general editing + some formatting fun

docs/_static/color.css

@@ -129,6 +129,16 @@
     text-decoration: line-through;
 }
 
+.bolditalic {
+  font-weight: bold;
+  font-style: italic;
+}
+
+.smallcaps {
+  font-variant: small-caps;
+  color: #8f4800;
+}
+
 .it {
     font-style: italic;
 }

docs/automation.rst

@@ -241,7 +241,7 @@ was called :file:`mysamples`, the new BlueSky command is called
 
 .. admonition:: Future Tech!
 
-   Convert spreadsheets to Bluesky queueserver input.
+   Convert spreadsheets to Bluesky |qs| input.
 
 
 .. _sample_wheel_automation:

docs/commonchores.rst

@@ -120,7 +120,7 @@ Once the hutch is secured and you are back at the computer:
    samples: ``RE(xafs_wheel.inner())`` and ``RE(xafs_wheel.outer())``.
    For other sample holders, move the appropriate sample stages.
 
-#. To import the spreadsheet into bsui (the data acquisition program):
+#. To import the spreadsheet into |bsui| (the data acquisition program):
    ``xlsx()`` You will be presented with a list of .xlsx file choices,
    pick the correct one by number and hit :key:`Enter`. You will then be
    presented with a list of tabs in the spreadsheet file, pick the
@@ -130,7 +130,7 @@ Once the hutch is secured and you are back at the computer:
 #. The output of the ``xlsx()`` command will display the command for
    reviewing the file (the one with ``??``) and the command for
    running the measurement sequence (the one with ``RE(
-   ... )``). Check to make sure it looks like ``bsui`` correctly
+   ... )``). Check to make sure it looks like |bsui| correctly
    imported the information from the spreadsheet (you did remember to
    save the spreadsheet, yes...?), then start the measurements.
 
@@ -285,7 +285,7 @@ Filling the 25 liter LN2 dewar
    the HMI panel. Push the door open manually.
 
 #. Open main LN2 valve.  Use the button on the "06BM utilities" CSS
-   screen or at the bsui command line do ``ln2.open()``.
+   screen or at the |bsui| command line do ``ln2.open()``.
 
    .. _fig-utilities:
    .. figure::  _images/BMM_utilities.png
@@ -336,7 +336,7 @@ Filling the 25 liter LN2 dewar
    hutch.
 
 #. Close main LN2 valve.  Use the button on the "06BM utilities" CSS
-   screen or at the bsui command line do ``ln2.close()``.
+   screen or at the |bsui| command line do ``ln2.close()``.
 
 #. Press the :green:`Front Right Maglock` button. The green light should be
    on. Manually close the right hutch door.

docs/data.rst

@@ -230,7 +230,8 @@ Accessing data from the beamline computers
 Under the new data security regime, the beamline computer does not
 have normal access to your data.  This is because all users run their
 experiment as the beamline operator.  If the beamline operator |nd|
-``xf06bm`` |nd| could see data, than any could look at anyone's data.
+``xf06bm`` |nd| could see data, than any user could look at any other
+user's data.
 
 Instead, data are stored on central storage with read permission
 granted to everyone named on the user proposal.  In this way, data are
@@ -241,7 +242,7 @@ To look at your data while at the beamline, do the following
 
 + Open a terminal window.  Normally a terminal window with a white
   background is open on screen and intended for this purpose.
-  ``bsui`` is typically run from a window with a black background, so
+  |bsui| is typically run from a window with a black background, so
   the white background is meant as a visual cue indicating that it is
   the place for data access.
 
@@ -258,16 +259,16 @@ To look at your data while at the beamline, do the following
   ``2024-2`` with the cycle of your visit and ``123456`` with your
   proposal number.
 
-Athena can be launched from the command line.  The best way to do this
+|athena| can be launched from the command line.  The best way to do this
 is to type
 
 .. code-block:: bash
 
    dathena 2&>1 &
 
 at the command line.  That incantation will suppress spurious screen
-messages and put Athena into the background so you can continue using
-the command line.  From there, simply use `Athena's File menu
+messages and put |athena| into the background so you can continue using
+the command line.  From there, simply use |athena|'s `File menu
 <https://bruceravel.github.io/demeter/documents/Athena/import/index.html>`__
 to load data from your proposal folder.
 
@@ -282,3 +283,24 @@ Accessing data via Jupyter
 --------------------------
 
 .. todo:: Details needed
+
+Why is data security important?
+-------------------------------
+
+For those who have been coming to NSLS-II over the last decade, this
+new emphasis on data security might be a bit surprising.  In short,
+the new data security model is consistent with Department of Energy
+data policies.
+
+Recently, there were a pair of incidents involving accidental leaks of
+sensitive synchrotron data to unauthorized parties.  This sort of
+violation of DOE policy can have an impact on the authorization to
+operate NSLS-II as a user facility.  Safe operations of the facility
+includes data security.
+
+As a result, our Data Science and Systems Integration team at NSLS-II
+has been begun moving the beamlines to a data acquisition model that
+includes sounds data security practices.  BMM volunteered to be an
+early adopter of the new data security practices.  We now provide an
+excellent user experience at BM that includes secure data management.
+

docs/desktop.rst

@@ -85,8 +85,8 @@ Data collection and visualization
 Data collection and visualization are separate things and should be
 managed separately.  
 
-On the main virtual desktop, open a terminal window for bsui.  At the
-command line type ``bsui``.  ``bsui`` startup at BMM is rather
+On the main virtual desktop, open a terminal window for |bsui|.  At the
+command line type ``bsui``.  |bsui| startup at BMM is rather
 time-consuming, but after a couple minutes it is ready to go.
 
 
@@ -100,7 +100,7 @@ plot workers as explained in :numref:`the section on Kafka workers
    :width: 80%
    :align: center
 
-   The tail end of the ``bsui`` startup messages and the
+   The tail end of the |bsui| startup messages and the
    command prompt.
 
 
@@ -117,20 +117,20 @@ experiment:
   Workspace folder
 
 Note that there is a button on the icon bar at the bottom of the
-screen for Hephaestus.
+screen for |hephaestus|.
 
-In the new data security regime, launching Athena as the beamline
+In the new data security regime, launching |athena| as the beamline
 account (``xf06bm``) is not very helpful given that it cannot access
 the data.  
 
-If data are accessed by opening a terminal window and doing
-``su - <username>`` followed by authentication with password and DUO,
-first ``cd`` to the proposal directory, the start Athena with this
-command: 
+If data are accessed by opening a terminal window and doing ``su -
+<username>`` followed by authentication with password and DUO (see
+:numref:`section %s <data>`), first ``cd`` to the proposal directory,
+then start |athena| with this command:
 
 .. code-block:: bash
 
    dathena > /dev/null 2>&1 &  
 
-That will open Athena and suppress the large stream of uniteresting
+That will open |athena| and suppress the large stream of uniteresting
 warning messages from the graphics tool kit.

docs/details.rst

@@ -16,6 +16,44 @@ This section is a scattershot assortment of details about things at
 the beamline.  This is basically an attempt to capture institutional
 knowledge ... someplace.
 
+Network configuration
+---------------------
+
+When introducing a new device to the beamline network:
+
++ Open a Jira ticket to request a new IP address and device name for
+  DNS.  As an example, a new Moxa terminal server was introduced.  In
+  the Jira ticket, we requested an IP address of 10.68.42.83 and a DNS
+  entry of ``xf06bm-tsrv13`` (full name:
+  ``xf06bm-tsrv13.nsls2.bnl.local``). 
+
++ In the case of a device that one in s series of similar devices, be
+  sure that the name matches the similar devices and that the number
+  is incremented.  In the case of the new Moxa server, there are 12
+  others at the beamline.  The numbers were incremented correctly for
+  both the name and the IP address
+
++ Identify a port on one of the servers that is available and
+  configured for the correct network.  The networks are:
+
+  + **SCI** (650): 10.68.40.xxx
+  + **CAM** (651): 10.68.41.xxx
+  + **INST** (652): 10.68.42.xxx
+  + **EPICS** (653): 10.68.43.xxx
+
+When configuring an individual device, here are the network configurations:
+
++ The gateway address on each network is ``xz.yy.zz.2``.  For example,
+  the gateway on the SCI network is 10.68.40.2. 
+
+* The netmask is ``255.255.255.0``.
+
++ There are two DNS servers:
+
+  + DNS1: 10.65.2.25
+  + DNS2: 10.65.2.26
+
+
 xf06bm-ws5, in-hutch Zoom calls
 -------------------------------
 
@@ -90,6 +128,13 @@ Needle valves are mounted on the outboard side of DM3. Quick connect
 outlets for the gases are mounted on the upstream/inboard corner of
 the XAFS table.  
 
+.. admonition::  Gaseous nitrogen supply
+   :class: note
+
+   BMM no longer uses a nitrogen cylinder as the supply of N\ :sub:`2`
+   for the ion chambers.  The house GN2 supplies N\ :sub:`2` to the
+   needle valves.
+
 .. _fig-inertgas:
 .. figure:: _images/Gas_handling.png
    :target: _images/Gas_handling.png
@@ -185,13 +230,15 @@ pointed to in databroker.  See:
 Pilatus 100K
 ------------
 
+.. todo::  Need to flesh this out with explanatory text and screenshots
+
 How files saving works
 ~~~~~~~~~~~~~~~~~~~~~~
 
 + tiff files to /disk2
 + /disk2 is mounted on xf06bm-ioc1
 + tiff and hdf5 AD plugins write files to proposal directories
-+ in bsui, there are pilatus and pilatus_tiff objects.  normally use
++ in |bsui|, there are pilatus and pilatus_tiff objects.  normally use
   pilatus, puilatus_tiff is helpful for testing tiff file writing,
   which is used by IBM
 

docs/instruments.rst

@@ -9,6 +9,8 @@
 
 .. _instruments:
 
+
+
 Beamline instrumentation
 ========================
 

docs/intro.rst

@@ -15,7 +15,7 @@ Introduction to BMM
 BMM is NIST's :red:`B`\ eamline for :red:`M`\ aterials :red:`M`\ easurement.
 
 At the unix command line, type ``bsui`` to start the BlueSky user
-interface.  bsui is simply an `Ipython shell <https://ipython.org/>`_
+interface.  |bsui| is simply an `Ipython shell <https://ipython.org/>`_
 with some customizations specific to BlueSky.  On top of that, there
 are a number of customizations specific to BMM.
 
@@ -66,7 +66,7 @@ Essential links
 The user experience
 -------------------
 
-The Ipython/bsui prompt at BMM is modified to provide at-a-glance
+The Ipython/|bsui| prompt at BMM is modified to provide at-a-glance
 information about the state of the beamline.
 
 .. _fig-prompt:
@@ -86,7 +86,7 @@ information about the state of the beamline.
   Si(111) monochromator (Section %s) <change-crystals>` is in use.
 
 * The green number in square brackets is an incremented count of how
-  many commands have been issued since ``bsui`` was started.
+  many commands have been issued since |bsui| was started.
 
 * If the prompt starts with three red exclamation points |nd| something like