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merging yt-4 into master #2437

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a4190a1
add test for name validator function
munkm Jan 17, 2020
438a56a
update pooch version requirement in test_requirements
munkm Jan 17, 2020
c0fccf0
Merge remote-tracking branch 'upstream/yt-4.0' into yt4-merge
matthewturk Jan 17, 2020
e0d200c
Merge remote-tracking branch 'upstream/master' into yt4-merge
matthewturk Jan 17, 2020
8dcc2fa
Merge pull request #2399 from brittonsmith/select
matthewturk Jan 23, 2020
3d87c62
Change py2-style print stmts to py3
cphyc Jan 28, 2020
19a0e0d
Fix erroneous docstrings
cphyc Jan 28, 2020
dbcf9c0
Remove extra () in docstrings
cphyc Jan 28, 2020
816301c
Merge pull request #2429 from cphyc/python3-prints
munkm Jan 28, 2020
0dc4584
WIP commit to put units in for the AREPO GFM_StellarFormationTime
dnarayanan Jan 30, 2020
b73839a
Update yt/frontends/arepo/fields.py
dnarayanan Jan 30, 2020
63e9c81
arepo stellar ages discriminate between cosmological and non cosmolog…
dnarayanan Jan 30, 2020
4af02db
Updating answer tests
matthewturk Feb 1, 2020
90d06ae
Updating py37 answer results
matthewturk Feb 3, 2020
b603db7
Use all available cores for both cythonize and build_ext
Xarthisius Feb 3, 2020
ce1abb6
Expanding docs and adding ability to list datasets
matthewturk Feb 3, 2020
7954759
Merge remote-tracking branch 'upstream/master' into yt4-merge
matthewturk Feb 3, 2020
f6407f2
Don't build in parallel on windows
Xarthisius Feb 3, 2020
8b59225
re-validizing yaml
matthewturk Feb 3, 2020
2b07fbb
Merge pull request #2438 from Xarthisius/parallel_build
munkm Feb 5, 2020
45f5e12
[setup] return 0 as number of cpus on windows to disable parallel build
Xarthisius Feb 5, 2020
d65aa2f
Drop unused import
Xarthisius Feb 5, 2020
1d1276d
Merge pull request #2441 from Xarthisius/parallel_build
matthewturk Feb 5, 2020
8073340
Merge remote-tracking branch 'upstream/master' into yt4-merge
matthewturk Feb 7, 2020
1050cdc
Unit objects need to have affiliated values
matthewturk Feb 7, 2020
fdeeb64
apply review suggestions from @cphyc
munkm Feb 12, 2020
87317d5
apply review suggestions from @neutrinoceros
munkm Feb 13, 2020
66d5c97
Merge pull request #2417 from jcoughlin11/pooch
ngoldbaum Feb 13, 2020
1dc8f40
Merge remote-tracking branch 'upstream/yt-4.0' into yt4-merge
matthewturk Mar 2, 2020
200728b
Merge remote-tracking branch 'upstream/master' into yt4-merge
matthewturk Mar 2, 2020
5656538
Missed a merge conflict that added a six import
matthewturk Mar 2, 2020
736039e
Mask is a slice in some cases, not an array.
matthewturk Mar 4, 2020
34049d6
Merge pull request #2472 from matthewturk/gadget_alldata_invarmass
munkm Mar 5, 2020
fd1e47c
Bump unyt to latest version for tests
Xarthisius Mar 10, 2020
667871c
Use proper name for B in cgs unit system
Xarthisius Mar 10, 2020
f8d3a4d
[streamlines] compute steps using unit sanitized values
Xarthisius Mar 10, 2020
e03694f
Merge branch 'upstream_master' into yt4-merge
Xarthisius Mar 10, 2020
a758ba0
Bump h5py for tests. h5py<=2.8.0 causes bugs in YTData serialization.
Xarthisius Mar 10, 2020
28401e8
Use floats to define start/end points
Xarthisius Mar 10, 2020
f209e1d
Temporarily drop units for answer comparison
Xarthisius Mar 16, 2020
b5963b2
Use requires_file instead _ds where appropriate
Xarthisius Mar 17, 2020
d41b04a
[ytdata] 'proj' -> 'quad_proj' for container_type
Xarthisius Mar 17, 2020
588a2a3
Temporarily disable part_traj test
Xarthisius Mar 17, 2020
cd43c48
Change order of multiplication in temp definition. Workaround for #2486
Xarthisius Mar 17, 2020
283a84a
make load_sample return load call
munkm Mar 22, 2020
056f8d5
Merge pull request #2496 from munkm/fix-loader
matthewturk Mar 22, 2020
c279201
add an annotate_list method
zingale Mar 24, 2020
aa20554
Adding repr methods for particle unions
matthewturk Mar 24, 2020
7b2d56b
clarify that the "height" in a disk region is from the midplane
zingale Mar 24, 2020
2a3d79f
address PR review
zingale Mar 25, 2020
63dd040
Merge pull request #2503 from zingale/disk_doc_fix
munkm Mar 25, 2020
08f46ea
remove IRC from communication channels
munkm Mar 25, 2020
258c82e
Merge pull request #2506 from munkm/comm-channels
munkm Mar 27, 2020
94819ce
Remove gperftools wrapper
matthewturk Mar 30, 2020
ab97110
Porting #2450 to yt-4.0
matthewturk Apr 1, 2020
4d15167
Responding to comments.
matthewturk Apr 1, 2020
ad35dc9
flake8 is throwing errors with 3.8
matthewturk Apr 1, 2020
7a56703
Merge remote-tracking branch 'upstream/yt-4.0' into yt4-merge
matthewturk Apr 1, 2020
a46431d
bump unyt to 2.7.1
matthewturk Apr 1, 2020
7f454ad
Conform to matplotlib 3.2+ API
matthewturk Apr 1, 2020
e63c13e
Adding in changes from #2448
matthewturk Apr 1, 2020
1438074
Attempt to get FLASH particle reads to work in yt-4.0
jzuhone Apr 7, 2020
42c9da0
Merge pull request #2515 from matthewturk/backport_filelike_png
matthewturk Apr 11, 2020
22c796a
Merge branch 'yt-4.0' of github.com:yt-project/yt into port-test-jobs…
matthewturk Apr 11, 2020
fe2cd24
Don't specify numpy version
matthewturk Apr 13, 2020
e01619c
bugfix for numpy 1.18: explicitly set dtype to int for variables used…
neutrinoceros Jan 17, 2020
0edb393
We only have answer results for 37, so use that
matthewturk Apr 13, 2020
c9ae3ae
Use master's py36 answer-stores
matthewturk Apr 13, 2020
aa92f0b
Cherry pick PR #2308
matthewturk Apr 13, 2020
db15daf
Removing answer-store subdirectory
matthewturk Apr 15, 2020
174790e
Track branch yt-4.0 in answer-store
matthewturk Apr 15, 2020
4cc3579
Merge pull request #2546 from matthewturk/answers_subrepo_yt40
munkm Apr 15, 2020
a529b89
Revert "Use master's py36 answer-stores"
matthewturk Apr 15, 2020
45d1d38
Merge branch 'yt-4.0' of github.com:yt-project/yt into port-test-jobs…
matthewturk Apr 15, 2020
c877900
Set a proper answer-store commit for yt-4.0
Xarthisius Apr 15, 2020
56215aa
Merge remote-tracking branch 'upstream/yt-4.0' into port-test-jobs-up…
matthewturk Apr 15, 2020
87548d6
Updating to new answer-store hash
matthewturk Apr 15, 2020
9385320
Merge pull request #2434 from dnarayanan/yt-4.0
munkm Apr 17, 2020
fecf079
Merge pull request #2513 from matthewturk/port-test-jobs-update
Xarthisius Apr 17, 2020
8fc0643
Merge branch 'yt-4.0' of github.com:yt-project/yt into remove_gperftools
matthewturk Apr 17, 2020
1ba3430
Merge branch 'yt-4.0' of github.com:yt-project/yt into union_repr
matthewturk Apr 17, 2020
efb3562
Change order of operations.
matthewturk Mar 17, 2020
79b68fe
Merge remote-tracking branch 'upstream/yt-4.0' into yt4-merge
matthewturk Apr 17, 2020
2c1c1a1
Merge remote-tracking branch 'upstream/master' into yt4-merge
matthewturk Apr 17, 2020
238f964
Add a latex_prefixes dict
matthewturk Apr 17, 2020
5fa44db
Fix two minor yt-4 updates
matthewturk Apr 17, 2020
693be3d
Just use "density" instead of a fake one
matthewturk Apr 17, 2020
c781b57
Fixing flake8
matthewturk Apr 17, 2020
40314a5
Merge branch 'master' of github.com:yt-project/yt into yt4-merge
matthewturk Apr 17, 2020
f9e6783
Merge pull request #2510 from matthewturk/remove_gperftools
matthewturk Apr 20, 2020
17bc285
Merge pull request #2487 from matthewturk/athena_order_of_op
munkm Apr 20, 2020
7e4d84a
Merge pull request #2502 from matthewturk/union_repr
munkm Apr 20, 2020
019c918
merging, resolving conflict
matthewturk Apr 22, 2020
595149f
Fixing FLASHParticleFile IO
matthewturk Apr 22, 2020
55fcc78
What, they were assigned to but never read?!
matthewturk Apr 22, 2020
6369053
dropped the second part of the slice
matthewturk Apr 23, 2020
862a30d
Merge branch 'flash_particles' of github.com:jzuhone/yt into fix_inco…
matthewturk Apr 23, 2020
f925775
Merging
matthewturk Apr 23, 2020
c2867fc
Merge branch 'fix_incompat_yt4' into yt4-merge
matthewturk Apr 23, 2020
7029c7c
Fix up reading particle coords
matthewturk Apr 23, 2020
73d4a67
Merge branch 'fix_incompat_yt4' into yt4-merge
matthewturk Apr 23, 2020
a7ab8d7
Fixing up particle field reading
matthewturk Apr 23, 2020
8bf1fbd
Merge branch 'fix_incompat_yt4' into yt4-merge
matthewturk Apr 23, 2020
1bd7177
annotate_list -> list_annotations
zingale Apr 26, 2020
c234925
Merge remote-tracking branch 'upstream/master' into yt4-merge
matthewturk Apr 27, 2020
d99f816
Merge pull request #2562 from zingale/annotate_list
munkm May 1, 2020
52d8b62
Merge branch 'master' of github.com:yt-project/yt into yt4-merge
matthewturk May 1, 2020
bb49bcb
Bumping AREPO answer test number
matthewturk May 1, 2020
4b5d7b6
Merge branch 'master' of github.com:yt-project/yt into yt4-merge
matthewturk May 1, 2020
c3ae3e0
First sketch of a particle selection tester
matthewturk May 4, 2020
0299776
Add in the smoothing length calculations
matthewturk May 4, 2020
073fbf9
Fix particle selection for sub-regions
matthewturk May 4, 2020
f3dd249
Had the logic for is_refined backwards
matthewturk May 5, 2020
7a99703
Updating tests to use particle selection comparison
matthewturk May 5, 2020
df4cf91
Update yt/geometry/particle_oct_container.pyx
matthewturk May 5, 2020
878e018
Update yt/geometry/particle_oct_container.pyx
matthewturk May 5, 2020
cc93f19
Update yt/geometry/particle_oct_container.pyx
matthewturk May 5, 2020
a8ef879
Updating from comments
matthewturk May 5, 2020
057aa91
Merge remote-tracking branch 'upstream/yt-4.0' into yt4-merge
matthewturk May 6, 2020
0a80070
Merge remote-tracking branch 'upstream/master' into yt4-merge
matthewturk May 6, 2020
63f935d
Execute setup only on parent thread to prevent failure with spawn. Fi…
Xarthisius May 6, 2020
dc76a48
Update the varia tests to match master
matthewturk May 6, 2020
83f38c4
fix: use '==/!=' for literal comparison instead of 'is'
neutrinoceros May 6, 2020
9c233f1
Merge pull request #2582 from Xarthisius/2581_osx_build
jzuhone May 6, 2020
04839c3
Coerce mx, my, mz to code-length
matthewturk May 6, 2020
55b17f5
Merge pull request #2584 from matthewturk/coerce_mxmymz_codelength
Xarthisius May 7, 2020
f44e867
Merge branch 'yt-4.0' of github.com:yt-project/yt into yt4-merge
matthewturk May 7, 2020
450f22b
Merge branch 'master' of github.com:yt-project/yt into yt4-merge
matthewturk May 7, 2020
d22947e
Refine tests a bit
matthewturk May 7, 2020
934a4eb
Add tests for wrapping on right
matthewturk May 7, 2020
402afa0
Rework periodic smoothing length calculations
matthewturk May 7, 2020
2e39ef1
Rework periodic smoothing length calculations
matthewturk May 7, 2020
404c244
Merge pull request #2583 from neutrinoceros/hotfix_literals_comp
Xarthisius May 7, 2020
0b68faf
We need bounds[i][1] + 1 for inclusive loops
matthewturk May 7, 2020
a5642b6
Merge branch 'fix_select_mi1mi2' of github.com:matthewturk/yt into fi…
matthewturk May 7, 2020
6f6dadc
Merge branch 'test_particle_selections' into fix_select_mi1mi2
matthewturk May 7, 2020
b20c3ed
remove unused import
matthewturk May 8, 2020
7356849
fixed typo in setup.py
AshKelly May 8, 2020
9647693
fix urllib.request import
AshKelly May 8, 2020
0f35f90
also import urllib.parse
AshKelly May 8, 2020
8cdf546
First, not-quite-working, pass at refined stuff.
matthewturk May 9, 2020
c284137
Merge pull request #2590 from AshKelly/yt-4.0-owlsfix
Xarthisius May 13, 2020
af135de
Temporary commit, still not working
matthewturk May 13, 2020
0062a98
Merge branch 'fix_select_mi1mi2' of github.com:matthewturk/yt into fi…
matthewturk May 13, 2020
e626e25
another pass
matthewturk May 15, 2020
b1c0d74
try to short circuit, and fix cython bugs
matthewturk May 15, 2020
2b59341
Merge pull request #2588 from AshKelly/yt-4.0-setup-typo
matthewturk May 19, 2020
bc7121c
Use expanded morton for faster BIGMAX selection
matthewturk May 19, 2020
300fc4a
Give up on hiding the C++ in EWAH
matthewturk May 19, 2020
2164393
Intermediate commit on way to working
matthewturk May 21, 2020
e89bd59
Keep a semi-running tally of bool array collections
matthewturk May 21, 2020
09aacb9
Switch to using BoolArray
matthewturk May 22, 2020
c82a015
Switch to word adding for refined EWAH.
matthewturk May 22, 2020
5c30b9a
Fixing a flake8 error
matthewturk May 22, 2020
a66be30
remove unused unordered_set import
matthewturk May 22, 2020
017768b
Fix testing calls; not working yet.
matthewturk May 23, 2020
d99d87f
Missed a logic check
matthewturk May 25, 2020
c5da911
Use bounded_morton_split_dds in coarse indexing
matthewturk May 26, 2020
ac32bb0
Fencepost error
matthewturk May 26, 2020
e8ce92b
Check for None in append()
matthewturk May 26, 2020
588b50e
Changing to uint32_t for Clang
matthewturk May 26, 2020
6488e10
Try to be more careful with uint/int distinctions.
matthewturk May 26, 2020
26a4ed4
Explicitly cast to uword
matthewturk May 26, 2020
e29599d
Update EWAH to 88b25a3345b82353ccd97a7de6064e6c179a7cc2
matthewturk May 27, 2020
9e1f34e
This fixes a compilation error
jzuhone May 29, 2020
bd1fb35
Make this platform-dependent
jzuhone May 29, 2020
25304b3
Update order-of-include and C++11 for particle_oct_container.pyx
matthewturk May 29, 2020
1384a35
Merge branch 'yt-4.0' into fix_select_mi1mi2
matthewturk May 29, 2020
e5847d8
Update to Bionic as per Kacper's suggestion
matthewturk May 29, 2020
3baa1bc
Merge branch 'fix_select_mi1mi2' of github.com:matthewturk/yt into fi…
matthewturk May 29, 2020
c85827e
Fix a handful of lint and style issues
matthewturk Jun 2, 2020
59290f0
Updating to new answer-store rev
matthewturk Jun 3, 2020
ad8fc19
Merge pull request #2575 from matthewturk/fix_select_mi1mi2
munkm Jun 5, 2020
844e19d
Merge branch 'yt-4.0' of github.com:yt-project/yt into yt4-merge
matthewturk Jun 5, 2020
8f45447
Abstract some particle tests
matthewturk Jun 5, 2020
5744cc4
missed a variable
matthewturk Jun 5, 2020
b620588
Adding PSC
matthewturk Jun 5, 2020
22e5b74
Adding AHF, Arepo, ART, Eagle, Flash, OWLS, Swift
matthewturk Jun 5, 2020
763e335
Fix two typo errors
matthewturk Jun 5, 2020
0ebed5e
Added extra dont cache case for when a bounding box has been applied
AshKelly Jun 6, 2020
c3939c0
Added ds.domain_override for cases when a bbox is applied
AshKelly Jun 6, 2020
56acf1b
Merge branch 'master' of github.com:yt-project/yt into yt4-merge
matthewturk Jun 8, 2020
737718c
Updating answer store
matthewturk Jun 8, 2020
ca536a2
Update bitmask_version for #2575
matthewturk Jun 8, 2020
eadc0e1
Update RAMSES particle counts to include 0 nbody
matthewturk Jun 8, 2020
15d337a
Add comments about what the run_defaults test does
matthewturk Jun 8, 2020
34871ac
Updating Athena++ answer values
matthewturk Jun 8, 2020
c0e8b9c
Merge pull request #2621 from matthewturk/update_bitmask_version_mi1mi2
munkm Jun 8, 2020
093a183
Merge branch 'yt-4.0' of github.com:yt-project/yt into yt4-merge
matthewturk Jun 8, 2020
66f6d57
Regenerate xray fields
matthewturk Jun 8, 2020
66d342b
Apply suggestions from code review
AshKelly Jun 9, 2020
cc1cb0a
Bump chombo answers
matthewturk Jun 9, 2020
e8626da
Athena answers now use different mu.
matthewturk Jun 9, 2020
c956572
Update boxlib, which has hash differences.
matthewturk Jun 9, 2020
7f8f179
change field name for xray fields
matthewturk Jun 9, 2020
53ae9b4
Bumping ARTIO tests.
matthewturk Jun 9, 2020
3d0cf68
Merge branch 'master' of github.com:yt-project/yt into yt4-merge
matthewturk Jun 9, 2020
ba07a82
Merge pull request #2618 from AshKelly/yt-4.0-bbox
matthewturk Jun 9, 2020
249d38f
Merge branch 'yt-4.0' of github.com:yt-project/yt into yt4-merge
matthewturk Jun 9, 2020
91bfb1c
Adding nbody answer tests using particle plots
matthewturk Jun 9, 2020
012144c
Removing unused import
matthewturk Jun 9, 2020
edae0cf
Update yt/utilities/answer_testing/framework.py
matthewturk Jun 11, 2020
ce00dcd
update gamer number
matthewturk Jun 12, 2020
99e1320
Updating xray:
matthewturk Jun 15, 2020
fc777a0
Don't allow edges to extend beyond domain for SPH region sources.
matthewturk Jun 16, 2020
ee001f8
Merge branch 'master' of github.com:yt-project/yt into yt4-merge
matthewturk Jun 16, 2020
594dfdc
Bumping answers for flash, gadget, tipsy, arepo, gizmo, owls
matthewturk Jun 17, 2020
7a585e8
Bumping enzo_p
matthewturk Jun 17, 2020
6627774
Change xray test names to be completely explicit.
matthewturk Jun 17, 2020
bff7270
Bump xray one last time.
matthewturk Jun 17, 2020
88219bd
Only do the bounds limiting for non-periodic datasets
matthewturk Jun 18, 2020
c7f0726
refactoring via comments
matthewturk Jun 18, 2020
96e6220
Merge branch 'master' of github.com:yt-project/yt into yt4-merge
matthewturk Jun 18, 2020
44eb8a8
Merge pull request #2617 from matthewturk/particle_tests
munkm Jun 18, 2020
04cbde2
fixing rename
matthewturk Jun 18, 2020
7a9f39a
adding comment
matthewturk Jun 18, 2020
565fe4c
Added extra dont cache case for when a bounding box has been applied
AshKelly Jun 6, 2020
77b06ed
Added ds.domain_override for cases when a bbox is applied
AshKelly Jun 6, 2020
3cfa46c
Apply suggestions from code review
AshKelly Jun 9, 2020
9fb8ee7
Add another dont_cache check for loading
matthewturk Jun 9, 2020
bc17bb0
Adding test
matthewturk Jun 9, 2020
3f1c8f3
Updating AREPO test numbers to update bounding box
matthewturk Jun 9, 2020
ce427fa
Minor fix for aesthetics of log output
matthewturk Jun 18, 2020
e78c485
Merge branch 'yt-4.0' into dont_cache_onload
matthewturk Jun 18, 2020
ec9a562
Merge pull request #2627 from matthewturk/nbody_tests
munkm Jun 19, 2020
59f9432
Merge pull request #2644 from matthewturk/edge_correction_sph
munkm Jun 19, 2020
37052e6
Merge pull request #2624 from matthewturk/dont_cache_onload
munkm Jun 19, 2020
256d30b
Merge branch 'yt-4.0' of github.com:yt-project/yt into yt4-merge
matthewturk Jun 19, 2020
3a33a24
Generate new answers and require new unyt version
matthewturk Jun 19, 2020
e2a75fa
Fix test names. Will bump after.
matthewturk Jun 19, 2020
8aa881f
let's go bowling
matthewturk Jun 19, 2020
755a885
Fix syntax error
Xarthisius Jun 19, 2020
49a1f85
Allow to modify answer name via suffix attribute
Xarthisius Jun 19, 2020
e2e652e
Use suffix to distinguish between xray fields tests
Xarthisius Jun 19, 2020
63dd61c
Update answers and fix periodicity issue with particle plots
matthewturk Jun 19, 2020
a1b84a9
I for one welcome our new unicode overlords
jzuhone Jun 19, 2020
6f04afc
Bump h5py version to avoid erroneous serialization of tuples in ytdat…
Xarthisius Jun 20, 2020
4432623
Add checks for periodicity in particle selection tests
matthewturk Jun 20, 2020
7a81a60
fix owls_subfind order of initialization
matthewturk Jun 20, 2020
80c8fc6
Update tipsy tests to use particle_types_raw
matthewturk Jun 20, 2020
58c9879
Change order of operations.
Xarthisius Jun 21, 2020
fe0ca6c
Disable owls_subfind as it hangs indefinitely
Xarthisius Jun 21, 2020
1f11752
Use nbody and sph answer tests for tipsy
matthewturk Jun 21, 2020
f07991c
Fix typo
Xarthisius Jun 21, 2020
28a9986
Fixing leftover testing state
matthewturk Jun 22, 2020
fd3535c
Fixing NoOldAnswers for Tipsy
matthewturk Jun 22, 2020
1e1e8cb
Re-add coordinate base data type for pkdgrav load
matthewturk Jun 22, 2020
b31f200
Merge branch 'yt4-merge' of github.com:matthewturk/yt into yt4-merge
matthewturk Jun 22, 2020
86e6e2a
Set coding to utf8
Xarthisius Jun 22, 2020
e5a08b5
Bump unyt for test minimal and appveyor
Xarthisius Jun 22, 2020
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9 changes: 9 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@ yt/geometry/oct_container.c
yt/geometry/oct_visitors.c
yt/geometry/particle_deposit.c
yt/geometry/particle_oct_container.c
yt/geometry/particle_oct_container.cpp
yt/geometry/particle_smooth.c
yt/geometry/selection_routines.c
yt/utilities/amr_utils.c
Expand All @@ -34,11 +35,16 @@ yt/utilities/lib/alt_ray_tracers.c
yt/utilities/lib/amr_kdtools.c
yt/utilities/lib/basic_octree.c
yt/utilities/lib/bitarray.c
yt/utilities/lib/bounded_priority_queue.c
yt/utilities/lib/bounding_volume_hierarchy.c
yt/utilities/lib/contour_finding.c
yt/utilities/lib/cykdtree/kdtree.cpp
yt/utilities/lib/cykdtree/utils.cpp
yt/utilities/lib/cyoctree.cpp
yt/utilities/lib/depth_first_octree.c
yt/utilities/lib/distance_queue.c
yt/utilities/lib/element_mappings.c
yt/utilities/lib/ewah_bool_wrap.cpp
yt/utilities/lib/fnv_hash.c
yt/utilities/lib/fortran_reader.c
yt/utilities/lib/freetype_writer.c
Expand All @@ -55,13 +61,16 @@ yt/utilities/lib/mesh_samplers.cpp
yt/utilities/lib/mesh_traversal.cpp
yt/utilities/lib/mesh_triangulation.c
yt/utilities/lib/mesh_utilities.c
yt/utilities/lib/pixelization_routines.cpp
yt/utilities/lib/misc_utilities.c
yt/utilities/lib/particle_kdtree_tools.cpp
yt/utilities/lib/particle_mesh_operations.c
yt/utilities/lib/partitioned_grid.c
yt/utilities/lib/primitives.c
yt/utilities/lib/origami.c
yt/utilities/lib/particle_mesh_operations.c
yt/utilities/lib/pixelization_routines.c
yt/utilities/lib/pixelization_routines.cpp
yt/utilities/lib/png_writer.c
yt/utilities/lib/points_in_volume.c
yt/utilities/lib/quad_tree.c
Expand Down
2 changes: 2 additions & 0 deletions .hgignore
Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@ yt/utilities/lib/contour_finding.c
yt/utilities/lib/depth_first_octree.c
yt/utilities/lib/distance_queue.c
yt/utilities/lib/element_mappings.c
yt/utilities/lib/ewah_bool_wrap.cpp
yt/utilities/lib/fnv_hash.c
yt/utilities/lib/fortran_reader.c
yt/utilities/lib/freetype_writer.c
Expand All @@ -54,6 +55,7 @@ yt/utilities/lib/mesh_traversal.cpp
yt/utilities/lib/mesh_triangulation.c
yt/utilities/lib/mesh_utilities.c
yt/utilities/lib/misc_utilities.c
yt/utilities/lib/particle_kdtree_tools.cpp
yt/utilities/lib/particle_mesh_operations.c
yt/utilities/lib/partitioned_grid.c
yt/utilities/lib/primitives.c
Expand Down
37 changes: 16 additions & 21 deletions .travis.yml
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
language: python
dist: xenial
sudo: required
dist: xenial
cache:
pip: true
directories:
Expand All @@ -10,6 +11,7 @@ addons:
apt:
packages:
- libhdf5-serial-dev
- libnetcdf-dev
- libproj-dev
- proj-data
- proj-bin
Expand All @@ -20,10 +22,6 @@ env:
global:
PIP=pip

env:
global:
PIP=pip

before_install:
- |
if [[ $TRAVIS_OS_NAME != 'osx' ]]; then
Expand Down Expand Up @@ -56,7 +54,9 @@ install:
# install dependencies yt
if [[ $TRAVIS_BUILD_STAGE_NAME != "Lint" ]]; then
if [[ $MINIMAL == 1 ]]; then
$PIP install numpy==1.10.4 cython==0.24
# Ensure numpy and cython are installed so dependencies that need to be built
# don't error out
$PIP install numpy==1.13.3 cython==0.26.1
$PIP install -r tests/test_minimal_requirements.txt
else
# Getting cartopy installed requires getting cython and numpy installed
Expand All @@ -75,24 +75,15 @@ install:
jobs:
include:
- stage: lint
python: 3.6
script: flake8 yt/

- stage: lint
python: 2.7
python: 3.7
script: flake8 yt/

- stage: tests
name: "Python: 2.7 Unit Tests"
python: 2.7
name: "Minimal Dependency Version Unit Tests"
python: 3.5
env: MINIMAL=1
script: coverage run $(which nosetests) -c nose_unit.cfg

- stage: tests
name: "Python: 2.7 Unit Tests"
python: 2.7
script: coverage run $(which nosetests) -c nose_unit.cfg

- stage: tests
name: "Python: 3.5 Unit Tests"
python: 3.5
Expand All @@ -104,15 +95,19 @@ jobs:
script: coverage run $(which nosetests) -c nose_unit.cfg

- stage: tests
name: "Python: 2.7 Minimal Dependency Answer Tests"
python: 2.7
name: "Python: 3.7 Unit Tests"
python: 3.7
script: coverage run $(which nosetests) -c nose_unit.cfg

- name: "Minimal Dependency Version Answer Tests"
python: 3.5
env: MINIMAL=1
script: coverage run $(which nosetests) -c nose_answer.cfg
after_failure: python tests/report_failed_answers.py -f -m --xunit-file "answer_nosetests.xml"

- stage: tests
name: "Python: 3.6 Answer Tests"
python: 3.6
name: "Python: 3.7 Answer Tests"
python: 3.7
script: coverage run $(which nosetests) -c nose_answer.cfg
after_failure: python tests/report_failed_answers.py -f -m --xunit-file "answer_nosetests.xml"

Expand Down
9 changes: 2 additions & 7 deletions CONTRIBUTING.rst
Original file line number Diff line number Diff line change
Expand Up @@ -405,12 +405,6 @@ the following subdirectories:
classes for data regions, covering grids, time series, and so on. This
also includes derived fields and derived quantities.

``analysis_modules``
This is where all mechanisms for processing data live. This includes
things like clump finding, halo profiling, halo finding, and so on. This
is something of a catchall, but it serves as a level of greater
abstraction that simply data selection and modification.

``gui``
This is where all GUI components go. Typically this will be some small
tool used for one or two things, which contains a launching mechanism on
Expand Down Expand Up @@ -762,6 +756,7 @@ Source code style guide

* In general, follow PEP-8 guidelines.
https://www.python.org/dev/peps/pep-0008/
* We no longer have a copyright blurb in every source file.
* Classes are ``ConjoinedCapitals``, methods and functions are
``lowercase_with_underscores``.
* Use 4 spaces, not tabs, to represent indentation.
Expand All @@ -784,7 +779,7 @@ Source code style guide
that occur on an object. See :ref:`docstrings` below for a fiducial example
of a docstring.
* Use only one top-level import per line. Unless there is a good reason not to,
imports should happen at the top of the file, after the copyright blurb.
imports should happen at the top of the file.
* Never compare with ``True`` or ``False`` using ``==`` or ``!=``, always use
``is`` or ``is not``.
* If you are comparing with a numpy boolean array, just refer to the array.
Expand Down
3 changes: 1 addition & 2 deletions MANIFEST.in
Original file line number Diff line number Diff line change
Expand Up @@ -3,14 +3,13 @@ include yt/visualization/mapserver/html/map.js
include yt/visualization/mapserver/html/map_index.html
include yt/utilities/mesh_types.yaml
exclude scripts/pr_backport.py
recursive-include yt *.py *.pyx *.pxd *.h README* *.txt LICENSE* *.cu
recursive-include yt *.py *.pyx *.pxd *.h *.hpp README* *.txt LICENSE* *.cu
recursive-include doc *.rst *.txt *.py *.ipynb *.png *.jpg *.css *.html
recursive-include doc *.h *.c *.sh *.svgz *.pdf *.svg *.pyx
include doc/README doc/activate doc/activate.csh doc/cheatsheet.tex
include doc/extensions/README doc/Makefile
prune doc/source/reference/api/generated
prune doc/build
recursive-include yt/analysis_modules/halo_finding/rockstar *.py *.pyx
recursive-include yt/visualization/volume_rendering/shaders *.fragmentshader *.vertexshader
prune yt/frontends/_skeleton
recursive-include yt/frontends/amrvac *.par
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6 changes: 4 additions & 2 deletions appveyor.yml
Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,8 @@ environment:
PYTHON: "C:\\Miniconda36-x64"

matrix:
- PYTHON_VERSION: "2.7"
- PYTHON_VERSION: "3.6"
NUMPY_VERSION: "1.16"

platform:
-x64
Expand All @@ -30,7 +30,9 @@ install:
- "python --version"

# Install specified version of numpy and dependencies
- "conda install --yes -c conda-forge numpy scipy nose setuptools ipython Cython sympy=1.4 fastcache h5py matplotlib mock pandas cartopy conda-build pyyaml"
- "conda install --yes -c conda-forge numpy==%NUMPY_VERSION% scipy nose setuptools ipython
Cython sympy=1.4 fastcache h5py matplotlib mock pandas cartopy conda-build unyt pyyaml"
# install yt
- "conda develop -b ."

# Not a .NET project
Expand Down
3 changes: 1 addition & 2 deletions doc/Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -49,8 +49,7 @@ html:
ifneq ($(READTHEDOCS),True)
SPHINX_APIDOC_OPTIONS=members,undoc-members,inherited-members,show-inheritance sphinx-apidoc \
-o source/reference/api/ \
-e ../yt ../yt/extern* $(shell find ../yt -name "*tests*" -type d) ../yt/utilities/voropp* \
../yt/analysis_modules/halo_finding/{fof,hop}
-e ../yt ../yt/extern* $(shell find ../yt -name "*tests*" -type d) ../yt/utilities/voropp*
endif
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
Expand Down
8 changes: 5 additions & 3 deletions doc/helper_scripts/show_fields.py
Original file line number Diff line number Diff line change
Expand Up @@ -54,8 +54,10 @@ def _strip_ftype(field):
unit_registry=ds.unit_registry)
for my_unit in ["m", "pc", "AU", "au"]:
new_unit = "%scm" % my_unit
ds.unit_registry.add(new_unit, base_ds.unit_registry.lut[my_unit][0],
dimensions.length, "\\rm{%s}/(1+z)" % my_unit)
my_u = Unit(my_unit, registry=ds.unit_registry)
ds.unit_registry.add(new_unit, my_u.base_value,
dimensions.length, "\\rm{%s}/(1+z)" % my_unit,
prefixable=True)



Expand Down Expand Up @@ -143,7 +145,7 @@ def print_all_fields(fl):
print(" * Units: :math:`%s`" % fix_units(df.units))
else:
print(" * Units: :math:`%s`" % fix_units(df.units, in_cgs=True))
print(" * Particle Type: %s" % (df.particle_type))
print(" * Sampling Method: %s" % (df.sampling_type))
print()
print("**Field Source**")
print()
Expand Down
7 changes: 0 additions & 7 deletions doc/helper_scripts/table.py
Original file line number Diff line number Diff line change
Expand Up @@ -23,13 +23,6 @@
("interacting/index.html", "Interacting with yt",
"Different ways -- scripting, GUIs, prompts, explorers -- to explore " +
"your data."),
("analysis_modules/index.html", "Analysis Modules",
"Discussions of some provided procedures for astrophysical analysis " +
"like halo finding and synthetic spectra. Halo finding, analyzing " +
"cosmology simulations, halo mass functions, halo profiling, light " +
"cone generator, making absorption spectrums, star particle " +
"analysis, two-point functions, halo merger trees, clump finding, " +
"radial column density, exporting to sunrise.")
]),
("Advanced Usage", [
("advanced/index.html", "Advanced yt usage",
Expand Down
49 changes: 1 addition & 48 deletions doc/install_script.sh
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,6 @@ INST_GIT=1 # Install git or not? If git is not already installed, yt
INST_EMBREE=0 # Install dependencies needed for Embree-accelerated ray tracing
INST_PYX=0 # Install PyX? Sometimes PyX can be problematic without a
# working TeX installation.
INST_ROCKSTAR=0 # Install the Rockstar halo finder?
INST_SCIPY=0 # Install scipy?
INST_H5PY=1 # Install h5py?
INST_ASTROPY=0 # Install astropy?
Expand Down Expand Up @@ -134,7 +133,6 @@ function write_config
echo INST_GIT=${INST_GIT} >> ${CONFIG_FILE}
echo INST_PYX=${INST_PYX} >> ${CONFIG_FILE}
echo INST_PY3=${INST_PY3} >> ${CONFIG_FILE}
echo INST_ROCKSTAR=${INST_ROCKSTAR} >> ${CONFIG_FILE}
echo INST_SCIPY=${INST_SCIPY} >> ${CONFIG_FILE}
echo INST_EMBREE=${INST_EMBREE} >> ${CONFIG_FILE}
echo INST_H5PY=${INST_H5PY} >> ${CONFIG_FILE}
Expand Down Expand Up @@ -286,17 +284,6 @@ then
PYEMBREE_URL="https://github.com/scopatz/pyembree/archive/master.zip"
fi

if [ $INST_ROCKSTAR -ne 0 ]
then
if [ $INST_YT_SOURCE -eq 0 ]
then
echo "yt must be compiled from source to install support for"
echo "the rockstar halo finder. Please set INST_YT_SOURCE to 1"
echo "and re-run the install script"
exit 1
fi
fi

echo
echo
echo "========================================================================"
Expand Down Expand Up @@ -330,10 +317,6 @@ printf "%-18s = %s so I " "INST_PYX" "${INST_PYX}"
get_willwont ${INST_PYX}
echo "be installing PyX"

printf "%-18s = %s so I " "INST_ROCKSTAR" "${INST_ROCKSTAR}"
get_willwont ${INST_ROCKSTAR}
echo "be installing Rockstar"

printf "%-18s = %s so I " "INST_H5PY" "${INST_H5PY}"
get_willwont ${INST_H5PY}
echo "be installing h5py"
Expand Down Expand Up @@ -598,16 +581,6 @@ then
popd &> /dev/null
fi

if [ $INST_ROCKSTAR -eq 1 ]
then
echo "Building Rockstar"
( ${GIT_EXE} clone https://github.com/yt-project/rockstar ${DEST_DIR}/src/rockstar/ 2>&1 ) 1>> ${LOG_FILE}
ROCKSTAR_PACKAGE=$(${DEST_DIR}/bin/conda build ${DEST_DIR}/src/yt_conda/rockstar --output)
log_cmd ${DEST_DIR}/bin/conda build ${DEST_DIR}/src/yt_conda/rockstar
log_cmd ${DEST_DIR}/bin/conda install $ROCKSTAR_PACKAGE
ROCKSTAR_DIR=${DEST_DIR}/src/rockstar
fi

# conda doesn't package pyx, so we install manually with pip
if [ $INST_PYX -eq 1 ]
then
Expand Down Expand Up @@ -650,13 +623,8 @@ else
then
echo $DEST_DIR > ${YT_DIR}/embree.cfg
fi
if [ $INST_ROCKSTAR -eq 1 ]
then
echo $ROCKSTAR_DIR > ${YT_DIR}/rockstar.cfg
ROCKSTAR_LIBRARY_PATH=${DEST_DIR}/lib
fi
pushd ${YT_DIR} &> /dev/null
( LIBRARY_PATH=$ROCKSTAR_LIBRARY_PATH ${DEST_DIR}/bin/${PYTHON_EXEC} setup.py develop 2>&1) 1>> ${LOG_FILE} || do_exit
( ${DEST_DIR}/bin/${PYTHON_EXEC} setup.py develop 2>&1) 1>> ${LOG_FILE} || do_exit
popd &> /dev/null
fi

Expand Down Expand Up @@ -697,21 +665,6 @@ echo "You can also update the init file appropriate for your shell"
echo "(e.g. .bashrc, .bash_profile, .cshrc, or .zshrc) to include"
echo "the same command."
echo
if [ $INST_ROCKSTAR -eq 1 ]
then
if [ $MYOS = "Darwin" ]
then
LD_NAME="DYLD_LIBRARY_PATH"
else
LD_NAME="LD_LIBRARY_PATH"
fi
echo
echo "For rockstar to work, you must also set $LD_NAME:"
echo
echo " export $LD_NAME=$DEST_DIR/lib:\$$LD_NAME"
echo
echo "or whichever invocation is appropriate for your shell."
fi
echo "========================================================================"
echo
echo "Oh, look at me, still talking when there's science to do!"
Expand Down
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