ipython-s6bm

User account for 6-BM-A using ipython

Installation of BlueSky control system

Install with conda

Install bluesky core packages first

As of 04/17/2019, python3.6 is the prefered version for running BlueSky.

conda install bluesky -c lightsource2-tag

then the apstools dependencies

conda install pyresttable -c prjemian

followed by installing apstools

conda install apstools -c aps-anl-dev

Before installing the metapackage jupyter, it is recommended to pin the package tornado to an older version until BlueSky dev team solve the related issue#1062. To do so, create a file named pinned under the directory CONDA_INSTALL_DIR/env/ENVNAME/conda-meta with the following content:

tornado<5

Then install jupyter and matplotlib with

conda install jupyter matplotlib

For update BlueSky packages, one can always do update with explicit channel name

conda update bluesky -c lightsource2-tag

Alternatively, a package configuration file .condarc can be placed under HOME (single env) or CONDA_INSTALL_DIR/envs/ENV_NAME (multi-env) with the following content

channels:
    - lightsource2-tag  
    - lightsource2-dev  
    - aps-anl-tag  
    - aps-anl-dev  
    - prjemian  
    - defaults  
    - conda-forge

NOTE: This is the recommended way to install BlueSky and associated dependencies.

Install with pip

Install bluesky and apstools with pip

pip install -U pip
pip install boltons mongoquery pims pyepics pyRestTable tzlocal jupyter suitcase matplotlib
pip install git+https://github.com/Nikea/historydict#egg=historydict \
            git+https://github.com/NSLS-II/amostra#egg=amostra \
            git+https://github.com/NSLS-II/bluesky#egg=bluesky \
            git+https://github.com/NSLS-II/databroker#egg=databroker \
            git+https://github.com/NSLS-II/doct#egg=doct \
            git+https://github.com/NSLS-II/event-model#egg=event_model \
            git+https://github.com/NSLS-II/ophyd#egg=ophyd \
            git+https://github.com/NSLS-II/hklpy#egg=hklpy
pip install apstools

Similarly, the package tornado need to be downgrade below 5.0 to avoid the runtime error.

Config Meta-data handler (MongoDB)

Copy the configuration file configs/mongodb_config.yml to HOME/.config/databroker/mongodb_config.yml to enable meta-data handler backed by a MongoDB server.

The entry host need to be changed to the IP of the machine that hosts the MongoDB service.

Ipython based control

Profile

The environment var IPYTHONDIR needs to be set where the profile folder is, or simply create symbolic link of the deisred profile to ~/.ipython/, which is the default location to store all IPython profiles.

>> export IPYTHONDIR=ipython_profiles/

Startup

Issue the following command in the terminal to run IPython with pre-configured environment for Tomo-characterization at 6-BM-A:

>> ipython --profile=s6bm