib_version.tar.gz ] ; then
         tar xf $AUTOBUILD_SOURCES/guile-lib-$guile_lib_version.tar.gz
      else
         exit
      fi
      (
      if [ ! -e $install_top_dir/bin/guile ] ; then
         echo no guile
         exit
      fi
      cd guile-lib-$guile_lib_version

      # sigh. I had to delete guile-3 installation, guile and guile-config being
      # correct for 2.2.7 was not enough.
      # (this uses PKG_CONFIG_PATH)
      if ./configure --prefix=$install_top_dir --with-guile-site=yes ; then
         if $MAKE ; then
            make install
         fi
      fi
      cd -
      ) > $HOSTLOGDIR/42-guile-lib.txt 2>&1
   fi
else
   echo not building guile-lib:
fi





if [ "$build_guile_gnome_platform" = true ] ; then
   skip_this=false
   if [ "$test_for_already_installed_dependencies" = true ] ; then
      if [ -e $install_top_dir/include/guile-gnome-2/guile-gnome-gobject.h ] ; then
         skip_this=true
      fi
   fi

   echo guile-gnome-platform skip_this $skip_this

   if [ $skip_this = false ] ; then
      echo BUILDING: gnome-gnome-platform
      echo BUILDING: gnome-gnome-platform $guile_gnome_platform_version >&2
      (
      unset LD_LIBRARY_PATH
      echo ========================= build guile-gnome-platform =================================
      if [ -e $AUTOBUILD_SOURCES/guile-gnome-platform-$guile_gnome_platform_version.tar.gz ] ; then
         tar xf $AUTOBUILD_SOURCES/guile-gnome-platform-$guile_gnome_platform_version.tar.gz
      else
         echo no file $AUTOBUILD_SOURCES/guile-gnome-platform-$guile_gnome_platform_version.tar.gz
         ${WGET} http://ftp.gnu.org/pub/gnu/guile-gnome/guile-gnome-platform/guile-gnome-platform-$guile_gnome_platform_version.tar.gz
         tar xf $AUTOBUILD_SOURCES/guile-gnome-platform-$guile_gnome_platform_version.tar.gz
      fi
      cd guile-gnome-platform-$guile_gnome_platform_version
      if ./configure --prefix=$install_top_dir ; then
         if $MAKE ; then
            make install
         fi
      fi
      ) > $HOSTLOGDIR/43-guile-gnome-platform.txt 2>&1
      echo BUILDING gnome-gnome-platform finished
   fi
else
   echo not building guile-gnome-platform
fi


###############################################################################
##########         Coot is now built from git repo                #############
###############################################################################
#

if test x$GITHUB_ENV = x ; then
    : # we are not in a hithub actions build
else
    # stop here because we build coot outside of this script in github actions
    exit
fi

echo Now Coot..... >&2
cd $start_dir
echo GITHUB_WORKSPACE is $GITHUB_WORKSPACE
date >&2
pwd >&2

if [ -e coot ] ; then
   echo CASE 1 coot directory exists
   echo CASE 1 coot directory exists >&2
   (
   pwd
   cd coot
   echo now in this dir:
   pwd
   echo 33333333333333333333333 and about to fetch and merge...
   git fetch

   if [ -e ltmain.sh    ] ; then rm ltmain.sh    ; fi
   if [ -e config.guess ] ; then rm config.guess ; fi
   if [ -e config.sub   ] ; then rm config.sub   ; fi

   git merge
   # if [ -e ltmain.sh ] ; then
   #   rm ltmain.sh
   # fi
   rm -rf autom4te.cache

   echo bash autogen.sh
   bash autogen.sh
   cd -
   ) > $HOSTLOGDIR/50-coot-fetch-merge-autogen.txt 2>&1
   echo  BUILDING: done merge
else
   echo CASE 2 coot directory not exists in $(pwd)
   echo CASE 2 coot directory not exists in $(pwd) >&2
   (
   save_dir=$(pwd)
   echo :::: $(pwd)
   echo cloning coot...
   echo cloning coot... >&2
   echo :::: git clone https://github.com/pemsley/coot.git -b main
   echo save_ld_library_path=$LD_LIBRARY_PATH
   # reset LD_LIBRARY_PATH for now. Do we need it set from now on actually?
   export LD_LIBRARY_PATH=
   if git clone https://github.com/pemsley/coot.git -b main --depth 2 ; then
      echo git clone https://github.com/pemsley/coot.git -b main without error status
      echo done clone
      cd coot
      rm -rf autom4te.cache
      if [ -e ltmain.sh    ] ; then rm ltmain.sh    ; fi
      if [ -e config.guess ] ; then rm config.guess ; fi
      if [ -e config.sub   ] ; then rm config.sub   ; fi
      bash autogen.sh
   else
      echo git clone https://github.com/pemsley/coot.git -b main failed
      echo done clone
      cd coot
   fi
   LD_LIBRARY_PATH=$save_ld_library_path
   cd $save_dir
   ) > $HOSTLOGDIR/50-clone-autogen.txt 2>&1
   echo  BUILDING: done checkout
fi

if test -n "$glib_installed" ; then
    coot_extra_args="$coot_extra_args --with-glib-prefix=$install_top_dir"
fi
if test -n "$gtk_installed" ; then
    coot_extra_args="$coot_extra_args --with-gtk-prefix=$install_top_dir"
fi


###############################################################################
##########         build Coot                                     #############
###############################################################################
#
echo BUILDING: coot
echo BUILDING: coot >&2

(

# 20091001 should not be needed.
# if [ "$ENABLE_PYTHON_COOT" = "no" ] ; then
#    echo INFO:: not a pythonized build
#    cp src/blank.cc src/coot_wrap_python.cc
# else
#    echo INFO:: A pythonized build
# fi

#      CXXFLAGS="-g -O"
# consider getting rid of $shared_static_flag, which does a --disable-shared.
# i.e. we should keep and use shared libs

#     $architecture is not set for Mac OS X.
coot_optim_args=
export CXXFLAGS="-g -O "

cbis_d=$(date +'%a %d %b %H%M.%S %Z %Y')
coot_build_info_string="build-host: $HOST on: $cbis_d"

if [ ! -z "$libintl_cflags" ] ; then
   CFLAGS=$libintl_cflags
   CPPFLAGS="$CPPFLAGS $libintl_cflags"
fi

cd $start_dir
if [ ! -d build-coot ] ; then
   mkdir build-coot
fi
cd build-coot


export LD_LIBRARY_PATH=$install_top_dir/lib64
unset LD_LIBRARY_PATH

echo From git repo now
echo building in: $PWD
echo CFLAGS: $CFLAGS
echo CXXFLAGS: $CXXFLAGS
echo CPPFLAGS: $CPPFLAGS
echo LDFLAGS: $LDFLAGS
echo PATH: $PATH
echo PKG_CONFIG_PATH: $PKG_CONFIG_PATH
# For external use, we need to have used git checkout for
# the gtk3 branch, have run autogen.sh
# and have placed that directory somewhere sensible relative to here


echo 33333
# 20220707-PE does this improve thie linking (get pass the problem with g_module_open_full)?
# We get checking dynamic linker characteristics... awk: symbol lookup error: /home/pemsley/autobuild/Linux-emsley-vm-fedora-2.lmb.internal-gtk4/lib/libreadline.so.8: undefined symbol: UP
# on fedora if LD_LIBRARY_PATH is set
if [ "$dist_name" = fedora ] ;  then
    :
else
    if [ "$dist_name" = arch ] ;  then
        :
    else
        export LD_LIBRARY_PATH=$install_top_dir/lib
    fi
fi

# add this when then are compiling and RDKIT is compiling

# if compiling with sound on ubuntu libvorbis-dev libasound2-dev

unset LD_LIBRARY_PATH
echo :::::::::::::::::::::::::::::::::::::::::::::::::::::::
echo LD_LIBRARY_PATH $LD_LIBRARY_PATH
echo :::::::::::::::::::::::::::::::::::::::::::::::::::::::

echo bash ../coot/configure $coot_prefix \
      --with-fftw-prefix=$install_top_dir  \
      COOT_BUILD_INFO_STRING="$coot_build_info_string" \
      SHELL=/bin/bash \
      PYTHON=python3 \
      --with-boost=$install_top_dir  \
      --with-boost-libdir=$install_top_dir/lib  \
      --with-enhanced-ligand-tools \
      --with-rdkit-prefix=$install_top_dir \
      --with-guile \
      $sqlite_config_args \
      $shared_static_flag \
      $coot_optim_args    \
      $coot_extra_args    \
      $extra_args_for_darwin

   bash ../coot/configure $coot_prefix \
      --with-fftw-prefix=$install_top_dir  \
      SHELL=/bin/bash \
      PYTHON=python3 \
      COOT_BUILD_INFO_STRING="$coot_build_info_string" \
      --with-boost=$install_top_dir  \
      --with-boost-libdir=$install_top_dir/lib  \
      --with-enhanced-ligand-tools \
      --with-rdkit-prefix=$install_top_dir \
      --with-guile \
      $sqlite_config_args \
      $shared_static_flag \
      $coot_optim_args    \
      $coot_extra_args    \
      $extra_args_for_darwin


$MAKE
# No rule to make target 'coot.py', needed by 'all-am'. Stop.
# but it's there! Timing problems?
echo === make again ===
make
status=$?
if [ "$status" != 0 ] ; then
    echo make failed.
    bad_coot_make=1
    exit 2
else
   echo 1 ---------------------------------------------------------------
   echo '                                ' make install
   echo 1 ----------------------------------------------------------------
   make install
   echo === make install again ===
   make install
   # if [ "$python_scripting" = '--with-python' ] ; then
      # echo copying src/coot.py $install_top_dir/share/coot/python
      # cp src/coot.py $install_top_dir/share/coot/python
   # fi
fi

) > $HOSTLOGDIR/50-coot.txt 2>&1


#         --with-gsl-prefix=$install_top_dir \
#        --with-glib-prefix=$install_top_dir \
#         --with-gtk-prefix=$install_top_dir \
#       --with-gtkgl-prefix=$install_top_dir \

coot_build_status=$?
if [ $coot_build_status != 0 ] ; then
    echo coot build failed, exiting.
    # echo fail-build $coot_revision > $LOGS/build-status
    my_exit 2 $coot_revision
else
    echo coot build was good.
    # echo pass-build $coot_revision > $LOGS/build-status
fi
echo done coot build.

# restore a sane environment for external programs (e.g. ftp)
#
unset LD_LIBRARY_PATH
unset CFLAGS
unset CPPFLAGS
unset LDFLAGS
unset PKG_CONFIG_PATH

# now, do we need to add the extra data files, the refmac monomer
# library and the reference structures?

# 20110505 we change to Garib's new dictionary
#refmac_mon_lib=refmac-monomer-library-20090929.tar.gz
#refmac_mon_lib=refmac-monomer-library-20091203.tar.gz
# mon_lib_dir=http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_experimental
# mon_lib_dir=http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary

# refmac_mon_lib=refmac_dictionary_v5.28.tar.gz
# refmac_mon_lib=refmac_dictionary_v5.29.tar.gz
# refmac_mon_lib=refmac_dictionary_v5.37.tar.gz
# refmac_mon_lib=refmac_dictionary_v5.38.tar.gz
# refmac_mon_lib=refmac_dictionary_v5.39.tar.gz
# refmac_mon_lib=refmac_dictionary_v5.41.tar.gz

# new style
mon_lib_dir=http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies
refmac_mon_lib=refmac-monomer-library.tar.gz

if [ -e $install_top_dir/share/coot/lib/data/monomers ] ; then
    echo INFO:: installation has refmac monomer library
else
    echo INSTALLING refmac monomer library...
    echo INSTALLING refmac monomer library... >&2
    $WGET $mon_lib_dir/$refmac_mon_lib
    mkdir -p $install_top_dir/share/coot/lib/data
    tar xzCf $install_top_dir/share/coot/lib/data $AUTOBUILD_SOURCES/$refmac_mon_lib
fi
if [ -e $install_top_dir/share/coot/reference-structures ] ; then
    echo INFO:: installation has reference structures
else
    echo GETTING reference structures tar...
    echo GETTING reference structures tar... >&2
    ${WGET} $extras_place/reference-structures.tar.gz
    if [ -e $AUTOBUILD_SOURCES/reference-structures.tar.gz ] ; then
       echo INSTALLING reference structures...
       tar xzCf $install_top_dir/share/coot $AUTOBUILD_SOURCES/reference-structures.tar.gz
    else
       echo FAIL wget for reference-structures.tar.gz failed.
    fi
fi

# clear up the library dependencies

if [ "$build_coot_prerelease" = 1 ] ; then
   pre_release_str=-pre-release
fi

clear_up_type=
if [ $shared_static_flag != "--disable-static" ] ; then
    clear_up_type=clear-static
fi
if [ $shared_static_flag != "--disable-shared" ] ; then
    clear_up_type=clear-dynamic
fi

if [ $clear_up_type != "" ] ; then
   if [ "$ENABLE_PYTHON_COOT" = "yes" ] ; then
      slim_dir=$(dirname $install_top_dir)/coot-${OS}-${systype}${pre_release_str}-gtk4-python
   else
      slim_dir=$(dirname $install_top_dir)/coot-${OS}-${systype}${pre_release_str}-gtk4
   fi
   echo post-install slim... >&2
   post_install_slim $install_top_dir $slim_dir $clear_up_type
fi

# clean up old status:
if [ -e $LOGS/test-status ] ; then
   rm $LOGS/test-status
fi


if [ "$run_tests" = true ] ; then
   # run test
   echo running tests:
   echo running tests: >&2
   if [ "$ENABLE_GUILE_COOT" = "yes" ] ; then
       echo running first test... >&2
      test_coot > $LOGS/test.log 2>&1
       r=$?
   else
       r=0
   fi

   # run python tests too, maybe (i.e. if we build with python)
   if [ "$ENABLE_PYTHON_COOT" = "yes" ] ; then
       echo running python test... >&2
       test_coot_python > $LOGS/test-python.log 2>&1
       rp=$?
   else
       rp=0
   fi

   # all gtk3 versions have python. No need for the python tag then
   if ( [ $r = 0 ] && [ $rp = 0 ] ); then
      echo ========================
      echo '   ' first coot test passed
      echo '   ' first coot test passed >&2
      echo ========----============
      echo pass-test > $LOGS/test-status
      if test "$do_nightlies" = "1" ; then
         if [ -d $BINARY_TAR_DEST_DIR ] ; then

            if [ ! -d $BINARY_TAR_DEST_DIR/holding ] ; then
               echo WARNING:: holding directory $BINARY_TAR_DEST_DIR/holding does not exist.
            else
               # regular path

               # original full fat:
               # make_tar `basename $install_top_dir` $BINARY_TAR_DEST_DIR/${coot_version}-binary-full-${OS}-${systype}${python_tag}${gtk2}.tar.gz
               # slimmed:
               bin_tar_file=$BINARY_TAR_DEST_DIR/${coot_version}-binary-${OS}-${systype}${gtk_version}.tar.gz
               holding_tar_file=$BINARY_TAR_DEST_DIR/holding/${coot_version}-binary-${OS}-${systype}${gtk_version}.tar.gz

       	       make_tar $(basename $slim_dir) $holding_tar_file

   	       # Now test the tar file by un-taring it and running the
   	       # tests.  Only if this test passes can we move tar file
	       # from holding to the binary pre-release dir.

	       if [ $run_second_test = true ] ; then
                  cd "$build_dir"
	          mkdir test-tar
	          cd test-tar
	          tar xzf $holding_tar_file
      	          echo cding into `basename $slim_dir`  from `pwd`
                  cd `basename $slim_dir`
   	          echo ln -s ../../$coot_dir_name/greg-tests .
	          ln -s ../../$coot_dir_name/greg-tests .
                  echo second coot test...
                  echo running second test... >&2
	          test_coot bin/coot > $LOGS/test-2.log 2>&1
                  test2_status=$?
               else
                  test2_status=0 # success
               fi

               if [ $test2_status = 0 ] ; then
                  echo ========================
                  echo second coot test passed
                  echo second coot test passed >&2
                  echo ========================
                  echo pass-2nd-test > $LOGS/test-status

                  mv $holding_tar_file $bin_tar_file
                  mv $holding_tar_file.md5sum $bin_tar_file.md5sum

                  # update the description of the latest binary tar file for
                  # this build-type.
                  binary_type_latest=$BINARY_TAR_DEST_DIR/type-binary-${OS}-${systype}${gtk_version}-latest.txt
	          echo $coot_version > $binary_type_latest

                  # update the ChangeLog, README and RELEASE-NOTES
                  cd "$build_dir"
                  cd $coot_dir_name
                  echo INFO:: in "$build_dir"/$coot_dir_name and about to copy over README and RELEASE-NOTES to $BINARY_TAR_DEST_DIR
                  cp ChangeLog $BINARY_TAR_DEST_DIR
                  cp README    coot-README
                  cp README    $BINARY_TAR_DEST_DIR/coot-README
                  cp RELEASE-NOTES    $BINARY_TAR_DEST_DIR/${coot_version}-RELEASE-NOTES
                  cp RELEASE-NOTES    $BINARY_TAR_DEST_DIR/PRE-RELEASE-NOTES

                  echo about to publish files:
                  echo about to publish files: >&2

                  # only copy over the binary files if they are not there
                  # already (checked by publish executable).
                  #
                  # reading the git logs adding $BINARY_TAR_DEST_DIR seems to have fixed something.
                  # Now, the transfer-to-web-server.sh scripts take the second arg
                  # and munge it to be the correct directory for the binary (and .txt) files.
	          echo $publish $bin_tar_file $BINARY_TAR_DEST_DIR
	          $publish      $bin_tar_file $BINARY_TAR_DEST_DIR
	          echo $publish $bin_tar_file.md5sum $BINARY_TAR_DEST_DIR
	          $publish      $bin_tar_file.md5sum $BINARY_TAR_DEST_DIR
	          # echo $publish $binary_type_latest
	          # publish $binary_type_latest
	          echo $publish --no-server-check ChangeLog
	          $publish --no-server-check ChangeLog
	          echo $publish --no-server-check coot-README
	          $publish --no-server-check coot-README
                  if [ -z "$build_coot_prerelease" ] ; then
                  echo $publish  --no-server-check RELEASE-NOTES
                  $publish --no-server-check RELEASE-NOTES
                  else
   	             echo $publish  --no-server-check $BINARY_TAR_DEST_DIR/PRE-RELEASE-NOTES
	             $publish --no-server-check $BINARY_TAR_DEST_DIR/PRE-RELEASE-NOTES
                  fi

	          echo done copy of README and RELEASE-NOTES
	       else
                  echo ========================
                  echo second coot test failed
                  echo second coot test failed >& 2
                  echo ========================
                  echo fail-2nd-test $date > $LOGS/test-status
               fi
            fi

         else
            echo Directory for binaries $BINARY_TAR_DEST_DIR does not exist.
	    echo Skipping tar.
         fi
      else
         echo not doing tar files for nightlies: $do_nightlies
      fi
   else
      echo ========================
      echo '  ' first coot test failed
      echo '  ' first coot test failed >&2
      echo ========================
      echo greg test status: $r
      echo python test status: $rp
      if [ $r = 0 ] ; then
         echo fail-test greg $date > $LOGS/test-status
      else
         if [ $rp = 0 ] ; then
            echo fail-test python $date > $LOGS/test-status
         else
            # this should not happen, AFAICS.
            echo fail-test $date > $LOGS/test-status
         fi
      fi
   fi
fi

$publish_logs $LOGS


echo finished.
echo finished.>&2


