Re: [yt-dev] yt-dev Digest, Vol 66, Issue 43

I can help fix the halo docs. I had started going through the old pages the last time I was working on this but got waylaid by traveling. I've got a bit of time now though! -Hilary

Message: 1 Date: Wed, 25 Jun 2014 08:42:53 -0700 From: Nathan Goldbaum To: "yt-dev@lists.spacepope.org" Subject: Re: [yt-dev] RFC: Staggered deprecation through 3.1 and 3.2 Message-ID: < CAJXewOksXTNE349-+8wkBR56oMqK+viX60iMYwS18quVCcuTLw@mail.gmail.com> Content-Type: text/plain; charset="utf-8"

There are still some vestiges of the old halo machinery in the docs. Britton, do you think you'd be up for looking over the halo analysis docs and updating it where necessary? I'm specifically referring to some of the errors and warnings in the docs build, (see http://tests.yt-project.org/job/yt-docs-3.0/lastSuccessfulBuild/consoleFull , search for "halo") but it probably also deserves a full proofread.

I haven't felt comfortable touching the halo finding docs since I'm not familiar with any of the halo analysis code.

On Wednesday, June 25, 2014, Britton Smith wrote:

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Getting all the cookbook recipes working is absolutely a blocker for 3.0. I think we're all in agreement on that. Someone should correct me if I'm wrong, but all of the existing recipes can and will be made to work by porting existing functionality to yt-3.0. This mostly involves adopting the various newisms, units, field names, etc. We will not release yt-3.0 with broken functionality. This is doable on a relatively short timescale I think. However, the new VR machinery will not be ready for a bit longer, so I think it's ok for that to come in 3.1.

As far as halos are concerned, here's the status there: - halo_analysis completely replaces the HaloProfiler. The halo_analysis functionality is fully documented (Thanks Hilary!) and the HaloProfiler has been removed from the source and the docs. - all halo finders have been ported and are now compliant with halo_analysis (Thanks again to Hilary). - HaloCatalogTimeSeries is a ways off and will need to be pushed to 3.1 or 3.2. This is functionality that never existed anywhere, so that's fine. - the other cards on the halo_analysis board are minor enhancements, not blockers - the halo mass function is almost ready and has an open PR that just needs a few things cleaned up and it's ready. - the big thing we are missing is a merger tree as neither of the old ones were ported. The idea is for them to work with the halo_analysis and HaloCatalogTimeSeries, which will probably require work akin to a redesign. For this reason, this will probably need to wait until 3.1.

Britton

On Wed, Jun 25, 2014 at 2:35 AM, Cameron Hummels javascript:_e(%7B%7D,'cvml','chummels@gmail.com');> wrote:

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I will continue to work on these, but you're right, we need more people working on these little issues or this will continue to be a big blocker and not get done. I can assign specific bugs to the specialists on those issues, if it is helpful (see below).

For all issues, see this page: https://trello.com/c/NJMfoXdl/22-be-able-to-run-the-cookbook . Reading the description can give you some clues as to the source of the error, but the best way to diagnose it is simply to go into the doc cookbook directory and try to run the python script:

e.g. $ cd $YT_DEST/doc/source/cookbook $ python script.py

* VR - KDTree issues (Sam Skillman? Matt Turk?) ----amrkdtree_downsampling.py ----camera_movement.py -- something going on with statusbar in brick counting! ----opaque_rendering.py -- same as camera_movement.py ----render_with_box_and_grids.py

* Light Rays and Light Cones (Britton Smith, John Zuhone, Devin Silvia) ----make_light_ray.py ----unique_light_cone_projections.py ----light_cone_projection.py ----light_cone_with_halo_mask.py

* Profiles (Matt Turk, Nathan Goldbaum, other?) ----global_phase_plots.py ----profile_with_variance.py ----rad_velocity.py ----radial_profile_styles.py? ----simple_profile.py ----time_series_profiles.py ----save_profiles.py

* Units working with everything in yt (Nathan Goldbaum, Matt Turk, John Zuhone) ----hse_field.py ----simple_off_axis_projection.py

* Miscellany ----aligned_cutting_plane.py -- something is wrong with the derived quantity AngularMomentumVector() in that it doesn't work fully for gas, but seems to work OK for particles. ----free_free_field.py--creating a new derived field (Matt Turk, Nathan Goldbaum) ----simple_slice_with_multiple_fields.py -- vorticity_squared fails as a field.

This is by no means a requirement to work on this, but it would help to take a look at it to see if you can help correct a small bug here and there if your name is listed here (or even if it isn't!)

Cameron

On Tue, Jun 24, 2014 at 6:09 PM, Nathan Goldbaum javascript:_e(%7B%7D,'cvml','nathan12343@gmail.com');> wrote:

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Ah - I see that now.

Yes, I agree that fixing the cookbook should be a blocker. FWIW that card is marked as such. As I said the other day, the blockers are on the yt-3.0 and the documentation board. We won't do the yt-3.0 release until all the cards marked as blockers are cleared.

This is a big task - any help we can get on this from anyone following along would be much appreciated. There are a lot of little tasks or tasks that can be completed in a couple hours by anyone that has a little with yt-3.0.

On Tue, Jun 24, 2014 at 6:04 PM, Cameron Hummels javascript:_e(%7B%7D,'cvml','chummels@gmail.com');> wrote:

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I think all of the cookbook items are blockers to be honest, because the cookbook recipes should be tests that are seen as failing.

https://trello.com/c/NJMfoXdl/22-be-able-to-run-the-cookbook

On Tue, Jun 24, 2014 at 5:32 PM, Nathan Goldbaum < nathan12343@gmail.com javascript:_e(%7B%7D,'cvml','nathan12343@gmail.com');> wrote:

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On Tuesday, June 24, 2014, Cameron Hummels javascript:_e(%7B%7D,'cvml','chummels@gmail.com');> wrote:

> I think there remain some issues in the VR working in 3.0, which I > identified on the cookbook post on the trello board for yt-3.0. For > example, I know the overlaying grids and overlaying boundaries does

...

> currently work. >

I don't see this on trello. Can you make a card and mark it as a blocker?

> That may be an easy fix, but it's something to keep in mind. I was > going to work on it last week as I was doing the cookbook update, but I > figured it was just going to get replaced with the scene interface, so it > wasn't worth the time. > > I guess I'd still like to have all of the API breakage occur in the > big jump from 2.x to 3.0, but if people really want to get 3.0 out

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> asap, then perhaps that isn't compatible. Personally, I'm +1 on waiting to > have all the halo+VR stuff in 3.0 instead of 3.1, but if everyone else > wants a 3.0 out sooner, I will not block it. I think having a super fancy > VR and awesome halo interface is one of the big pulls to getting

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> have not yet switched to join 3.0 (from both 2.x as well as non-users) even > if it takes a few more months, but I may be the minority here. > > Cameron > > > On Tue, Jun 24, 2014 at 10:08 AM, Nathan Goldbaum < > nathan12343@gmail.com> wrote: > >> Ok - I think the script in the issue description is sufficient. Let >> me know if you need something more detailed. >> >> >> On Tue, Jun 24, 2014 at 10:07 AM, Matthew Turk < >> matthewturk@gmail.com> wrote: >> >>> That's the one -- you mentioned it in a blockers email a few days >>> ago. >>> >>> On Tue, Jun 24, 2014 at 12:06 PM, Nathan Goldbaum < >>> nathan12343@gmail.com> wrote: >>> > Sorry - not sure which issue you're talking about - this one >>> maybe? >>> > >>> > >>> https://bitbucket.org/yt_analysis/yt/issue/827/enzo-particle-fields-work-dif... >>> > >>> > >>> > >>> > >>> > On Tue, Jun 24, 2014 at 10:02 AM, Matthew Turk < >>> matthewturk@gmail.com> >>> > wrote: >>> >> >>> >> Related to that, do you have a reproducible script for the >>> particle >>> >> issue you reported? If so, could you add that to either an >>> issue or a >>> >> trello card so I can work on it? >>> >> >>> >> On Tue, Jun 24, 2014 at 11:58 AM, Nathan Goldbaum < >>> nathan12343@gmail.com> >>> >> wrote: >>> >> > I'd be +1 on this plan, although we should note that this is >>> the plan in >>> >> > the >>> >> > release announcement. We may also want to note that there are >>> some >>> >> > issues >>> >> > with volume rendering of oct and particle data at the moment >>> (I believe >>> >> > that's the case - let me know if I'm wrong there). >>> >> > >>> >> > I think that leaves analysis modules and documentation as the >>> main >>> >> > blockers >>> >> > for a 3.0 release. >>> >> > >>> >> > -Nathan >>> >> > >>> >> > >>> >> > >>> >> > On Tue, Jun 24, 2014 at 9:53 AM, John ZuHone < >>> jzuhone@gmail.com> wrote: >>> >> >> >>> >> >> +1 on Matt's proposal. -1 on a beta. >>> >> >> >>> >> >> My worry about a beta release is that it will slow adoption, >>> whether >>> >> >> rightly or wrongly. I think we agree that we're ready to >>> encourage >>> >> >> adoption >>> >> >> of 3.0. >>> >> >> >>> >> >> John ZuHone >>> >> >> Laboratory for High-Energy Astrophysics >>> >> >> NASA/Goddard Space Flight Center >>> >> >> 8800 Greenbelt Rd., Mail Code 662 >>> >> >> Greenbelt, MD 20771 >>> >> >> (w) 301-286-2531 >>> >> >> (m) 781-708-5004 >>> >> >> john.zuhone@nasa.gov >>> >> >> jzuhone@gmail.com >>> >> >> >>> >> >> > On Jun 24, 2014, at 12:38 PM, Matthew Turk < >>> matthewturk@gmail.com> >>> >> >> > wrote: >>> >> >> > >>> >> >> > I think Britton covered the halos, but the VR works as-is. >>> As far as >>> >> >> > 3.0beta, I'm a bit nervous about that as we want to avoid >>> the >>> >> >> > situation where we are in beta for 1+ years... I am worried >>> about the >>> >> >> > perception of a "beta" tag. Is that overblown? Would >>> calling it >>> >> >> > "yt-3.0-2014" work? >>> >> >> > >>> >> >> >> On Tue, Jun 24, 2014 at 10:32 AM, Nathan Goldbaum >>> >> >> >> wrote: >>> >> >> >> Do the old VR and halo interfaces work? Not much effort >>> has gone >>> >> >> >> into >>> >> >> >> porting them, I think. >>> >> >> >> >>> >> >> >> >>> >> >> >>> On Tuesday, June 24, 2014, Sam Skillman < >>> samskillman@gmail.com> >>> >> >> >>> wrote: >>> >> >> >>> >>> >> >> >>> I'm +1 on this, particularly since I'm at fault for not >>> pushing on >>> >> >> >>> the >>> >> >> >>> VR >>> >> >> >>> as much as I'd like to. >>> >> >> >>> >>> >> >> >>> >>> >> >> >>> On Tue, Jun 24, 2014 at 7:44 AM, Matthew Turk >>> >> >> >>> >>> >> >> >>> wrote: >>> >> >> >>>> >>> >> >> >>>> Hi all, >>> >> >> >>>> >>> >> >> >>>> One thing we really tried to do with 3.0 was break all >>> the APIs we >>> >> >> >>>> thought we'd need to before release. This included >>> things like >>> >> >> >>>> ds/pf, >>> >> >> >>>> index/hierarchy, the way data selections were made, etc. >>> >> >> >>>> >>> >> >> >>>> It's starting to become clear that we are approaching >>> maturity at >>> >> >> >>>> different rates in these initiatives. I am wondering if >>> perhaps >>> >> >> >>>> we >>> >> >> >>>> should de-couple the release from all of the API >>> breakages, and >>> >> >> >>>> instead note which interfaces we know are going to >>> change in the >>> >> >> >>>> future. >>> >> >> >>>> >>> >> >> >>>> Pragmatically, what this would mean is: >>> >> >> >>>> >>> >> >> >>>> * Release a 3.0 with the old VR and halo finding >>> interfaces >>> >> >> >>>> * Release a 3.1 with either the new VR or the new halo >>> finding (or >>> >> >> >>>> both) >>> >> >> >>>> * Do the same for 3.2 >>> >> >> >>>> >>> >> >> >>>> This doesn't fit with the usual "major numbers are where >>> APIs >>> >> >> >>>> break" >>> >> >> >>>> philosophy that comes from semantic versioning, but I >>> think from >>> >> >> >>>> the >>> >> >> >>>> perspective of pragmatism, if we identify those

not the door people who sections

...

>>> of the >>> >> >> >>>> code >>> >> >> >>>> that are *going* to change, and we pitch 3.0 as the >>> first part of >>> >> >> >>>> a >>> >> >> >>>> staged release of totally rewritten infrastructure, we >>> can likely >>> >> >> >>>> come >>> >> >> >>>> out okay. >>> >> >> >>>> >>> >> >> >>>> I'd like to put this out there for discussion. >>> >> >> >>>> >>> >> >> >>>> -Matt >>> >> >> >>>> _______________________________________________ >>> >> >> >>>> yt-dev mailing list >>> >> >> >>>> yt-dev@lists.spacepope.org >>> >> >> >>>> >>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >>> >> >> >> >>> >> >> >> _______________________________________________ >>> >> >> >> yt-dev mailing list >>> >> >> >> yt-dev@lists.spacepope.org >>> >> >> >> >>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >>> >> >> > _______________________________________________ >>> >> >> > yt-dev mailing list >>> >> >> > yt-dev@lists.spacepope.org >>> >> >> > >>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >>> >> >> _______________________________________________ >>> >> >> yt-dev mailing list >>> >> >> yt-dev@lists.spacepope.org >>> >> >> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >>> >> > >>> >> > >>> >> > >>> >> > _______________________________________________ >>> >> > yt-dev mailing list >>> >> > yt-dev@lists.spacepope.org >>> >> > http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >>> >> > >>> >> _______________________________________________ >>> >> yt-dev mailing list >>> >> yt-dev@lists.spacepope.org >>> >> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >>> > >>> > >>> > >>> > _______________________________________________ >>> > yt-dev mailing list >>> > yt-dev@lists.spacepope.org >>> > http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >>> > >>> _______________________________________________ >>> yt-dev mailing list >>> yt-dev@lists.spacepope.org >>> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >>> >> >> >> _______________________________________________ >> yt-dev mailing list >> yt-dev@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org >> >> > > > -- > Cameron Hummels > Postdoctoral Researcher > Steward Observatory > University of Arizona > http://chummels.org >

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