Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

PR 407 + tweaks #421

Merged
merged 84 commits into from
Sep 4, 2024
Merged

PR 407 + tweaks #421

merged 84 commits into from
Sep 4, 2024

Commits on Jul 18, 2024

  1. Added ExportNML.py file to export SWC into NeuroML

    @AdityaPandeyCN
    AdityaPandeyCN committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    c24a91b View commit details
    Browse the repository at this point in the history

  2. removed example usage

    @AdityaPandeyCN
    AdityaPandeyCN committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    d61a66b View commit details
    Browse the repository at this point in the history

  3. removed unused variable

    @AdityaPandeyCN
    AdityaPandeyCN committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    8860733 View commit details
    Browse the repository at this point in the history

Commits on Jul 26, 2024

  1. refactored the whole code

    @AdityaPandeyCN
    AdityaPandeyCN committed Jul 26, 2024
    Configuration menu
    Copy the full SHA
    90de9ce View commit details
    Browse the repository at this point in the history

Commits on Jul 29, 2024

  1. Merge branch 'development' of https://github.com/NeuroML/pyNeuroML in… 

    …to feat/ExportSWC
    @AdityaPandeyCN
    AdityaPandeyCN committed Jul 29, 2024
    Configuration menu
    Copy the full SHA
    d12cd95 View commit details
    Browse the repository at this point in the history

Commits on Jul 31, 2024

  1. refactored for handling wrong node types

    @AdityaPandeyCN
    AdityaPandeyCN committed Jul 31, 2024
    Configuration menu
    Copy the full SHA
    609dfaa View commit details
    Browse the repository at this point in the history

  2. added logger

    @AdityaPandeyCN
    AdityaPandeyCN committed Jul 31, 2024
    Configuration menu
    Copy the full SHA
    b845beb View commit details
    Browse the repository at this point in the history

Commits on Aug 5, 2024

  1. refactored the code with reference to using the neuroml library

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 5, 2024
    Configuration menu
    Copy the full SHA
    6223b02 View commit details
    Browse the repository at this point in the history

  2. removed unused imports

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 5, 2024
    Configuration menu
    Copy the full SHA
    7bd56db View commit details
    Browse the repository at this point in the history

Commits on Aug 6, 2024

  1. added SWCGraph and removed Segment.type

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 6, 2024
    Configuration menu
    Copy the full SHA
    e1886b1 View commit details
    Browse the repository at this point in the history

  2. added __init__.py file

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 6, 2024
    Configuration menu
    Copy the full SHA
    2da58d1 View commit details
    Browse the repository at this point in the history

  3. added unittest file

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 6, 2024
    Configuration menu
    Copy the full SHA
    c617ef2 View commit details
    Browse the repository at this point in the history

  4. removed absolute import

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 6, 2024
    Configuration menu
    Copy the full SHA
    1bd17ce View commit details
    Browse the repository at this point in the history

  5. refactored to add component_factory

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 6, 2024
    Configuration menu
    Copy the full SHA
    2112586 View commit details
    Browse the repository at this point in the history

Commits on Aug 7, 2024

  1. renmaed the test file

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 7, 2024
    Configuration menu
    Copy the full SHA
    6e1a738 View commit details
    Browse the repository at this point in the history

  2. renmaed the test file

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 7, 2024
    Configuration menu
    Copy the full SHA
    ca5c326 View commit details
    Browse the repository at this point in the history

  3. renmaed the test file

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 7, 2024
    Configuration menu
    Copy the full SHA
    4dd5006 View commit details
    Browse the repository at this point in the history

  4. added comments to provide more clarity

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 7, 2024
    Configuration menu
    Copy the full SHA
    f46f933 View commit details
    Browse the repository at this point in the history

Commits on Aug 8, 2024

  1. removed component_factory

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 8, 2024
    Configuration menu
    Copy the full SHA
    9fa84cc View commit details
    Browse the repository at this point in the history

Commits on Aug 14, 2024

  1. refactored the Export file

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 14, 2024
    Configuration menu
    Copy the full SHA
    3a5a8cc View commit details
    Browse the repository at this point in the history

Commits on Aug 18, 2024

  1. refactored the code for better segment formation

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 18, 2024
    Configuration menu
    Copy the full SHA
    ab280ac View commit details
    Browse the repository at this point in the history

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

    @AdityaPandeyCN
    AdityaPandeyCN authored Aug 18, 2024
    Configuration menu
    Copy the full SHA
    fcca73b View commit details
    Browse the repository at this point in the history

  3. refactore docstrings

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 18, 2024
    Configuration menu
    Copy the full SHA
    38c24b0 View commit details
    Browse the repository at this point in the history

  4. Merge branch 'feat/ExportSWC' of https://github.com/AdityaBITMESRA/py… 

    …NeuroML into feat/ExportSWC
    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 18, 2024
    Configuration menu
    Copy the full SHA
    e7dc36b View commit details
    Browse the repository at this point in the history

  5. refactored docstrings

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 18, 2024
    Configuration menu
    Copy the full SHA
    aa40ae5 View commit details
    Browse the repository at this point in the history

Commits on Aug 19, 2024

  1. used relative imports

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 19, 2024
    Configuration menu
    Copy the full SHA
    34642ac View commit details
    Browse the repository at this point in the history

Commits on Aug 20, 2024

  1. removed the segment duplication error

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 20, 2024
    Configuration menu
    Copy the full SHA
    6d98ec2 View commit details
    Browse the repository at this point in the history

Commits on Aug 21, 2024

  1. some changes

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 21, 2024
    Configuration menu
    Copy the full SHA
    ad92502 View commit details
    Browse the repository at this point in the history

  2. changes

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 21, 2024
    Configuration menu
    Copy the full SHA
    5bad25f View commit details
    Browse the repository at this point in the history

  3. changes

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 21, 2024
    Configuration menu
    Copy the full SHA
    89b5fd9 View commit details
    Browse the repository at this point in the history

  4. resolved the non-processing of non soma points error

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 21, 2024
    Configuration menu
    Copy the full SHA
    1509d16 View commit details
    Browse the repository at this point in the history

  5. resolved the non-processing of non soma points error

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 21, 2024
    Configuration menu
    Copy the full SHA
    b88b1a3 View commit details
    Browse the repository at this point in the history

Commits on Aug 22, 2024

  1. added detailed docstrings

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    d1d75f4 View commit details
    Browse the repository at this point in the history

  2. refactored multipoint soma handling

    @AdityaPandeyCN
    AdityaPandeyCN committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    7290dc9 View commit details
    Browse the repository at this point in the history

Commits on Aug 27, 2024

  1. Merge branch 'development' into feat/ExportSWC-ankur

    @sanjayankur31
    sanjayankur31 committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    612815d View commit details
    Browse the repository at this point in the history

  2. chore(swc): remove a few redundant bits

    @sanjayankur31
    sanjayankur31 committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    763d35a View commit details
    Browse the repository at this point in the history

  3. chore: update docstrings

    @sanjayankur31
    sanjayankur31 committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    d00bfc3 View commit details
    Browse the repository at this point in the history

  4. chore(export-nml): update imports

    @sanjayankur31
    sanjayankur31 committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    d6f02fd View commit details
    Browse the repository at this point in the history

  5. chore(export-nml): make methods private

    @sanjayankur31
    sanjayankur31 committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    d523cba View commit details
    Browse the repository at this point in the history

  6. feat: add new pynml-swc2nml command line

    @sanjayankur31
    sanjayankur31 committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    5f6bd55 View commit details
    Browse the repository at this point in the history

  7. chore(swc2nml): correct command line arg

    @sanjayankur31
    sanjayankur31 committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    2af654f View commit details
    Browse the repository at this point in the history

  8. feat(swc2nml): use debug for more logging

    @sanjayankur31
    sanjayankur31 committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    05036cc View commit details
    Browse the repository at this point in the history

  9. feat(load-swc): reduce warning logging

    @sanjayankur31
    sanjayankur31 committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    a81c280 View commit details
    Browse the repository at this point in the history

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

    @sanjayankur31
    sanjayankur31 committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    5554ea8 View commit details
    Browse the repository at this point in the history

  11. chore(swc2nml): remove unused variables 

    Also make the order of arguments consistent
    @sanjayankur31
    sanjayankur31 committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    780c60c View commit details
    Browse the repository at this point in the history

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

    @sanjayankur31
    sanjayankur31 committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    49ff1f3 View commit details
    Browse the repository at this point in the history

  13. chore(swc2nml): move notes to morphology element

    @sanjayankur31
    sanjayankur31 committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    ae244b7 View commit details
    Browse the repository at this point in the history

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

    Just for consistency, we don't like spaces in ids/names
    @sanjayankur31
    sanjayankur31 committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    d59a2b7 View commit details
    Browse the repository at this point in the history

  15. feat(swc2nml): allow exporting standalone Morphology element

    @sanjayankur31
    sanjayankur31 committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    37ded70 View commit details
    Browse the repository at this point in the history

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

    @sanjayankur31
    sanjayankur31 committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    9d5e697 View commit details
    Browse the repository at this point in the history

  17. feat(swc2nml): use graph root as start point 

    We don't need to find this again, we already know the tree root.
    @sanjayankur31
    sanjayankur31 committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    c11a4ff View commit details
    Browse the repository at this point in the history

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

    @sanjayankur31
    sanjayankur31 committed Aug 27, 2024
    Configuration menu
    Copy the full SHA
    fc882de View commit details
    Browse the repository at this point in the history

Commits on Aug 29, 2024

  1. chore: comment purpose of class variables

    @sanjayankur31
    sanjayankur31 committed Aug 29, 2024
    Configuration menu
    Copy the full SHA
    3c57468 View commit details
    Browse the repository at this point in the history

  2. wip: reviewing

    @sanjayankur31
    sanjayankur31 committed Aug 29, 2024
    Configuration menu
    Copy the full SHA
    c2ab280 View commit details
    Browse the repository at this point in the history

Commits on Sep 3, 2024

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

    @sanjayankur31
    sanjayankur31 committed Sep 3, 2024
    Configuration menu
    Copy the full SHA
    398f4aa View commit details
    Browse the repository at this point in the history

  2. feat(swc2nml): refactor general segment creation

    @sanjayankur31
    sanjayankur31 committed Sep 3, 2024
    Configuration menu
    Copy the full SHA
    ce8f4ae View commit details
    Browse the repository at this point in the history

  3. feat(swc2nml): strip down tests 

    While checking the XML string is fine, checking the NeuroML object tree
is more future proof. We'll modify the tests to do that as we go.
    @sanjayankur31
    sanjayankur31 committed Sep 3, 2024
    Configuration menu
    Copy the full SHA
    326988d View commit details
    Browse the repository at this point in the history

  4. feat(swc2nml): return NeuroMLDocument for programmatic access 

    Otherwise, one has to then re-load the written NeuroML file again.
    @sanjayankur31
    sanjayankur31 committed Sep 3, 2024
    Configuration menu
    Copy the full SHA
    21eb3cb View commit details
    Browse the repository at this point in the history

  5. chore: ignore .coverage everywhere

    @sanjayankur31
    sanjayankur31 committed Sep 3, 2024
    Configuration menu
    Copy the full SHA
    d3ed6bb View commit details
    Browse the repository at this point in the history

  6. chore: logger.warn -> logger.warning

    @sanjayankur31
    sanjayankur31 committed Sep 3, 2024
    Configuration menu
    Copy the full SHA
    b77390d View commit details
    Browse the repository at this point in the history

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

    @sanjayankur31
    sanjayankur31 committed Sep 3, 2024
    Configuration menu
    Copy the full SHA
    bcf71c4 View commit details
    Browse the repository at this point in the history

  8. test(swc2nml): checkin CVApp generated nml files 

    We'll use these to test our implementation
    @sanjayankur31
    sanjayankur31 committed Sep 3, 2024
    Configuration menu
    Copy the full SHA
    e9e2e60 View commit details
    Browse the repository at this point in the history

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

    @sanjayankur31
    sanjayankur31 committed Sep 3, 2024
    Configuration menu
    Copy the full SHA
    477e9ae View commit details
    Browse the repository at this point in the history

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

    @sanjayankur31
    sanjayankur31 committed Sep 3, 2024
    Configuration menu
    Copy the full SHA
    35c3e41 View commit details
    Browse the repository at this point in the history

  11. refactor(swc2nml): comment code, other cosmetic changes

    @sanjayankur31
    sanjayankur31 committed Sep 3, 2024
    Configuration menu
    Copy the full SHA
    0a881c7 View commit details
    Browse the repository at this point in the history

  12. feat(swc2nml): improve handle_soma documentation and structure

    @sanjayankur31
    sanjayankur31 committed Sep 3, 2024
    Configuration menu
    Copy the full SHA
    8612387 View commit details
    Browse the repository at this point in the history

  13. fix(swc2nml): correctly include parent info

    @sanjayankur31
    sanjayankur31 committed Sep 3, 2024
    Configuration menu
    Copy the full SHA
    0bb18a9 View commit details
    Browse the repository at this point in the history

  14. wip(swc2nml): improve tests

    @sanjayankur31
    sanjayankur31 committed Sep 3, 2024
    Configuration menu
    Copy the full SHA
    3c56f28 View commit details
    Browse the repository at this point in the history

  15. chore: remove unused import

    @sanjayankur31
    sanjayankur31 committed Sep 3, 2024
    Configuration menu
    Copy the full SHA
    e79c23b View commit details
    Browse the repository at this point in the history

Commits on Sep 4, 2024

  1. test(swc2nml): parameterize tests

    @sanjayankur31
    sanjayankur31 committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    cf0d077 View commit details
    Browse the repository at this point in the history

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

    `create_unbranche_segment` adds one to the root segments of all
unbranched segment groups
    @sanjayankur31
    sanjayankur31 committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    0b72255 View commit details
    Browse the repository at this point in the history

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

    The first two points belong to the first segment in this case also, and
that needed to be correctly recorded. Otherwise, other segments that
have the second point as the parent were not referring to the first
segment as the parent segment---they were referring to the next segment
where the second point was the proximal, not the distal.
    @sanjayankur31
    sanjayankur31 committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    99f0b0f View commit details
    Browse the repository at this point in the history

  4. test(swc2nml): also match all the segments individually

    @sanjayankur31
    sanjayankur31 committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    0cd7e50 View commit details
    Browse the repository at this point in the history

  5. chore(swc2nml): remove unused import

    @sanjayankur31
    sanjayankur31 committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    57a86a5 View commit details
    Browse the repository at this point in the history

  6. chore(swc2nml): add man page 

    Also regenerates all man pages

[skip ci]
    @sanjayankur31
    sanjayankur31 committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    0755ed2 View commit details
    Browse the repository at this point in the history

  7. feat(swc2nml): improve multi-point soma conversion 

    Use better variable names to clarify what point is being used.
Also correctly map points to their corresponding segments.
    @sanjayankur31
    sanjayankur31 committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    1367ec5 View commit details
    Browse the repository at this point in the history

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

    @sanjayankur31
    sanjayankur31 committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    a486102 View commit details
    Browse the repository at this point in the history

  9. chore(pre-commit): allow 2MB files 

    Otherwise some of our test files don't get committed.
    @sanjayankur31
    sanjayankur31 committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    9f4e478 View commit details
    Browse the repository at this point in the history

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

    @sanjayankur31
    sanjayankur31 committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    4a0eda4 View commit details
    Browse the repository at this point in the history

  11. chore(swc): tweak info message

    @sanjayankur31
    sanjayankur31 committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    c2a4f38 View commit details
    Browse the repository at this point in the history

  12. feat(swc2nml): improve segment group creation 

    There's no need to store the segment groups in another data structure
and do another pass to create them. We can keep adding the segments to
the segment groups as we go.
    @sanjayankur31
    sanjayankur31 committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    9eda784 View commit details
    Browse the repository at this point in the history

  13. test(swc2nml): allow skipping detailed checks 

    For some files, iterating over both files takes quite a while.
    @sanjayankur31
    sanjayankur31 committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    e45cbc1 View commit details
    Browse the repository at this point in the history

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

    @sanjayankur31
    sanjayankur31 committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    1ee37a2 View commit details
    Browse the repository at this point in the history

  15. chore: remove stray print 

    [skip ci]
    @sanjayankur31
    sanjayankur31 committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    6aee352 View commit details
    Browse the repository at this point in the history