arrays moved to bundle

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core
ChimeraX Version: 1.0 (2020-05-05)
Description
Something seems to have gone a little wonky with the include directories... my build against the latest RC fails with:

src/symmetry_cpp/symmetry.cpp:35:32: fatal error: arrays/pythonarray.h: No such file or directory
 #include <arrays/pythonarray.h>
 

... and if I look for pythonarray.h in the ChimeraX install directory it's at:

/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/arrays/include/arrays/pythonarray.h

... whereas for an older 0.93 daily build it was at:

/opt/UCSF/ChimeraX-daily/include/arrays/pythonarray.h


Log:
UCSF ChimeraX version: 1.0rc202005052344 (2020-05-05)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 440.33.01
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)
	Subsystem: NVIDIA Corporation Device [10de:11df]
	Kernel driver in use: nvidia

[Tristan Croll]

To add to this, I *am* declaring arrays as a dependency in the 
bundle_info.xml:

       <Library>atomstruct</Library>
       <Library>arrays</Library>

... but that doesn't appear to be carried through to the compiler 
command:

c++ -pipe -fPIC -std=gnu99 
-fdebug-prefix-map=/tmp/chx-release-v1.0.FlCc0Z/build=. 
-fstack-protector-strong -I/tmp/chx-release-v1.0.FlCc0Z/build/include 
-L/tmp/chx-release-v1.0.FlCc0Z/build/lib -DUSE_DYLD_GLOBAL_NAMESPACE 
-pthread -shared -O3 -Wall -Wextra -D_FORTIFY=2 -fvisibility=hidden 
-fvisibility-inlines-hidden -s -Wl,-rpath,$ORIGIN 
src/clipper_ext/xtal_mgr.o src/clipper_ext/edcalc_ext.o 
src/clipper_ext/sfcalc_obs_vdw.o -L/opt/UCSF/ChimeraX/lib -Lsrc 
-L/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/lib 
-lclipper -latomstruct -lelement -o src/libclipper_cx.so
C compiler: gcc -pipe -fPIC -std=gnu99 -fstack-protector-strong 
-DUSE_DYLD_GLOBAL_NAMESPACE -pthread -Wno-unused-result -Wsign-compare 
-DNDEBUG -g -O3 -Wall -D_FORTIFY=2 -fstack-protector-strong -fPIC

compile options: '-std=c++11 -fvisibility=hidden 
-fvisibility-inlines-hidden -DDYNAMIC_LIBRARY=1 
-I/opt/UCSF/ChimeraX/include 
-I/opt/UCSF/ChimeraX/lib/python3.7/site-packages/numpy/core/include 
-I/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/include 
-I/opt/UCSF/ChimeraX/include/python3.7m -c'
gcc: src/symmetry_cpp/symmetry.cpp


On 2020-05-06 09:39, ChimeraX wrote:

[Tristan Croll]

Oh - I get it now. It's been moved from core to the bundles, so now I 
need to explicitly declare it in the <Dependencies> list:

     <Dependency name="ChimeraX-Arrays" version="~=1.0"/>

... and everything works again.

On 2020-05-06 09:44, ChimeraX wrote: