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Add support for graph operations#355

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jnsbck wants to merge 72 commits intomainjaxleyverse/jaxley:mainfrom 334-support-for-graph-operationsjaxleyverse/jaxley:334-support-for-graph-operationsCopy head branch name to clipboard

+1,734-22

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Commits on Jan 13, 2025

• add: add to_graph method

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• add: add from_graph method

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• fix: isort and rm obs import

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• doc: added more comments

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• wip: started adding new swc import function

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• wip: save dev wip

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• add: implement graph2jaxley method, that imposes branch structure on some graph

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• fix: small fixes

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• enh: add prelim version of xyzr

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• wip: save wip

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• enh: refactor of swc->graph->jaxley->module pipeline

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• enh: cleanup

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• fix: small fix, now from graph runs on compartmentalized morphology

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• doc: add docstrings and type hints

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• doc: more comments added

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• fix: small fixes.

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• fix: rm undefined from groups at import

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• wip: save wip

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• wip: save wip

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• rm: remove dev notebook from tracking

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• add: add tests for graph functionalities

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• fix: added more tests and they are now passing

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• fix: test fixes

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• wip: save wip working on graph and swc io

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• fix: radius import fixed

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• wip: save wip

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• enh: massive overhaul complete of graph pipeline compared to before. now much simpler and neuron comparison tests pass.

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• wip: save wip

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• wip: save wip

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• fix: some fixes added

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• wip: save wip

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• wip: save wip tests

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• wip: test look better than before.

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• wip: remove complexity and improve test MSE. still not there though

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• wip: save wip.

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• rm: rm notebooks from pr

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• wip: save wip

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• enh: small refactor of swc -> initial graph pipe

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• enh: massive overhaul auf graph pipe. add documentation. passes tests now

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• wip: start adding tests.

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• enh: incl graphIO in tutorial

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• wip: progress on tests and tutorial

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• wip: tests are passing. except for voltages, which only passes in notebook but not in pytest

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• rm: dev notebook removed

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• fix: tests passing for non-single soma morpho

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• enh: Tests are finally passing

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• fix: add misssing kwarg in simulate_trace_error

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• fix: fix diff with main

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• fix: rm diff in modules/base

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• fix: add __eq__ back in for comparisons of cells attr in net and fix asteric

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• chore: ran black

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• fix: change read_swc to io imports

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• chore: add license header

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• enh: fixup of wording

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• fix: fix merge artefact

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• rm: rm tutorials left from rebase

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• wip: swc pipe now works up until module import

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• wip: in/out pipeline working for morphology, but w.o. attrs like recordings.

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• fix: update tutorial

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• fix: fix tutorial and synapses and input output

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• fix: add networkx as dep

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• fix rebase io/swc.py to main

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• doc: add more function documentation

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• wip: step 1 on getting tests to pass

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• fix: reduce diff

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• fix: ammend last commit

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• fix: pop l when converting graph

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• wip: working on tests

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Commits on Jan 14, 2025

• wip: all but one test passing, working on import export cycle validation

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• fix: finished import export tests and all tests are passing

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• fix: speed up tests and add docs

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• chore: edit changelog

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