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Handle skeleton encoding internally #1970

Merged
merged 40 commits into from
Sep 25, 2024
Merged

Handle skeleton encoding internally #1970

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034cffb
start class `SkeletonEncoder`
eberrigan Sep 20, 2024
dd4865d
start class `SkeletonEncoder`
eberrigan Sep 21, 2024
f66a12d
_encoded_objects need to be a dict to add to
eberrigan Sep 21, 2024
7c48903
add notebook for testing
eberrigan Sep 23, 2024
4a75924
format
eberrigan Sep 23, 2024
57ec9d3
fix type in docstring
eberrigan Sep 23, 2024
58b2398
finish classmethod for encoding Skeleton as a json string
eberrigan Sep 23, 2024
8aedebd
test encoded Skeleton as json string by decoding it
eberrigan Sep 23, 2024
b9973c2
add test for decoded encoded skeleton
eberrigan Sep 24, 2024
4d77a68
update jupyter notebook for easy testing
eberrigan Sep 24, 2024
6c96a0e
constraining attrs in dev environment to make sure decode format is a…
eberrigan Sep 24, 2024
c78e9a9
encode links first then encode source then target then type
eberrigan Sep 24, 2024
5935b6a
save first enconding statically as an input to _get_or_assign_id so t…
eberrigan Sep 24, 2024
cab40c2
save first encoding statically
eberrigan Sep 24, 2024
2068fdd
first encoding is passed to _get_or_assign_id
eberrigan Sep 24, 2024
61c7cc0
use first_encoding variable to determine if we should assign a py/id
eberrigan Sep 24, 2024
c4f5be9
add print statements for debugging
eberrigan Sep 24, 2024
839d67c
update notebook for easy testing
eberrigan Sep 24, 2024
5bcea83
black
eberrigan Sep 24, 2024
167ef77
remove comment
eberrigan Sep 24, 2024
28f0c61
adding attrs constraint to show this passes for certain attrs version…
eberrigan Sep 24, 2024
fd14ad0
add import
eberrigan Sep 24, 2024
7fa9517
switch out jsonpickle.encode
eberrigan Sep 24, 2024
1d98177
oops remove import
eberrigan Sep 24, 2024
949fbe6
can attrs be unconstrained?
eberrigan Sep 24, 2024
6490d1f
forgot comma
eberrigan Sep 24, 2024
c199061
pin attrs for testing
eberrigan Sep 24, 2024
345dbc0
test Skeleton from json, template, with symmetries, and template
eberrigan Sep 24, 2024
4a8c326
use SkeletonEncoder.encode
eberrigan Sep 24, 2024
c57e64d
black
eberrigan Sep 24, 2024
4c8bdd6
try removing None values in EdgeType reduced
eberrigan Sep 24, 2024
6444378
Handle case when nodes are replaced by integer indices from caller
eberrigan Sep 25, 2024
c232ae6
Remove prototyping notebook
talmo Sep 25, 2024
2a56e88
Merge branch 'develop' into elizabeth/handle-skeleton-encoding-intern…
talmo Sep 25, 2024
5319e5a
Remove attrs pins
talmo Sep 25, 2024
b1d757b
Remove sort keys (which flips the neccessary ordering of our py/ids)
roomrys Sep 25, 2024
e7fb00a
Do not add extra indents to encoded file
roomrys Sep 25, 2024
743e406
Only append links after fully encoded (fat-finger)
roomrys Sep 25, 2024
02865f8
Remove outdated comment
roomrys Sep 25, 2024
83a2704
Lint
roomrys Sep 25, 2024
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2 changes: 1 addition & 1 deletion environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ channels:

dependencies:
# Packages SLEAP uses directly
- conda-forge::attrs >=21.2.0 #,<=21.4.0
- conda-forge::attrs >=21.2.0 #,<=21.4.0
- conda-forge::cattrs ==1.1.1
- conda-forge::imageio-ffmpeg # Required for imageio to read/write videos with ffmpeg
- conda-forge::jsmin
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2 changes: 1 addition & 1 deletion environment_no_cuda.yml
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Expand Up @@ -11,7 +11,7 @@ channels:

dependencies:
# Packages SLEAP uses directly
- conda-forge::attrs >=21.2.0 #,<=21.4.0
- conda-forge::attrs >=21.2.0 #,<=21.4.0
- conda-forge::cattrs ==1.1.1
- conda-forge::imageio-ffmpeg # Required for imageio to read/write videos with ffmpeg
- conda-forge::jsmin
Expand Down
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