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Add support for graph operations #355

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1fa713d
add: add to_graph method
jnsbck Apr 25, 2024
2ebb66f
add: add from_graph method
jnsbck Apr 25, 2024
142bf2d
fix: isort and rm obs import
jnsbck Apr 26, 2024
1dc3234
doc: added more comments
jnsbck Apr 26, 2024
d98292d
wip: started adding new swc import function
jnsbck Apr 29, 2024
e0f30cb
wip: save dev wip
jnsbck Apr 29, 2024
a495984
add: implement graph2jaxley method, that imposes branch structure on …
jnsbck May 1, 2024
54b1f30
fix: small fixes
jnsbck May 1, 2024
5232707
enh: add prelim version of xyzr
jnsbck May 2, 2024
961d7ff
wip: save wip
jnsbck May 2, 2024
d420c03
enh: refactor of swc->graph->jaxley->module pipeline
jnsbck May 3, 2024
6a8fab9
enh: cleanup
jnsbck May 3, 2024
ce48595
fix: small fix, now from graph runs on compartmentalized morphology
jnsbck May 3, 2024
ce120f5
doc: add docstrings and type hints
jnsbck May 6, 2024
1a047ae
doc: more comments added
jnsbck May 6, 2024
abf6b3c
fix: small fixes.
jnsbck May 6, 2024
1660a10
fix: rm undefined from groups at import
jnsbck May 6, 2024
3394167
wip: save wip
jnsbck May 6, 2024
5bdf747
wip: save wip
jnsbck May 6, 2024
da58074
rm: remove dev notebook from tracking
jnsbck May 6, 2024
73b3eed
add: add tests for graph functionalities
jnsbck May 7, 2024
af874df
fix: added more tests and they are now passing
jnsbck May 7, 2024
e606da0
fix: test fixes
jnsbck May 7, 2024
e1a496e
wip: save wip working on graph and swc io
jnsbck May 27, 2024
2a0be27
fix: radius import fixed
jnsbck Jun 3, 2024
f3a825e
wip: save wip
jnsbck Jun 10, 2024
bd2a17a
enh: massive overhaul complete of graph pipeline compared to before. …
jnsbck Jun 10, 2024
6ac8373
wip: save wip
jnsbck Jun 16, 2024
bd142c4
wip: save wip
jnsbck Jun 16, 2024
9e32bc4
fix: some fixes added
jnsbck Jun 17, 2024
2858d85
wip: save wip
jnsbck Jun 18, 2024
5688472
wip: save wip tests
jnsbck Jun 19, 2024
38a79b3
wip: test look better than before.
jnsbck Jul 12, 2024
7540a65
wip: remove complexity and improve test MSE. still not there though
jnsbck Jul 12, 2024
80dca4a
wip: save wip.
jnsbck Aug 15, 2024
f970c31
rm: rm notebooks from pr
jnsbck Aug 15, 2024
72f8599
wip: save wip
jnsbck Aug 23, 2024
dd07d2c
enh: small refactor of swc -> initial graph pipe
jnsbck Aug 23, 2024
004e292
enh: massive overhaul auf graph pipe. add documentation. passes tests…
jnsbck Aug 23, 2024
528c500
wip: start adding tests.
jnsbck Aug 23, 2024
552c8f8
enh: incl graphIO in tutorial
jnsbck Aug 23, 2024
3d7222f
wip: progress on tests and tutorial
jnsbck Aug 27, 2024
49443fd
wip: tests are passing. except for voltages, which only passes in not…
jnsbck Aug 27, 2024
21d905d
rm: dev notebook removed
jnsbck Aug 27, 2024
b3781f8
fix: tests passing for non-single soma morpho
jnsbck Aug 27, 2024
bfb377f
enh: Tests are finally passing
jnsbck Aug 30, 2024
5f4d046
fix: add misssing kwarg in simulate_trace_error
jnsbck Aug 30, 2024
833f908
fix: fix diff with main
jnsbck Aug 30, 2024
8be9cfd
fix: rm diff in modules/base
jnsbck Sep 2, 2024
8a18037
fix: add __eq__ back in for comparisons of cells attr in net and fix …
jnsbck Sep 2, 2024
355ea2b
chore: ran black
jnsbck Sep 2, 2024
07ca101
fix: change read_swc to io imports
jnsbck Sep 2, 2024
1d63067
chore: add license header
jnsbck Sep 2, 2024
2843b9f
enh: fixup of wording
jnsbck Sep 2, 2024
412c84b
fix: fix merge artefact
jnsbck Dec 18, 2024
53895a4
rm: rm tutorials left from rebase
jnsbck Dec 18, 2024
1ee82cc
wip: save wip
jnsbck Dec 19, 2024
de93766
wip: swc pipe now works up until module import
jnsbck Dec 20, 2024
dbe990b
wip: in/out pipeline working for morphology, but w.o. attrs like reco…
jnsbck Dec 20, 2024
4df31e9
fix: update tutorial
jnsbck Dec 21, 2024
e8b93c3
fix: fix tutorial and synapses and input output
jnsbck Dec 21, 2024
39f5f35
fix: add networkx as dep
jnsbck Dec 22, 2024
6fee9c3
fix rebase io/swc.py to main
jnsbck Dec 22, 2024
dde6999
doc: add more function documentation
jnsbck Dec 22, 2024
82fb9c9
wip: step 1 on getting tests to pass
jnsbck Dec 22, 2024
54ba32b
fix: reduce diff
jnsbck Dec 22, 2024
574c26e
fix: ammend last commit
jnsbck Dec 22, 2024
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282 changes: 269 additions & 13 deletions docs/tutorials/08_importing_morphologies.ipynb

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5 changes: 5 additions & 0 deletions jaxley/io/__init__.py
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
# This file is part of Jaxley, a differentiable neuroscience simulator. Jaxley is
# licensed under the Apache License Version 2.0, see <https://www.apache.org/licenses/>

# from jaxley.io.graph import from_graph, to_graph
from jaxley.io.swc import read_swc
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