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Discussion of Python in High Energy Physics https://hepsoftwarefoundation.org/activities/pyhep.html

Dear colleague,

We are pleased to announce the second "Python in HEP" workshop organised by the HEP Software Foundation (HSF). The PyHEP, "Python in HEP", workshops aim to provide an environment to discuss and promote the usage of Python in the HEP community at large.

PyHEP 2019 will be held in Abingdon, near Oxford, United Kingdom, from 16-18 October 2019.

The workshop will be a forum for the participants and the community at large to discuss developments of Python packages and tools, exchange experiences, and steer where the community needs and wants to go. There will be ample time for discussion.

The agenda will be composed of plenary sessions, a highlight of which is the following:

1) A keynote presentation from the Data Science domain.

2) A topical session on histogramming including a talk and a hands-on tutorial.

3) Lightning talks from participants.

4) Presentations following up from topics discussed at PyHEP 2018.

We encourage community members to propose presentations on any topic (email: pyhep2019-organisation@cern.ch). We are particularly interested in new(-ish) packages of broad relevance.

The agenda will be made available on the workshop indico page (https://indico.cern.ch/event/833895/) in due time. It is also linked from the PyHEP WG homepage http://hepsoftwarefoundation.org/activities/pyhep.html.

Registration will open very soon, and we will provide detailed travel and accommodation information at that time.

Travel funds may be available at a modest level. To be confirmed once registration opens.

You are encouraged to register to the PyHEP WG Gitter channel (https://gitter.im/HSF/PyHEP) and/or to the HSF forum (https://groups.google.com/forum/#!forum/hsf-forum) to receive further information concerning the organisation of the workshop.

Looking forward to your participation!

Eduardo Rodrigues & Ben Krikler, for the organising committee

R.I.P. rootpy documentation:

http://rootpy.org/

http://rootpy.org/

`NOTICE: This domain name expired on 7/11/2019 and is pending renewal or deletion.`

Hi @kreczko, try getting in touch with Noel Dawe, see https://github.com/ndawe. He's probably still responsible for the site - just my best guess.

@kreczko here's an option that also delays the reindex of b and preserves the order of first-seen values:

```
import numpy as np, awkward
a = np.array([1, 12, 1, 10, 50, 10])
b = np.array([10, 20, 30, 40, 50, 60])
arg = a.argsort(kind='stable')
offsets, = np.where(np.r_[True, np.diff(a[arg]) > 0])
output = awkward.JaggedArray.fromoffsets(offsets.flatten(), awkward.IndexedArray(arg, b))
```

in other news,

`np.where([0, 1, 0, 0, 1])[0].base`

is surprisingly 2d (hence the flatten)
since the knowledge in this channel proved invaluable before, another question :)

I have

```
group_1 = np.array([(1, 2), (3, 3), (5, 7), (4, 4)])
test_elements = np.array([(1, 2), (3, 3), (3, 5)])
```

and would like to test if the elements in `test_elements`

are in `group_1`

. I expect the result

`[True, True, False]`

as I take the tuples as unique objects.

Numpy has the function `isin`

where

`np.isin(group_1, test_elements)`

will return

`[[True, True], [True, True], [True, False], [False, False]]`

OK, so this is inverse to what I want, fine.

```
np.isin(group_1, test_elements)
# returns
[[True, True], [True, True], [True, True]]
```

Clearly it compares element by element and since both `3`

and `5`

are contained, therefore `(3,5)`

should be as well, right?

Well, not in my case. Is there a way to do this comparison for each 2-vector instead of element-wise? For loop (even with numba) is quite slow

Yes, you can do that. The idea is: make a comparison of all possible combinations of each element with each other element. This gives you a rank three boolean object with: number of elements in the group, number of elements to test, dimension of an element. Then make two reduce operations: 1. `reduce all`

on the axis of the tuple, requiring that true is if in a tuple everything is true and 2. a `reduce any`

on the axis of all the possible combinations, since at least one tuple has to be fully contained.

For example (may change the axis for convenience):

```
test_elements_expanded = np.expand_dims(test_elements, axis=1)
entries_equal = group_1 == test_elements_expanded
tuple_equal = np.all(entries_equal, axis=2)
tuple_contained = np.any(tuple_equal, axis=0)
```

The dimension of

`entries_equal`

is off :(
Axis 0 lists all test samples. In axis 1 are the possible combinations. In axis 2 is the tuple itself. Reducing axis 2 with all means that an entry is *all* elements in a tuple are true, otherwise false, reducing axis 1 with *at least one* matching tuple is true. So your left with the axis 0.

`true`

where `any`

means that an entry with
thanks!

You can also map the tuples to scalars (easy if you have some idea what the values are going to be), e.g:

```
def squash(x):
return 10000 * x[:,0] + x[:,1]
np.in1d(squash(test_elements), squash(group_1))
```

This should be more memory-efficient and faster if both arrays are large.

If you are going to do membership testing repeatedly on the same array, it might be even better to convert it to a set, dictionary or some other object backed by a hash table, so membership tests are a constant time operation.

@JelleAalbers Where does the

`10000`

come from?
it's interesting how many solutions exist for the same operation

It's just a placeholder, you can put in whatever the maximum value you expect to be is. If your numbers are e.g. arbitrary-sized floats I guess this solution doesn't work. Though you can probably replace 'squash' with some other function (if you want to go really overboard you can use some cryptographic hash function, though then forget about speed :-)

Comparing the two solutions:

yours: 28366.0 microseconds

stackoverflow: 10999.0 microseconds

So essentially same speed *for this exact problem*. At this point, it matters, if: you call it once or a million times? How big is your array really? That's when things like presorting can make the difference. My advice: use which ever method you *understand/like better* (not from the speed, from the concept) and try only to improve on it if it proves to be a bottleneck.

Registration is now open for PyHEP 2019, in Abingdon, UK, from the 16th to 18th of October! The registration fee for the 2.5 days has been set at £80; it includes the venue, lunches, dinners, and refreshments. We also have about 46 rooms at Cosener’s House, available on a first-come-first-served basis. The actual payment system will not be online for a few more days, however, so you’ll only be able to complete registration then including the room booking.

The agenda is also shaping up with talks confirmed on topics ranging from histogramming, statistical methods, distributed workflows, visualisation, and even GPU-programming. Several speakers from industry are confirmed, including our keynote speaker on the PyViz library.

Since the PyHEP series is all about growing a “Python in High Energy Physics” community, this year we’re also including a session of lighting talks where 30 people can present any topic of their choosing for 3 minutes with a single slide as a way for everyone, especially newcomers and early careers researchers, to introduce themselves.

Community members can also propose presentations on any topic (email: pyhep2019-organisation@cern.ch). We are particularly interested in new(-ish) packages of broad relevance.

More details can be found on the indico page (https://indico.cern.ch/e/PyHEP2019) or from the PyHEP WG homepage http://hepsoftwarefoundation.org/activities/pyhep.html. You can also join the HSF forum (https://groups.google.com/forum/#!forum/hsf-forum) to get more information about the workshop and community

Help us spread the word! :slight_smile:

Not true in my case...

I can't book any rooms.

Thanks Hans and Chris. Chris is correct. The payment system is still not set up (the company we've had to use have been extremely difficult to work with, I've been trying to reach them by the phone every working day for the last week). We'll let you know straight away, I expect to have it in the next day or two.

It is no problem for me, I was just surprised, thanks for clearing this up!

Kind reminder on the PyHEP workshop: the available slots are being filled up at a nice pace, so don't delay registration too much, if you intend to come and participate - we hope you do! See https://indico.cern.ch/e/PyHEP2019 …

We kindly ask you to broadcast information of the workshop to your communities/groups/colleagues. Many thanks!

We kindly ask you to broadcast information of the workshop to your communities/groups/colleagues. Many thanks!

@/all Interested in a Pythonic Postdoc? The XENON Dark Matter experiment software stack is in Python and there's a job to work in that direction (with ML component): https://jobs.rice.edu/postings/20856

If you know somebody who might be interested, feel free to share.

Hi @all We are looking for **PhD students** in in physics, computer science, and data science to attend a **three-day OpenHack in September** to analyze real physics data from the **LHCb experiment at CERN using Microsoft AI technologies**.

An OpenHack is challenge rather than instruction-based. Students will work directly with physicists from CERN and Cloud Advocates from Microsoft. They will progress through these challenges to analyze data from LHCb and search for the “unexpected” in particle collisions:

```
Data exploration and visualization
Classification and anomaly detection
Source control and automation
AML experimentation
AML for hyperparameter tuning
Real-world application of data
```

The **OpenHack will be held Sept. 11-13 in northern Italy at Fondazione Bruno Kessler**, a scientific research institute affiliated with CERN. Students need pay only for their travel and lodging – there is no registration fee for the OpenHack itself. We will help find lodging.

The registration form is here. Please encourage your students to attend this unique training event and to contact monicar@microsoft.com with any questions.

To @all:

Registration for the PyHEP 2019 workshop has been extended to September 15th.

As a reminder, the registration fees for the 2.5 days has been set at £80. It includes the venue, lunches, dinners, and refreshments.

We still have rooms available at Cosener’s House, the venue, available on a first-come-first-served basis.

The agenda is also shaping up with talks confirmed on topics ranging from histogramming, statistical methods, distributed workflows,

visualisation, and even GPU-programming. Two speakers from industry are confirmed, including our keynote speaker on the PyViz visualisation project.

Since the PyHEP series is all about growing a community, this year we’re also including a session of lighting talks

where 30 people can present any topic of their choosing for 3 minutes, with a single slide, as a way for everyone,

especially newcomers and early careers researchers, to introduce themselves.

Community members can also propose presentations on any topic (email: pyhep2019-organisation@cern.ch).

We are particularly interested in new(-ish) packages of broad relevance.

**Note that partial travel support for some U.S. participants (in particular, students and early-career postdocs)may be available from the IRIS-HEP institute. Please contact Peter Elmer (Peter.Elmer@cern.ch) to enquire about details.**

More details can be found on the indico page https://indico.cern.ch/e/PyHEP2019

or from the PyHEP WG homepage http://hepsoftwarefoundation.org/activities/pyhep.html.

You can also join the PyHEP WG Gitter channel (https://gitter.im/HSF/PyHEP) and/or

the HSF forum (https://groups.google.com/forum/#!forum/hsf-forum) to get more information about the workshop and community.

Hope to see you there!

Eduardo Rodrigues & Ben Krikler, for the organising committee

**HSF PyHEP WG topical meeting on fitting tools, Sep. 11th @ 17h CET**

Dear Python enthusiasts,

The HSF PyHEP WG is restarting activities post-Summer with topical meetings (not to be confused with the workshop in the UK ;-)).

The first one will be on the hot and important topic of fitting (tools)! It will take place on Wednesday September 11th at 17h CET.

The agenda, which you can find at https://indico.cern.ch/event/834210/, contains 2 presentations,

one from HEP, and one from an astroparticle physics community colleague:

- The zfit project, Jonas Eschle (Universitaet Zuerich)
- Numpy-based Python fitting frameworks Astropy & Sherpa, Christoph Deil (MPI for Nuclear Physics, Heidelberg)

Take this opportunity of cross-exchange to come and discuss needs, technical design, functionality requirements, etc.!

Hoping to see you there!

Eduardo, for the PyHEP WG conveners

P.S.: Note that a second topical meeting on fitting tools will likely happen as a follow-up.

Has anyone here ever been involved with Hacktoberfest: https://hacktoberfest.digitalocean.com/ ?

have two t-shirts that say "yes, I have"

I've just heard through the UK's Software Sustainability Institute of the US' Better Scientific Software community. They have a fellowship scheme for researchers that are affiliated to a US institute which lasts for a year and provides funds for specific activities. The application for 2020 is now open until mid-October: https://bssw.io/. Share around and let's see if we can't get some particle physicists on it :)