Merge branch 'main' into 169-beamline

README.md

@@ -1,147 +1,20 @@
 # README.md
 
-This repository, via [Jupyter](https://jupyter.org/) notebooks, demonstrates use
-of the Bluesky framework at a typical beamline scenario for a BCDA-sponsored
-class.
+This repository provides training materials for [APS](https://www.aps.anl.gov)
+beamlines to use the [Bluesky](https://blueskyproject.io) framework.
+
+- [HowTo guides, tutorials, & references](https://bcda-aps.github.io/bluesky_training/)
+  demonstrating use of the Bluesky framework at a typical beamline.
+- a [template](./bluesky/) for beamlines to configure their instrument
+- a [list of APS instrument](https://github.com/BCDA-APS/bluesky_training/wiki/)
+  repositories
 
 Unit Tests | License | GH tag
 --- | --- | ---
 [![Unit Tests](https://github.com/BCDA-APS/bluesky_training/workflows/Unit%20Tests/badge.svg)](https://github.com/BCDA-APS/bluesky_training/actions/workflows/unit_tests.yml) | [![license: ANL](https://img.shields.io/badge/license-ANL-brightgreen)](/LICENSE.txt) | [![tag](https://img.shields.io/github/tag/BCDA-APS/bluesky_training.svg)](https://github.com/BCDA-APS/bluesky_training/tags)
 
-<!-- consider this new structure
-
-      Introductory
-         Bluesky Hello, World!
-         Connect with EPICS
-         APS 101
-      Basic hardware configuration and measurement
-         scaler
-         motor
-         step scan
-      Measurement using the instrument package
-         area detector
-         count a scaler
-         watch a temperature
-         lineup 1-D peak
-         locate 2-D peak on area detector image
-         custom bluesky plans
-         bluesky for SPEC users
-      After the measurement: processing, reduction, analysis, export or copy data
-      Training
-      Instrument template
-      Conda
-      Version control
-      References
-
-Also take note of
+<!-- take note of
 
    * https://diataxis.fr/
    * https://stackoverflow.com/questions/42843288/is-there-any-way-to-make-markdown-tables-sortable
 -->
-
-- [README.md](#readmemd)
-  - [Introductory](#introductory)
-  - [Basic hardware configuration and measurement](#basic-hardware-configuration-and-measurement)
-    - [Hardware Configuration - Advanced](#hardware-configuration---advanced)
-  - [Measurement using the `instrument` package](#measurement-using-the-instrument-package)
-    - [Measurement - Advanced](#measurement---advanced)
-  - [Post-measurement (such as Analysis)](#post-measurement-such-as-analysis)
-    - [Data Processing, Reduction, and/or Analysis](#data-processing-reduction-andor-analysis)
-  - [Review](#review)
-  - [Install as Bluesky `instrument` package](#install-as-bluesky-instrument-package)
-
-name | URL
---- | ---
-Documentation | https://BCDA-APS.github.io/bluesky_training
-Instrument template | https://github.com/BCDA-APS/bluesky_training/tree/main/bluesky/instrument
-APS instruments | https://github.com/BCDA-APS/bluesky_training/wiki/
-Bluesky Framework | https://blueskyproject.io/
-bluesky | https://blueskyproject.io/bluesky
-ophyd | https://blueskyproject.io/ophyd
-databroker | https://blueskyproject.io/databroker
-databroker-pack | https://blueskyproject.io/databroker-pack
-apstools | https://BCDA-APS.github.io/apstools
-APS Data Management | https://confluence.aps.anl.gov/display/DMGT/Infrastructure
-
-## Introductory
-
-The best introduction to Bluesky might come through a _Hello, World!_ example
-and then an example connecting EPICS to Bluesky.
-
-- [Bluesky *Hello, World!*](https://bcda-aps.github.io/bluesky_training/tutor/hello_world.html)
-- [Connect with EPICS](https://bcda-aps.github.io/bluesky_training/tutor/connect_epics.html)
-
-These notebooks, and the notebooks in the next section, comprise the **_APS
-Bluesky 101_** introductory course.  You can review the [presenter's
-notes](https://bcda-aps.github.io/bluesky_training/tutor/_aps101_notes.html) for
-details on that course.
-
-## Basic hardware configuration and measurement
-
-These notebooks demonstrate the basics of hardware configuration
-([ophyd](https://blueskyproject.io/ophyd)) and custom measurement plans
-([bluesky](https://blueskyproject.io/bluesky)), in addition to measurement
-activities.
-
-1. [scaler](https://bcda-aps.github.io/bluesky_training/tutor/_basic_a.html)
-1. [motor](https://bcda-aps.github.io/bluesky_training/tutor/_basic_b.html)
-1. [step scan](https://bcda-aps.github.io/bluesky_training/tutor/_basic_c.html)
-
-### Hardware Configuration - Advanced
-
-- [Run a Linux command as an `ophyd.Device`](https://bcda-aps.github.io/bluesky_training/howto/_doodle.html)
-- [Store Images, Darks, and Flats frames separately in HDF5 files](https://bcda-aps.github.io/bluesky_training/howto/_images_darks_flats.html)
-
-## Measurement using the `instrument` package
-
-As the configuration of a system becomes more complex, it may be easier to
-describe (and startup) by making the steps into Python package that can be
-`import`ed.  These notebooks start with an `instrument` package that is
-preconfigured to use the general purpose `gp:` IOC and the area detector `ad:`
-IOC.
-
-1. [Count the scaler](https://bcda-aps.github.io/bluesky_training/howto/_count_scaler.html)
-1. [Watch a temperature](https://bcda-aps.github.io/bluesky_training/example/_watch_temperature.html)
-1. [Lineup a 1-D peak](https://bcda-aps.github.io/bluesky_training/howto/_lineup_1d_peak.html)
-1. [Locate peak on 2-D area detector image](https://bcda-aps.github.io/bluesky_training/howto/_locate_image_peak.html)
-1. [Plot $(x,y)$ data from a databroker run](https://bcda-aps.github.io/bluesky_training/howto/_plot_x_y_databroker.html)
-1. [Custom bluesky plan](https://bcda-aps.github.io/bluesky_training/howto/_custom_plan.html)
-
-### Measurement - Advanced
-
-- [Move 2 motors with dynamic limits](https://bcda-aps.github.io/bluesky_training/howto/_dynamic_limits_2motor.html)
-  : EPICS : Demo of dynamic limit signal to avoid collision of two motors
-- [XAFS scan, multi-segment](https://bcda-aps.github.io/bluesky_training/example/_xafs_scan.html)
-  :  step scan (note: detector data is random numbers)
-
-## Post-measurement (such as Analysis)
-
-Typically, measurement data is sent to Bluesky's
-[databroker](https://blueskyproject.io/databroker) package for storage in a
-MongoDB database (or a structured set of folders) for access and analysis.
-These notebooks use data recorded previously and stored in a structured set of
-folders (created by tools from Bluesky's
-[databroker-pack](https://blueskyproject.io/databroker-pack/) package.)
-
-### Data Processing, Reduction, and/or Analysis
-
-- [Access data later, after the measurement](https://bcda-aps.github.io/bluesky_training/howto/_after_measurement.html)
-  using Data Broker
-- [Analyze a 2-D image](https://bcda-aps.github.io/bluesky_training/howto/_locate_image_peak.html)
-- [Plot $(x,y)$ data from a databroker run](https://bcda-aps.github.io/bluesky_training/howto/_plot_x_y_databroker.html)
-  using Data Broker
-
-## Review
-
-- [Command Review](https://bcda-aps.github.io/bluesky_training/tutor/_command_review.html)
-- [Overview of the `instrument` package](https://bcda-aps.github.io/bluesky_training/instrument/describe_instrument.html)
-
-## Install as Bluesky `instrument` package
-
-The [`bluesky`](https://github.com/BCDA-APS/bluesky_training/tree/main/bluesky)
-directory of this [repository](https://github.com/BCDA-APS/bluesky_training)
-serves as a template for creating a new bluesky `instrument` package.  See these
-installation
-[instructions](https://bcda-aps.github.io/bluesky_training/instrument/_install_new_instrument.html#setup-a-bluesky-instrument).
-The process to install on Mac OS and Windows is similar but support for those
-operating systems is not provided here.

bluesky/README.md

@@ -9,7 +9,7 @@ Contains:
 
 description | item(s)
 --- | ---
-Introduction | [`intro2bluesky.md`](intro2bluesky.md)
+Introduction | [`intro2bluesky.md`](https://bcda-aps.github.io/bluesky_training/reference/_intro2bluesky.html)
 IPython console startup | [`console/`](console/README.md)
 Bluesky queueserver support | [introduction](qserver.md), `*qs*`
 Instrument configuration | `instrument/`

bluesky/qserver.md

@@ -8,23 +8,23 @@ work-in-progress: *very* basic notes for now
     - [diagnostics and testing](#diagnostics-and-testing)
   - [graphical user interface](#graphical-user-interface)
 
-**IMPORTANT**:  When the queueserver starts, it **must** find only one `/.py` file in this directory and it must find `instrument/` in the same directory.  Attempts to place the qserver files in a sub directory result in `'instrument/' directory not found` as queueserver starts.
+**IMPORTANT**:  When the queueserver starts, it **must** find only one `.py` file in this directory and it must find `instrument/` in the same directory.  Attempts to place the qserver files in a sub directory result in `'instrument/' directory not found` as queueserver starts.
 
 ## Run the queuserver
 
 ### operations
 
 Run in a background screen session.
 
-`./qserver start`
+`./qserver.sh start`
 
 Stop this with
 
-`./qserver stop`
+`./qserver.sh stop`
 
 ### diagnostics and testing
 
-`./qserver run`
+`./qserver.sh run`
 
 ## graphical user interface
 
@@ -33,4 +33,5 @@ Stop this with
 - connect to the server
 - open the environment
 - add tasks to the queue
-- run the queue
+- run the queue
+- 

docs/source/howto/_bluesky_queueserver.md

@@ -20,15 +20,15 @@ from the [APS beamline data pipelines.
 
 Install `redis` package in OS (if not already installed):
 
-```bash
-sudo apt install redis
-```
+<pre>
+$ <b>sudo apt install redis</b>
+</pre>
 
 Create conda environment
 
-```bash
-conda create -y -n qserver -c conda-forge bluesky-queueserver
-```
+<pre>
+$ <b>conda create -y -n qserver -c conda-forge bluesky-queueserver</b>
+</pre>
 
 ## Start a monitor on a qserver
 
@@ -43,6 +43,8 @@ Here, the `training` catalog is subscribed to the RunEngine, in addition to a 0M
 
 <details>
 
+<pre>
+$ <b>start-re-manager --zmq-publish-console ON --databroker-config training</b>
 <pre>
 $ <b>start-re-manager --zmq-publish-console ON --databroker-config training</b>
 INFO:bluesky_queueserver.manager.manager:Starting ZMQ server at 'tcp://*:60615'