nsls-ii-opls / profile_collection Goto Github PK

Previsit

• Make sure that the current latest environments are pushed to all the bl machines
• Skim the IPython startup files in profile_collection
  • Check if it's safe to start bsui remotely (does it touch any hardware?) - use git grep .put or git grep caput
• Check for outstanding PRs and issues on beamline repos
• Check if beamline specific packages pushed to the BL machines
• (Optional) Enable CI

Housekeeping

• Add BL staff to the BL GitHub organization as owners
• Work with BL staff to commit any un-committed changes to their profiles
• Tag the profile as-found as 2019C3.x
• Discuss with BL staff which conda envs they want to keep/delete and perform the cleanup
• Check/update the beamline's inventory with the BL staff (in https://github.com/NSLS-II/playbooks/blob/master/production)

Test deployment

• In ~/.bashrc add the following and remember to source ~/.bashrc afterward.

  BLUESKY_LOG_FILE=/var/log/bluesky.log
  BLUESKY_IPYTHON_LOG_FILE=/var/log/bluesky_ipython.log
  

  and (if needed) create those directories, making them world-read/write-able.
• Append to 00-startup.py https://gist.github.com/jklynch/a4366b8900ec0c03883403455ae711b2
• Run profile against new environment
  • BS_ENV=collection-2020-2.0rc7 bsui
• Update the profile as needed to run:
  • Replace .value -> .get() if it's in a Device, or with yield from bps.read() if in a plan
  • history.sqlite issue - see https://blueskyproject.io/bluesky/metadata.html#persistence-between-sessions
  • potential issue with images in databroker V2
• Run acceptance tests (if any) and run a representative set of scans for the beamline
• Tag the updated profile as 2020C2.0
• Update BSUI via ansible to use the new environment (http://nsls-ii.github.io/deployment/upgrading-beamlines.html#change-bsui-s-default-environment)

Previsit

• Make sure that the current latest environments are pushed to all the bl machines

  conda env list
  

• Skim the IPython startup files in profile_collection
  • Check if it's safe to start bsui remotely (does it touch any hardware?) - use git grep .put or git grep caput
• Check for outstanding PRs and issues on beamline repos
• (Optional) Enable CI

Housekeeping

• Update conda

  $ su - <your-controls-account>
  $ sudo su -
  # conda activate base  # should be activated by default, but just in case.
  # conda install conda -c https://repo.anaconda.com/pkgs/main/
  

• Add BL staff to the BL GitHub organization as owners
• Work with BL staff to commit any un-committed changes to their profiles
• Tag the profile as-found as 2020C2.1
• Discuss with BL staff which conda envs they want to keep/delete and perform the cleanup
• Check/update the beamline's inventory with the BL staff (in https://github.com/NSLS-II/playbooks/blob/master/production)
• In ~/.bashrc, if necessary, update the logging environment variables to use directory /var/log/bluesky/... and add umask 0002.

  umask u=rwx,g=rwx,o=rx  # 0002
  export BLUESKY_LOG_FILE=/var/log/bluesky/bluesky.log
  export BLUESKY_IPYTHON_LOG_FILE=/var/log/bluesky/bluesky_ipython.log
  

  and (if needed) create that directory with the following permissions and ownership:

  sudo mkdir /var/log/bluesky
  sudo chown -Rv xf12id1:xf12id1 /var/log/bluesky
  sudo chmod -Rv g+rws /var/log/bluesky
  

  Remember to source ~/.bashrc.
• Remove explicit setting of ophyd logging level from the first startup script
• Double-check that if there is an open PR removing handlers, it is merged (and tested).
• Update vendored copy of PersistentDict to bug-fixed version (see the updated gist snippet: https://gist.github.com/jklynch/a4366b8900ec0c03883403455ae711b2).
• Make sure all repos have the BSD-3-Clause licenses (see NSLS-II-SRX/profile_collection#16 as an example)

Test deployment

• Run profile against new environment
  • BS_ENV=collection-2021-1.0 bsui
• Update the profile as needed to run
• Test databroker v2

  from databroker import catalog
  cat = catalog['beamline_name']
  cat[-1].read()
  

• Run acceptance tests (if any) and run a representative set of scans for the beamline
• Tag the updated profile as 2021C1.0
• Update BSUI via ansible to use the new environment (http://nsls-ii.github.io/deployment/upgrading-beamlines.html#change-bsui-s-default-environment)

This is blocked by changes to the playbooks to provide the opls configuration files.

two quick sketches for how to make use of multiple LivePlots in one scan:

from functools import partial

from ophyd.sim import hw as _hw

from bluesky import RunEngine
from bluesky.plans import scan
from bluesky.callbacks.mpl_plotting import LivePlot
import bluesky.callbacks
import bluesky.preprocessors as bpp


hw = _hw()

bluesky.callbacks.mpl_plotting.initialize_qt_teleporter()

RE = RunEngine({})

def same_axes():
   def get_ax():
       import matplotlib.pyplot as plt
       return plt.figure('my plot').gca()

   lt =  LivePlot('det', 'motor', marker='x', markersize=10, ax=get_ax)
   lt2 =  LivePlot('det1', 'motor', marker='o', markersize=10, ax=get_ax)   
   return (yield from bpp.subs_wrapper(scan([hw.det, hw.det1], hw.motor, -5, 5, 30), [lt, lt2]))


def same_figure():
   def get_ax(i):
       import matplotlib.pyplot as plt
       fig = plt.figure('my plot')
       if len(fig.axes) == 0:
           fig.subplots(1, 2)
       return fig.axes[i]

   lt =  LivePlot('det', 'motor', marker='x', markersize=10, ax=partial(get_ax, i=0))
   lt2 =  LivePlot('det1', 'motor', marker='o', markersize=10, ax=partial(get_ax, i=1))   
   return (yield from bpp.subs_wrapper(scan([hw.det, hw.det1], hw.motor, -5, 5, 30), [lt, lt2]))


RE(same_figure())

In your actual use the hard coded lt and lt2 can be replaced with a loop over the y-values of interest.