NeXus Code Camp - January 2020¶

The 2020 NeXus Code Camp is scheduled for 3 days in January 2020: Jan 21 (Tuesday) - 23 (Thursday). The code camp will take place at the Advanced Photon Source, Argonne National Laboratory, IL, USA (near Chicago).

(We used an online poll to help decide the exact dates.)

Purpose¶

NeXus periodically convenes a Code Camp to develop NeXus software components through intense effort by small groups working on specific projects and tasks. It is expected that those attending the 2020 NeXus Code Camp will already have a strong foundation and understanding in aspects of the NeXus software and come ready with knowledge, tools, and ideas to make significant progress during the event.

Specific projects and tasks are described on the GitHub issue tracker. Issues for consideration at 2020 NeXus Code Camp will be added to the Code Camp’s Topics page (edit here). These issues will be prioritized on the first day for handling at the Code Camp.

(For more info on code camps, try searching Google for “code camp” or “codeathon”. Events such as the EPICS Codeathon would be reasonable templates for this NeXus code camp.)

Attendees¶

The list of Attendees is here.

Remote Attendees¶

We will open certain time slots for remote attendees to participate using Bluejeans video conference software. Connection details will be provided here. Please make sure your computer is configured to run Bluejeans before the session.

Teleconference will be available during the organizational periods in the schedule listed below:

9 - 9:30 AM CST, daily planning
5 - 6 PM CST, daily summary
Meeting ID: 150 847 021
URL: https://bluejeans.com/150847021
Phone Dial-in: +1.408.317.9254 (US (San Jose)) -or- +1.866.226.4650 (US Toll Free)
Global Numbers: https://www.bluejeans.com/premium-numbers
Room System 199.48.152.152 or bjn.vc
Want to test your video connection? https://bluejeans.com/111

Registration¶

You must notify the host of your visit in advance to arrange site access. Also, see the section below titled ANL Visitor Registration.

Costs¶

Conference fee: no fee
- food at morning and afternoon breaks will be provided
- perhaps (no guarantee) a small meeting souvenir
regular meals (breakfast, lunch, dinner) will be traveler’s expense

ANL Visitor Registration¶

The Argonne visitor registration form is for individuals who are visiting employees.

Argonne visitor registration form: https://apps.anl.gov/registration/visitors/

Indicate that you are visiting Pete Jemian.

Host¶

Pete Jemian
- X-ray Science Division
- Advanced Photon Source, Argonne National Laboratory
- 9700 South Cass Avenue
- Argonne, IL 60439 USA
- email: jemian@anl.gov
- office phone: +1-630-252-3189 (forwards to mobile)
- Google voice: +1-847-859-9775 (forwards to mobile)

Meeting Place¶

Building 437 (LOM 437 on the sign), Conference Room C010 (Advanced Photon Source)

map: google

Recommended Lodging¶

Please reserve your own rooms directly with the hotel:

Argonne Guest House
Argonne National Laboratory
9700 S. Cass Avenue - Building 460
Argonne, IL 60439
Web site: http://www.anlgh.org/
telephone: +1-800-632-8990, +1-630-739-6000
fax: +1-630-739-1000
map: google
General information: Visiting the APS

Directions¶

airport:
- Chicago O’Hare (ORD): international
- Chicago Midway (MDW): domestic
- Milwaukee, WI Mitchell Field (MKE): distant alternative
taxi:
- Call for a taxi pickup only after you have all your bags
- Must be a taxi that goes to Chicago suburbs
- suburban taxi will pickup in second lane of arrivals at Chicago O’Hare airport
- http://www.americantaxi.com, 1-800-244-1177 (automated system)
- … others …
airport bus: http://www.airportexpress.com/shuttles/ohare.html
commuter train:
- inconvenient

Practical Matters¶

Equipment¶

item	quantity	who provides?
projector & screen		host
LCD displays, keyboards, & mice		host
120 VAC, 60 Hz, US-style 3-prong extension cords	sufficient	host
foreign electrical power adapter	as needed	traveler
Wi-Fi connections	sufficient	hotel

Meals¶

No meals are provided by the code camp.
Light refreshments will be available for the breaks.
Attendees of the Code Camp will decide ad hoc on where to have their meals.

Agenda¶

Business Matters¶

Since this is not to be a meeting of the full NIAC, no business matters can be resolved.

Goal¶

Resolve issues and milestone to prepare next release of NXDL.

Suggestions:

We should take this opportunity to provide the standard Introduction to NeXus as a public presentation.
We should allow time for an open, working lunch on one of the days to interact with the community able to attend.
If someone wishes to make any other public presentation, either during, before, or after the Code Camp, please contact the host.

Schedule¶

arrive evening before the Code Camp
conference check-in Day 1 morning
meet Day 1
meet Day 2
meet Day 3
checkout next day morning

Here is the daily schedule (teleconference for remote attendees will be available during the organizational periods, see above for connection details). All times listed are Central Standard Time (CST):

time	description	comments
9:00 - 9:30 AM	organizational	daily planning (plenary)
9:30 - 10:15 AM	meeting	work on projects and tasks
10:15 - 10:45 AM	morning break	(included)
10:45 AM - 12:00 PM	meeting	work on projects and tasks
12:00 - 1:15 PM	lunch	offsite, traveler’s expense
1:15 - 3:15 PM	meeting	work on projects and tasks
3:15 - 3:30 PM	afternoon break	(included)
3:30 - 5:00 PM	meeting	work on projects and tasks
5:00 - 6:00 PM	organizational	daily summary (plenary)

Notes:

late-afternoon wrap-up (plenary) each day
morning and afternoon breaks will be included in amenities charge
breakfast, lunch, dinner will be in a local restaurant at traveler’s expense

Day 1¶

Check-in, Welcome, and introductions
Decide which topics to work on and resolve during this code camp.
- this took longer than expected (about 90 minutes)
- we used a shared Google Docs spreadsheet to list GitHub issues, assign priorities, note workers, and report status
AOB?
work on issues

Day 2¶

work on issues

Day 3¶

work on issues
make release (or release candidate) of NXDL per release procedure
AOB?

Minutes for the meeting¶

We don’t typically record minutes for the Code Camps.
Rather, the work progress is recorded in the GitHub issue trackers for the various repositories involved.

We’ll note here certain progress items or any questions or recommendations for the NIAC.

We are looking to publish the manual through GitHub Pages: https://manual.nexusformat.org
We made excellent progress on the Gold Standard for NXmx, helping both the MX, FEL, and synchrotron communities and the vendor support.
We have registered a DOI with zenodo that updates with each release of the definitions repository. The DOI link is noted on our GitHub home page.
We expect to make a release of NXDL 2020.1 on 2020-01-31.

Code Camp Tasks¶

We list here the various tasks we handled during the code camp, with a disposition for each, as copied from the Google Sheet we shared.

repository	task	disposition
definitions	NXDL data type vs NAPI type vs NeXus data type: clarify and simplify!	Done
definitions	more prominently document existing scheme for uncertainties	Done
definitions	Recording time-stamped data	Done
definitions	Create structure to incorporate PDB definitions into NeXus	Done
definitions	use consistent terms when names are flexible	Done
definitions	NIAC has decided about how to report errors/uncertainties	Done
definitions	[DOC] C example uses old style NXdata	Done
definitions	Added documentation for variants to datarules.rst	Done
definitions	How to specify per-shot wavelength	Done
definitions	close branch pixel_as_length_issue_511	Done
definitions	integrate NIAC decision on errors & uncertainties	Done
definitions	NXDL release 2020.1	expected 2020-01-31
exampledata	Can we remove the file trees from the readme files as they are out of date and need to be manually updated	Done
exampledata	separate out non-compliant data files	Done
exampledata	Example thaumatin multisample NXmx/NXreflections file.	Done
definitions	Clarify note on IUCr coordinate system.	Done
definitions	add “uncertainties” attribute to fieldType in nxdl.xsd	closed as wontfix
definitions	“Are there examples of NeXus data?” - asked at Nobugs 2018	Done
definitions	“Are there examples of code that reads NeXus data?” - asked at Nobugs 2018	Done
definitions	docs: add text when a group name is suggested	Done
definitions	can NXscan be extended to include 1-D data?	moved to next milestone
definitions	update Sphinx config	Done
definitions	consider publishing docs in GitHub pages	Done
definitions	examples of axes/AXISNAME_indices attributes	moved to next milestone
definitions	datarules.rst contains information on 2014 discussions	moved to next milestone
definitions	clarify how to name fields and groups	NIAC to review
definitions	clarify naming convention	NIAC to review
exampledata	some example files for NXptycho	after code camp
definitions	Is use of UPPER case names described in the manual?	Done
definitions	Need new links to h5toText program	Done
exampledata	critique.py was not working	Done
definitions	Slow/fast axis inconsistent in NXdetector_module	Done
definitions	adjust links for h5toText, now punx tree	Done
definitions	update copyright date to 2020	Done
definitions	2020 copyright	Done
definitions	some unit tests fail since flexible names are UPPER case	Done
definitions	certain unit tests had failed	Done
definitions	NXmx has fields that may not have to be required	Done
definitions	update Sphinx config to 2.3.1	Done
definitions	DATASET_errors naming convention should appear in manual	Done
definitions	PDF manual does not build	Done
definitions	Remove references to NAPI from schema and documentation	Done
definitions	describe field suffixes reserved by NeXus	Done
definitions	Improved documentation about time stamped data	Done
definitions	cleanup in nxdl.xsd	Done
definitions	cleanup in nxdl.xsd (PR to #725)	Done
definitions	Remove some references to NAPI for #699	Done
definitions	Makefile can’t build the PDF manual	Done
definitions	editing needed in datarules.rst new content	Done
definitions	Clarify the nature of NeXus application definitions	Done
definitions	Clarify the nature of NeXus application definitions	Done
definitions	GitHub API authentication has changed : affects the release process	Done
definitions	Revise release note scripting	Done
definitions	create_release_notes.py should use SHA credentials	Done
definitions	added type=”NX_FLOAT”	Done
definitions	NXstxm nxdl does not specify a type for the energy field for [/NXentry/NXinstrument/NXmonochromator/energy]	Done
definitions	cite API contributions	Done
definitions	Update example for new axes syntax and for HDF 1.8.0 and above	Done
definitions	Reduce number of mandatory fields in NXcxi_ptycho	Done
definitions	adjust doc string in NXcxi_ptycho	Done
definitions	writer_2_1 example broken	Done
definitions	Bad indentation in NXcxi_ptycho	Done
definitions	add h5py example reader using attributes to find default plottable data	Done
definitions	From code camp, clarify NXmx/NXdetector depends_on field.	Done
definitions	From code camp, Make NXmx/NXdata optional.	Done
definitions	From code camp, add note to NXmx that file_name and file_time are recommended	Done
definitions	in release notes, TOC link to each subsection	Done
definitions	in release notes TOC, add link to each subsection	Done

page source: GitHub link