It means that signac is better integrated within the scientific Python ecosystem and that the NumFOCUS organization is going to help us improve the sustainability of the project. There are no immediate changes besides that we have another platform to promote the project to potential users and developers. Concretely, we hope to significantly increase the number of contributors across different institutions in the next couple of months.
To achieve this, we are going to try to increase the transparency of our development process. All future development meetings and sprints are open to anyone. We also hope to host more user meetings and tutorials at conferences.
Good morning! I am having some trouble with signac view. It returns: Error: <lambda>() takes 1 positional argument but 2 were given. The project was initialized with the script
# init.py
import signac
project = signac.init('fmria_project')
sp = {'monomer':'nfa'}
job = project.open_job(sp)
job.init()I am using signac version 1.1.0 and python version 3.7.3 on CentOS version 6.10 (Final)
Any and all help would be appreciated! Thank you!
https://github.com/glotzerlab/signac/issues/new/choose
subprocess is not as straightforward as i'd hoped
Hey @atravitz , This is not exactly the same as what you are wanting to do, but one of our (MoSDeF) python libraries mBuild uses the PACKMOL binary for packing our systems, and we generate input files that are directly fed to packmol. So its not exactly a python wrapper, but if you just need to pack some smaller molecules in a box or region, mbuild.packing abstracts away a lot of the necessary inputs for PACKMOL into function arguments. If you already have a structure file for your molecules, you can have a packed system in no time!
If you need this very soon, it might take a bit of time to get up and running, but you can swing by our gitter channel for additional help!
A few of us in our group all use the signac workflow in combination with our tools at mosdef.org and have had great success!
function move_logs() {
# Put logs into subdirectories.
verify_project_dir
if [ -n "$(find . -maxdepth 1 -name "$RESUB_LOG_GLOB" -print -quit)" ]; then
mkdir -p logs
for resublog in $RESUB_LOG_GLOB; do
mv -v $resublog logs/
done
else
echo "No resubmit logs found."
fi
if [ -n "$(find . -maxdepth 1 -name "$JOB_LOG_GLOB" -print -quit)" ]; then
for joblog in $JOB_LOG_GLOB; do
signacid=$(echo $joblog | sed -rn "s/^([a-f0-9]+).*/\1/p")
remainder=$(echo $joblog | sed -rn "s/^[a-f0-9]+-(.*)/\1/p")
if [ -d workspace/${signacid} ]; then
mv -v $joblog workspace/${signacid}/job-${remainder}
else
echo "workspace/${signacid} does not exist. Moving to logs."
mv -v $joblog logs/
fi
done
else
echo "No job logs found."
fi
}
function clear_logs() {
# Remove logs.
verify_project_dir
find . -maxdepth 1 -name "$JOB_LOG_GLOB" -exec rm {} +
find . -maxdepth 1 -name "$RESUB_LOG_GLOB" -exec rm {} +
rm -r logs
echo "Logs cleared.”
}
Traceback (most recent call last):
File "src/project.py", line 188, in <module>
Project().main()
File "/home/telezki/Hoomd/venv/lib/python3.6/site-packages/flow/project.py", line 2721, in main
_exit_or_raise()
File "/home/telezki/Hoomd/venv/lib/python3.6/site-packages/flow/project.py", line 2689, in main
args.func(args)
File "/home/telezki/Hoomd/venv/lib/python3.6/site-packages/flow/project.py", line 2362, in _main_status
self.print_status(jobs=jobs, **args)
File "/home/telezki/Hoomd/venv/lib/python3.6/site-packages/flow/legacy.py", line 230, in wrapper
return func(self, jobs=jobs, *args, **kwargs)
File "/home/telezki/Hoomd/venv/lib/python3.6/site-packages/flow/project.py", line 1105, in print_status
tmp = self._fetch_status(jobs, err, ignore_errors, no_parallelize)
File "/home/telezki/Hoomd/venv/lib/python3.6/site-packages/flow/project.py", line 994, in _fetch_status
self._fetch_scheduler_status(jobs, err, ignore_errors)
File "/home/telezki/Hoomd/venv/lib/python3.6/site-packages/flow/project.py", line 975, in _fetch_scheduler_status
scheduler_info = {sjob.name(): sjob.status() for sjob in self.scheduler_jobs(scheduler)}
File "/home/telezki/Hoomd/venv/lib/python3.6/site-packages/flow/project.py", line 975, in <dictcomp>
scheduler_info = {sjob.name(): sjob.status() for sjob in self.scheduler_jobs(scheduler)}
File "/home/telezki/Hoomd/venv/lib/python3.6/site-packages/flow/project.py", line 856, in scheduler_jobs
for sjob in self._expand_bundled_jobs(scheduler.jobs()):
File "/home/telezki/Hoomd/venv/lib/python3.6/site-packages/flow/project.py", line 832, in _expand_bundled_jobs
for job in scheduler_jobs:
File "/home/telezki/Hoomd/venv/lib/python3.6/site-packages/flow/scheduling/torque.py", line 99, in jobs
nodes = _fetch(user=self.user)
File "/home/telezki/Hoomd/venv/lib/python3.6/site-packages/flow/scheduling/torque.py", line 31, in _fetch
tree = ET.parse(source=result)
File "/opt/rh/rh-python36/root/usr/lib64/python3.6/xml/etree/ElementTree.py", line 1196, in parse
tree.parse(source, parser)
File "/opt/rh/rh-python36/root/usr/lib64/python3.6/xml/etree/ElementTree.py", line 597, in parse
self._root = parser._parse_whole(source)
xml.etree.ElementTree.ParseError: syntax error: line 2, column 0
Hi! I'll be live-streaming the public part of my Ph.D. defense tomorrow (Wed) at 11am EDT. I'll be presenting my work on inverse design, software development in academic environments, and of course signac. ;) Tune in live or watch later if you’re interested to know what I’ve been working on in the past 5 years. :)
os.system() that calls the container exec function? and perhaps passing the job data as flag arguments to the container? I don't know of a better form. Thanks.
flow.cmd