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prjemian committed Apr 28, 2024
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1 change: 1 addition & 0 deletions bluesky/instrument/framework/initialize.py
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Expand Up @@ -56,6 +56,7 @@ def get_md_path():
logger.info("RunEngine metadata saved in directory: %s", str(path))
return str(path)


# Set up a RunEngine and use metadata backed PersistentDict
RE = RunEngine({})
RE.md = PersistentDict(get_md_path())
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1 change: 1 addition & 0 deletions docs/requirements.txt
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Expand Up @@ -9,4 +9,5 @@ pydata-sphinx-theme
pygments >=2.12
pygments-ipython-console
sphinx <6
sphinx-design
sphinx-tabs
3 changes: 3 additions & 0 deletions docs/source/conf.py
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Expand Up @@ -26,8 +26,10 @@
sphinx.ext.viewcode
nbsphinx
myst_parser
sphinx_design
""".split()
extensions.append("sphinx_tabs.tabs") # issue #129: this must be last
myst_enable_extensions = ["colon_fence"]

templates_path = ["_templates"]
source_suffix = ".rst .md".split()
Expand All @@ -43,6 +45,7 @@

html_static_path = ["_static"]
html_theme = "pydata_sphinx_theme"
html_title = project

autodoc_mock_imports = """
bluesky
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2 changes: 1 addition & 1 deletion docs/source/howto/index.rst
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Expand Up @@ -15,7 +15,7 @@ How-To Guides
How-to guides are directions that take the reader through the steps required to
solve a real-world problem. How-to guides are *goal-oriented*.
Tutorials often involve more depth than HowTo guides.
(Tutorials often involve more depth than HowTo guides.)

.. toctree::
:maxdepth: 2
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117 changes: 47 additions & 70 deletions docs/source/index.rst
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@@ -1,14 +1,6 @@
APS Bluesky Training
====================

The APS Bluesky Training repository [#]_ demonstrates use of the Bluesky
framework at a typical APS beamline. Its ``bluesky/`` directory [#]_ also
serves as a template for new beamline installations.

.. [#] repository: https://github.com/BCDA-APS/bluesky_training
.. [#] ``bluesky/`` directory: new beamline
`template <https://github.com/BCDA-APS/bluesky_training/tree/main/bluesky>`__
.. for documentation authors:
Documentation may be created in restructured text (.rst), markdown (.md)
of Jupyter notebooks (.ipynb). Add new documents to the appropriate folder
Expand All @@ -17,79 +9,64 @@ serves as a template for new beamline installations.
files which do not start with a "_" are added explicitly to the toctree in
the `index.rst` file of that folder.
In addition to these highlights, additional content is available in each section
of the documentation.

- :ref:`howto`
- `Bluesky Cheat Sheet <howto/bluesky_cheat_sheet.md>`_:
First Steps to use Bluesky after installation.
- `Plot x, y data from a databroker run <https://bcda-aps.github.io/bluesky_training/howto/_plot_x_y_databroker.html>`_
- `Working with data after the measurement <https://bcda-aps.github.io/bluesky_training/howto/_after_measurement.html>`_
- :ref:`instrument`
- `Installation Guide <https://bcda-aps.github.io/bluesky_training/instrument/_install_new_instrument.html>`_:
Install the components of the Bluesky framework.
- `Template <https://github.com/BCDA-APS/bluesky_training/tree/main/bluesky/instrument>`_
for a bluesky ``instrument``
- `Instrument Package Guide <instrument/guide.md>`__:
Building the ``instrument`` package.
- `About the instrument package <file:///home/prjemian/Documents/projects/BCDA-APS/bluesky_training/docs/build/html/instrument/describe_instrument.html>`_
- :ref:`examples`
- `XAFS scan <https://bcda-aps.github.io/bluesky_training/example/_xafs_scan.html>`_ : Example multi-segment XAFS scan.
- :ref:`Tutorials and Lessons <tutorials>`
- `Hello, World <https://bcda-aps.github.io/bluesky_training/tutor/hello_world.html>`_
- `Connect Bluesky with EPICS <https://bcda-aps.github.io/bluesky_training/tutor/connect_epics.html>`_
- :ref:`reference`
- `bluesky training wiki <https://github.com/BCDA-APS/bluesky_training/wiki>`_:
Includes list of APS instruments
- `General Bluesky Documentation (for APS) <https://wiki-ext.aps.anl.gov/blc/index.php?title=Controls_Software_Documentation#Bluesky>`_
This APS Bluesky Training repository demonstrates use of the Bluesky framework
at a typical APS beamline.

.. icons: https://fonts.google.com/icons
.. grid:: 2

.. grid-item-card:: :material-regular:`list_alt;3em` :ref:`instrument.install`

Install a new ``bluesky`` directory and get started.

.. grid-item-card:: :material-regular:`precision_manufacturing;3em` :ref:`instrument`

Customize your control system with Bluesky.

.. grid-item-card:: :material-regular:`straight;3em` :ref:`examples`

See real-case scenarios of the Bluesky framework in action.

.. grid-item-card:: :material-regular:`alt_route;3em` :ref:`howto`

Step-by-step instructions tailored for you to master specific Bluesky tasks.

.. grid-item-card:: :material-regular:`school;3em` :ref:`tutorials`

Step-by-step guides to help you get started and learn through doing.

.. grid-item-card:: :material-regular:`precision_manufacturing;3em` `Template <https://github.com/BCDA-APS/bluesky_training/tree/main/bluesky>`_

The pristine model of your ``bluesky`` directory.

.. grid-item-card:: :material-regular:`question_mark;3em` :ref:`FAQ`

Some commonly-asked questions concerning Bluesky.

.. grid-item-card:: :material-regular:`collections_bookmark;3em` :ref:`reference`

Learn more about Bluesky.

.. toctree::
:maxdepth: 1
:hidden:

howto/index
instrument/index
example/index
howto/index
tutor/index
reference/index
changes

Other resources
==================

* apstools
* home: https://bcda-aps.github.io/apstools/latest/
* source: https://github.com/BCDA-APS/apstools
* PyPI: https://pypi.org/project/apstools/
* conda: https://anaconda.org/conda-forge/apstools
* Bluesky framework
* home: https://blueskyproject.io
* source: https://github.com/bluesky
* conda: all packages available on conda-forge channel
* MongoDB
* home: https://www.mongodb.com/
* PyDM
* home: https://slaclab.github.io/pydm/
* source: https://github.com/slaclab/pydm
* PyPI: https://pypi.org/project/pydm/
* conda: https://anaconda.org/conda-forge/pydm
* PyEPICS
* home: https://pyepics.github.io/pyepics/
* source: https://github.com/pyepics/pyepics
* PyPI: https://pypi.org/project/pyepics/
* conda: https://anaconda.org/conda-forge/pyepics
* APS Data Management
* home: https://confluence.aps.anl.gov/display/DMGT/

Revision History
==================

:ref:`History of code changes <changes>`

Index
==================

* :ref:`genindex`
About
-----

:home: https://bcda-aps.github.io/bluesky_training/
:source: https://github.com/bcda-aps/bluesky_training
:published: |today|
:revisions: :ref:`History of code changes <changes>`
:index: :ref:`genindex`

.. * :ref:`modindex`
.. * :ref:`search`
46 changes: 46 additions & 0 deletions docs/source/instrument/_activate_environment.rst
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.. _instrument.activate_bluesky_conda_environment:

Activate the bluesky conda environment
--------------------------------------

.. note:: Consider merging with :ref:`reference.create_bluesky_enviroment`

.. TODO: instead of dropdown, make a paragraph that references the extra help page
If you need to install a bluesky conda environment, see these instruction...
See these instructions (link) if you need to create a bluesky conda environment.
MAKE SURE THE TITLE names match. Use :ref: anchors.
.. raw:: html

<details>
<summary>How to create a conda environment for bluesky?</summary>

See <a href="https://bcda-aps.github.io/bluesky_training/reference/_create_conda_env.html">here</a>.

</details>

To use bluesky, you first need to activate the bluesky conda environment:

.. raw:: html

<pre>
$ <b>conda activate bluesky_2023_3</b>
</pre>

The prompt changes to display ``(bluesky_2023_3)`` .

.. raw:: html

<details>
<summary>How to create an alias to activate the bluesky environment?</summary>

See <a href="https://bcda-aps.github.io/bluesky_training/reference/_create_conda_env.html#create-an-alias-to-activate-the-bluesky-environment">here</a>.
</details>



This activation will remain in effect for the duration of the session
(*i.e.* as long as the terminal stays open), unless you activate a
different environment or deactivate it using the ``conda deactivate``
command.

142 changes: 0 additions & 142 deletions docs/source/instrument/_configure_bluesky_instrument.md

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