BUG: Track blockless particles

[matthewturk]

This is a first step at tracking blockless particles, as noted in #3681. It needs two things before it can go in:

• Whatever we end up with in _read_particle_coords (which I'm hoping someone will have suggestions to improve) needs to be mirrored in _read_particle_fields.
• We need to add a test dataset to catch and verify this behavior.

[matthewturk]

While I was implementing the other part of it, I realized that there may be issues with sub-chunking. I think what we need to ensure is that we don't need to read backwards as well as extra-forwards. I think we do not, but I'm keeping this note here just in case.

[matthewturk]

I have convinced myself that start should always be the lower bound, so we don't need bidirectional buffering.

@jzuhone I think this is ready for review, and I'm happy to walk through it with you if that would help.

[neutrinoceros]

a couple comments. I have not reviewed the rest in detail yet. In any case my review shouldn't be required to get this in.

[jzuhone]

@matthewturk can we set up a time for you to walk me through this?

[matthewturk]

@jzuhone Yeah, absolutely. What if we did something on Friday afternoon?

[jzuhone]

This looks good to me, but we just need a test, as you say

[jzuhone]

What should we do to get this over the finish line?

[matthewturk]

@jzuhone I think I need to set aside time to add the test. I will put it on my schedule for today or tomorrow. If you want to try, have at it, but I suspect you've got stuff on your plate too.

[neutrinoceros]

adding this to the 4.0.3 milestone since it looks close to completion.

[matthewturk]

The new test data can be found at: http://use.yt/upload/d6e42681

[jzuhone]

I think we just need to get the file on the machine, right?

[neutrinoceros]

New datasets need to be registered in yt-project/website as well as yt/sample_data_registry.json

[neutrinoceros]

Here's the required patch for this branch

--- a/yt/sample_data_registry.json
+++ b/yt/sample_data_registry.json
@@ -271,6 +271,12 @@
     "load_name": "plt00015",
     "url": "https://yt-project.org/data/Laser.tar.gz"
   },
+  "LocBub_dust.tar.gz": {
+    "hash": "1ad9728ca982616686d9bd6c1c959fece3c067ecbbba64ff8c2c5bfcc1deed01",
+    "load_kwargs": {},
+    "load_name": "LocBub_dust_hdf5_plt_cnt_0220",
+    "url": "https://yt-project.org/data/LocBub_dust.tar.gz"
+  },
   "MagneticumCluster.tar.gz": {
     "hash": "403c2224c205a44ee92a5925053be8aef6e5d530d9297c18151cdb0f588c32a7",
     "load_kwargs": {

[neutrinoceros]

And here's the companion PR on the website repo : yt-project/website#113

[neutrinoceros]

I took the liberty to push the patch above to register the new data sample, and confirm that yt.load_sample("LocBub_dust") now works as expected.

Provided tests pass, I think this is now ready to merge since it was previously approved by @jzuhone

[neutrinoceros]

Ah, looks like the dataset wasn't properly installed on the testing server yet. Maybe @Xarthisius can handle this ?

[matthewturk]

@Xarthisius I don't think I know how to do that. :(

[Xarthisius]

@yt-fido test this please.

[neutrinoceros]

thanks !

[neutrinoceros]

@meeseeksdev backport to yt-4.0.x

[lumberbot-app]

Owee, I'm MrMeeseeks, Look at me.

There seem to be a conflict, please backport manually. Here are approximate instructions:

1. Checkout backport branch and update it.

git checkout yt-4.0.x
git pull

2. Cherry pick the first parent branch of the this PR on top of the older branch:

git cherry-pick -x -m1 d56de5e01cf0f3565facf5dd2a9978c4bad31e18

3. You will likely have some merge/cherry-pick conflict here, fix them and commit:

git commit -am 'Backport PR #3683: BUG: Track blockless particles'

4. Push to a named branch:

git push YOURFORK yt-4.0.x:auto-backport-of-pr-3683-on-yt-4.0.x

5. Create a PR against branch yt-4.0.x, I would have named this PR:

"Backport PR #3683 on branch yt-4.0.x (BUG: Track blockless particles)"

And apply the correct labels and milestones.

Congratulations — you did some good work! Hopefully your backport PR will be tested by the continuous integration and merged soon!

Remember to remove the Still Needs Manual Backport label once the PR gets merged.

If these instructions are inaccurate, feel free to suggest an improvement.

[neutrinoceros]

manually backported as #3894