NeuroML/pyNeuroML issues and pull requests

#440 - [Bug]

Issue - State: open - Opened by adampdp 8 days ago

#439 - [WIP] utility function list params in ComponentType

Pull Request - State: open - Opened by samkitshah1262 21 days ago - 2 comments
Labels: T: enhancement

#438 - Help! pynml: command not found

Issue - State: closed - Opened by LucianSheen about 1 month ago - 2 comments

#437 - wip: improve `pynml-summary`

Pull Request - State: closed - Opened by sanjayankur31 3 months ago - 2 comments

#436 - Fix file compatibility check

Pull Request - State: closed - Opened by sanjayankur31 3 months ago - 7 comments
Labels: T: enhancement

#435 - Improve model standard detection from files

Issue - State: closed - Opened by sanjayankur31 3 months ago
Labels: T: enhancement

#434 - Fix pynml archive

Pull Request - State: closed - Opened by sanjayankur31 3 months ago

#433 - Add utility function to enumerate all model parameters

Issue - State: open - Opened by sanjayankur31 3 months ago - 4 comments
Labels: T: enhancement, Help wanted, good first issue

#432 - feat: support py3.13

Pull Request - State: open - Opened by sanjayankur31 4 months ago - 2 comments

#431 - Time series plotting tweaks

Pull Request - State: closed - Opened by sanjayankur31 4 months ago
Labels: T: enhancement

#430 - Feat: util to create + include new components in NeuroMLDocuments

Pull Request - State: closed - Opened by sanjayankur31 4 months ago - 3 comments
Labels: T: enhancement

#429 - Fixes for validating - should be possible to validate xml files as nml too...

Pull Request - State: closed - Opened by pgleeson 5 months ago

#428 - Added segment picking from faces

Pull Request - State: closed - Opened by lej0hn 5 months ago - 3 comments
Labels: T: enhancement

#427 - Refactor LEMSSimulation to remove the need of an explicit dict (just use `vars(self)` instead

Pull Request - State: closed - Opened by sanjayankur31 5 months ago

#426 - Add functionality to overlay data on to 3D visualisations

Issue - State: open - Opened by sanjayankur31 5 months ago - 6 comments
Labels: T: enhancement

#425 - feat(vispy): simplify mesh creation

Pull Request - State: closed - Opened by sanjayankur31 5 months ago

#424 - Feat: improve cached method invocations

Pull Request - State: closed - Opened by sanjayankur31 5 months ago

#423 - Cached functions: cast arguments to hashable types before invocation

Issue - State: closed - Opened by sanjayankur31 5 months ago
Labels: T: enhancement

#422 - Tracking: multiple 3D vispy based visualisations do not work in a single jupyter notebook

Issue - State: open - Opened by sanjayankur31 5 months ago
Labels: T: bug

#421 - PR 407 + tweaks

Pull Request - State: closed - Opened by sanjayankur31 5 months ago

#420 - Add segment picking ability in 3D

Pull Request - State: closed - Opened by lej0hn 6 months ago - 4 comments

#419 - To v1.3.8; allows xml or sbml files to be validated as SBML

Pull Request - State: closed - Opened by pgleeson 6 months ago

#418 - Changes for NeuroML v2.3.1 release

Pull Request - State: closed - Opened by pgleeson 6 months ago

#417 - To v1.3.7 & use jnml v0.13.3

Pull Request - State: closed - Opened by pgleeson 6 months ago

#416 - Changes from master merged in

Pull Request - State: closed - Opened by pgleeson 6 months ago

#415 - Visualization: handle referenced morphologies

Pull Request - State: closed - Opened by sanjayankur31 6 months ago - 2 comments
Labels: T: enhancement

#414 - Morphology plotting: handle cells where morphology is a standalone element that is referenced in cell

Issue - State: closed - Opened by sanjayankur31 6 months ago - 3 comments
Labels: T: bug

#413 - Improve checks to ensure that the right input files are provided for each pynml command

Pull Request - State: closed - Opened by sanjayankur31 6 months ago - 2 comments
Labels: S: ready for review

#412 - Test multiple shading filters

Pull Request - State: closed - Opened by lej0hn 6 months ago - 7 comments

#411 - fix(moose): correct math operator

Pull Request - State: closed - Opened by sanjayankur31 6 months ago

#410 - Installation issues: Vispy and Conda?

Issue - State: closed - Opened by sanjayankur31 7 months ago - 2 comments
Labels: T: bug

#409 - docs: add stellaprins as a contributor for code, and ideas

Pull Request - State: closed - Opened by allcontributors[bot] 7 months ago

#408 - Feat/upright 2d plotter: enable upright for 2d morph plots also

Pull Request - State: closed - Opened by sanjayankur31 7 months ago - 1 comment
Labels: T: enhancement

#407 - Feat/export swc:- This aims to add a file which exports SWC file into neuroml.

Pull Request - State: closed - Opened by AdityaBITMESRA 7 months ago - 15 comments
Labels: S: ready for review

#406 - Check if users are passing the correct file type for various pynml commands

Issue - State: closed - Opened by sanjayankur31 7 months ago - 5 comments
Labels: T: enhancement, good first issue

#405 - feature/Added lighting

Pull Request - State: closed - Opened by lej0hn 7 months ago - 8 comments
Labels: T: enhancement

#404 - Feat/export swc-Adds function to export SWC graph to a new SWC file

Pull Request - State: closed - Opened by AdityaBITMESRA 7 months ago - 3 comments

#403 - Add SWC exporter

Issue - State: closed - Opened by sanjayankur31 7 months ago - 2 comments
Labels: T: enhancement

#402 - Add function to export SWC graph to a new SWC file

Issue - State: closed - Opened by sanjayankur31 7 months ago - 1 comment
Labels: T: enhancement

#401 - add downloads URL as biosimulations.submit_simulation_archive return value

Pull Request - State: closed - Opened by stellaprins 7 months ago - 3 comments

#400 - Review of #384 with a few tweaks

Pull Request - State: closed - Opened by sanjayankur31 7 months ago

#399 - feat/Make 3d visualization compatibile with jupyter notebooks

Pull Request - State: closed - Opened by lej0hn 7 months ago - 5 comments

#398 - Support visualisation of morphology only files

Pull Request - State: closed - Opened by sanjayankur31 7 months ago - 1 comment
Labels: T: enhancement

#397 - Allow visualization of morphology only NML files

Issue - State: closed - Opened by sanjayankur31 7 months ago
Labels: T: enhancement

#396 - To v1.3.2 and use jnml v0.13.2; pinning numpy<2.0

Pull Request - State: closed - Opened by pgleeson 8 months ago - 1 comment

#395 - Deps and CI fixes

Pull Request - State: closed - Opened by sanjayankur31 8 months ago - 3 comments

#394 - ci: tweak pip command

Pull Request - State: closed - Opened by sanjayankur31 8 months ago

#393 - WIP: testing with py3.13

Pull Request - State: closed - Opened by sanjayankur31 8 months ago

#392 - Use jnml jar 0.13.1; fixes to allow for cells with external morphology/biophysicalProperties

Pull Request - State: closed - Opened by pgleeson 8 months ago - 1 comment

#391 - ci: update comment bit to also work on PRs from forks

Pull Request - State: closed - Opened by sanjayankur31 8 months ago

#390 - Add `bqbiol.is`

Pull Request - State: closed - Opened by sanjayankur31 8 months ago - 1 comment

#389 - Error: pyneuroml/povray/OverlaySimulation.py:279:31: F821 Undefined name `volts`

Issue - State: closed - Opened by sanjayankur31 8 months ago
Labels: T: bug

#388 - Speed up unit tests

Issue - State: closed - Opened by sanjayankur31 8 months ago - 1 comment
Labels: T: enhancement

#387 - ci: add coverage to pull requests

Pull Request - State: closed - Opened by sanjayankur31 8 months ago - 4 comments

#386 - Feat/coverage

Pull Request - State: closed - Opened by sanjayankur31 8 months ago

#385 - Enable coverage info on the repo

Issue - State: closed - Opened by sanjayankur31 8 months ago - 1 comment

#384 - Feat/swc loaderfile Adding SWC loader to load SWC file

Pull Request - State: closed - Opened by AdityaBITMESRA 8 months ago - 17 comments
Labels: T: enhancement

#383 - chore: linter fixes

Pull Request - State: closed - Opened by sanjayankur31 8 months ago

#382 - Feat/make generate plot clicky

Pull Request - State: closed - Opened by sanjayankur31 8 months ago

#381 - docs: add AdityaBITMESRA as a contributor for code, and review

Pull Request - State: closed - Opened by allcontributors[bot] 8 months ago

#380 - Feat/loadswc Adding SWC loader to load SWC file

Pull Request - State: closed - Opened by AdityaBITMESRA 8 months ago

#379 - Feature Draft/ Use PCA to visualize cell 'upwards'

Pull Request - State: closed - Opened by lej0hn 8 months ago - 29 comments

#378 - fix(setup.cfg): include template channel file in data

Pull Request - State: closed - Opened by sanjayankur31 8 months ago

#377 - issue 303: plot spikes

Pull Request - State: closed - Opened by sanjayankur31 8 months ago - 4 comments

#376 - Tests on master failing

Issue - State: closed - Opened by pgleeson 8 months ago

#375 - Add a SWC loader

Issue - State: closed - Opened by sanjayankur31 8 months ago - 3 comments
Labels: T: enhancement

#374 - Feat/plotting checks

Pull Request - State: closed - Opened by sanjayankur31 8 months ago - 1 comment

#373 - Feat/get ks channel states

Pull Request - State: closed - Opened by sanjayankur31 8 months ago

#372 - Make getting model file list SBML aware

Issue - State: open - Opened by sanjayankur31 8 months ago
Labels: T: enhancement

#371 - chore: improve contributing documentation

Pull Request - State: closed - Opened by sanjayankur31 9 months ago
Labels: C: docs

#370 - docs: add lej0hn as a contributor for code

Pull Request - State: closed - Opened by allcontributors[bot] 9 months ago

#369 - Implement exporting to Neuroglancer formats

Issue - State: open - Opened by sanjayankur31 9 months ago - 1 comment
Labels: T: enhancement

#368 - Better handling of nested if statements in xpp parser

Pull Request - State: closed - Opened by pgleeson 9 months ago

#367 - Added translate_cell function

Pull Request - State: closed - Opened by lej0hn 9 months ago - 10 comments

#366 - Added function translate_cell

Pull Request - State: closed - Opened by lej0hn 9 months ago

#365 - Feat/test animate plots

Pull Request - State: closed - Opened by sanjayankur31 9 months ago

#364 - docs: add YBCS as a contributor for code, and test

Pull Request - State: closed - Opened by allcontributors[bot] 9 months ago

#363 - docs: add lej0hn as a contributor for review

Pull Request - State: closed - Opened by allcontributors[bot] 9 months ago

#362 - Implement vispy based viewing of SWC files

Issue - State: closed - Opened by sanjayankur31 9 months ago - 3 comments
Labels: T: enhancement

#361 - feat(rotation): allow users to pick if they want a copy

Pull Request - State: closed - Opened by sanjayankur31 9 months ago - 2 comments
Labels: S: ready for review

#360 - Add utility function to translate cell to that soma is at origin

Issue - State: closed - Opened by sanjayankur31 9 months ago
Labels: T: enhancement

#359 - vispy-viewer: make it run in jupyter notebooks using jupyter_rfb

Issue - State: closed - Opened by sanjayankur31 9 months ago - 1 comment
Labels: T: enhancement

#358 - [Bug] pynml-plotmorph: vispy: no mouse events

Issue - State: open - Opened by Sietse20 9 months ago - 3 comments
Labels: T: bug

#357 - Add analysis of KineticState channels to `pynml-channelanalysis`

Issue - State: open - Opened by sanjayankur31 9 months ago
Labels: T: enhancement

#356 - fix(nml-channel-analysis): include `ionChannelVShift`

Pull Request - State: closed - Opened by sanjayankur31 9 months ago

#355 - Updates to xpp running/plotting

Pull Request - State: closed - Opened by pgleeson 9 months ago

#354 - Annotations: completes exporting and extraction of annotations that we use in NeuroML

Pull Request - State: closed - Opened by sanjayankur31 9 months ago
Labels: T: enhancement

#353 - More annotation tweaks: remove unused ids, use `rdf:li`

Pull Request - State: closed - Opened by sanjayankur31 9 months ago
Labels: T: enhancement

#352 - feat(pynml-modchananalysis): add labels and fix file name

Pull Request - State: closed - Opened by sanjayankur31 10 months ago - 2 comments
Labels: T: enhancement

#351 - LEMS does not like RDF metadata (while using `pynml-channelanalysis`)?

Issue - State: open - Opened by sanjayankur31 10 months ago - 1 comment
Labels: T: bug

#350 - feat(annotations): improve for use as embedded annotations

Pull Request - State: closed - Opened by sanjayankur31 10 months ago

#349 - feat(annotations): extend to allow both miriam and biosimulations styles

Pull Request - State: closed - Opened by sanjayankur31 10 months ago
Labels: T: enhancement

#348 - animate matplotlib plots

Pull Request - State: closed - Opened by YBCS 10 months ago - 5 comments
Labels: T: enhancement

#347 - Extend `pynml` to include a `-biosimulations` flag to submit simulations

Issue - State: open - Opened by sanjayankur31 10 months ago
Labels: T: enhancement

#346 - feat(optional-deps): add warnings to inform users of optional packages

Pull Request - State: closed - Opened by sanjayankur31 10 months ago
Labels: T: enhancement, S: ready for review

#345 - chore: move to ruff

Pull Request - State: closed - Opened by sanjayankur31 10 months ago

#344 - creating and sending omex archives to biosimulations

Pull Request - State: closed - Opened by sanjayankur31 10 months ago - 1 comment
Labels: T: enhancement

#343 - Minor fixes and tests for XPP export; to v1.2.10

Pull Request - State: closed - Opened by pgleeson 10 months ago

#342 - Feat/recv2- Recording functionality

Pull Request - State: closed - Opened by AdityaBITMESRA 10 months ago - 1 comment
Labels: S: waiting on reporter

#341 - Draft - Added cell realignment with pca

Pull Request - State: closed - Opened by lej0hn 10 months ago
Labels: T: enhancement

GitHub / NeuroML/pyNeuroML issues and pull requests