DOC: Sample notebook error

[zhafen]

Bug report

As of this moment, the sample notebook hosted at https://yt-project.org/doc/examining/generic_particle_data.html appears to be failing with RuntimeError: length_unit (pc) is invalid.
It's the first google result for "yt particle data", so it's a relatively visible failure.

No code for reproduction necessary. I'm referring to the html page generated and hosted at the above link.

[neutrinoceros]

I'm going to look into this, sorry it's taken so long.
So, we already know that the first error is easily fixed thanks to #3542, but there is at least one other problem that seems harder to track down.
This failure seems to go so far back in our history that I can't even git bisect it easily as I'm stumbling on pip/cython errors using present-day versions.
At the moment the only point in time that I was able to get a stable run for is 42c037d

[neutrinoceros]

So I tried again to bisect this problem using git bisect skip for commits that I cannot compile on my laptop but the process is daunting. Here's what I got so far

git bisect log

git bisect start
# bad: [564450aa2b0efe5195811b11c533561f4926adca] Merge pull request #3831 from neutrinoceros/migrate2tomli
git bisect bad 564450aa2b0efe5195811b11c533561f4926adca
# bad: [2c1c46b686155a2c337b1ac97240e8e869c5d28f] Merge pull request #3551 from yt-project/pre-commit-ci-update-config
git bisect bad 2c1c46b686155a2c337b1ac97240e8e869c5d28f
# good: [42c037dce30e37010792511c039e3d9c5c50e68e] Merge branch 'master' of github.com:yt-project/yt
git bisect good 42c037dce30e37010792511c039e3d9c5c50e68e
# bad: [60fd5f31a4f36399e35a7260162afe554a97d878] Merge pull request #2696 from Xarthisius/amrvac_test_ds
git bisect bad 60fd5f31a4f36399e35a7260162afe554a97d878
# bad: [7dae7a31b2675501596218d73924517de5975d4e] Fix the species list
git bisect bad 7dae7a31b2675501596218d73924517de5975d4e
# skip: [43237a90787f9a6ff122f8efcaef6d7f61eb0082] reimplemeneted richcmp operator overload
git bisect skip 43237a90787f9a6ff122f8efcaef6d7f61eb0082
# skip: [43237a90787f9a6ff122f8efcaef6d7f61eb0082] reimplemeneted richcmp operator overload
git bisect skip 43237a90787f9a6ff122f8efcaef6d7f61eb0082
# good: [b886b59e3f264f1ba4e909bc01f97800a93d637b] Merge pull request #2079 from adammcmaster/fix-field-data
git bisect good b886b59e3f264f1ba4e909bc01f97800a93d637b
# skip: [3bea08b52c395ba6631cca081e24afed8cee979a] fixed a bug with the struct sizes
git bisect skip 3bea08b52c395ba6631cca081e24afed8cee979a
# skip: [da2183ab1426b5dc8219076c2d759f7d1009aed6] merging with matt's work that added per-file chunking to Gadget HDF5
git bisect skip da2183ab1426b5dc8219076c2d759f7d1009aed6
# skip: [7334e8c737d76efa7ca86641fc9572945536c2e4] Updating bitarray
git bisect skip 7334e8c737d76efa7ca86641fc9572945536c2e4
# skip: [720647d7b0c15d02d076e2d49de71e0f1a568b6c] Removed compile-time directive GhostsAfter
git bisect skip 720647d7b0c15d02d076e2d49de71e0f1a568b6c
# skip: [b9ea661c416f94489aa6fb7813859959594a85b4] fixed the swift dataset tests
git bisect skip b9ea661c416f94489aa6fb7813859959594a85b4
# bad: [8108b176ca11959f7af9ac4f97f479fc6539a8ef] remove h5py string saving hack
git bisect bad 8108b176ca11959f7af9ac4f97f479fc6539a8ef
# skip: [50bfbf840b93f324e0c464b64bf2970502d7f8f5] removed shrink to fit and further work on the ytoctree get_data method
git bisect skip 50bfbf840b93f324e0c464b64bf2970502d7f8f5
# skip: [c9b0a163df223ddc1b480cdc488238e5449eebcc] Center tests
git bisect skip c9b0a163df223ddc1b480cdc488238e5449eebcc
# skip: [72d53547ef9260134dd4f66a7e31afe90aee5e26] Removing n_ref and over_refine_factor from the stream frontend
git bisect skip 72d53547ef9260134dd4f66a7e31afe90aee5e26
# good: [a1e5d60c3f5c3aa5f28f9537b40f87820f40a0ef] move cartopy helper functions to standalone file
git bisect good a1e5d60c3f5c3aa5f28f9537b40f87820f40a0ef
# skip: [424d84170db1961c3c3992310ffee841205dee06] fixed bug in pid bounded priority queue, this is working now with its own validation function
git bisect skip 424d84170db1961c3c3992310ffee841205dee06
# skip: [d78e7a98ad71b26688e2cd250a3239a603f20726] Merging
git bisect skip d78e7a98ad71b26688e2cd250a3239a603f20726
# skip: [a1a429cc9eb94175bff18ddf1a23093cc2e10f65] added scatter/gather approach to the new octree - very rough around the edges
git bisect skip a1a429cc9eb94175bff18ddf1a23093cc2e10f65
# skip: [270d00dd9558b1f17f2d10eb0a8fb1fa361afc44] minor changes and additions for morton functions"
git bisect skip 270d00dd9558b1f17f2d10eb0a8fb1fa361afc44
# skip: [33b80201bd1b149f498b69f6afe8487966d46999] fixing undefined behaviour bug in the offaxisprojection
git bisect skip 33b80201bd1b149f498b69f6afe8487966d46999
# good: [e921e23db9c3fe12a4f6268576bc1eca35a64e2f] one more try to fix permissions issue
git bisect good e921e23db9c3fe12a4f6268576bc1eca35a64e2f
# skip: [55dad77628ebb2e4e03c7c152f2eb2969c37aa82] finally wired up the _fill_sph_particles for YTArbitraryGrid. this appears to be working
git bisect skip 55dad77628ebb2e4e03c7c152f2eb2969c37aa82
# skip: [afc2b0c11633aa873f567d6fc5999db7f906509b] changed all the prange to range until the cython issue is addressed
git bisect skip afc2b0c11633aa873f567d6fc5999db7f906509b
# skip: [3a01e85a987843293bcb1db51e0a6dd15a0e7dbe] fix cython compiler error
git bisect skip 3a01e85a987843293bcb1db51e0a6dd15a0e7dbe
# skip: [48c4f5c1ca775f85841efcc6fc8272106b180124] Fixed the bug in the sph arbritrary grid! note to self (and anyone else) always debug cython code with bounds checking on
git bisect skip 48c4f5c1ca775f85841efcc6fc8272106b180124
# skip: [7b6861579b08460631a0ee9bb8777f28d911f9e5] safer memory allocation, fix func return types and neatened up doc
git bisect skip 7b6861579b08460631a0ee9bb8777f28d911f9e5
# skip: [33b358fb38d0aab6a8b2117d126c1dfacfd27adc] delete exceptions that have been moved to unyt
git bisect skip 33b358fb38d0aab6a8b2117d126c1dfacfd27adc
# skip: [b8932ca356b1b448d6ca52f96e1d1f48616f3046] Fix chained selectors for particle data, add test
git bisect skip b8932ca356b1b448d6ca52f96e1d1f48616f3046
# skip: [df9961e7361c75fa401be87c28822dfbb24040e1] moved the generate_sph_field method to the arbitrary grid class.
git bisect skip df9961e7361c75fa401be87c28822dfbb24040e1
# skip: [b357bcd3aceff42bf396f80fc5a9667f2164eabd] Merge branch 'yt-4.0' of https://github.com/yt-project/yt into yt-4.0-octree
git bisect skip b357bcd3aceff42bf396f80fc5a9667f2164eabd
# good: [7e0ae14afcb201a03963d7db47a8de8dec3891c7] skip UTM in answer tests as well
git bisect good 7e0ae14afcb201a03963d7db47a8de8dec3891c7
# skip: [5821d696df1c8041e7254d20e2e408de6bb8bc73] modified to only call the method for arbitrary grids and not any yt data container
git bisect skip 5821d696df1c8041e7254d20e2e408de6bb8bc73
# skip: [73873f47a320001a8535a4cd30e336848de0ed2c] remove over_refine_factor and n_ref from FLASHParticleDataset
git bisect skip 73873f47a320001a8535a4cd30e336848de0ed2c
# skip: [a26e242d4141d80bba7dbd45c26081f00c1caddc] hook up SPH slice pixelizer
git bisect skip a26e242d4141d80bba7dbd45c26081f00c1caddc
# skip: [09d378a49357fc4a07823d965499ccfb971e5b7b] use inverse matrix to do rotations for SPH off-axis projections
git bisect skip 09d378a49357fc4a07823d965499ccfb971e5b7b
# bad: [73d4f281b568bfb306bba91969e051bfa404754a] Implement chunked io in _read_particle_positions.
git bisect bad 73d4f281b568bfb306bba91969e051bfa404754a
# skip: [4b0b3ee300b656b06ae4c5699d23ce342b32881d] try to fix compiling on windows
git bisect skip 4b0b3ee300b656b06ae4c5699d23ce342b32881d
# skip: [7765003eb8b775abba891b7fa0e1f84d6c86a1b3] Adapt to the new semantics for the MaxLocation derived quantity
git bisect skip 7765003eb8b775abba891b7fa0e1f84d6c86a1b3
# skip: [c097be8cd8d88e4fe96ec7aabeaa5cfde29a80e5] Add an index_octree and finalize method to the forest.
git bisect skip c097be8cd8d88e4fe96ec7aabeaa5cfde29a80e5
# skip: [f4492748bc6d2b8c9244bdf8735079818cec27be] clear conflicts
git bisect skip f4492748bc6d2b8c9244bdf8735079818cec27be
# good: [1bccd8a78b413fe10ae7258e01ccd0345b9e8916] Added support for multiresultion N-body particles for artio frontend
git bisect good 1bccd8a78b413fe10ae7258e01ccd0345b9e8916
# skip: [3c5569a2e022344a75985ce820e8858ccb0ae8fb] teach test_load_particles_types about the nbody particle union
git bisect skip 3c5569a2e022344a75985ce820e8858ccb0ae8fb
# skip: [f64338697f50d6c11e2db0ca7b2e11fec93e1aed] re-structued the progress bar for the arbitrary_grid function
git bisect skip f64338697f50d6c11e2db0ca7b2e11fec93e1aed
# skip: [3a4b8dbc939d44daeee90e939f46bc7a14538f55] Merge branch 'master' into yt-4.0
git bisect skip 3a4b8dbc939d44daeee90e939f46bc7a14538f55
# skip: [fc9f09b633e612fd3ebe71c8605bfeb6efc8d16a] update gitignore
git bisect skip fc9f09b633e612fd3ebe71c8605bfeb6efc8d16a
# skip: [30f5320cd9c2d70de03a0f66a8bfcc783c9955b8] Remove analysis_modules from table.py.
git bisect skip 30f5320cd9c2d70de03a0f66a8bfcc783c9955b8
# skip: [74ba220afd6aa4db3a58be7cf42ae3dec4709261] fix domain_width not being initialized correctly
git bisect skip 74ba220afd6aa4db3a58be7cf42ae3dec4709261
# skip: [d4b2fa33034843616fa7ff005a534ddbf014c790] Merge pull request #2071 from ngoldbaum/yt-4.0
git bisect skip d4b2fa33034843616fa7ff005a534ddbf014c790
# skip: [a136f43a85a0e598cc7d1b1114b182b4cfed31ae] updated the comments to sph slice projection
git bisect skip a136f43a85a0e598cc7d1b1114b182b4cfed31ae
# skip: [b4d010ac1f4c2e6b6e62255dc143b95fde23e25f] Passing index
git bisect skip b4d010ac1f4c2e6b6e62255dc143b95fde23e25f
# skip: [f21e3694d7993cff3fe0773abc15b7605ce74c85] Merge branch 'master' into sph-viz
git bisect skip f21e3694d7993cff3fe0773abc15b7605ce74c85
# skip: [ebf402f6efa80d9154e5888c8cee0cd38f9c0e6a] Merge pull request #1997 from jzuhone/fix_min
git bisect skip ebf402f6efa80d9154e5888c8cee0cd38f9c0e6a
# skip: [c9a3de52627ee63a631e81a498a7bf206b822ae3] Merge pull request #2 from chummels/weight
git bisect skip c9a3de52627ee63a631e81a498a7bf206b822ae3
# skip: [b12311a4b637be2c9bd66c917b2615837e00f262] added some documentation for the new octree
git bisect skip b12311a4b637be2c9bd66c917b2615837e00f262
# skip: [dedf4edaf83fee0021c351d70810808da33c2842] fix unintentional API break for the min and max location derived quantities
git bisect skip dedf4edaf83fee0021c351d70810808da33c2842
# skip: [006a40521f7ed50759227b97aa78a49adff91f4b] adding py37 answers
git bisect skip 006a40521f7ed50759227b97aa78a49adff91f4b
# skip: [7b7baecb41f34fa56a64919e6ae95488cfc6ad24] fix cut region field access
git bisect skip 7b7baecb41f34fa56a64919e6ae95488cfc6ad24
# skip: [0cbcf221f65b54924b79f24b65c64d212cce4853] refactored the octree scatter and gather methods and added pbars
git bisect skip 0cbcf221f65b54924b79f24b65c64d212cce4853
# skip: [d210865567a795be3e24b7345d3b4dc1428b53c3] Add basic KDTree projection data object, does not actually work
git bisect skip d210865567a795be3e24b7345d3b4dc1428b53c3
# skip: [b9cfa553b6a34a7bf103920bf4a0f4cafce829f4] merging with upstream
git bisect skip b9cfa553b6a34a7bf103920bf4a0f4cafce829f4
# skip: [12c7ef97cf666fddb6e8b7a0a637c0ecfacb9002] Abort when we detect a negative smoothing length
git bisect skip 12c7ef97cf666fddb6e8b7a0a637c0ecfacb9002
# skip: [7b36f9df38112f386bae6aef79caeb3201e61948] Fixed issue with ewah that left hanging reference
git bisect skip 7b36f9df38112f386bae6aef79caeb3201e61948
# skip: [667d1c5a103e20a447a0a1bc56309f0fe375964d] teach test_stream_particles about the nbody particle type
git bisect skip 667d1c5a103e20a447a0a1bc56309f0fe375964d
# skip: [d075e391e397351455cc8c641a491b6580eee129] removed use of hasattr
git bisect skip d075e391e397351455cc8c641a491b6580eee129
# skip: [b7d77ccc5ccbc02b933d4f807e80b4004efd09db] Adding new interpolation table class
git bisect skip b7d77ccc5ccbc02b933d4f807e80b4004efd09db
# skip: [7e7be2a05ea722dd70376b5709367ee8a0ecaf22] add tests for sphere, disk, and ray
git bisect skip 7e7be2a05ea722dd70376b5709367ee8a0ecaf22
# skip: [47220d2133360bfd2e5450a7aee815a29f4a0d29] Adjust selectors for SPH fields.
git bisect skip 47220d2133360bfd2e5450a7aee815a29f4a0d29
# skip: [f4207c62267a49b925c83852e886dabf9e631177] fix failing tests
git bisect skip f4207c62267a49b925c83852e886dabf9e631177
# skip: [12f97419b98ff7c9da782ce303c7243d34e960d2] Begin buffer mask work.
git bisect skip 12f97419b98ff7c9da782ce303c7243d34e960d2
# skip: [3d0e6ab56df415f40e590ea3473c2f4d835a97e2] remove unused keyword arguments from RockstarDataset
git bisect skip 3d0e6ab56df415f40e590ea3473c2f4d835a97e2
# skip: [374927aba98b103113b2d61e6c36090b9edb702b] Fixing missing parameter from merge
git bisect skip 374927aba98b103113b2d61e6c36090b9edb702b
# skip: [da1a39cebd776bde23525ebf44da0e1a653ba584] Make particle datasets do an I/O pass to infer the bounding box if it is unset
git bisect skip da1a39cebd776bde23525ebf44da0e1a653ba584
# skip: [105a535684f141a4c1c4924a0b88029ad94ac268] Fix factors of 2 issues in the calculation of the 'dts' field
git bisect skip 105a535684f141a4c1c4924a0b88029ad94ac268
# skip: [54fa05b6ed61ee27beb8ec79e6ad66c4e4fa8701] further additions to the code which should be able to loop through pixels finding the nearest neighbours and their pids
git bisect skip 54fa05b6ed61ee27beb8ec79e6ad66c4e4fa8701
# skip: [b71d56a83c96dd07790483b33e9775e309eeca02] Merging from upstream
git bisect skip b71d56a83c96dd07790483b33e9775e309eeca02
# skip: [52c23200f16a235308f745fef78ef8b710372817] added some name mangled functions to the bounded priority queue to deal with a second array of particle id's so it is possible to know which neighbours are the closest
git bisect skip 52c23200f16a235308f745fef78ef8b710372817
# skip: [35af648932b06aaa4b480b156da0f079c4d4139e] Add a keys map to BoolArrayCollection.
git bisect skip 35af648932b06aaa4b480b156da0f079c4d4139e
# skip: [88b4fc05f370f9febc983a20407bc889a3cd3041] Fix I/O for tipsy.
git bisect skip 88b4fc05f370f9febc983a20407bc889a3cd3041
# skip: [62a8d50ff20bbe64ffaaa9b43587605252654515] do linting on python3.7
git bisect skip 62a8d50ff20bbe64ffaaa9b43587605252654515
# skip: [13e9e064c5b5eafcc09b69336806bba4a735c7c4] accidentally changed an import -- fixed now
git bisect skip 13e9e064c5b5eafcc09b69336806bba4a735c7c4
# skip: [eb8e3718dadaea1eda12617ea91f87465e6ac7f5] Added option to only refine and add ghost zones at selector edges
git bisect skip eb8e3718dadaea1eda12617ea91f87465e6ac7f5
# skip: [ad56642b1f806130cab2a87d16242a216afbbe3e] Merge branch 'master' of github.com:ngoldbaum/yt into sph-viz
git bisect skip ad56642b1f806130cab2a87d16242a216afbbe3e
# skip: [67fbab35ccd4d7473a3b98a8cec3768d7c934e77] Checking
git bisect skip 67fbab35ccd4d7473a3b98a8cec3768d7c934e77
# skip: [fcade2598dba53599f65b9d879136e8165e26117] attempting to add an sph interface to the arbitrary grid
git bisect skip fcade2598dba53599f65b9d879136e8165e26117
# skip: [1619dea08c23649a7bc78bbae9f6dec8f7b89188] Particle counts attempt
git bisect skip 1619dea08c23649a7bc78bbae9f6dec8f7b89188
# skip: [5fc949e84d50ba082c81e5946414c8b980ec83df] Merge pull request #1795 from ngoldbaum/yt-4-version-numbers
git bisect skip 5fc949e84d50ba082c81e5946414c8b980ec83df
# skip: [f840288b89da395682245471065ee93fc12d12bd] used boilerplate gather all data in more places
git bisect skip f840288b89da395682245471065ee93fc12d12bd
# skip: [8d1d46f44eb2e237bad36553cf29e3f13f8492c1] Add hashing step to particle data ingestion
git bisect skip 8d1d46f44eb2e237bad36553cf29e3f13f8492c1
# skip: [b0ec4eaa75b10ff103a27664595dc5e11b8739e3] Merging from upstream
git bisect skip b0ec4eaa75b10ff103a27664595dc5e11b8739e3
# skip: [0ac6a483e8bd087e94eff04451b6f412f6ccd104] Implementing weighted projections in cython pixelization routine.
git bisect skip 0ac6a483e8bd087e94eff04451b6f412f6ccd104
# skip: [a63bb9e825b2facd961ef399d26bf02ebeb0465f] Merge pull request #1984 from ngoldbaum/precision-issues
git bisect skip a63bb9e825b2facd961ef399d26bf02ebeb0465f
# skip: [e67fcc0e90faf961d95d46567a8389b2be673446] Ensure _initialize_index gets called for Gadget binary data
git bisect skip e67fcc0e90faf961d95d46567a8389b2be673446
# skip: [3a7d70a485704f58b8ea8fd0f09b46b947ed8de3] added a basic frontend to support the Swift output
git bisect skip 3a7d70a485704f58b8ea8fd0f09b46b947ed8de3
# skip: [305820a443daacb0d0087976d3e32811f29b1553] delete unused code in particle_oct_container.pyx
git bisect skip 305820a443daacb0d0087976d3e32811f29b1553
# skip: [572a985dbb25cbe84c88a6b5d96e92ba2b48b52c] remove use of GNU-only C standard library code
git bisect skip 572a985dbb25cbe84c88a6b5d96e92ba2b48b52c
# skip: [613f7cdee3650dcf7a1293299607889cf414fc83] Seprate YTQuadTreeProj into two classes for easier subclassing
git bisect skip 613f7cdee3650dcf7a1293299607889cf414fc83
# skip: [a6c7e509bb438c113fc8c9074849add3760de676] Changed refined index to include smoothing in mask
git bisect skip a6c7e509bb438c113fc8c9074849add3760de676
# skip: [614a72de5490cb38f1241bb76a360e41e2aff86c] fix gadget binary IO offsets
git bisect skip 614a72de5490cb38f1241bb76a360e41e2aff86c
# skip: [ed95b1ac2f7105092b1116f9c76568ae27024751] Removed compile-time directive BoolType
git bisect skip ed95b1ac2f7105092b1116f9c76568ae27024751
# good: [5a44545059b06c069bb7484606fa8de12eedaef4] Add support for omega_radiation to Enzo frontend and add it as an attribute for cosmological datasets.
git bisect good 5a44545059b06c069bb7484606fa8de12eedaef4
# skip: [3a10896b2a032bbabb6a6f850645f3cb52501002] merging with master
git bisect skip 3a10896b2a032bbabb6a6f850645f3cb52501002
# skip: [41c655dfd916d4e1721d1631d3045fe3bc4d49a9] Merge branch 'master' into yt-4.0
git bisect skip 41c655dfd916d4e1721d1631d3045fe3bc4d49a9
# skip: [55f5388898c08c3e126692dbf4489dd28a369544] Add a new VisibleDeprecationWarning class
git bisect skip 55f5388898c08c3e126692dbf4489dd28a369544
# skip: [fd4941b7b2e9efa96e6adbc7d75356a1e498842b] Delete unused code and print statements in test_particle_octree and convert yield asserts to plain asserts
git bisect skip fd4941b7b2e9efa96e6adbc7d75356a1e498842b
# skip: [d786bca874a7f1220e0883b31357cb9b41711298] add test for SPH field semantics
git bisect skip d786bca874a7f1220e0883b31357cb9b41711298
# skip: [7e0174ea7513affe478f93190ac0db38b65f5141] Fixed mistakes in yt4differences
git bisect skip 7e0174ea7513affe478f93190ac0db38b65f5141
# skip: [5a9550797627d9d2d2539c0faf8c6c3dc7ece49a] Refactor calculation of 'dts' and 't' field for SPH ray
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# skip: [d02013ca7ad1092defd2b88ba93f0826a14338d0] removed some redundant comments in the bounded priority queue
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# skip: [38a2f498d6efe6f4f49ee5f379a83b4ee72330ba] Added support for bitwise addition of > 1
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# skip: [7e11853f34b55fba37ee4a6cfead72f4d8af28fd] Added most of the off-axis logic
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# skip: [746c80cd72c41c7caceb70c5ac2ec2e93b21a8b4] re-enabled normalizatio
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# skip: [4803922b3e7e6cca0b2f059a0f968b76db1b0921] Added a new test data set for sph data and used this to test the ability of arbitrary grid to load sph data and to test the accuracy of the arbitrary grid pixelization routine
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# skip: [d3345d6adb549170b95c9f3e249983a3829b26ae] Merge branch 'master' into sph-viz
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# skip: [4b76dd960cb961e9167f1cff219f67434cad3678] Merge pull request #2085 from MatthewTurk/flake8_nits_4
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# skip: [767761386c94ce6b4c0a85fa79529f8ee41832f9] updated the comments on the pixelize_sph_kernel_arbitrary_grid cython function
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# skip: [60280839c79615476100bba9439198f43741c305] fixed flake8 failiure
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# skip: [9fe749fc38eb71aa528b999cfbc631918ad4cd47] Fix I/O for non-SPH tipsy fields
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# skip: [05e720d8cc7786cd24263444a68f066ff462f8ac] Adding test using north_vector in OAP.
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# skip: [c82113d75c16e2a16b96095fed33d0afa8455008] Merge pull request #1934 from ngoldbaum/sph-oap-rotation
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# skip: [6b1ed7ec67497bd9bd373cbf1cb3fb3485634fb4] skip add_smoothed_particle_field test until we decide about deprecation
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# skip: [4f52d8de8b34e47326cb15eeb86d341bf4433820] improved perfomance on random number of neighbors
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# skip: [e33c1d3e7d4f5ee30362f58f473046b294740ad2] fix rockstar I/O
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# skip: [bb20d4abf199a8766a2bc323f4d2e9632d3da19b] fixed bug in the bounded priority queue
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# skip: [e0198d75c841360bbc6ef6865e690f581841fc89] More optimizations
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# skip: [9665b2a820a77c62482e4efe1ca7f7d5bdbd96a2] Merge with Nathan
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# skip: [2b751118fd229c4293c89572b874e98ab4327925] ensure that the warning about using sampling type is raised at a more useful level in the call stack
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# skip: [86b5af77f2840ba6a7a0fe989e34fe2d5e8e8be0] narrowed issue to something going wrong when resetting the kdtree
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# skip: [3a56a520c90390e8df5f7ecc99a48abf7e1748b3] Adding EWAHBoolArray from https://github.com/lemire/EWAHBoolArray
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# skip: [ffb51320f7cf5828bb44bc4ca25fabc9bf4f5011] Unit consistency
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# skip: [777c4be1c93976fb717759a64736b512cc6a421d] Merge pull request #2138 from MatthewTurk/gadget_binary_fix_header
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# skip: [de92b7f47144c475971c86bedc1944d331a0c8b0] adding utility functions to allow passing of certain particle types to the octree
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# skip: [dfea49455e1ea364ed91dc80b38dcc49eae3bee5] Some changes to compile
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# skip: [8858c339c164aa0eaf9e1c2443c36afb5f4b3320] Fix I/O for Tipsy data.
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# skip: [a112b7a7c8faf3bdce2e1ce49569a34175cf6c6f] Merge pull request #2095 from ngoldbaum/yt-4.0
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# skip: [e631b655246e28a2e711e30aac488d51e4a2ccc8] Remove rockstar from install script.
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# skip: [c752780ad3687de0a666d3435c3c9faaa0b8778d] fixed some comments in the arbitrary pixelization routines and switched to code units for the arbitrary grid wiring
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# skip: [93d4e5e4c9ad9370ba01b24ac699df4833035d7f] Plots for paper in testing for now
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# skip: [3aaa7f5c6bae53ca4b159fbe526adb70d1b1a41b] add cykdtree to appveyor build
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# skip: [ef4bba5c8ffb58e272a435e9d7836a58c88bca60] Merge pull request #1889 from AshKelly/yt-4.0-octree
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# skip: [93a3dd8067bcc5b5bc028d0fdc9edd56840d6f22] fix photon simulator test failure
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# skip: [9d2c37eb697fe861b024974373f3c9c8db1a6fd6] fixed the density factor, finished up the tests and removed some redundant setters
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# skip: [18b68fb18e6eec4176a35829e139ffb7d1d3d891] Merge branch 'yt-4.0' of https://github.com/yt-project/yt into yt-4.0-covering-grid
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I suspect that the reason so many commits fail to compile is that I'm running this on MacOS. Hopefully it would be much easier to perform this bisection on Linux.

[neutrinoceros]

Not much more luck with Linux actually. At this point I would really like some pointers from @matthewturk
AFAICT we are not exercising the field ˋ("deposit", "all_cic")` anywhere else in the code base anymore so I'm not even sure it was supposed to survive into yt 4.0

[chrishavlin]

This error seems to be just that all of the loaders expect the unit parameters to be strings, not unyt units. e.g.,

ds = yt.load_particles(data, length_unit='parsec')

works but

ds = yt.load_particles(data, length_unit=unyt.parsec)

fails with RuntimeError: length_unit (parsec) is invalid.

All the other loaders (load_uniform_grid, load_octree, etc.) clearly state that all the unit parameters should be strings, but the load_particles docstring looks very out of date:

"""
...
    length_unit : float
        Conversion factor from simulation length units to centimeters
    bbox : array_like (xdim:zdim, LE:RE), optional
        Size of computational domain in units of the length_unit
    sim_time : float, optional
        The simulation time in seconds
    mass_unit : float
        Conversion factor from simulation mass units to grams
    time_unit : float
        Conversion factor from simulation time units to seconds
"""

So that docstring should probably be updated along with fixing the notebook. I do think it'd make sense to have the loaders accept unyt units in addition to strings but I'm not sure how hard that might be. I assume they used to accept unyt units since this notebook must have worked at one point...

[chrishavlin]

oh, just read throuhg the longer discussion in the PR that was closed so my comment above isn't super relevant. Ignore :)