yt-dev September 2015

yt-dev@python.org

16 participants
32 discussions

PR Triage Hangout
by Hilary Egan 23 Nov '15

23 Nov '15

Hi all, Here's the link for next week's PR triage hangout and a reminder that they will now be Mondays at 2pm EST! https://plus.google.com/b/107728486871834552760/events/car4cot30l8gu65a3b6e… -- Hilary Egan Astrophysical and Planetary Science Department University of Colorado Boulder

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Numpy-like ops YTEP
by Matthew Turk 06 Oct '15

06 Oct '15

Hi all, I'd very much appreciate feedback on this YTEP: https://bitbucket.org/yt_analysis/ytep/pull-requests/55/ytep-0026-numpy-lik… The related PR that starts implementing them is here: https://bitbucket.org/yt_analysis/yt/pull-requests/1763/wip-proposed-set-of… Two things that I think need some bikeshedding -- histogram and the step argument to slicing. -Matt

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Issue #1087: python seg faults when trying to load face-centered Enzo MHDCT fields (yt_analysis/yt)
by Nathan Goldbaum 30 Sep '15

30 Sep '15

New issue 1087: python seg faults when trying to load face-centered Enzo MHDCT fields https://bitbucket.org/yt_analysis/yt/issues/1087/python-seg-faults-when-try… Nathan Goldbaum: Dataset is here: http://use.yt/upload/58d7f69e Test script: ``` #!python import yt ds = yt.load('DD0004/DD0004') ad = ds.all_data() ad['BxF'] ``` The traceback the Apple crash reporter generates doesn't have anything particularly illuminating in it. The error message that gets printed to my console is: ``` #! Python(56127,0x7fff742f5300) malloc: *** error for object 0x7ffb01f54608: incorrect checksum for freed object - object was probably modified after being freed. *** set a breakpoint in malloc_error_break to debug ```

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Pre-YTEP: remove caching of datasets
by Matthew Turk 25 Sep '15

25 Sep '15

Hi all, Before I get too far into writing up a YTEP, I wanted to know if anyone would object to disabling "caching" of datasets in-memory. Right now, if you do: ds1 = yt.load("something") ds2 = yt.load("something") "ds1 is ds2" will return True; this was done so that you could load a dataset, then unpickle an object with a reference to that dataset, and get the dataset back rather than a newly-loaded one. But I think a) folks don't pickle much b) it causes a lot of problems. So I'm wondering if it would be okay to just turn this off. -Matt

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Issue #1086: derived_field_list not updated after add_volume_weighted_smoothed_field (yt_analysis/yt)
by Bili Dong 25 Sep '15

25 Sep '15

New issue 1086: derived_field_list not updated after add_volume_weighted_smoothed_field https://bitbucket.org/yt_analysis/yt/issues/1086/derived_field_list-not-upd… Bili Dong: When ``add_volume_weighted_smoothed_field`` is used to add a smoothed field to a dataset (``ds`` thereafter) as shown below, ``ds.derived_field_list`` remains the same before and after the operation. The issue is that ``ds.field_info`` is supposed to be passed to ``add_volume_weighted_smoothed_field``. Then ``ds.field_info.add_field`` is called to add the field, which updates ``ds.field_info`` but not ``ds.derived_field_list``. One way to fix it is to call ``registry.ds.add_field`` instead of ``registry.add_field`` in ``add_volume_weighted_smoothed_field`` (here ``registry`` is supposed to be ``ds.field_info``. But I'm not sure if this is the best way to do it. ``` python import yt ds = yt.load('GadgetDiskGalaxy/snapshot_200.hdf5') ds.index from yt.fields.particle_fields import add_volume_weighted_smoothed_field add_volume_weighted_smoothed_field('PartType0', 'Coordinates', 'Masses', 'SmoothingLength', 'Density', 'particle_ones', ds.field_info) ad = ds.all_data() field = ('deposit', 'PartType0_smoothed_particle_ones') print(field in ds.derived_field_list) ad[field] ``` BTW, ``('deposit', 'PartType0_smoothed_particle_ones')`` can be accessed with no problem.

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Nominate Allyson Julian as a yt project member
by Nathan Goldbaum 24 Sep '15

24 Sep '15

Hi all, Today I issued a pull request with some updates for YTEP-1776: http://ytep.readthedocs.org/en/latest/YTEPs/YTEP-1776.html This reminded me that we should be on the lookout for new contributors who have made or are making substantial contributions to the codebase. To that end, I'd like to nominate Allyson Julian as a new member. Allyson has been working for the past few months on a frontend for the Exodus II unstructured mesh data format. We are getting ready to merge the frontend into the experimental bookmark soon and I think her work will be extremely useful for expanding yt's ability to load unstructured mesh data natively. Once I've heard back from enough of you in support of Allyson's nomination, I'll add Allyson to the member list. -Nathan

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Fwd: [Matplotlib-devel] Fwd: [NumFOCUS Projects] grant opportunity
by Nathan Goldbaum 24 Sep '15

24 Sep '15

---------- Forwarded message ---------- From: Thomas Caswell <tcaswell(a)gmail.com> Date: Wed, Sep 23, 2015 at 10:51 PM Subject: [Matplotlib-devel] Fwd: [NumFOCUS Projects] grant opportunity To: matplotlib development list <matplotlib-devel(a)python.org> If anyone has some downtime and would like to be paid to hack on open source. Submissions are due Sept 30 Tom ---------- Forwarded message --------- From: Gina Helfrich <gina(a)numfocus.org> Date: Fri, Sep 18, 2015 at 12:10 PM Subject: [NumFOCUS Projects] grant opportunity To: <projects(a)numfocus.org> Hi all, Wanted to bring this opportunity to your attention: Stripe is looking to host three to four developers at their San Francisco office for three months to work full-time on an open-source project. The grant is no-strings-attached: $7,500 per month in addition to desk space at our office and meals during the week. "We want to provide everything needed to focus and have a substantial impact on an open-source project." More info: https://stripe.com/blog/open-source-retreat-2016 The program will run from January 15th until April 15th, 2016 at Stripe HQ in the Mission District of San Francisco. Best, Gina -- *Gina Helfrich, Ph.D.* *Communications Director* NumFOCUS <http://www.numfocus.org/> | Open Code, Better Science gina(a)numfocus.org | 512-222-5449 -- You received this message because you are subscribed to the Google Groups "Fiscally Sponsored Project Representatives" group. To unsubscribe from this group and stop receiving emails from it, send an email to projects+unsubscribe(a)numfocus.org. To post to this group, send email to projects(a)numfocus.org. Visit this group at http://groups.google.com/a/numfocus.org/group/projects/. To view this discussion on the web visit https://groups.google.com/a/numfocus.org/d/msgid/projects/CAFhTXRPxOsUubAHE… <https://groups.google.com/a/numfocus.org/d/msgid/projects/CAFhTXRPxOsUubAHE…> . _______________________________________________ Matplotlib-devel mailing list Matplotlib-devel(a)python.org https://mail.python.org/mailman/listinfo/matplotlib-devel

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Fwd: [Numpy-discussion] ANN: numtraits v0.2
by Nathan Goldbaum 23 Sep '15

23 Sep '15

Hi all, This might be useful for us. Both numtraits and traitlets are pure python packages that would not be difficult to add as dependencies. -Nathan ---------- Forwarded message ---------- From: Thomas Robitaille <thomas.robitaille(a)gmail.com> Date: Wed, Sep 23, 2015 at 11:39 AM Subject: [Numpy-discussion] ANN: numtraits v0.2 To: "Discussions about using IPython. http://ipython.org" < ipython-user(a)scipy.org>, Discussion of Numerical Python < numpy-discussion(a)scipy.org>, SciPy Users List <scipy-user(a)scipy.org> Hi everyone, We have released a small experimental package called numtraits that builds on top of the traitlets package and provides a NumericalTrait class that can be used to validate properties such as: * number of dimension (for arrays) * shape (for arrays) * domain (e.g. positive, negative, range of values) * units (with support for astropy.units, pint, and quantities) The idea is to be able to write a class like: class Sphere(HasTraits): radius = NumericalTrait(domain='strictly-positive', ndim=0) position = NumericalTrait(shape=(3,)) and all the validation will then be done automatically when the user sets 'radius' or 'position'. In addition, tuples and lists can get automatically converted to arrays, and default values can be specified. You can read more about the package and see examples of it in use here: https://github.com/astrofrog/numtraits and it can be easily installed with pip install numtraits The package supports both Python 3.3+ and Legacy Python (2.7) :) At this point, we would be very interested in feedback - the package is still very young and we can still change the API if needed. Please open issues with suggestions! Cheers, Tom and Francesco _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion(a)scipy.org https://mail.scipy.org/mailman/listinfo/numpy-discussion

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notes from team meeting
by Britton Smith 23 Sep '15

23 Sep '15

HI all, Notes from yesterday's team meeting can be found here: https://docs.google.com/document/d/10-WC-t6XhU75IRR4YXXoRjrFRE7Gva4ooYFsURG… Keep up the good work, everyone! Britton

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Need help to create new frontend
by Grassinger, Daniel 21 Sep '15

21 Sep '15

Hi developers, I make an internship at a German reasearcher institute. My job is to write a frontend for yt to load a special kind of HDF5 files. Most parts of the code are are working now. So the yt.load() function create a dataset without throwing errors. But I have still some erros when I wand to make a plot. The reason is I have problems with the code in the io.py. Can you please help me with further explanation of the class in io.py. Thank you for helping. Daniel Grassinger

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yt-dev September 2015