more work moving stuff from wiki into github doc

devtools/conda-envs/docs_env.yaml

@@ -20,5 +20,5 @@ dependencies:
   - sphinx-math-dollar
   - sphinx-subfigure
   - sphinx-design
-
+  - sphinxcontrib.bibtex  
 

docs/automation.rst

@@ -189,6 +189,8 @@ was called :file:`mysamples`, the new BlueSky command is called
    Convert spreadsheets to Bluesky queueserver input.
 
 
+.. _sample_wheel_automation:
+
 Sample wheel automation
 -----------------------
 

docs/before.rst

@@ -0,0 +1,200 @@
+..
+   This document was developed primarily by a NIST employee. Pursuant
+   to title 17 United States Code Section 105, works of NIST employees
+   are not subject to copyright protection in the United States. Thus
+   this repository may not be licensed under the same terms as Bluesky
+   itself.
+
+   See the LICENSE file for details.
+
+.. _before:
+
+Before your Beamtime
+====================
+
+Register for BNL Site Access
+----------------------------
+
+Upon receipt of notification of your beamtime, verify that all
+the team members attending your experiment have a valid BNL Guest
+registration. 
+
+.. note::
+
+   + New registration requests as well as the extensions requests for
+     expired registrations shall be submitted as soon as possible.
+   + Approvals for guest registrations can take as long as two
+     months for some non-US citizens.
+
+To apply for a BNL Guest appointment: https://www.bnl.gov/ps/userguide/beforearrival.php 
+
+.. caution::  Without an active appointment, you will not be allowed
+	      on site and will be turned away at the main gate. 
+
+BNL Domain Account
+------------------
+
+When your BNL Guest registration becomes active, you should receive an
+email with instructions for enabling your BNL domain account. You must
+complete that step, which includes setting your password and signing
+up for DUO Federal two-factor authentication. If you need to request
+an account, go to https://www.bnl.gov/accounts/ and click the button
+that says "Submit account registration form".
+
+Enabling your BNL account is non-optional. You must have an active
+account in order to unlock the computers at the beamline. 
+
+.. caution:: Without an active account, a known password, and DUO
+	     Federal two-factor authentication, you will be unable to
+	     perform your experiment.
+
+Safety Approval Form
+--------------------
+
+Submit your Safety Approval Form (SAF) AT LEAST two weeks before the
+above starting date. Your SAF should provide a complete and accurate
+description of the experiment, including all samples, chemicals,
+solvents, reference materials, and equipment that will be used during
+the experiment and preparation. In addition, any additional equipment
+not provided by the beamline has to be identified and described in the
+SAF. Provide detailed information on sample processing and any safety
+measures necessary.
+
+.. caution:: An approved SAF is required on the first day of beamtime.
+	     Without enough time for approval, you may lose your
+	     beamtime beamtime.
+
+To submit a SAF: https://pass.bnl.gov
+
+If your experiment requires chemicals, compressed gases, lab access,
+or other equipment, please contact `Bruce Ravel
+<mailto:[email protected]>`__ well ahead of your expriment.
+Transportation of hazardous materials related to your experiment to
+the BNL site and back to the home institution is your responsibility.
+
+
+Support Laboratories
+--------------------
+
+Currently, four labs support user activities at BMM.  They are:
+
++ Lab 3L-L06: XAS Sample Prep Lab
++ Lab 3L-L07: Environmental Science Wet Lab
++ Lab 3L-L09: XAS Chemistry Lab
++ Lab 4L-L09: Electrochemistry Lab
+
+See https://www.bnl.gov/nsls2/labs/
+
+If you prepare or treat samples on-site, you must request use of the
+appropriate NSLS-II User Laboratory when you submit your Safety
+Approval Form.
+
+You cannot request a laboratory after an SAF has been approved.  
+
+
+Here is some advice on selecting the correct lab:
+
+Unbound nanoparticles
+  Please note that supported nanoparticles or nanoparticles in
+  solution are not considered “unbound”.  If your samples are indeed
+  unbound, please contact BMM beamline scientist Bruce Ravel
+  ([email protected]) as soon as possible.  
+
+Solid sample preparation (pellet pressing, spreading on tape etc)
+  Request Lab 3L-L06.
+
+Liquid samples (organic solvents, acids, bases)
+  Request Lab 3L-L09.
+
+Hydrofluoric acid treatment
+  Request Lab 3L-L09 and notify Cognizant Space Manager, Syed Khalid
+  at [email protected], as soon as possible. 
+
+Environment and earth science sample preparation and treatment
+  Request Lab 3L-L07.
+
+Electrochemistry and battery science
+  Request Lab 4L-L09.
+
+Radionuclide samples must be prepared and properly contained at the
+home institution. NSLS-II has no lab available for work on
+radiological materials. Samples with depleted uranium and uranium at
+low or environmentally relevant concentrations are considered
+radiological samples at NSLS-II and must be treated accordingly.
+
+Requests for using gloveboxes should be discussed prior to submitting
+the SAF, with Bruce Ravel ([email protected]) and/or Syed Khalid
+([email protected])
+
+.. note:: Each lab you select on your safety approval form makes work
+	  for the lab stewards.  Only request the lab(s) that you
+	  actually intend to use.
+
+Training
+--------
+
+Please complete all required online user training at least one week
+before the starting date.  Failure to complete training will result in a
+delay starting your experiment.
+
+To complete your training, follow the training instructions at:
+https://www.bnl.gov/ps/userguide/beforearrival.php
+
+
+Electrical Equipment
+--------------------
+
+Any equipment with an electrical cable including low-voltage
+instruments and sample holderss are considered electrical equipment
+(laptop computers are excluded). 
+
+If you plan to bring electrical equipment for your experiment, please
+contact Jerome Malley, Electrical Equipment Inspection (EEI) Manager
+at [email protected] as soon as practical and at least two weeks before
+the start of your experiment.  Be prepared to provide manuals, photos,
+electrical diagrams, and schematics.
+
+Please include beamline staff (Bruce Ravel <[email protected]> for all
+experiments; Vesna Stanic <[email protected]> & Jean Jordan-Sweet
+<[email protected]> for XRD experiments) in your communication as some
+pre-approved electrical equipment (e.g., potentiostat, heaters,
+temperature meters, and controllers) may be available at the beamline.
+
+.. note:: Failure to comply with EEI will result in a delay to your
+	  experiment.  Equipment that cannot pass EEI may not be used
+	  at NSLS-II.
+
+Research Equipment Pool
+-----------------------
+
+Many experimental tools are available from `the NSLS-II Research
+Equipment Pool
+<https://public.bnl.gov/sites/rep/SitePages/Home.aspx>`__.  If you
+wish to use any items from equipment pool, contact `Bruce Ravel
+<mailto:[email protected]>`__ well ahead of your experiment.
+
+
+Shipping things to the beamline
+-------------------------------
+
+Things should be shipped to
+
+.. code-block:: none
+
+   Bruce Ravel / Beamline 6BM
+   Building 740
+   Brookhaven National Laboratory
+   Upton NY 11973
+
+The Day of your Experiment
+--------------------------
+
+.. note:: Unless told otherwise, your experiment starts at 8 am.  
+
+You should consider having all team members arrive the afternoon prior
+to the first day of the beamtime to check in at `the GUV Center
+<https://www.bnl.gov/guv/>`__ and to complete beamline specific
+training.
+
+Please consult `NSLS-II user guide <https://www.bnl.gov/ps/userguide/>`__
+or contact BMM beamline staff for more information.

docs/commonchores.rst

@@ -15,6 +15,61 @@
 Common chores
 =============
 
+Search the Hutch
+----------------
+
+The buttons on the hutch interlock panel are labeled with black
+stickers with white numbers.  Those labels correspond to the numbering
+in these lists:
+
+To OPEN the hutch
+~~~~~~~~~~~~~~~~~
+
++ 6. Close the shutter
++ 5. Press the "SBE" button
++ 4. ∙∙∙
++ 3. Make sure the “Front Left Maglock” button is not green
++ 2. Press the green “Open Door” button, wait for the slow door to open
++ 1. Enter the hutch
+
+
+To CLOSE the hutch
+~~~~~~~~~~~~~~~~~~
+
+Everyone but the person performing the search should leave the hutch.
+
+The search is done by and only one person.  Only one person pushes all
+the buttons.  The serach **is not** a team sport!
+
+1. Complete the hutch search 
+
+   + Look in the mirror to see that no one is behind the table
+   + Press search button 1
+   + Visually inspect the length of the hutch, verifying that it is empty of people
+   + Press search button 2
+   + Exit the hutch
+
+2. ∙∙∙
+3. Push the “Front Left Maglock” button. It should be lit green
+4. Push and hold the yellow “Close Door” button. Listen for the magnetic latch
+5. Push the "SBE" button, wait for the loud noise to finish
+6. You can now open the shutter
+
+Hutch search sign
+~~~~~~~~~~~~~~~~~
+
+These instructions are printed, laminated, mounted on a magnetic
+sheet, and hung near the search station.  I would like to make these
+signs in various languages.  If you would like to help by translating
+this sign, download the Word document below.  Make a translation into
+your language and mail the Word doc back to Bruce.  He will print and
+mount the new translation!  I am most eager for Chinese, Russian, and
+German translations.
+
+:download:`Word document with hutch search instructions <_static/HutchSearch.docx>`.
+
+
+
 Change energy and prepare for fluorescence measurements
 -------------------------------------------------------
 

docs/details.rst

@@ -114,8 +114,8 @@ Bluesky. The heart of the implementation is a system call to
 ``fswebcam``. From there, the image is saved as an asset and correctly
 pointed to in databroker.  See:
 
-+ https://github.com/NSLS-II-BMM/profile_collection/blob/master/startup/BMM/user_ns/detectors.py#L253
-+ https://github.com/NSLS-II-BMM/profile_collection/blob/master/startup/BMM/camera_device.py#L62-L164
++ `BMM/user_ns/detectors.py <https://github.com/NSLS-II-BMM/profile_collection/blob/master/startup/BMM/user_ns/detectors.py#L253>`__
++ `BMM/camera_device.py <https://github.com/NSLS-II-BMM/profile_collection/blob/master/startup/BMM/camera_device.py#L62-L164>`__
 
 
 DI Water Flow

docs/index.rst

@@ -21,6 +21,7 @@ BMM is NIST's Beamline for Materials Measurement
    :caption: Running the beamline
 
    intro.rst
+   before.rst
    instruments.rst
    motors.rst
    pds.rst
@@ -29,8 +30,8 @@ BMM is NIST's Beamline for Materials Measurement
    automation.rst
    log.rst
    manage.rst
-   cheatsheet.rst
    commonchores.rst
+   cheatsheet.rst
    trouble.rst
 
 .. appendix::