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PR 407 + tweaks#421

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sanjayankur31 merged 84 commits intodevelopmentNeuroML/pyNeuroML:developmentfrom feat/ExportSWC-ankurNeuroML/pyNeuroML:feat/ExportSWC-ankurCopy head branch name to clipboardSep 4, 2024

+97,178-30

Commits

Commits on Jul 18, 2024

• Added ExportNML.py file to export SWC into NeuroML

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• removed example usage

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• removed unused variable

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Commits on Jul 26, 2024

• refactored the whole code

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Commits on Jul 29, 2024

• Merge branch 'development' of https://github.com/NeuroML/pyNeuroML into feat/ExportSWC

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Commits on Jul 31, 2024

• refactored for handling wrong node types

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• added logger

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Commits on Aug 5, 2024

• refactored the code with reference to using the neuroml library

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• removed unused imports

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Commits on Aug 6, 2024

• added SWCGraph and removed Segment.type

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• added __init__.py file

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• added unittest file

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• removed absolute import

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• refactored to add component_factory

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Commits on Aug 7, 2024

• renmaed the test file

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• renmaed the test file

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• renmaed the test file

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• added comments to provide more clarity

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Commits on Aug 8, 2024

• removed component_factory

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Commits on Aug 14, 2024

• refactored the Export file

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Commits on Aug 18, 2024

• refactored the code for better segment formation

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• Delete pyneuroml/swc/dCH-cobalt.CNG.nml

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• refactore docstrings

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• Merge branch 'feat/ExportSWC' of https://github.com/AdityaBITMESRA/pyNeuroML into feat/ExportSWC

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• refactored docstrings

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Commits on Aug 19, 2024

• used relative imports

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Commits on Aug 20, 2024

• removed the segment duplication error

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Commits on Aug 21, 2024

• some changes

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• changes

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• changes

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• resolved the non-processing of non soma points error

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• resolved the non-processing of non soma points error

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Commits on Aug 22, 2024

• added detailed docstrings

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• refactored multipoint soma handling

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Commits on Aug 27, 2024

• Merge branch 'development' into feat/ExportSWC-ankur

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• chore(swc): remove a few redundant bits

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• chore: update docstrings

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• chore(export-nml): update imports

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• chore(export-nml): make methods private

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• feat: add new pynml-swc2nml command line

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• chore(swc2nml): correct command line arg

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• feat(swc2nml): use debug for more logging

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• feat(load-swc): reduce warning logging

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• chore(load-swc): also print line number for non-header comments

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• chore(swc2nml): remove unused variables

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• feat(load-swc): add filename in metadata if not included

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• chore(swc2nml): move notes to morphology element

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• chore(swc2nml): replace spaces with _ in segment names

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• feat(swc2nml): allow exporting standalone Morphology element

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• feat(load-swc): check that first point line is root, with parent '-1'

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• feat(swc2nml): use graph root as start point

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• chore(swc2nml): re-order method args for consistency

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Commits on Aug 29, 2024

• chore: comment purpose of class variables

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• wip: reviewing

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Commits on Sep 3, 2024

• chore(swc2nml): use try/except instead of check

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• feat(swc2nml): refactor general segment creation

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• feat(swc2nml): strip down tests

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• feat(swc2nml): return NeuroMLDocument for programmatic access

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• chore: ignore .coverage everywhere

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• chore: logger.warn -> logger.warning

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• feat(swc2nml): allow main generate function to also only do morph

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• test(swc2nml): checkin CVApp generated nml files

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• chore(load-swc): start line count from 0

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• test(swc2nml): re-do to compare created Python objects

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• refactor(swc2nml): comment code, other cosmetic changes

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• feat(swc2nml): improve handle_soma documentation and structure

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• fix(swc2nml): correctly include parent info

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• wip(swc2nml): improve tests

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• chore: remove unused import

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Commits on Sep 4, 2024

• test(swc2nml): parameterize tests

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• feat(swc2nml): note addition of proximal point to "cable" roots

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• fix(swc2nml): correct generation of multi-point soma segments

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• test(swc2nml): also match all the segments individually

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• chore(swc2nml): remove unused import

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• chore(swc2nml): add man page

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• feat(swc2nml): improve multi-point soma conversion

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• fix(swc2nml): handle all other soma cases, not just ones with >3 points

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• chore(pre-commit): allow 2MB files

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• test(swc2nml): check in test swc + CVapp NML files

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• chore(swc): tweak info message

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• feat(swc2nml): improve segment group creation

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• test(swc2nml): allow skipping detailed checks

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• feat(plot-morph): use default group colours for single cells

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• chore: remove stray print

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