Catkin 0.7.8 Does Not Compile

Here for visibility.
allenh1@hunter-laptop ~/work/poky/rpi-build $ bitbake rpi-basic-image
WARNING: Host distribution "gentoo" has not been validated with this version of the build system; you may possibly experience unexpected failures. It is recommended that you use a tested distribution.
Loading cache: 100% |############################################| Time: 0:00:01
Loaded 4877 entries from dependency cache.
Parsing recipes: 100% |##########################################| Time: 0:00:05
Parsing of 4030 .bb files complete (4024 cached, 6 parsed). 4875 targets, 85 skipped, 0 masked, 0 errors.
WARNING: No recipes available for:
  /home/allenh1/work/poky/meta-cloud-services/meta-openstack/recipes-extended/libvirt/libvirt_1.%.bbappend
  /home/allenh1/work/poky/meta-cloud-services/meta-openstack/recipes-httpd/apache2/apache2_2.4.%.bbappend
NOTE: Resolving any missing task queue dependencies

Build Configuration:
BB_VERSION        = "1.36.0"
BUILD_SYS         = "x86_64-linux"
NATIVELSBSTRING   = "universal"
TARGET_SYS        = "arm-poky-linux-gnueabi"
MACHINE           = "raspberrypi2"
DISTRO            = "poky"
DISTRO_VERSION    = "2.4"
TUNE_FEATURES     = "arm armv7ve vfp thumb neon vfpv4 callconvention-hard cortexa7"
TARGET_FPU        = "hard"
meta
meta-poky
meta-yocto-bsp    = "rocko:f7b90ab3eaf832bd81f3efc1dab4dcf6863ac284"
meta-raspberrypi  = "rocko:a1cfeb3324c458a73507e34ffcf28c25591b8052"
meta-ros          = "master:7de7cdba597cf56eacd23d66407d2c6ffcc36520"
meta-odroid       = "master:6dc821e74c29bf3c56babf1e54db745f05c12c31"
meta-clutter      = "master:b370de472e14f3b6a562fa8fcdf9d012613cdcb7"
meta-browser      = "master:a8bb1e779bc3565beacceadc4414816670f33475"
meta-cloud-services
meta-openstack    = "rocko:62f3fed67f8cf07de5e342f57e4faf911f001c12"
meta-oe
meta-multimedia
meta-networking
meta-gnome
meta-xfce
meta-python       = "master:34aa4c3202b427f59f843dc43a4e1afda4f81d13"

WARNING: The Linux kernel on your build host was not configured to provide process I/O statistics. (CONFIG_TASK_IO_ACCOUNTING is not set)
Initialising tasks: 100% |#######################################| Time: 0:00:15
NOTE: Executing SetScene Tasks
NOTE: Executing RunQueue Tasks
ERROR: catkin-0.7.8-r0 do_configure: Function failed: do_configure (log file is located at /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/temp/log.do_configure.16797)
ERROR: Logfile of failure stored in: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/temp/log.do_configure.16797
Log data follows:
| DEBUG: Executing shell function do_configure
| -- The C compiler identification is GNU 7.2.0
| -- The CXX compiler identification is GNU 7.2.0
| -- Check for working C compiler: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/bin/arm-poky-linux-gnueabi/arm-poky-linux-gnueabi-gcc
| -- Check for working C compiler: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/bin/arm-poky-linux-gnueabi/arm-poky-linux-gnueabi-gcc -- works
| -- Detecting C compiler ABI info
| -- Detecting C compiler ABI info - done
| -- Detecting C compile features
| -- Detecting C compile features - done
| -- Check for working CXX compiler: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/bin/arm-poky-linux-gnueabi/arm-poky-linux-gnueabi-g++
| -- Check for working CXX compiler: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/bin/arm-poky-linux-gnueabi/arm-poky-linux-gnueabi-g++ -- works
| -- Detecting CXX compiler ABI info
| -- Detecting CXX compiler ABI info - done
| -- Detecting CXX compile features
| -- Detecting CXX compile features - done
| -- Using CATKIN_DEVEL_PREFIX: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/devel
| -- Using CMAKE_PREFIX_PATH: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot/opt/ros/lunar;/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot/usr;                        /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/opt/ros/lunar;/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr
| -- Found PythonInterp: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/bin/python-native/python (found version "2.7.13")
| -- Using PYTHON_EXECUTABLE: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/bin/python-native/python
| -- Using default Python package layout
| -- Found PY_em: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/lib/python2.7/site-packages/em.pyc
| -- Using empy: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/lib/python2.7/site-packages/em.pyc
| -- Using CATKIN_ENABLE_TESTING: 0
| -- catkin 0.7.8
| /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/devel/setup.sh: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/devel/_setup_util.py: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr: bad interpreter: Permission denied
| Traceback (most recent call last):
|   File "/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/catkin_generated/generate_cached_setup.py", line 22, in <module>
|     code = generate_environment_script('/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/devel/env.sh')
|   File "/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/catkin-release-release-lunar-catkin-0.7.8-0/cmake/../python/catkin/environment_cache.py", line 62, in generate_environment_script
|     env_after = ast.literal_eval(output.decode('utf8'))
|   File "/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/lib/python2.7/ast.py", line 49, in literal_eval
|     node_or_string = parse(node_or_string, mode='eval')
|   File "/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/lib/python2.7/ast.py", line 37, in parse
|     return compile(source, filename, mode, PyCF_ONLY_AST)
|   File "<unknown>", line 1
|     Failed to run '"/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/devel/_setup_util.py" /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/bin/python-native/python -c import os; print(dict(os.environ))': return code 126
|             ^
| SyntaxError: invalid syntax
| CMake Error at cmake/safe_execute_process.cmake:11 (message):
|
|   execute_process(/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/bin/python-native/python
|   "/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/catkin_generated/generate_cached_setup.py")
|   returned error code 1
| Call Stack (most recent call first):
|   cmake/all.cmake:186 (safe_execute_process)
|   CMakeLists.txt:8 (include)
|
|
| -- Configuring incomplete, errors occurred!
| See also "/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/CMakeFiles/CMakeOutput.log".
| WARNING: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/temp/run.do_configure.16797:1 exit 1 from 'cmake $oecmake_sitefile /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/catkin-release-release-lunar-catkin-0.7.8-0 -DCMAKE_INSTALL_PREFIX:PATH=/usr -DCMAKE_INSTALL_BINDIR:PATH=bin -DCMAKE_INSTALL_SBINDIR:PATH=sbin -DCMAKE_INSTALL_LIBEXECDIR:PATH=libexec -DCMAKE_INSTALL_SYSCONFDIR:PATH=/etc -DCMAKE_INSTALL_SHAREDSTATEDIR:PATH=../com -DCMAKE_INSTALL_LOCALSTATEDIR:PATH=/var -DCMAKE_INSTALL_LIBDIR:PATH=lib -DCMAKE_INSTALL_INCLUDEDIR:PATH=include -DCMAKE_INSTALL_DATAROOTDIR:PATH=share -DCMAKE_INSTALL_SO_NO_EXE=0 -DCMAKE_TOOLCHAIN_FILE=/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/toolchain.cmake -DCMAKE_VERBOSE_MAKEFILE=1 -DCMAKE_NO_SYSTEM_FROM_IMPORTED=1 -DCMAKE_PREFIX_PATH='/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot/opt/ros/lunar;/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot/usr;                        /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/opt/ros/lunar;/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr' -DCMAKE_INSTALL_PREFIX:PATH='/opt/ros/lunar' -DSETUPTOOLS_DEB_LAYOUT=OFF -DCATKIN_ENABLE_TESTING=0 -DCATKIN_BUILD_BINARY_PACKAGE=1 ${PACKAGECONFIG_CONFARGS} -Wno-dev'
| ERROR: Function failed: do_configure (log file is located at /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/temp/log.do_configure.16797)
ERROR: Task (/home/allenh1/work/poky/meta-ros/recipes-ros-lunar/catkin/catkin_0.7.8.bb:do_configure) failed with exit code '1'
NOTE: Tasks Summary: Attempted 5659 tasks of which 5650 didn't need to be rerun and 1 failed.

Summary: 1 task failed:
  /home/allenh1/work/poky/meta-ros/recipes-ros-lunar/catkin/catkin_0.7.8.bb:do_configure
Summary: There were 3 WARNING messages shown.
Summary: There was 1 ERROR message shown, returning a non-zero exit code.

@tfoote FYI

This might be a quoting issue for the subprocess bash/python interpretation.
tfoote@snowman:~ Last: [2] (0s Seconds)
$ python -c 'import os; print(dict(os.environ))' > /dev/null ; echo $?
0
tfoote@snowman:~ Last: [0] (0s Seconds)
$ python -c import os; print(dict(os.environ))
bash: syntax error near unexpected token `dict'
tfoote@snowman:~ Last: [2] (0s Seconds)
$ echo $?
2

@tfoote thanks for the tip! Looked into it more and devised this patch.
diff --git a/python/catkin/environment_cache.py b/python/catkin/environment_cache.py
index dd5e353..a5463ab 100644
--- a/python/catkin/environment_cache.py
+++ b/python/catkin/environment_cache.py
@@ -57,7 +57,7 @@ def generate_environment_script(env_script):
     env = os.environ

     # fetch environment after calling setup
-    python_code = 'import os; print(dict(os.environ))'
+    python_code = "'import os; print(dict(os.environ))'"
     output = subprocess.check_output([env_script, sys.executable, '-c', python_code])
     env_after = ast.literal_eval(output.decode('utf8'))

Unfortunately, the patch isn't doing the trick yet, but I definitely found what's tripping up: https://github.com/ros/catkin/blob/a7f81d0087f87449f35ff2c0380be7373f44de3d/python/catkin/environment_cache.py#L56-L62
In this case, the command being run is:
'"/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/devel/_setup_util.py" /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/bin/python-native/python -c 'import os; print(dict(os.environ))''

But that all seems fine to me -- do you have any ideas?

Update: This happens if I run that command in the terminal.
allenh1@hunter-laptop ~/work/poky/rpi-build $ "/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/devel/_setup_util.py" /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/bin/python-native/python -c "import os; print(dict(os.environ))"
bash: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/devel/_setup_util.py: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr: bad interpreter: Permission denied

sigh I figured it out.
From linux:
#ifndef _LINUX_BINFMTS_H
#define _LINUX_BINFMTS_H

#include <unistd.h>
#include <linux/capability.h>

struct pt_regs;

/*
 * These are the maximum length and maximum number of strings passed to the
 * execve() system call.  MAX_ARG_STRLEN is essentially random but serves to
 * prevent the kernel from being unduly impacted by misaddressed pointers.
 * MAX_ARG_STRINGS is chosen to fit in a signed 32-bit integer.
 */
#define MAX_ARG_STRLEN (sysconf(_SC_PAGESIZE) * 32)
#define MAX_ARG_STRINGS 0x7FFFFFFF

/* sizeof(linux_binprm->buf) */
#define BINPRM_BUF_SIZE 128

#endif /* _LINUX_BINFMTS_H */

The #! interpreter line thus has a length BINPRM_BUF_SIZE - 1 (-1 for \0).
allenh1@hunter-laptop ~/catkin-release-release-lunar-catkin-0.7.8-0
$ python3
Python 3.5.4 (default, Nov 11 2017, 15:58:51)
[GCC 6.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> print('#!/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/bin/python-native/python'[:127])
#!/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr

Which is exactly what the "bad interpreter" was when mentioned in the log previously. I'm sure a clever symlink could fix this, but I think this will involve tricking OE into making it somehow.
Regardless, that's definitely a bummer.

It looks like this is a common issue for python virtual envs: https://github.com/pypa/virtualenv/issues/596
This forwarder script seems like it might be the best approach to workaround the limit: https://github.com/spack/spack/pull/497

On my new kernel now with the longer limit (because I want to make sure this all works before getting buried in patches).
This is the new build output.
allenh1@hunter-laptop ~/work/poky/rpi-build $ bitbake catkin
WARNING: Host distribution "gentoo" has not been validated with this version of the build system; you may possibly experience unexpected failures. It is recommended that you use a tested distribution.
Loading cache: 100% |############################################| Time: 0:00:01
Loaded 4878 entries from dependency cache.
Parsing recipes: 100% |##########################################| Time: 0:00:05
Parsing of 4030 .bb files complete (4024 cached, 6 parsed). 4875 targets, 85 skipped, 0 masked, 0 errors.
WARNING: No recipes available for:
  /home/allenh1/work/poky/meta-cloud-services/meta-openstack/recipes-extended/libvirt/libvirt_1.%.bbappend
  /home/allenh1/work/poky/meta-cloud-services/meta-openstack/recipes-httpd/apache2/apache2_2.4.%.bbappend
NOTE: Resolving any missing task queue dependencies

Build Configuration:
BB_VERSION        = "1.36.0"
BUILD_SYS         = "x86_64-linux"
NATIVELSBSTRING   = "universal"
TARGET_SYS        = "arm-poky-linux-gnueabi"
MACHINE           = "raspberrypi2"
DISTRO            = "poky"
DISTRO_VERSION    = "2.4"
TUNE_FEATURES     = "arm armv7ve vfp thumb neon vfpv4 callconvention-hard cortexa7"
TARGET_FPU        = "hard"
meta
meta-poky
meta-yocto-bsp    = "rocko:f7b90ab3eaf832bd81f3efc1dab4dcf6863ac284"
meta-raspberrypi  = "rocko:a1cfeb3324c458a73507e34ffcf28c25591b8052"
meta-ros          = "master:676d272654953255cb64deb268829a01b5f3f765"
meta-odroid       = "master:6dc821e74c29bf3c56babf1e54db745f05c12c31"
meta-clutter      = "master:b370de472e14f3b6a562fa8fcdf9d012613cdcb7"
meta-browser      = "master:a8bb1e779bc3565beacceadc4414816670f33475"
meta-cloud-services
meta-openstack    = "rocko:62f3fed67f8cf07de5e342f57e4faf911f001c12"
meta-oe
meta-multimedia
meta-networking
meta-gnome
meta-xfce
meta-python       = "master:34aa4c3202b427f59f843dc43a4e1afda4f81d13"

WARNING: The Linux kernel on your build host was not configured to provide process I/O statistics. (CONFIG_TASK_IO_ACCOUNTING is not set)
Initialising tasks: 100% |#######################################| Time: 0:00:03
NOTE: Executing SetScene Tasks
NOTE: Executing RunQueue Tasks
ERROR: catkin-0.7.8-r0 do_configure: Function failed: do_configure (log file is located at /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/temp/log.do_configure.7699)
ERROR: Logfile of failure stored in: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/temp/log.do_configure.7699
Log data follows:
| DEBUG: Executing shell function do_configure
| -- The C compiler identification is GNU 7.2.0
| -- The CXX compiler identification is GNU 7.2.0
| -- Check for working C compiler: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/bin/arm-poky-linux-gnueabi/arm-poky-linux-gnueabi-gcc
| -- Check for working C compiler: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/bin/arm-poky-linux-gnueabi/arm-poky-linux-gnueabi-gcc -- works
| -- Detecting C compiler ABI info
| -- Detecting C compiler ABI info - done
| -- Detecting C compile features
| -- Detecting C compile features - done
| -- Check for working CXX compiler: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/bin/arm-poky-linux-gnueabi/arm-poky-linux-gnueabi-g++
| -- Check for working CXX compiler: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/bin/arm-poky-linux-gnueabi/arm-poky-linux-gnueabi-g++ -- works
| -- Detecting CXX compiler ABI info
| -- Detecting CXX compiler ABI info - done
| -- Detecting CXX compile features
| -- Detecting CXX compile features - done
| -- Using CATKIN_DEVEL_PREFIX: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/devel
| -- Using CMAKE_PREFIX_PATH: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot/opt/ros/lunar;/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot/usr;                        /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/opt/ros/lunar;/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr
| -- Found PythonInterp: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/bin/python-native/python (found version "2.7.13")
| -- Using PYTHON_EXECUTABLE: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/bin/python-native/python
| -- Using default Python package layout
| -- Found PY_em: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/lib/python2.7/site-packages/em.pyc
| -- Using empy: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/lib/python2.7/site-packages/em.pyc
| -- Using CATKIN_ENABLE_TESTING: 0
| -- catkin 0.7.8
| Traceback (most recent call last):
|   File "/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/catkin_generated/generate_cached_setup.py", line 22, in <module>
|     code = generate_environment_script('/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/devel/env.sh')
|   File "/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/catkin-release-release-lunar-catkin-0.7.8-0/cmake/../python/catkin/environment_cache.py", line 62, in generate_environment_script
|     env_after = ast.literal_eval(output.decode('utf8'))
|   File "/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/lib/python2.7/ast.py", line 49, in literal_eval
|     node_or_string = parse(node_or_string, mode='eval')
|   File "/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/lib/python2.7/ast.py", line 37, in parse
|     return compile(source, filename, mode, PyCF_ONLY_AST)
|   File "<unknown>", line 0
|
|     ^
| SyntaxError: unexpected EOF while parsing
| CMake Error at cmake/safe_execute_process.cmake:11 (message):
|
|   execute_process(/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/bin/python-native/python
|   "/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/catkin_generated/generate_cached_setup.py")
|   returned error code 1
| Call Stack (most recent call first):
|   cmake/all.cmake:186 (safe_execute_process)
|   CMakeLists.txt:8 (include)
|
|
| -- Configuring incomplete, errors occurred!
| See also "/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/CMakeFiles/CMakeOutput.log".
| WARNING: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/temp/run.do_configure.7699:1 exit 1 from 'cmake $oecmake_sitefile /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/catkin-release-release-lunar-catkin-0.7.8-0 -DCMAKE_INSTALL_PREFIX:PATH=/usr -DCMAKE_INSTALL_BINDIR:PATH=bin -DCMAKE_INSTALL_SBINDIR:PATH=sbin -DCMAKE_INSTALL_LIBEXECDIR:PATH=libexec -DCMAKE_INSTALL_SYSCONFDIR:PATH=/etc -DCMAKE_INSTALL_SHAREDSTATEDIR:PATH=../com -DCMAKE_INSTALL_LOCALSTATEDIR:PATH=/var -DCMAKE_INSTALL_LIBDIR:PATH=lib -DCMAKE_INSTALL_INCLUDEDIR:PATH=include -DCMAKE_INSTALL_DATAROOTDIR:PATH=share -DCMAKE_INSTALL_SO_NO_EXE=0 -DCMAKE_TOOLCHAIN_FILE=/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/toolchain.cmake -DCMAKE_VERBOSE_MAKEFILE=1 -DCMAKE_NO_SYSTEM_FROM_IMPORTED=1 -DCMAKE_PREFIX_PATH='/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot/opt/ros/lunar;/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot/usr;                        /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/opt/ros/lunar;/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr' -DCMAKE_INSTALL_PREFIX:PATH='/opt/ros/lunar' -DSETUPTOOLS_DEB_LAYOUT=OFF -DCATKIN_ENABLE_TESTING=0 -DCATKIN_BUILD_BINARY_PACKAGE=1 ${PACKAGECONFIG_CONFARGS} -Wno-dev'
| ERROR: Function failed: do_configure (log file is located at /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/temp/log.do_configure.7699)
ERROR: Task (/home/allenh1/work/poky/meta-ros/recipes-ros-lunar/catkin/catkin_0.7.8.bb:do_configure) failed with exit code '1'
NOTE: Tasks Summary: Attempted 1316 tasks of which 1315 didn't need to be rerun and 1 failed.

Summary: 1 task failed:
  /home/allenh1/work/poky/meta-ros/recipes-ros-lunar/catkin/catkin_0.7.8.bb:do_configure
Summary: There were 3 WARNING messages shown.
Summary: There was 1 ERROR message shown, returning a non-zero exit code.

@tfoote More progress after removing the patch to quote the string.
ERROR: Logfile of failure stored in: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/temp/log.do_install.30799
Log data follows:
| DEBUG: Executing python function extend_recipe_sysroot
| NOTE: Direct dependencies are ['virtual:native:/home/allenh1/work/poky/meta/recipes-devtools/pseudo/pseudo_1.8.2.bb:do_populate_sysroot', '/home/allenh1/work/poky/meta/recipes-devtools/python/python-native_2.7.13.bb:do_populate_sysroot', '/home/allenh1/work/poky/meta/recipes-devtools/cmake/cmake-native_3.8.2.bb:do_populate_sysroot', '/home/allenh1/work/poky/meta/recipes-core/glibc/glibc_2.26.bb:do_populate_sysroot', 'virtual:native:/home/allenh1/work/poky/meta-ros/recipes-devtools/python/python-catkin-pkg_0.3.9.bb:do_populate_sysroot', '/home/allenh1/work/poky/meta/recipes-devtools/gcc/gcc-runtime_7.2.bb:do_populate_sysroot', '/home/allenh1/work/poky/meta/recipes-devtools/cmake/cmake_3.8.2.bb:do_populate_sysroot', '/home/allenh1/work/poky/meta/recipes-devtools/quilt/quilt-native_0.65.bb:do_populate_sysroot', 'virtual:native:/home/allenh1/work/poky/meta-ros/recipes-devtools/python/python-empy_3.3.2.bb:do_populate_sysroot', '/home/allenh1/work/poky/meta/recipes-devtools/gcc/gcc-cross_7.2.bb:do_populate_sysroot']
| NOTE: Installed into sysroot: ['pseudo-native']
| NOTE: Skipping as already exists in sysroot: ['python-native', 'cmake-native', 'glibc', 'python-catkin-pkg-native', 'gcc-runtime', 'cmake', 'quilt-native', 'python-empy-native', 'gcc-cross-arm', 'automake-native', 'bzip2-native', 'readline-native', 'zlib-native', 'libtool-native', 'pkgconfig-native', 'expat-native', 'openssl-native', 'xz-native', 'gnu-config-native', 'autoconf-native', 'sqlite3-native', 'curl-native', 'linux-libc-headers', 'python-setuptools-native', 'bzip2', 'curl', 'expat', 'ncurses', 'xz', 'zlib', 'libarchive', 'libgcc', 'libmpc-native', 'binutils-cross-arm', 'texinfo-dummy-native', 'gmp-native', 'mpfr-native', 'ncurses-native', 'pigz-native', 'makedepend-native', 'cryptodev-linux-native', 'gettext-minimal-native', 'm4-native', 'unzip-native', 'opkg-utils', 'gnutls', 'attr', 'libxml2', 'acl', 'bison-native', 'flex-native', 'xproto-native', 'util-macros-native', 'libidn', 'nettle', 'libunistring', 'gmp', 'python3', 'db', 'readline', 'gdbm', 'sqlite3', 'libffi', 'openssl', 'cryptodev-linux']
| DEBUG: Python function extend_recipe_sysroot finished
| DEBUG: Executing shell function do_install
| NOTE: DESTDIR=/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image cmake --build /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build --target install -- -j6
| /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/bin/cmake -H/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/catkin-release-release-lunar-catkin-0.7.8-0 -B/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build --check-build-system CMakeFiles/Makefile.cmake 0
| /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/bin/cmake -E cmake_progress_start /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/CMakeFiles /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/CMakeFiles/progress.marks
| make -f CMakeFiles/Makefile2 all
| make[1]: Entering directory '/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build'
| make[1]: Nothing to be done for 'all'.
| make[1]: Leaving directory '/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build'
| /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/bin/cmake -E cmake_progress_start /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/CMakeFiles 0
| make -f CMakeFiles/Makefile2 preinstall
| make[1]: Entering directory '/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build'
| make[1]: Nothing to be done for 'preinstall'.
| make[1]: Leaving directory '/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build'
| Install the project...
| /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/bin/cmake -P cmake_install.cmake
| -- Install configuration: ""
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/lib/pkgconfig/catkin.pc
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/catkinConfig.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/catkinConfig-version.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/package.xml
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/LICENSE
| -- Up-to-date: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/all.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/assert.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/atomic_configure_file.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/catkin_add_env_hooks.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/catkin_destinations.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/catkin_download.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/catkin_generate_environment.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/catkin_install_python.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/catkin_libraries.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/catkin_metapackage.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/catkin_package_xml.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/catkin_python_setup.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/catkin_workspace.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/debug_message.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/em
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/em/order_packages.cmake.em
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/em/pkg.pc.em
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/em_expand.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/empy.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/env-hooks
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/env-hooks/05.catkin_make.bash
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/env-hooks/05.catkin_make_isolated.bash
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/find_program_required.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/interrogate_setup_dot_py.py
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/legacy.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/list_append_deduplicate.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/list_append_unique.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/list_insert_in_workspace_order.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/order_paths.py
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/parse_package_xml.py
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/platform
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/platform/lsb.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/platform/ubuntu.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/platform/windows.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/python.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/safe_execute_process.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/shell.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/stamp.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/string_starts_with.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/Doxyfile.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/__init__.py.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/_setup_util.py.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/cfg-extras.context.py.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/env-hook.context.py.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/env.bat.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/env.sh.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/generate_cached_setup.py.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/order_packages.context.py.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/pkg.context.pc.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/pkgConfig-version.cmake.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/python_distutils_install.bat.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/python_distutils_install.sh.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/relay.py.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/rosinstall.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/safe_execute_install.cmake.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/script.bash.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/script.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/script.py.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/script.sh.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/setup.bash.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/setup.bat.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/setup.sh.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/setup.zsh.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/templates/pkgConfig.cmake.in
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/test
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/test/catkin_download_test_data.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/test/download_checkmd5.py
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/test/gtest.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/test/nosetests.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/test/remove_test_results.py
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/test/run_tests.py
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/test/tests.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/tools
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/tools/bz2.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/tools/doxygen.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/tools/libraries.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/tools/rt.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/tools/threads.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/toplevel.cmake
| -- Installing: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/share/catkin/cmake/catkin_package.cmake
| + cd /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/catkin-release-release-lunar-catkin-0.7.8-0
| + mkdir -p /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image/opt/ros/lunar/lib/python2.7/site-packages
| + /usr/bin/env PYTHONPATH=/opt/ros/lunar/lib/python2.7/site-packages:/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/lib/python2.7/site-packages:/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/opt/ros/lunar/lib/python2.7/site-packages CATKIN_BINARY_DIR=/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot-native/usr/bin/python-native/python /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/catkin-release-release-lunar-catkin-0.7.8-0/setup.py build --build-base /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build install --root=/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image --prefix=/opt/ros/lunar --install-scripts=/opt/ros/lunar/bin
| running build
| running build_py
| creating /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/lib
| creating /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/lib/catkin
| copying python/catkin/__init__.py -> /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/lib/catkin
| copying python/catkin/builder.py -> /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/lib/catkin
| copying python/catkin/cmake.py -> /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/lib/catkin
| copying python/catkin/environment_cache.py -> /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/lib/catkin
| copying python/catkin/find_in_workspaces.py -> /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/lib/catkin
| copying python/catkin/init_workspace.py -> /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/lib/catkin
| copying python/catkin/package_version.py -> /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/lib/catkin
| copying python/catkin/terminal_color.py -> /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/lib/catkin
| copying python/catkin/test_results.py -> /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/lib/catkin
| copying python/catkin/tidy_xml.py -> /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/lib/catkin
| copying python/catkin/workspace.py -> /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/lib/catkin
| copying python/catkin/workspace_vcs.py -> /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/lib/catkin
| running build_scripts
| creating /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/scripts-2.7
| copying bin/catkin_find -> /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/scripts-2.7
| copying bin/catkin_init_workspace -> /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/scripts-2.7
| copying bin/catkin_make -> /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/scripts-2.7
| copying bin/catkin_make_isolated -> /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/scripts-2.7
| copying bin/catkin_package_version -> /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/scripts-2.7
| copying bin/catkin_prepare_release -> /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/scripts-2.7
| copying bin/catkin_test_results -> /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/scripts-2.7
| copying bin/catkin_topological_order -> /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/scripts-2.7
| running install
| error: invalid Python installation: unable to open /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/recipe-sysroot/usr/lib/python2.7/config/Makefile (No such file or directory)
| CMake Error at catkin_generated/safe_execute_install.cmake:4 (message):
|
|   execute_process(/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build/catkin_generated/python_distutils_install.sh)
|   returned error code
| Call Stack (most recent call first):
|   cmake_install.cmake:59 (include)
|
|
| make: *** [Makefile:121: install] Error 1
| WARNING: /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/temp/run.do_install.30799:1 exit 2 from 'DESTDIR='/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/image' cmake --build '/home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/build' --target install -- -j6'
| ERROR: Function failed: do_install (log file is located at /home/allenh1/work/poky/rpi-build/tmp/work/cortexa7hf-neon-vfpv4-poky-linux-gnueabi/catkin/0.7.8-r0/temp/log.do_install.30799)
ERROR: Task (/home/allenh1/work/poky/meta-ros/recipes-ros-lunar/catkin/catkin_0.7.8.bb:do_install) failed with exit code '1'
NOTE: Tasks Summary: Attempted 2712 tasks of which 2707 didn't need to be rerun and 2 failed.

Summary: 2 tasks failed:
  /home/allenh1/work/poky/meta-ros/recipes-ros-lunar/ros-comm-msgs/rosgraph-msgs_1.11.2.bb:do_configure
  /home/allenh1/work/poky/meta-ros/recipes-ros-lunar/catkin/catkin_0.7.8.bb:do_install
Summary: There were 2 WARNING messages shown.
Summary: There were 2 ERROR messages shown, returning a non-zero exit code.

That comes for libpython2.7-dev on ubuntu. Maybe it's a missing dependency/expected in the ROS bootstrap installation?

That comes for libpython2.7-dev on ubuntu.

Ok, I found that there's no python2.7 in that folder (but there is python3.5). I'm attempting to switch catkin to 3.5 for the moment.


add julials

Sorry I forgot to update README

Hello! Cool! Have you seen the discussions in #143 btw? Due to how the Julia package manager works, we lose a lot of the control and guarantees that is necessary to ensure the plugin behaves in a reliable manner (this is discussed more in #143).
I've spent some time today looking into how the VSCdoe extension does this, and it seems like they bundle the LanguageServer and all its dependencies, like so. The server is started like so, which runs main.jl. From this, I've been able to set up a simplified version which seems to be working pretty well actually.
Could you see whether branch add-julials (#429) works fine for you? I'm not a Julia dev so I can't really tell. It seems a bit "broken" on projects that only has a Project.toml and not a Manifest.toml (it wont find dependencies, you need to run Pkg.instantiate() and then restart neovim for the LSP to find dependencies).

Oh, sorry, I didn't notice you already worked on julia.
Sure, I'm looking into that.

I just removed my changes which are no longer needed and formatted the script to a "Julia style". https://github.com/williamboman/nvim-lsp-installer/pull/432

Oh, sorry, I didn't notice you already worked on julia. Sure, I'm looking into that.

No worries! We had actually gotten a bit stuck haha, this PR prompted me to take a 2nd look :)


Add functions to list keys of Function Apps

Adds mixin functions to wrap ARM API calls to List Keys of Function Apps, as described in this issue.
Required for #295 or in case we want to support non-anonymous HTTP callback functions.
A function getServiceClientCredentials got introduced in core package. It might be useful for any REST interaction with the Azure Management API.
I enabled "format on save" in my VS Code, so some old lines got re-formated. Let me know if that's too annoying.

Note that we might get this Terraform on some point, but they are blocked upstream, so probably not in short-term. See https://github.com/terraform-providers/terraform-provider-azurerm/issues/699

Done with review pass.  LGTM, but i did hav ea question about something odd...


Refactor the Maxwellian correction routine in gyrokinetics based on successful refactoring in Vlasov

This branch takes the work of the Vlasov-Maxwell refactor of the Maxwellian correction routine (the LTE correction routine for Vlasov since Vlasov is agnostic to non-relativistic vs. relativistic) and hooks the results in to the gyrokinetic app. The big picture changes are as follows:

The correction algorithm converges in the cell averages of (n, u_par, T/m) and does not try to converge in all the moments (i.e., does not try to converge point-wise). This is a change both in iterating on the primitive moments and only using the cell averages.
We utilize a relative error instead of an absolute error, which allows us to reduce finite precision errors when running with SI units. Note that for the u_par convergence we check if fabs(u_par) < 1.0 (i.e., if u_par is O(1)) because we can safely use absolute errors in that case and avoid dividing by 0.0 (since some cells will have very small u_par while other cells may have large flows, like near the sheath).
The option to utilize the last iteration if one wants to utilize a small fixed number of iterations (like 2-5 iterations) so that even if you "fail to converge" you may still get some benefit from the correction routine.

The details of these big picture changes are as follows:

The creation of a new updater: gyrokinetic_maxwellian_moments, which computes (n, u_par, T/m) with the option to return n with or without the Jacobian factor, depending on how one is projecting the Maxwellian (either just using the velocity space Jacobian, or the total Jacobian).
This new updater also addresses issue https://github.com/ammarhakim/gkylzero/issues/265 by giving an option to compute the bi-Maxwellian moments (n, u_par, T_par/m, T_perp/m).
The deletion of the old correction routine and the addition of the updater gyrokinetic_maxwellian_correct, which has been hooked in to both the app and unit test
We can write out the correction status as an optional diagnostic, which for GK returns a dynvector of size 5 (the number of iterations, the status (whether or not it converged, 0 means converged), the maximum error in n, the maximum error in u_par, and the maximum error in T/m)
A small change to proj_gkmaxwellian_prim_moms to take a single array of (n, u_par, T/m) (@manauref want to draw your attention to this change in the hopes that conflicts with the non-uniform velocity-space work are minimized).
Clean up of the app to utilize this new infrastructure, including a big of streamlining of the logic and the option to "correct_all_moms" in both the projection routine and the BGK operator
Hooking in the Vlasov correction routine and projection objects to the neutral species.
A small change to gk_species_react (@tnbernard @akashukla) to accommodate the fact that gkmaxwellian_prim_moms expects a single array now (we might want to slightly refactor this change since it's a little convoluted).

We have a new regression test: gk_periodic_bgk_sod_shock_p1, which does a 1x sod shock set up in the gyrokinetic app with no evolution of the potential, so similar to a 1x3v Vlasov sod shock. We can converge the primitive moments in 5-8 iterations to 1.0e-14 error and thus obtain perfect energy conservation (if you do not correct the moments, the error in the conservation is 1-10 percent).
If you want to correct initial conditions or sources, you can now do so with the parameter "correct_all_moms" in the projection object. Give it a shot! So far my experience is universally positive.
Next steps:

This PR comments out the cross-species collisions in BGK because the BGK cross species collisional moments should now be the primitive moments u_{rs} T_{rs}. We need to generate new kernels and deploy these new kernels.

My goodness. A War and Peace length PR comment!

Thanks for making these changes. I'm overall approving, and I think this will greatly improve simulations with Maxwellian projections/BGK (cost TBD). Aside from the relatively minor things I brought up in individual comments I have 1 request, 1 suggestion, and 3 questions:

Request: did you run the relevant unit and reg tests and make sure they work and that they are valgrind free? i'm thinking the unit tests modified here + bgk,step,react reg tests. Especially since I think I spotted at least one memory leak.
Suggestion: that we implement the cross-species BGK moments here so we can wrap the BGK stuff up.
Question 1: In your PR message you said this addresses issue Implement T_parallel and T_perp into prim_moms #265. Does allow me to request prim_moms with Tpar/Tperp from the input file? how?
Question 2: Can you clarify, maybe by editing the PR message, what the default setting is now for BGK collision and reaction operators, with regards to corrections? are they do it? with how many iterations, etc.
Question 3: Is it clear to you if the maxwellian_correction routine could be easily written in a way that also works for bimaxwellians?

Good catch on things like the memory leak and the allreduce_host. Yes this PR has not been extensively vetted yet by the regression system because I'm traveling but I wanted to file it and get your comments now before the next week and a half is busy with writing
We can push ahead with the cross-species BGK refactor, but since these changes were self-contained and @dingyunl is still working on implementing the refactored BGK cross moments, I wanted to file the PR and get people's eyes on this now. There is other clean up of this work I'd like to do but did not do to minimize the overall number of changes for this refactor (big example: in Vlasov the density correction is just part of the projection routine as opposed to a separate method in the correction updater, but I avoided doing this because I didn't want to make a bunch of changes to the project Maxwellian routines and create conflicts with the non-uniform velocity space work. Another example: the reaction routines could switch to utilizing the Vlasov LTE projection object which does give density correction for free and hooks in more seamlessly to the correction routine).
There are two new diagnostic moment options: "MaxwellianMoments" and "BiMaxwellianMoments" which return (n, u_par, T/m) and (n, u_par, T_par/m, T_perp/m). These moments are returned this way because of how they are utilized by the correction updater and projection updaters. We could add options to unpack some of them but my chief ambition was to finally be able to write out T_par and T_perp and get rid of the need to set write_collisions=true for writing out the primitive moments. If you have a preferred name change please let me know. I am happy to change names.
No solver or updater turns on corrections by default. You must set the "correct_all_moms=true" flag.
Yes this is as close to trivial as I am willing to call things trivial. It literally could be an option to the correction updater as is (set the number of corrected components to either 3 or 4 depending on whether you're doing a Maxwellian or Bimaxwellian).

With respect to names. I made the deliberate choice to rename things as gyrokinetic_* so that it was more clear that certain objects went together (gyrokinetic_maxwellian_moments and gyrokinetic_maxwellian_correct). This naming convention I have adopted for Vlasov (see all the vlasov_lte functions) and if anything I think in the refactor of proj_maxwellian, since we should not need the Vlasov version anymore, we can repurpose this object as gyrokinetic_maxwellian_proj_on_basis.

Thanks Jimmy for revising the maxwellian correction routine. One thing I notice is that in this new routine, the density is also corrected by iteration instead of rescaling, which saves some lines of code but seems to increase the dimension of the iteration. Do we want to keep the rescaling for density correction?


Go to definition for project imports

This adds the ability to jump to a source file by making a goto definition request on an import statement.
This also adds a map of imported module names to the GHC module cache to support it.
Closes #688
Todo

[x] Write tests (waiting on #691)

Concept LGTM, need to get the tests to pass though.


How to send udp massage from RakNet Client to Boos::asio server

I try to send simple udp massage to simple boost::asio server
for this example i used the boost::asio echo server
and the raknet tutorial .
The server accept the client massage but i have problem translate in boost::asio concepts the use of RakNet.
How do i use the RakNet::BitStream inside the Boost::Asio server
to the raknet client could understand it , or even can i do that ?
In short what i need to change in this simple example so it could work .
    class server
    {
    public:
        server(boost::asio::io_service& io_service, short port)
            : socket_(io_service, udp::endpoint(udp::v4(), port))
        {
            socket_.async_receive_from(
                boost::asio::buffer(data_, max_length), sender_endpoint_,
                boost::bind(&server::handle_receive_from, this,
                boost::asio::placeholders::error,
                boost::asio::placeholders::bytes_transferred));
        }

        void handle_receive_from(const boost::system::error_code& error,
            size_t bytes_recvd)
        {
            if (!error && bytes_recvd > 0)
            {
                socket_.async_send_to(
                    boost::asio::buffer(data_, bytes_recvd), sender_endpoint_,
                    boost::bind(&server::handle_send_to, this,
                    boost::asio::placeholders::error,
                    boost::asio::placeholders::bytes_transferred));
            }
            else
            {
                socket_.async_receive_from(
                    boost::asio::buffer(data_, max_length), sender_endpoint_,
                    boost::bind(&server::handle_receive_from, this,
                    boost::asio::placeholders::error,
                    boost::asio::placeholders::bytes_transferred));
            }
        }

        void handle_send_to(const boost::system::error_code& /*error*/,
            size_t /*bytes_sent*/)
        {
            socket_.async_receive_from(
                boost::asio::buffer(data_, max_length), sender_endpoint_,
                boost::bind(&server::handle_receive_from, this,
                boost::asio::placeholders::error,
                boost::asio::placeholders::bytes_transferred));
        }

    private:
        udp::socket socket_;
        udp::endpoint sender_endpoint_;
        enum { max_length = 1024 };
        char data_[max_length];
    };

    int main(int argc, char* argv[])
    {
        try
        {

            boost::asio::io_service io_service;

            using namespace std; // For atoi.
            server s(io_service, 9991);
            std::cout << "Starting server on 9991" <<std::endl;
            io_service.run();
        }
        catch (std::exception& e)
        {
            std::cerr << "Exception: " << e.what() << "\n";
        }

        return 0;
    }

And the RakNet Client

    void RakNetWrapper::Init()
    {
        char str[512];
        strcpy(str, "<IP_ADDRESS>");
        RakNet::SocketDescriptor sd;
        RakNet::StartupResult startupResult = peer->Startup(1, &sd, 1);
        RakNet::ConnectionAttemptResult connectionAttemptResult = peer->Connect(str, SERVER_PORT, 0, 0);
        StartReciveLoop();
    }

    void RakNetWrapper::StartReciveLoop()
    {
        while (1)
        {
            for (packet = peer->Receive(); packet; peer->DeallocatePacket(packet), packet = peer->Receive())
            {
                switch (packet->data[0])
                {
                case ID_REMOTE_DISCONNECTION_NOTIFICATION:
                    log("Another client has disconnected.\n");
                    break;
                case ID_REMOTE_CONNECTION_LOST:
                    log("Another client has lost the connection.\n");
                    break;
                case ID_REMOTE_NEW_INCOMING_CONNECTION:
                    log("Another client has connected.\n");
                    break;
                case ID_CONNECTION_REQUEST_ACCEPTED:
                {
                    log("Our connection request has been accepted.\n");

                    // Use a BitStream to write a custom user message
                    // Bitstreams are easier to use than sending casted structures, and handle endian swapping automatically
                    RakNet::BitStream bsOut;
                    bsOut.Write((RakNet::MessageID)ID_GAME_MESSAGE_1);
                    bsOut.Write("Hello world");
                    peer->Send(&bsOut, HIGH_PRIORITY, RELIABLE_ORDERED, 0, packet->systemAddress, false);
                }
                break;
                case ID_NEW_INCOMING_CONNECTION:
                    log("A connection is incoming.\n");
                    break;
                case ID_NO_FREE_INCOMING_CONNECTIONS:
                    log("The server is full.\n");
                    break;
                case ID_DISCONNECTION_NOTIFICATION:
                    {
                        log("We have been disconnected.\n");
                    }
                    break;
                case ID_CONNECTION_LOST:
                    {
                        log("Connection lost.\n");

                    }
                    break;

                case ID_GAME_MESSAGE_1:
                {
                    RakNet::RakString rs;
                    RakNet::BitStream bsIn(packet->data, packet->length, false);
                    bsIn.IgnoreBytes(sizeof(RakNet::MessageID));
                    bsIn.Read(rs);
                    log("%s\n", rs.C_String());
                }
                break;

                default:
                    log("Message with identifier %i has arrived.\n", packet->data[0]);
                    break;
                }
            }
        }
    }

From what I can see you do not even handle RakNet handshakes in your boost implementation.


Master becomes locked in distributed mode

OrientDB Version: 3.0.1
Java Version: 1.8
OS: Ubuntu 16.04.2
We start two nodes in distributed mode. One master and one replica. Initially, the system behaves normally, but after a while the master is blocked and write operations are not executed.
Expected behavior
All write operations are performed on the master and then sent to the replica. A replica creates a full backup every 3 hours.
Actual behavior
Write operations are not executed after the following lines from the master log.
2018-06-04 12:57:19:048 INFO  [master]->[replica1] Creating delta backup of database 'test' (startLSN=OLogSequenceNumber{segment=5, position=52}) in directory: /tmp/orientdb/backup_replica1_test_server0.zip...
2018-06-04 12:57:19:049 INFO  Cannot find requested LSN=OLogSequenceNumber{segment=5, position=52} for database sync operation (last available LSN is OLogSequenceNumber{segment=21, position=214419})
2018-06-04 12:57:19:050 FINE  [master]->[replica1] Sending response com.orientechnologies.orient.server.distributed.task.ODistributedDatabaseDeltaSyncException: Requested database delta sync with LSN=OLogSequenceNumber{segment=5, position=52} but not found in database back (reqId=id=1. 26236 task=deploy_delta_db)

In replica log the master has backup status, but it should not do backups.
2018-06-04 12:57:19:189 WARNI [replica1]<-[master] Error on installing database delta for 'test' (err=Requested database delta sync with LSN=OLogSequenceNumber{segment=5, position=52} but not found in database)
2018-06-04 12:57:19:189 INFO  [replica1] Requesting full sync for database 'test'...
2018-06-04 12:57:19:189 INFO  [replica1]->[[master]] Requesting deploy of database 'test' on local server...
2018-06-04 12:57:19:206 INFO  [replica1]<-[master] Received updated status master.test=BACKUP
2018-06-04 12:57:19:207 INFO  [replica1] Distributed servers status (*=current @=lockmgr[master]):

Steps to reproduce
Replica has following config.
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<orient-server>
    <handlers>
        <handler class="com.orientechnologies.orient.server.hazelcast.OHazelcastPlugin">
            <parameters>
                <parameter value="${distributed}" name="enabled"/>
                <parameter value="${ORIENTDB_HOME}/config/default-distributed-db-config.json" name="configuration.db.default"/>
                <parameter value="${ORIENTDB_HOME}/config/hazelcast.xml" name="configuration.hazelcast"/>
                <parameter value="replica1" name="nodeName"/>
            </parameters>
        </handler>
        ...
        <handler class="com.orientechnologies.orient.server.handler.OAutomaticBackup">
            <parameters>
                <parameter value="true" name="enabled"/>
                <parameter value="${ORIENTDB_HOME}/config/automatic-backup.json" name="config"/>
            </parameters>
        </handler>
        ...
    </orient-server>
</handlers>

Master has following.
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<orient-server>
    <handlers>
        <handler class="com.orientechnologies.orient.server.hazelcast.OHazelcastPlugin">
            <parameters>
                <parameter value="${distributed}" name="enabled"/>
                <parameter value="${ORIENTDB_HOME}/config/default-distributed-db-config.json" name="configuration.db.default"/>
                <parameter value="${ORIENTDB_HOME}/config/hazelcast.xml" name="configuration.hazelcast"/>
                <parameter value="master" name="nodeName"/>
            </parameters>
        </handler>
        ...
        <handler class="com.orientechnologies.orient.server.handler.OAutomaticBackup">
            <parameters>
                <parameter value="false" name="enabled"/>
                <parameter value="${ORIENTDB_HOME}/config/automatic-backup.json" name="config"/>
            </parameters>
        </handler>
        ....
    </handlers>
</orient-server>

Distributed configuration is the same for both.
{
  "autoDeploy": true,
  "readQuorum": 1,
  "writeQuorum": "majority",
  "executionMode": "undefined",
  "readYourWrites": true,
  "newNodeStrategy": "dynamic",
  "servers": {
    "master": "master",
    "*": "replica"
  },
  "clusters": {
    "internal": {
    },
    "*": {
      "servers": ["<NEW_NODE>"]
    }
  }
}

Hi @artbez,
We fixed some similar issue in 3.0.2 that is beening released now, anyway could you share a thread dump so we can be sure about your specific problem.
Regards

Hi @artbez,
There is no public issue of that, anyway this is the commit that solve the problem: https://github.com/orientechnologies/orientdb/commit/71edf2df4b8bde6f47dd3d7293ea4028dcfc1c39
Regards


A number of TC test scripts that use Open Commissioning Window use a problematic setup payload

The setup payload MT:-24J0AFN00KA0648G00 and corresponding verifier have been copy / pasted into a number of test scripts. However this payload contains the test vendor ID (0xFFF1), causing a discovery failure during PASE establishment if the DUT is using a real vendor id.
For good measure we should also use a discriminator and passcode that differ from the default values used by the example apps.

Fixing a few of these in #35784, I'll put up a PR for the rest tomorrow.


⚠ Bofrost.lu has degraded performance

In c64a3f8, Bofrost.lu (https://www.bofrost.lu) experienced degraded performance:

HTTP code: 200
Response time: 2142 ms

Resolved: Bofrost.lu performance has improved in cd80377 after 9 minutes.


autoscroll to the end of output buffer

Hi! To see a result of ant command execution I'm forced to switch to output window and navigate to the buffer end. I guess it would be handy to autoscroll to the end of output buffer.

Take a look at the variable compilation-scroll-output.

Great, thanks! Sorry for noise.


Map drawing

Could not see the "type" attribute propagates as part of the event...(also could not find trace in the code for it)
anyone got it working?
thanks

Sorry - not sure what/where you mean ? propagate when ? do you have a small example flow to show the issue ?

According to the documentation,
The property "type" (shape type) should be part of the event coming back from the map to the flow when a map drawing entity created. I could not get the property "type" as part of the event (I do get all other properties).
please take a look  the event message object content I got:


Implement cryptographic keys as instance IDs

Currently we generated a random number as the instance ID
We should start generating device public/private key pairs, where we use the public key as the instance ID.
Part of
https://github.com/uProxy/uproxy/issues/702

Closing as this is not a priority right now.


TP-Link device tracker not working

Make sure you are running the latest version of Home Assistant before reporting an issue.
You should only file an issue if you found a bug. Feature and enhancement requests should go in the Feature Requests section of our community forum:
**Home Assistant release (hass --version):0.52
Python release (python3 --version):
**Component/platform:TP-link
**Description of problem: Device traces not working, not loaded.
**Expected: working
Problem-relevant configuration.yaml entries and steps to reproduce:
Error log entry:
2017-08-27 14:56:54 ERROR (MainThread) [homeassistant.components.device_tracker] Error setting up platform tplink
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/requests/packages/urllib3/response.py", line 302, in _error_catcher
yield
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/requests/packages/urllib3/response.py", line 384, in read
data = self._fp.read(amt)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py", line 449, in read
n = self.readinto(b)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py", line 493, in readinto
n = self.fp.readinto(b)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/socket.py", line 586, in readinto
return self._sock.recv_into(b)
ConnectionResetError: [Errno 54] Connection reset by peer

1.
2.
3.

**Traceback (if applicable):**
```bash

Additional info:

Please fill in the issue template. Without more info it's not possible to fix the problem.

Issue template updated.

#9120 is about the same issue.

Thanks! I'll close this as duplicate and we'll continue tracking in #9120.


docs: Change relabelling -> relabeling

Signed-off-by: Julien Pivotto<EMAIL_ADDRESS>

So has it been decided to go with this spelling? Because it can be either way: https://www.merriam-webster.com/dictionary/relabel

I have taken the one with more use.


MOD: OSGi manifest headers

Introduced bundle packaging through maven-bundle-plugin.
java-app-lib solely depends on org.eclipse.paho/org.eclipse.paho.client.mqttv3 and org.json/json: both this artifacts are built as Java OSGi bundles.
I have added the maven-bundle-plugin to the POM and changed the packaging mode to "bundle": this way the generated JAR has all the needed manifest headers to be a proper OSGi bundle itself.
The usage of the JAR as a simple standalone Java library is totally unchanged, but now the same library can properly execute inside an OSGi runtime, like Apache Felix, Eclipse Equinox and so on.

 Thank you for your submission, we really appreciate it. Like many open source projects, we ask that you sign our Contributor License Agreement before we can accept your contribution.

Thanks @IOOOTA!

Fine. Thanks for your contribution @IOOOTA !

@cambierr now you can!

Great, thanks !

It's a pleasure @cambierr, thanks to TTN for the opportunity :+1:


Strict borrow drop checks

Wasmtime's resources implementation strictly verifies that components drop borrows before a call completes.
We should implement the same thing in jco to ensure that components are conformant.

Fixed in https://github.com/bytecodealliance/jco/pull/262.


show both images and video in gallery screen

Thanks for awesome library.
Is there any option that show both images and videos in
gallery screen.
Thanks.

+1

+1

Thank you for the kind words. We will however be removing support for loading photos from the gallery in future updates. I encourage you to check out the excellent replacement library, which I have also contributed to as well:
https://github.com/react-native-cameraroll/react-native-cameraroll
The maintainers there are really great.


direct stdin to a process

Typical setup for me is having concurrently run nodemon, for which you can trigger a restart by typing rs in your terminal. I presume concurrently is ignoring stdin?

Yes, we are currently doing nothing to the stdin pipe of the child processes.
If you use --raw, however, stdin will work.

brilliant, that worked, thanks!

@rotexhawk it's not a nodemon flag, it's a concurrently one.
Also make sure to check #128, it will bring stdin handling.

Awesome. Thanks for clarifying it. Hopefully #128 will be merged soon.


k3s doesn't work on Chrome OS Crostini

Describe the bug
k3s fails on Crostini
To Reproduce
Install k3s and attempt to start Kubernetes cluster
Expected behavior
Kubernetes cluster starts
Actual behavior
Cluster fails to start
Additional context
Speaking with Darren Sheperd at Kubecon, he said that k3s would need some changes to work in Crostini, if it was even possible.  I'm opening this issue as a reminder to please look into it.

Really want this to work on my Pixelbook please.

It seems like the vxlan moduke is missing

Another pixelbook user here that needs this.

Doen't work on my chromebook as well
k3s service starts but i get no node  would be great if someone can add chromebook support when possible
Thanks

I am seeing the same issue. The logs show that we are lack of OVERLAY_FS and BRIDGE_NETFILTER support. Similar issue for minikube here: https://github.com/kubernetes/minikube/issues/6411

related:

https://richrose.dev/posts/chromeos/productivity/chromeos-minikube/
https://github.com/kubernetes-sigs/kind/issues/763#issuecomment-1219133506

Based on https://twitter.com/ibuildthecloud/status/1571718481133064193 & https://twitter.com/ibuildthecloud/status/1571736993725566976
I just tried as:
apt install -y fuse3
curl -sfL [https://get.k3s.io](https://t.co/1Ezuadk0kx) | sh -s - --snapshotter fuse-overlayfs --kubelet-arg 'feature-gates=KubeletInUserNamespace=true' --kube-proxy-arg 'proxy-mode=ipvs' --write-kubeconfig-mode 0644

And it seems to work just fine:
eminguez@k3s:~$ k get po -A
NAMESPACE              NAME                                        READY   STATUS      RESTARTS      AGE
kube-system            helm-install-traefik-crd-w949j              0/1     Completed   0             111m
kube-system            helm-install-traefik-tqxt9                  0/1     Completed   2             111m
kube-system            metrics-server-668d979685-x9lc4             1/1     Running     0             111m
kubernetes-dashboard   dashboard-metrics-scraper-8c47d4b5d-h9n4d   1/1     Running     0             106m
kube-system            local-path-provisioner-7b7dc8d6f5-h48x4     1/1     Running     0             111m
kube-system            coredns-b96499967-bz897                     1/1     Running     0             111m
kube-system            traefik-7cd4fcff68-s5x8b                    1/1     Running     0             109m
kube-system            svclb-traefik-1b183594-vwsw8                2/2     Running     0             109m
kubernetes-dashboard   kubernetes-dashboard-67bd8fc546-6w5s4       1/1     Running     1 (13m ago)   106m
default                hello-world-nginx-66c656756f-rxx6r          1/1     Running     0             5m58s
default                hello-world-nginx-66c656756f-s9xrq          1/1     Running     0             5m58s
default                hello-world-nginx-66c656756f-222dw          1/1     Running     0             5m58s
eminguez@k3s:~$ k get ingress
NAME          CLASS    HOSTS   ADDRESS          PORTS   AGE
hello-world   <none>   *       <IP_ADDRESS>   80      6m
eminguez@k3s:~$ curl http://<IP_ADDRESS>
<html>
<head>
  <title>Hello World!</title>
</head>
<body>Hello World!</body>
</html>

It doesn't fully work because iptables bridge filtering is not supported by the kernel. This will manifest itself easily by the fact that DNS is broken inside pods. Inside a pod just run "ping www.google.com" and you'll see the DNS fails to resolve. This is because the request going to <IP_ADDRESS> (for coredns) is not getting processed by the kube proxy iptables rules.

Possibly there is an approach to use nftables instead of iptables. I haven't investigated that.

Not planning on adding ChromeOS support at this time.


Remove the unnecessary 'creationTimestamp' fields in sample's yamls

creationTimestamp will be created at runtime, so it's not necessary to define it in the yamls

[APPROVALNOTIFIER] This PR is NOT APPROVED
This pull-request has been approved by: crystaldust
To fully approve this pull request, please assign additional approvers.
We suggest the following additional approvers: chxchx, frankbu
Assign the PR to them by writing /assign @chxchx @frankbu in a comment when ready.
The full list of commands accepted by this bot can be found here.
The pull request process is described here

Needs approval from an approver in each of these files:

samples/OWNERS
tests/OWNERS

Approvers can indicate their approval by writing /approve in a comment
Approvers can cancel approval by writing /approve cancel in a comment

Hi @crystaldust. Thanks for your PR.
I'm waiting for a istio member to verify that this patch is reasonable to test. If it is, they should reply with /ok-to-test on its own line. Until that is done, I will not automatically test new commits in this PR, but the usual testing commands by org members will still work. Regular contributors should join the org to skip this step.
I understand the commands that are listed here.

Instructions for interacting with me using PR comments are available here.  If you have questions or suggestions related to my behavior, please file an issue against the kubernetes/test-infra repository.


Dump database

Related Issues: #277
Requested Reviewers: @andrewtarzia
Note for Reviewers: If you accept the review request add a :+1: to this post

This PR adds a new test, test_dump_molecule_structures(), which
is responsible for dumping the molecular structures to files and
placing them into a MongoDB database. Previously the file dumping
was done in the test_get_atoms() test, but I think having a
separate test for this is better, because it keeps better to the single
responsibility principle.
The PR also updates the CI to dump the MongoDB database after
the tests have been run, so that it can be downloaded and viewed
locally, for example with stk-vis. To help viewing with stk-vis
the file tests/mongo-config.json has been added. It can be
loaded into stk-vis and configures it so that the developer does
not have to manually change the database name or the molecule
key name.
The PR also adds a new utility script drop_test_database.py which
just drops the databases which running the tests creates. This script
is meant to be run manually if a developer wants to remove the
databases for some reason.
Finally, the PR also removes all uses of the MongoDB action with a
MongoDB service container in the CI. This just seems more idiomatic
to me.

It does require it, but has for a while now.