NeuroML/pyNeuroML issues and pull requests

#332 - feat(LEMSSimulation): allow using float/str for duration/dt

Pull Request - State: closed - Opened by sanjayankur31 7 months ago - 1 comment
Labels: T: enhancement, S: ready for review

#331 - docs: add YBCS as a contributor for code

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

#330 - [Bug] ExportSWC: exceptions are wrong

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

#329 - Add option to generate SEDML file from LEMS and use this as master in exported OMEX archive

Issue - State: open - Opened by pgleeson 7 months ago
Labels: T: enhancement, Help wanted, good first issue

#328 - Add utility function to create SpikeArray from file

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

#327 - figures generated by `pynml-modchananalysis` are saved by default

Pull Request - State: closed - Opened by YBCS 8 months ago - 6 comments

#326 - add -swc in pynml

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

#325 - Feat/issue 321: add a parallel runner

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

#324 - docs: add AdityaBITMESRA as a contributor for bug, and ideas

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

#323 - docs: add Dhruvanshu-Joshi as a contributor for bug, and ideas

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

#322 - docs: add lej0hn as a contributor for bug, and ideas

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

#321 - [simulation] Add method to run multiple sims in parallel using pp

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

#320 - Added warning for missing included files

Pull Request - State: closed - Opened by lej0hn 8 months ago - 4 comments
Labels: S: waiting on reporter

#319 - [cell analysis] Implement morphological statistics for NeuroML cell models

Issue - State: open - Opened by sanjayankur31 8 months ago
Labels: T: enhancement, Help wanted, good first issue

#318 - [vispy viewer] investigate if we can record a video of the rotating image

Issue - State: open - Opened by sanjayankur31 8 months ago - 2 comments
Labels: T: enhancement, Help wanted, good first issue

#317 - [vispy viewer] align cells along its first principal component

Issue - State: closed - Opened by sanjayankur31 8 months ago - 3 comments
Labels: T: enhancement, Help wanted, good first issue

#316 - <feat> : Added feature to save vispy obj and gz files

Pull Request - State: closed - Opened by Dhruvanshu-Joshi 8 months ago - 14 comments
Labels: T: enhancement

#315 - Add warnings about missing files of model during visualisation

Issue - State: open - Opened by lej0hn 9 months ago - 1 comment
Labels: T: enhancement

#314 - feat: split vispy into qt5 and qt6 deps

Pull Request - State: closed - Opened by sanjayankur31 9 months ago
Labels: T: enhancement, S: ready for review

#313 - Feat/issue 303: de-duplicate plot spikes code

Pull Request - State: closed - Opened by AdityaBITMESRA 9 months ago - 67 comments
Labels: T: enhancement, S: ready for review, S: needs info, S: waiting on reporter

#312 - To v1.2.7 and some updates to -run-tellurium

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

#311 - plot-timeseries: expose option in cli to allow saving plot to a file

Pull Request - State: closed - Opened by sanjayankur31 9 months ago
Labels: T: enhancement, S: ready for review

#310 - To v1.2.4; include pyneuroml.utils.misc in pynml imports

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

#309 - Refactored the PlotSpikes.py file

Pull Request - State: closed - Opened by AdityaBITMESRA 9 months ago - 3 comments
Labels: S: ready for review, S: waiting on reporter

#308 - Ascertain and set `NEURON_HOME` if the environment variable is not set

Issue - State: open - Opened by sanjayankur31 9 months ago - 5 comments
Labels: T: enhancement, Help wanted, good first issue

#307 - Feat: Add method and cli to plot time series

Pull Request - State: closed - Opened by sanjayankur31 9 months ago - 1 comment
Labels: T: enhancement, S: ready for review

#306 - Document sbml

Pull Request - State: closed - Opened by sanjayankur31 9 months ago - 1 comment
Labels: T: enhancement, C: docs

#305 - Feat/ run tellurium

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

#304 - Feat/ run tellurium

Pull Request - State: closed - Opened by robertvi 9 months ago - 1 comment

#303 - Refactor: de-duplicate PlotSpikes code

Issue - State: closed - Opened by sanjayankur31 9 months ago - 2 comments
Labels: T: enhancement, Help wanted, good first issue

#302 - Updated jnml jar with SED-ML file writing

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

#301 - Improve default positioning of legend on plots

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

#300 - Feat/ run tellurium

Pull Request - State: closed - Opened by robertvi 9 months ago - 2 comments

#299 - Chore: run `no_implicit_optional` on code base

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

#298 - Adds util method to generate simulation scripts in a different, clean directory

Pull Request - State: closed - Opened by sanjayankur31 10 months ago - 3 comments
Labels: T: enhancement, S: ready for review

#297 - WIP: module to enable conversion of sim data to nwb

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

#296 - feat(pynml): respect `JNML_MAX_MEMORY_LOCAL` env variable

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

#295 - added -sbml-sedml option passing through to jnml

Pull Request - State: closed - Opened by robertvi 10 months ago - 3 comments

#294 - feat: morphology plotting: allow marking/highlighting individual segments

Pull Request - State: closed - Opened by sanjayankur31 11 months ago - 1 comment
Labels: T: enhancement

#293 - Issue compiling .mod files on Apple Silicon [Bug]

Issue - State: closed - Opened by olitr20 11 months ago - 5 comments
Labels: T: question

#292 - fix(vispy): use proximal and distal radii for mesh

Pull Request - State: closed - Opened by sanjayankur31 11 months ago
Labels: T: bug, T: enhancement

#291 - To v1.1.10 & black formatting

Pull Request - State: closed - Opened by pgleeson 11 months ago

#290 - Tested sedml validate changes

Pull Request - State: closed - Opened by pgleeson 11 months ago

#289 - added -validate-sedml option

Pull Request - State: closed - Opened by robertvi 12 months ago - 1 comment

#288 - added SEDML validate option (rebased)

Pull Request - State: closed - Opened by robertvi 12 months ago

#287 - added SEDML validate option

Pull Request - State: closed - Opened by robertvi 12 months ago - 5 comments

#286 - feat(archive): also handle h5 files

Pull Request - State: open - Opened by sanjayankur31 12 months ago
Labels: T: enhancement

#285 - archiving/nsg: include HDF5 exports

Issue - State: open - Opened by sanjayankur31 12 months ago - 2 comments
Labels: T: enhancement

#284 - feat(py312): mark 3.12 as supported

Pull Request - State: closed - Opened by sanjayankur31 12 months ago - 2 comments
Labels: T: enhancement

#283 - Drop explicit inspyred installation in CI

Pull Request - State: closed - Opened by sanjayankur31 12 months ago

#282 - feat!: drop Py3.7 support

Pull Request - State: closed - Opened by sanjayankur31 12 months ago - 1 comment
Labels: T: enhancement, S: ready for review

#281 - Master changes -> dev

Pull Request - State: closed - Opened by pgleeson 12 months ago

#280 - fix(nsgr-netpyne): include model files in NSG zip also

Pull Request - State: closed - Opened by sanjayankur31 12 months ago
Labels: T: bug, S: ready for review

#279 - Include generation of animated matplotlib plots

Issue - State: closed - Opened by sanjayankur31 12 months ago - 13 comments
Labels: T: enhancement, Help wanted, good first issue

#278 - Add option to save vispy generated meshdata

Issue - State: closed - Opened by sanjayankur31 12 months ago - 5 comments
Labels: T: enhancement, Help wanted, good first issue

#277 - Add option to validate SED-ML files

Issue - State: closed - Opened by pgleeson 12 months ago - 2 comments
Labels: T: enhancement, Help wanted

#276 - docs: add robertvi as a contributor for code, and test

Pull Request - State: closed - Opened by allcontributors[bot] 12 months ago

#275 - Tweaks to sbml; fix generate_plot() in pynml; to v1.1.7

Pull Request - State: closed - Opened by pgleeson about 1 year ago

#274 - Test sbml

Pull Request - State: closed - Opened by pgleeson about 1 year ago

#273 - wip(vispy): add lighting

Pull Request - State: closed - Opened by sanjayankur31 about 1 year ago - 1 comment
Labels: T: enhancement

#272 - Chord diagram and other connectivity plot related refactoring

Pull Request - State: open - Opened by sanjayankur31 about 1 year ago
Labels: T: enhancement

#271 - feat(plotter): use matplotlib rcparams defaults for missing options

Pull Request - State: closed - Opened by sanjayankur31 about 1 year ago
Labels: T: enhancement

#270 - feat(graph-generator): allow passing kwargs to GraphVizHandler

Pull Request - State: closed - Opened by sanjayankur31 about 1 year ago
Labels: T: enhancement, S: ready for review

#269 - feat(pynml): do not import plotters if mpl is not already imported

Pull Request - State: closed - Opened by sanjayankur31 about 1 year ago

#268 - Add tests running simple neuron + netpyne sims on nsg

Issue - State: open - Opened by sanjayankur31 about 1 year ago - 1 comment
Labels: T: enhancement, good first issue

#267 - Testing sbml

Pull Request - State: closed - Opened by pgleeson about 1 year ago

#266 - added -validate-sbml option

Pull Request - State: closed - Opened by robertvi about 1 year ago - 5 comments
Labels: T: enhancement, S: ready for review

#265 - Development

Pull Request - State: closed - Opened by robertvi about 1 year ago

#264 - Close cylindrical meshes for vispy viewer

Pull Request - State: closed - Opened by sanjayankur31 about 1 year ago - 2 comments
Labels: T: enhancement, S: ready for review, S: release pending

#263 - For 1.1.3 release

Pull Request - State: closed - Opened by sanjayankur31 about 1 year ago

#262 - Expose `meta` in LEMSSimulation

Pull Request - State: closed - Opened by sanjayankur31 about 1 year ago
Labels: T: enhancement, S: ready for review

#261 - chore(deps): remove unused pandas

Pull Request - State: closed - Opened by sanjayankur31 about 1 year ago
Labels: T: enhancement

#260 - Improve performance of vispy plotter using meshes and their instances

Pull Request - State: closed - Opened by sanjayankur31 about 1 year ago - 5 comments
Labels: T: enhancement, S: ready for review

#259 - To 1.1.2

Pull Request - State: closed - Opened by sanjayankur31 about 1 year ago

#258 - Reduce memory usage when generating morph plots and a few minor fixes

Pull Request - State: closed - Opened by sanjayankur31 about 1 year ago
Labels: T: bug, T: enhancement

#257 - Changes for NML v2.3 release

Pull Request - State: closed - Opened by pgleeson about 1 year ago

#256 - To v1.1.0; uses jnml jar 0.12.4

Pull Request - State: closed - Opened by pgleeson about 1 year ago

#255 - feat(write): include HDF5 writing

Pull Request - State: closed - Opened by sanjayankur31 about 1 year ago
Labels: T: enhancement, S: ready for review

#254 - To v1.1.0; Update to jnml v0.12.3 jar

Pull Request - State: closed - Opened by pgleeson about 1 year ago

#253 - Feat/hybrid plots: allow users to specify how they want various cells in networks to be plotted

Pull Request - State: closed - Opened by sanjayankur31 about 1 year ago
Labels: T: enhancement, S: ready for review

#252 - fix(plots): provide axis for colorbar

Pull Request - State: closed - Opened by sanjayankur31 about 1 year ago

#251 - fix(vispy-morph): get title from cell object if no network is found

Pull Request - State: closed - Opened by sanjayankur31 about 1 year ago
Labels: S: ready for review

#250 - Add option to validate SBML

Issue - State: closed - Opened by pgleeson about 1 year ago - 3 comments
Labels: T: enhancement, Help wanted, good first issue

#249 - feat(pynml): include more info in version

Pull Request - State: closed - Opened by sanjayankur31 over 1 year ago
Labels: T: enhancement, S: ready for review

#248 - feat(morph-plots): improve colouring of cells/groups in schematic plot

Pull Request - State: closed - Opened by sanjayankur31 over 1 year ago
Labels: T: enhancement, S: ready for review

#247 - To v1.0.10; removed 'experimental' build config, uses 'dev' as development env/dependencies

Pull Request - State: closed - Opened by pgleeson over 1 year ago

#246 - allow netpyne runner to also return command output

Pull Request - State: closed - Opened by pgleeson over 1 year ago

#245 - To v1.0.9

Pull Request - State: closed - Opened by pgleeson over 1 year ago

#244 - Remove argparse dependency

Pull Request - State: closed - Opened by pgleeson over 1 year ago

#243 - Feat/nsgr integration

Pull Request - State: closed - Opened by sanjayankur31 over 1 year ago - 4 comments
Labels: T: enhancement, S: ready for review

#242 - Feat/chan den analysis

Pull Request - State: closed - Opened by sanjayankur31 over 1 year ago - 1 comment
Labels: T: enhancement, S: ready for review

#241 - Add function to generate LFP plots

Issue - State: open - Opened by sanjayankur31 over 1 year ago - 2 comments
Labels: T: enhancement, Help wanted, P: low

#240 - Feat/add all contributors

Pull Request - State: closed - Opened by sanjayankur31 over 1 year ago

#239 - feat(pynml-netpyne): allow netpyne runner to also return command output

Pull Request - State: closed - Opened by sanjayankur31 over 1 year ago
Labels: T: enhancement, S: ready for review

#238 - Feat: extend morphology plotting methods to accept a file path and objects; move vispy bits to separate module to reduce import errors (breaking)

Pull Request - State: closed - Opened by sanjayankur31 over 1 year ago - 1 comment
Labels: T: enhancement, S: ready for review

GitHub / NeuroML/pyNeuroML issues and pull requests