IPython profile configuration - Collection
nsls-ii-amx / profile_collection Goto Github PK
View Code? Open in Web Editor NEWIPython profile configuration - Collection
License: BSD 3-Clause "New" or "Revised" License
profile_collection's Introduction
profile_collection's People
Contributors
Watchers
profile_collection's Issues
Deployment 2020-2.0 checklist
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
bsuiremotely (does it touch any hardware?) - usegit grep .putorgit grep caput
- Check if it's safe to start
- 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
- 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 aDevice, or withyield from bps.read()if in a plan -
history.sqliteissue - see https://blueskyproject.io/bluesky/metadata.html#persistence-between-sessions - potential issue with images in databroker V2
- Replace
- 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)
Resolve JupyterLab live plotting issue
Tried to figure it out with @jklynch on 7/10/2019, were able to enable the live plotting in the classic notebook, but it still failed for the JupyterLab.
Here is the environment on xf17id2-ca:
$ conda list
WARNING conda.core.prefix_data:_load_site_packages(272): Problem reading non-conda package record at lib/python3.7/site-packages/fabio-0.8.0-py3.7-linux-x86_64.egg-info/PKG-INFO. Please verify that you still need this, and if so, that this is still installed correctly. Reinstalling this package may help.
# packages in environment at /opt/conda_envs/collection-2019-3.0-amx:
#
# Name Version Build Channel
17-id-amx-collection 2019C3.0 0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
amostra 0.2 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
anaconda-client 1.7.2 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
analysis 2019C3.0 0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
appdirs 1.4.3 py37h28b3542_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
asciitree 0.3.3 py_2 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
asn1crypto 0.24.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
asteval 0.9.12 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
astropy 3.1.2 py37h7b6447c_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
atomicwrites 1.3.0 py37_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
attrs 19.1.0 py37_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
backcall 0.1.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
blas 1.0 mkl https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
bleach 3.1.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
bluesky 1.5.3 py37_1 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
bluesky-browser 0.1.0a1 py37_1 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
bluesky-kafka 0.1 0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
bokeh 1.2.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
boltons 16.3.1 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
bottleneck 1.2.1 py37h035aef0_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
bzip2 1.0.6 h14c3975_5 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
ca-certificates 2019.5.15 0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
cairo 1.14.12 h8948797_3 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
caproto 0.4.0 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
certifi 2019.3.9 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
cffi 1.12.3 py37h2e261b9_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
cftime 1.0.3.4 py37hdd07704_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
chardet 3.0.4 py37_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
click 7.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
cloudpickle 1.1.1 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
clyent 1.2.2 py37_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
collection 2019C3.0 0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
controls-doctor 0.0.1 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
cryptography 2.7 py37h1ba5d50_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
curio 0.9 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
curl 7.64.1 hbc83047_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
cycler 0.10.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
cytoolz 0.9.0.1 py37h14c3975_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
dask 1.1.4 py37_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
dask-core 1.1.4 py37_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
databroker 0.13.0 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
datamuxer 0.3.0 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
dbus 1.13.6 h746ee38_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
decorator 4.4.0 py37_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
defusedxml 0.6.0 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
dill 0.2.9 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
distributed 1.26.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
doct 1.0.5 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
entrypoints 0.3 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
epics-base 3.15.6 0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
et_xmlfile 1.0.1 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
event-model 1.10.0 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
expat 2.2.6 he6710b0_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
fabio 0.8.0 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
fast-histogram 0.7 py37hdd07704_1000 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
fastcache 1.1.0 py37h7b6447c_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
fasteners 0.14.1 py_3 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
ffmpeg 4.0 hcdf2ecd_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
fftw 3.3.8 h7b6447c_3 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
flake8 3.7.7 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
fontconfig 2.13.0 h9420a91_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
freetype 2.9.1 h8a8886c_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
fribidi 1.0.5 h7b6447c_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
gevent 1.4.0 py37h7b6447c_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
glib 2.56.2 hd408876_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
glue-core 0.14.2 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
glue-vispy-viewers 0.11 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
glueviz 0.13.3 0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
gmp 6.1.2 h6c8ec71_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
gmpy2 2.0.8 py37h10f8cd9_2 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
graphite2 1.3.13 h23475e2_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
graphviz 2.40.1 h21bd128_2 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
greenlet 0.4.15 py37h7b6447c_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
grid-strategy 0.0.1 py37_1 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
gst-plugins-base 1.14.0 hbbd80ab_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
gstreamer 1.14.0 hb453b48_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
h5py 2.9.0 py37h7918eee_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
harfbuzz 1.8.8 hffaf4a1_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
hdf4 4.2.13 h3ca952b_2 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
hdf5 1.10.4 hb1b8bf9_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
heapdict 1.0.0 py37_2 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
historydict 1.2.3 py_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
holoviews 1.12.1 py_2 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
humanize 0.5.1 py37_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
icu 58.2 h9c2bf20_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
idna 2.8 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
imageio 2.5.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
importlib_metadata 0.17 py37_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
intake 0.5.1 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
intake-bluesky 0.1.0a8 2 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
intake-xarray 0.3.0 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
intel-openmp 2019.4 243 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
ipykernel 5.1.1 py37h39e3cac_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
ipympl 0.1.1 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
ipython 7.5.0 py37h39e3cac_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
ipython_genutils 0.2.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
ipywidgets 7.2.1 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jdcal 1.4.1 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jedi 0.13.3 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jeepney 0.4 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jinja2 2.10.1 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jpeg 9b h024ee3a_2 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jsonschema 3.0.1 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jupyter 1.0.0 py37_7 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jupyter_client 5.2.4 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jupyter_console 6.0.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jupyter_core 4.4.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jupyterlab 0.35.5 py37hf63ae98_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
jupyterlab_server 0.2.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
kafka-python 1.4.2 py_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
kazoo 2.6.1 py_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
keyring 18.0.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
kiwisolver 1.1.0 py37he6710b0_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
krb5 1.16.1 h173b8e3_7 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libcurl 7.64.1 h20c2e04_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libedit 3.1.20181209 hc058e9b_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libffi 3.2.1 hd88cf55_4 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libgcc-ng 8.2.0 hdf63c60_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libgcrypt 1.8.4 h7b6447c_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libgfortran-ng 7.3.0 hdf63c60_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libgpg-error 1.32 hf484d3e_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libgsasl 1.8.0 h7b6447c_3 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libnetcdf 4.6.1 h11d0813_2 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libntlm 1.5 h7b6447c_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libopus 1.3 h7b6447c_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libpng 1.6.37 hbc83047_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
librdkafka 1.0.1 0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
libsodium 1.0.16 h1bed415_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libssh2 1.8.2 h1ba5d50_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libstdcxx-ng 8.2.0 hdf63c60_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libtiff 4.0.10 h2733197_2 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libuuid 1.0.3 h1bed415_2 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libvpx 1.7.0 h439df22_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libxcb 1.13 h1bed415_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
libxml2 2.9.9 he19cac6_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
lmfit 0.9.9 pyh5ca1d4c_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
locket 0.2.0 py37_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
lz4-c 1.8.1.2 h14c3975_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
markupsafe 1.1.1 py37h7b6447c_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
matplotlib 3.1.0 py37h5429711_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
mccabe 0.6.1 py37_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
mistune 0.8.4 py37h7b6447c_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
mkl 2019.4 243 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
mkl_fft 1.0.12 py37ha843d7b_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
mkl_random 1.0.2 py37hd81dba3_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
mongoquery 1.1.0 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
monotonic 1.5 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
more-itertools 7.0.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
mpc 1.1.0 h10f8cd9_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
mpfr 4.0.1 hdf1c602_3 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
mpi 1.0 openmpi https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
mpi4py 3.0.0 py37_openmpi_1004 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
mpl-scatter-density 0.5 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
mpmath 1.1.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
msgpack-numpy 0.4.4.2 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
msgpack-python 0.6.1 py37hfd86e86_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
nbconvert 5.5.0 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
nbformat 4.4.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
ncurses 6.1 he6710b0_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
netcdf4 1.4.2 py37h808af73_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
netifaces 0.10.7 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
networkx 2.3 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
nodejs 10.13.0 he6710b0_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
notebook 5.7.8 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
nslsii 0.0.10 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
numcodecs 0.5.4 py37he6710b0_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
numpy 1.16.4 py37h7e9f1db_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
numpy-base 1.16.4 py37hde5b4d6_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
olefile 0.46 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
openmpi 3.1.1 1000 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
openpyxl 2.6.2 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
openssl 1.1.1 h7b6447c_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
ophyd 1.3.3 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
oscars 2.1.8 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
packaging 19.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pandas 0.24.2 py37he6710b0_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pandoc 2.2.3.2 0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pandocfilters 1.4.2 py37_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pango 1.42.4 h049681c_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
param 1.9.0 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
parso 0.4.0 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
partd 0.3.10 py37_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pcre 8.43 he6710b0_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
peakutils 1.1.1 py_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
pexpect 4.7.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pickleshare 0.7.5 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pillow 6.0.0 py37h34e0f95_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pims 0.4.1 py_1 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
pip 19.1.1 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pixman 0.38.0 h7b6447c_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
plotly 3.9.0 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pluggy 0.12.0 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
prettytable 0.7.2 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
prometheus_client 0.6.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
prompt_toolkit 2.0.9 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
psutil 5.6.2 py37h7b6447c_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
ptyprocess 0.6.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
py 1.8.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pycodestyle 2.5.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pycparser 2.19 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pyepics 3.3.0 py37_1 https://conda.nsls2.bnl.gov/conda/overrides
pyfftw 0.11.1 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
pyflakes 2.1.1 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pygments 2.4.2 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pykafka 2.8.0 py37_1000 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
pymongo 3.7.2 py37he6710b0_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pyolog 4.4.2 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
pyopengl 3.1.1a1 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pyopenssl 19.0.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pyparsing 2.4.0 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pyqt 5.9.2 py37h22d08a2_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pyrsistent 0.14.11 py37h7b6447c_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pyserial 3.4 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pysocks 1.7.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pytest 4.6.2 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pytest-arraydiff 0.3 py37h39e3cac_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pytest-astropy 0.5.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pytest-doctestplus 0.3.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pytest-openfiles 0.3.2 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pytest-remotedata 0.3.1 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
python 3.7.3 h0371630_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
python-confluent-kafka 1.0.0 py37_1002 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
python-dateutil 2.8.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
python-graphviz 0.10.1 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
python-snappy 0.5.4 py37he6710b0_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pytz 2019.1 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pyviz_comms 0.7.2 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pywavelets 1.0.3 py37hdd07704_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pyyaml 5.1 py37h7b6447c_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
pyzmq 18.0.0 py37he6710b0_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
qt 5.9.7 h5867ecd_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
qtconsole 4.5.1 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
qtpy 1.7.1 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
readline 7.0 h7b6447c_5 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
requests 2.22.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
retrying 1.3.3 py37_2 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
ruamel_yaml 0.15.46 py37h14c3975_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
scikit-beam 0.0.14 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
scikit-image 0.15.0 py37he6710b0_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
scipy 1.2.1 py37h7c811a0_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
secretstorage 3.1.1 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
send2trash 1.5.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
setuptools 41.0.1 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
sip 4.19.13 py37he6710b0_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
six 1.12.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
slicerator 0.9.8 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
snappy 1.1.7 hbae5bb6_3 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
sortedcontainers 2.1.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
sqlite 3.28.0 h7b6447c_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
suitcase-jsonl 0.1.1 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
suitcase-utils 0.1.1 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
super_state_machine 1.0 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
sympy 1.4 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
tabulate 0.8.3 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
tblib 1.4.0 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
terminado 0.8.2 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
testpath 0.4.2 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
tifffile 0.15.1 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
tk 8.6.8 hbc83047_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
toolz 0.9.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
tornado 4.5.3 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
tqdm 4.31.1 py37_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
traitlets 4.3.2 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
tzlocal 1.5.1 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
ujson 1.35 py37h14c3975_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
urllib3 1.24.2 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
wcwidth 0.1.7 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
webencodings 0.5.1 py37_1 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
wheel 0.33.4 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
widgetsnbextension 3.4.2 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
xarray 0.12.1 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
xlrd 1.2.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
xlwt 1.3.0 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
xray-vision 0.0.9 py37_0 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
xraylib 3.3.0 py37_1 https://conda.nsls2.bnl.gov/conda/nsls-ii-2019C3.0
xz 5.2.4 h14c3975_4 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
yaml 0.1.7 had09818_2 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
zarr 2.2.0 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
zeromq 4.3.1 he6710b0_3 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
zict 0.1.4 py37_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
zipp 0.5.1 py_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
zlib 1.2.11 h7b6447c_3 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
zstd 1.3.7 h0b5b093_0 https://conda.nsls2.bnl.gov/conda/defaults-2019C3.0
attn @danielballan
Deployment 2020-2.0 checklist
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
bsuiremotely (does it touch any hardware?) - usegit grep .putorgit grep caput
- Check if it's safe to start
- 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
- 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 aDevice, or withyield from bps.read()if in a plan -
history.sqliteissue - see https://blueskyproject.io/bluesky/metadata.html#persistence-between-sessions - potential issue with images in databroker V2
- Replace
- 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)
fix centroid mode ADCompVision plugin ROI for low mag camera
If a scan doesn't get aborted cleanly the Array Port for the ADCompVision plugin gets stuck on an ROI that doesn't make sense. We need to specify the ROI in stage_sigs for the "centroid" low mag cam mode to prevent errors on subsequent scans.
stack trace indicating where check_value throws an exception on attempted move:
File "/nsls2/data/amx/shared/config/bluesky/profile_collection/startup/97-plan_development.py", line 166, in align_centroid
yield from move_centroid_inner(n_steps)
File "/nsls2/data/amx/shared/config/bluesky/profile_collection/startup/97-plan_development.py", line 162, in move_centroid_inner
yield from bps.mvr(x_axis, delta_x)
File "/nsls2/conda/envs/2023-1.0-py310/lib/python3.10/site-packages/bluesky/plan_stubs.py", line 300, in mvr
return (yield from inner_mvr())
File "/nsls2/conda/envs/2023-1.0-py310/lib/python3.10/site-packages/bluesky/utils/__init__.py", line 1147, in dec_inner
return (yield from plan)
File "/nsls2/conda/envs/2023-1.0-py310/lib/python3.10/site-packages/bluesky/preprocessors.py", line 1075, in relative_set_wrapper
return (yield from plan)
File "/nsls2/conda/envs/2023-1.0-py310/lib/python3.10/site-packages/bluesky/preprocessors.py", line 245, in msg_mutator
ret = yield msg
File "/nsls2/conda/envs/2023-1.0-py310/lib/python3.10/site-packages/bluesky/preprocessors.py", line 195, in plan_mutator
inner_ret = yield msg
File "/nsls2/conda/envs/2023-1.0-py310/lib/python3.10/site-packages/bluesky/preprocessors.py", line 195, in plan_mutator
inner_ret = yield msg
File "/nsls2/conda/envs/2023-1.0-py310/lib/python3.10/site-packages/bluesky/preprocessors.py", line 195, in plan_mutator
inner_ret = yield msg
[Previous line repeated 1 more time]
File "/nsls2/conda/envs/2023-1.0-py310/lib/python3.10/site-packages/bluesky/run_engine.py", line 1583, in _run
new_response = await coro(msg)
File "/nsls2/conda/envs/2023-1.0-py310/lib/python3.10/site-packages/bluesky/run_engine.py", line 2088, in _set
ret = obj.set(*msg.args, **kwargs)
File "/nsls2/conda/envs/2023-1.0-py310/lib/python3.10/site-packages/ophyd/positioner.py", line 92, in set
return self.move(new_position, wait=wait, moved_cb=moved_cb, timeout=timeout)
File "/nsls2/conda/envs/2023-1.0-py310/lib/python3.10/site-packages/ophyd/utils/epics_pvs.py", line 202, in wrapper
return fcn(self, *args, **kwargs)
File "/nsls2/conda/envs/2023-1.0-py310/lib/python3.10/site-packages/ophyd/epics_motor.py", line 179, in move
status = super().move(position, **kwargs)
File "/nsls2/conda/envs/2023-1.0-py310/lib/python3.10/site-packages/ophyd/positioner.py", line 195, in move
self.check_value(position)
File "/nsls2/conda/envs/2023-1.0-py310/lib/python3.10/site-packages/ophyd/epics_motor.py", line 248, in check_value
self.user_setpoint.check_value(pos)
File "/nsls2/conda/envs/2023-1.0-py310/lib/python3.10/site-packages/ophyd/signal.py", line 1861, in check_value
raise LimitError(
ophyd.utils.errors.LimitError: gonio_gx_user_setpoint: value nan outside of range: [-16000.0, 16000.0]
[I 2023-03-13 06:30:58,069.069 IPKernelApp ipkernel:448] Exception in execute request:
LimitError: gonio_gx_user_setpoint: value nan outside of range: [-16000.0, 16000.0]
Filestore database name is wrong
database should be 'filestore' not 27017
https://github.com/NSLS-II-AMX/profile_collection/blob/master/startup/01-bluesky.py#L46
Make rotation axis alignment plan more robust under varied lighting
Rotation axis alignment plan occasionally fails to determine the true rotation axis and requires 2-3 attempts to bring the cross hairs into +/- 2 um of true rotation axis. This failure may be due to new lighting conditions around the sample position following installation of front light, holey mirror realignment, microscope focus, or some combination of these factors.
A more robust algorithm is required, things to try:
- Use canny edge -> contour detection instead of AD stats max pixels
- take more measurements for least squares regression
- fly scan pin position for focus scan
- disable mpeg server during scan to avoid disrupting LSDC camera loops
Bluesky deployment 2022-04-20
see also slack discussion:
https://nsls2.slack.com/archives/C01QJ5Y9UV8/p1650462398989789
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