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Install Bluesky packages

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Pete R Jemian edited this page Feb 17, 2021 · 25 revisions

Install Bluesky Packages

revision: 2021-02-17

(Linux) Instructions to install bluesky packages into a new conda environment. Also short tests are shown for key packages.

Overview

This describes how to install the Python packages needed to run the Bluesky Framework at the Advanced Photon Source. The packages will be installed in a conda environment that is marked with a version corresponding to the APS Run Cycle for which is used. The environment setup file is configured with package and version requirements for the components to be used.

Comparable environment files for Windows and Mac OSX also may be available. Check the repository directory for availability. For each of these OS platforms, run the same conda env create -f env_file.yml from a bash shell to create the conda environment.

More information about conda environments

Recommendations

  • Use a conda environment to:
    • allow local package customizations
    • maintain stability when/if /APSshare is updated
  • Use base environment: (/APSshare/miniconda)
    • bare minimum number of packages
    • intended for use this way
    • faster then /APSshare/anaconda3/x86_64 to do administrative work
  • Define CONDA_ENVIRONMENT environment variable in ~/.bash_aliases
  • Note: /APSshare/anaconda3/Bluesky requires no installation but cannot be customized by end users.

Activate base environment

source /APSshare/miniconda/x86_64/bin/activate

Define environment vairable

export CONDA_ENVIRONMENT=bluesky_2021_1

Installation

After activating the base environment , create the Bluesky environment following these steps:

Use the bash shell (if not already using it):

bash

Download file environment_2021_1.yml to a temporary directory (such as /tmp on Linux). You only need this file once, to create the conda environment:

cd /tmp
wget https://raw.githubusercontent.com/BCDA-APS/use_bluesky/main/python_installation/environment_2021_1.yml

The environment file is a text file in YAML format that describes the packages (and versions) that are needed.

Run the installer (takes ~10 minutes or so to finish, usually):

conda env create -f /tmp/environment_2021_1.yml

This will create the new conda environment bluesky_2021_1.

Testing

EPICS Test PV

This is the EPICS PV for the APS Storage Ring Current (the single quotes are needed by the python tests below):

export TEST_PV="'S:SRcurrentAI'"

If you have caget as a command line tool, then check the PV without any python code:

(bluesky_2021_1) jemian@wow /tmp $ caget S:SRcurrentAI
S:SRcurrentAI                  102.255

Test EPICS Support

This shows a test that the pyepics package has been installed, loads in python, connects with an expected PV, and prints its value.

(bluesky_2021_1) jemian@wow /tmp $ export TEST_PV="'S:SRcurrentAI'"
(bluesky_2021_1) jemian@wow /tmp $ python -c "import epics; print(epics.caget(${TEST_PV}))"
102.38126717909132

NOTE: In Bluesky, we don't call pyepics directly but rather use ophyd to manage the use of pyepics..

Test Bluesky Packages

Test ophyd

Same test, now using ophyd:

(bluesky_2021_1) jemian@wow /tmp $ python -c "import ophyd; pv= ophyd.EpicsSignal(${TEST_PV}, name='pv'); print(pv.get())"
101.78977005909132

Another ophyd test, showing more information:

(bluesky_2021_1) jemian@wow /tmp $ python -c "import ophyd; pv= ophyd.EpicsSignal(${TEST_PV}, name='pv'); pv.wait_for_connection(); print(pv.read())"
{'pv': {'value': 101.81930405909134, 'timestamp': 1613588453.43987}}

Test apstools

Reformat that information with the apstools package. (The test command has become more complex so we'll build it by parts.)

(bluesky_2021_1) jemian@wow /tmp $ cmd="python -c \""
(bluesky_2021_1) jemian@wow /tmp $ cmd+="from apstools.utils import listdevice; "
(bluesky_2021_1) jemian@wow /tmp $ cmd+="import ophyd; "
(bluesky_2021_1) jemian@wow /tmp $ cmd+="pv= ophyd.EpicsSignal(${TEST_PV}, name='pv'); "
(bluesky_2021_1) jemian@wow /tmp $ cmd+="pv.wait_for_connection(); "
(bluesky_2021_1) jemian@wow /tmp $ cmd+="listdevice(pv)"
(bluesky_2021_1) jemian@wow /tmp $ cmd+=\"
(bluesky_2021_1) jemian@wow /tmp $ echo $cmd
python -c "from apstools.utils import listdevice; import ophyd; pv= ophyd.EpicsSignal('S:SRcurrentAI', name='pv'); pv.wait_for_connection(); listdevice(pv)"
(bluesky_2021_1) jemian@wow /tmp $ eval $cmd
==== ================== ==========================
name value              timestamp
==== ================== ==========================
pv   102.31602881909133 2021-02-17 13:09:32.439845
==== ================== ==========================

If you are at an APS beamline, then show additional information about the storage ring:

(bluesky_2021_1) jemian@wow /tmp $ cmd="python -c \""
(bluesky_2021_1) jemian@wow /tmp $ cmd+="from apstools.utils import listdevice; "
(bluesky_2021_1) jemian@wow /tmp $ cmd+="from apstools.devices import ApsMachineParametersDevice; "
(bluesky_2021_1) jemian@wow /tmp $ cmd+="aps = ApsMachineParametersDevice(name='aps'); "
(bluesky_2021_1) jemian@wow /tmp $ cmd+="aps.wait_for_connection(); "
(bluesky_2021_1) jemian@wow /tmp $ cmd+="listdevice(aps)"
(bluesky_2021_1) jemian@wow /tmp $ cmd+=\"
(bluesky_2021_1) jemian@wow /tmp $ echo $cmd
python -c "from apstools.utils import listdevice; from apstools.devices import ApsMachineParametersDevice; aps = ApsMachineParametersDevice(name='aps'); aps.wait_for_connection(); listdevice(aps)"
(bluesky_2021_1) jemian@wow /tmp $ eval $cmd
========================================== ===================== ==========================
name                                       value                 timestamp
========================================== ===================== ==========================
aps_current                                102.03240813909133    2021-02-17 13:24:31.439878
aps_lifetime                               9.16753387531647      2021-02-17 13:24:31.737008
aps_aps_cycle                              2021-1                2021-02-17 13:24:31.863255
aps_machine_status                         USER OPERATIONS       2021-02-16 08:00:01.341010
aps_operating_mode                         Delivered Beam        2021-02-16 15:16:39.600022
aps_shutter_permit                         PERMIT                2021-02-16 15:16:39.601252
aps_fill_number                            7.0                   2021-02-16 15:16:39.600275
aps_orbit_correction                       0.0                   2021-01-25 15:01:30.180411
aps_global_feedback                        On                    2021-02-16 15:06:38.076138
aps_global_feedback_h                      On                    2021-02-17 13:24:31.423398
aps_global_feedback_v                      On                    2021-02-17 13:24:31.423398
aps_operator_messages_operators            Grodecki, Berg        2021-02-17 07:05:06.113157
aps_operator_messages_floor_coordinator    Clay White (2-0101)   2021-02-17 07:51:19.871657
aps_operator_messages_fill_pattern         0+24x1 RHB            2021-01-30 23:37:24.294902
aps_operator_messages_last_problem_message Top-up resumed @11:53 2021-02-17 12:37:16.681556
aps_operator_messages_last_trip_message    L1 VSWR trip          2021-02-17 12:37:16.680389
aps_operator_messages_message6                                   2021-02-17 12:37:31.121230
aps_operator_messages_message7                                   2021-01-21 18:01:22.341254
aps_operator_messages_message8                                   2021-01-21 18:01:18.413236
========================================== ===================== ==========================

Test hklpy

Test diffractometer support package 'hklpy' is installed:

(bluesky_2021_1) jemian@wow /tmp $ python -c "import gi; gi.require_version('Hkl', '5.0'); import hkl.diffract ; print(hkl.diffract.Diffractometer.__doc__)"
Diffractometer pseudopositioner

    .. autosummary::

        ~calc
        ~engine
        ~forward
        ~inverse
        ~_energy_changed
        ~_update_calc_energy

    This has a corresponding calculation engine from **hklpy** that does
    forward and inverse calculations.

    If instantiating a specific diffractometer class such as `E4C`, `E6C`,
    neither the `calc_inst` or the `calc_kw` parameters are required.

    However, there is the option to either pass in a calculation
    instance (with `calc_inst`) or keywords for the default calculation
    class (using `calc_kw`) to instantiate a new one.

    Parameters
    ----------
    prefix : str
        PV prefix for all components
    calc_kw : dict, optional
        Initializer arguments for the calc class
    decision_fcn : callable, optional
        The decision function to use when multiple solutions exist for a given
        forward calculation. Defaults to arbitrarily picking the first
        solution.
    read_attrs : list, optional
        Read attributes default to all pseudo and real positioners
    configuration_attrs : list, optional
        Defaults to the UB matrix and energy
    parent : Device, optional
        Parent device
    name : str, optional
        Device name

    Attributes
    ----------
    calc_class : sub-class of CalcRecip
        Reciprocal calculation class used with this diffractometer.
        If None (as in `hkl.diffract.Diffractometer`, `calc_inst` must be
        specified upon initialization.

    See Also
    --------
    :class:`hkl.diffract.E4CH`
    :class:`hkl.diffract.E4CV`
    :class:`hkl.diffract.E6C`
    :class:`hkl.diffract.K4CV`
    :class:`hkl.diffract.K6C`
    :class:`hkl.diffract.Med2p3`
    :class:`hkl.diffract.Petra3_p09_eh2`
    :class:`hkl.diffract.SoleilMars`
    :class:`hkl.diffract.SoleilSiriusKappa`
    :class:`hkl.diffract.SoleilSiriusTurret`
    :class:`hkl.diffract.SoleilSixs`
    :class:`hkl.diffract.SoleilSixsMed1p2`
    :class:`hkl.diffract.SoleilSixsMed2p2`
    :class:`hkl.diffract.TwoC`
    :class:`hkl.diffract.Zaxis`

Remove conda environment

In case you want to remove the conda environment (such as for reinstall):

conda deactivate
conda env remove -n ${CONDA_ENVIRONMENT}
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