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Recent Releases of pyneuroml

pyneuroml - v1.3.21

What's Changed

  • fix(file-list): correct recursive file listing by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/456

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.3.20...v1.3.21

- Python
Published by sanjayankur31 8 months ago

pyneuroml - v1.3.20

What's Changed

  • feat(deps): unpin pyopengl-acclerate by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/455

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.3.19...v1.3.20

- Python
Published by sanjayankur31 8 months ago

pyneuroml - v1.3.19

What's Changed

  • ci: remove numpy pin by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/453
  • Feat test py313 by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/445
  • fix(vispy): handle case where no rotation is required by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/451
  • Feat: provide jnml command that will use the bundled jar by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/450

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.3.18...v1.3.19

- Python
Published by sanjayankur31 8 months ago

pyneuroml - v1.3.18

What's Changed

  • Use latest nmllite etc by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/448
  • fix: drop unused import by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/449

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.3.17...v1.3.18

- Python
Published by sanjayankur31 9 months ago

pyneuroml - v1.3.17

What's Changed

  • fix(morph-plot): handle files with single point cell types by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/441
  • Whitespace changes & bump to v1.3.17 - update to require latest pylems/libneuroml/neuromllite by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/444
  • feat: remove numpy version pin by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/446

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.3.15...v1.3.17

- Python
Published by sanjayankur31 9 months ago

pyneuroml - v1.3.15

What's Changed

  • Uses jNeuroML v0.14.0
  • Add example testing executecommandin_dir etc. by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/442

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.3.13...v1.3.14

- Python
Published by pgleeson about 1 year ago

pyneuroml - v1.3.13

What's Changed

  • Changes for NeuroML v2.3.1 release by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/418
  • Refactor LEMSSimulation to remove the need of an explicit dict (just use vars(self) instead by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/427
  • Fixes for validating - should be possible to validate xml files as nml too... by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/429
  • Added segment picking from faces by @lej0hn in https://github.com/NeuroML/pyNeuroML/pull/428
  • Feat: util to create + include new components in NeuroMLDocuments by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/430
  • Time series plotting tweaks by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/431
  • Fix pynml archive by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/434
  • wip: improve pynml-summary by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/437
  • Fix file compatibility check by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/436

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.3.12...v1.3.13

- Python
Published by sanjayankur31 about 1 year ago

pyneuroml - v1.3.12

What's Changed

  • feat(vispy): simplify mesh creation by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/425

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.3.11...v1.3.12

- Python
Published by sanjayankur31 over 1 year ago

pyneuroml - v1.3.11

What's Changed

  • Feat: improve cached method invocations by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/424

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.3.10...v1.3.11

- Python
Published by sanjayankur31 over 1 year ago

pyneuroml - v1.3.10

  • feat(morph-plot): also allow plotting of swc files: https://github.com/NeuroML/pyNeuroML/commit/3d9a27f0210b8f4cb7ecc6881f753749af4635a9

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.3.9...v1.3.10

- Python
Published by sanjayankur31 over 1 year ago

pyneuroml - v1.3.9

What's Changed

  • Visualization: handle referenced morphologies by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/415
  • PR 407 + tweaks by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/421
  • Feat/export swc:- This aims to add a file which exports SWC file into neuroml. by @AdityaBITMESRA in https://github.com/NeuroML/pyNeuroML/pull/407

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.3.8...v1.3.9

- Python
Published by sanjayankur31 over 1 year ago

pyneuroml - v1.3.8

What's Changed

  • To v1.3.8; allows xml or sbml files to be validated as SBML by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/419

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.3.7...v1.3.8

- Python
Published by pgleeson over 1 year ago

pyneuroml - v1.3.7

What's Changed

  • docs: add lej0hn as a contributor for bug, and ideas by @allcontributors in https://github.com/NeuroML/pyNeuroML/pull/322
  • docs: add Dhruvanshu-Joshi as a contributor for bug, and ideas by @allcontributors in https://github.com/NeuroML/pyNeuroML/pull/323
  • docs: add AdityaBITMESRA as a contributor for bug, and ideas by @allcontributors in https://github.com/NeuroML/pyNeuroML/pull/324
  • docs: add YBCS as a contributor for code by @allcontributors in https://github.com/NeuroML/pyNeuroML/pull/331
  • docs: add lej0hn as a contributor for review by @allcontributors in https://github.com/NeuroML/pyNeuroML/pull/363
  • docs: add YBCS as a contributor for code, and test by @allcontributors in https://github.com/NeuroML/pyNeuroML/pull/364
  • docs: add lej0hn as a contributor for code by @allcontributors in https://github.com/NeuroML/pyNeuroML/pull/370
  • fix(setup.cfg): include template channel file in data by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/378
  • docs: add AdityaBITMESRA as a contributor for code, and review by @allcontributors in https://github.com/NeuroML/pyNeuroML/pull/381
  • docs: add stellaprins as a contributor for code, and ideas by @allcontributors in https://github.com/NeuroML/pyNeuroML/pull/409
  • Improve checks to ensure that the right input files are provided for each pynml command by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/413
  • Changes from master merged in by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/416
  • To v1.3.7 & use jnml v0.13.3 by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/417

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.3.5...v1.3.7

- Python
Published by pgleeson over 1 year ago

pyneuroml - v1.3.5

What's Changed

  • fix(moose): correct math operator by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/411

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.3.4...v1.3.5

- Python
Published by sanjayankur31 over 1 year ago

pyneuroml - v1.3.4

What's Changed

  • Review of #384 with a few tweaks by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/400
  • Feat/swc loaderfile Adding SWC loader to load SWC file by @AdityaBITMESRA in https://github.com/NeuroML/pyNeuroML/pull/384
  • add downloads URL as biosimulations.submitsimulationarchive return value by @stellaprins in https://github.com/NeuroML/pyNeuroML/pull/401
  • feat/Make 3d visualization compatibile with jupyter notebooks by @lej0hn in https://github.com/NeuroML/pyNeuroML/pull/399
  • Feat/export swc-Adds function to export SWC graph to a new SWC file by @AdityaBITMESRA in https://github.com/NeuroML/pyNeuroML/pull/404

New Contributors

  • @AdityaBITMESRA made their first contribution in https://github.com/NeuroML/pyNeuroML/pull/384
  • @stellaprins made their first contribution in https://github.com/NeuroML/pyNeuroML/pull/401

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.3.3...v1.3.4

- Python
Published by sanjayankur31 over 1 year ago

pyneuroml - v1.3.3

What's Changed

  • Feature Draft/ Use PCA to visualize cell 'upwards' by @lej0hn in https://github.com/NeuroML/pyNeuroML/pull/379
  • Support visualisation of morphology only files by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/398

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.3.2...v1.3.3

- Python
Published by sanjayankur31 over 1 year ago

pyneuroml - v1.3.2

What's Changed

  • ci: tweak pip command by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/394
  • Deps and CI fixes by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/395
  • To v1.3.2 and use jnml v0.13.2; pinning numpy<2.0 by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/396

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.3.0...v1.3.2

- Python
Published by pgleeson over 1 year ago

pyneuroml - v1.3.0

What's Changed

  • Added translate_cell function by @lej0hn in https://github.com/NeuroML/pyNeuroML/pull/367
  • Annotations: completes exporting and extraction of annotations that we use in NeuroML by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/354
  • chore: improve contributing documentation by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/371
  • Feat/get ks channel states by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/373
  • Feat/plotting checks by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/374
  • issue 303: plot spikes by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/377
  • Feat/make generate plot clicky by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/382
  • chore: linter fixes by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/383
  • Feat/coverage by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/386
  • ci: add coverage to pull requests by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/387
  • Add bqbiol.is by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/390
  • ci: update comment bit to also work on PRs from forks by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/391
  • Use jnml jar 0.13.1; fixes to allow for cells with external morphology/biophysicalProperties by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/392

New Contributors

  • @lej0hn made their first contribution in https://github.com/NeuroML/pyNeuroML/pull/367

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.2.14...v1.3.0

- Python
Published by pgleeson over 1 year ago

pyneuroml - v1.2.14

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.2.13...v1.2.14

  • bugfix: adds progressbar as a default dependency

- Python
Published by sanjayankur31 almost 2 years ago

pyneuroml - v1.2.13

What's Changed

  • feat(annotations): improve for use as embedded annotations by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/350
  • More annotation tweaks: remove unused ids, use rdf:li by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/353
  • fix(nml-channel-analysis): include ionChannelVShift by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/356
  • Updates to xpp running/plotting by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/355
  • feat(rotation): allow users to pick if they want a copy by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/361
  • animate matplotlib plots by @YBCS in https://github.com/NeuroML/pyNeuroML/pull/348
  • Feat/test animate plots by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/365
  • feat(pynml-modchananalysis): add labels and fix file name by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/352
  • Better handling of nested if statements in xpp parser by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/368

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.2.12...v1.2.13

- Python
Published by pgleeson almost 2 years ago

pyneuroml - v1.2.12

What's Changed

  • feat(annotations): extend to allow both miriam and biosimulations styles by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/349

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.2.11...v1.2.12

- Python
Published by sanjayankur31 almost 2 years ago

pyneuroml - v1.2.11

What's Changed

  • feat(optional-deps): add warnings to inform users of optional packages by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/346

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.2.10...v1.2.11

- Python
Published by sanjayankur31 almost 2 years ago

pyneuroml - v1.2.10

What's Changed

  • Minor fixes and tests for XPP export; to v1.2.10 by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/343
  • feat(annotations): add wrapper to write annotations by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/339
  • chore: move to ruff by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/345
  • creating and sending omex archives to biosimulations by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/344

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.2.9...v1.2.10

- Python
Published by sanjayankur31 almost 2 years ago

pyneuroml - v1.2.9

What's Changed

  • feat: split vispy into qt5 and qt6 deps by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/314
  • Feat/issue 321: add a parallel runner by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/325
  • add -swc in pynml by @YBCS in https://github.com/NeuroML/pyNeuroML/pull/326
  • feat(LEMSSimulation): allow using float/str for duration/dt by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/332
  • figures generated by pynml-modchananalysis are saved by default by @YBCS in https://github.com/NeuroML/pyNeuroML/pull/327
  • pynml-archive: add -sedml by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/335
  • Initial version of pynml-xpp, for parsing XPP files and converting to LEMS by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/338

New Contributors

  • @YBCS made their first contribution in https://github.com/NeuroML/pyNeuroML/pull/326

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.2.7...v1.2.9

- Python
Published by pgleeson almost 2 years ago

pyneuroml - v1.2.7

What's Changed

  • To v1.2.7 and some updates to -run-tellurium by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/312

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.2.5...v1.2.7

- Python
Published by pgleeson almost 2 years ago

pyneuroml - v1.2.5

What's Changed

  • plot-timeseries: expose option in cli to allow saving plot to a file by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/311

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.2.4...v1.2.5

- Python
Published by sanjayankur31 almost 2 years ago

pyneuroml - v1.2.4

What's Changed

  • Feat/ run tellurium by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/305
  • To v1.2.4; include pyneuroml.utils.misc in pynml imports by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/310

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.2.2...v1.2.4

- Python
Published by sanjayankur31 about 2 years ago

pyneuroml - v1.2.2

What's Changed

  • Feat: Add method and cli to plot time series by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/307

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.2.1...v1.2.2

- Python
Published by sanjayankur31 about 2 years ago

pyneuroml - v1.2.1

  • fix: removes the import of the nsgr submodule from pynml that was mistakenly introduced in 1.2.0

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.2.0...v1.2.1

- Python
Published by sanjayankur31 about 2 years ago

pyneuroml - v1.2.0

What's Changed

  • Improve default positioning of legend on plots by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/301
  • Updated jnml jar with SED-ML file writing by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/302
  • Adds util method to generate simulation scripts in a different, clean directory by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/298
  • feat(py312): mark 3.12 as supported by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/284
  • Feat/ run tellurium by @robertvi in https://github.com/NeuroML/pyNeuroML/pull/304
  • Document sbml by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/306

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.1.13...v1.2.0

- Python
Published by sanjayankur31 about 2 years ago

pyneuroml - v1.1.13

What's Changed

  • feat(pynml): respect JNML_MAX_MEMORY_LOCAL env variable by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/296
  • added -sbml-sedml option passing through to jnml by @robertvi in https://github.com/NeuroML/pyNeuroML/pull/295

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.1.12...v1.1.13

- Python
Published by sanjayankur31 about 2 years ago

pyneuroml - v1.1.12

What's Changed

  • feat: morphology plotting: allow marking/highlighting individual segments by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/294

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.1.11...v1.1.12

- Python
Published by sanjayankur31 about 2 years ago

pyneuroml - v1.1.11

What's Changed

  • fix(vispy): use proximal and distal radii for mesh by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/292

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.1.10...v1.1.11

- Python
Published by sanjayankur31 about 2 years ago

pyneuroml - v1.1.10

What's Changed

  • docs: add robertvi as a contributor for code, and test by @allcontributors in https://github.com/NeuroML/pyNeuroML/pull/276
  • feat!: drop Py3.7 support by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/282
  • Master changes -> dev by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/281
  • Drop explicit inspyred installation in CI by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/283
  • Tested sedml validate changes by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/290
  • added -validate-sedml option by @robertvi in https://github.com/NeuroML/pyNeuroML/pull/289
  • To v1.1.10 & black formatting by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/291

New Contributors

  • @allcontributors made their first contribution in https://github.com/NeuroML/pyNeuroML/pull/276

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.1.8...v1.1.10

- Python
Published by pgleeson about 2 years ago

pyneuroml - v1.1.8

What's Changed

  • fix(nsgr-netpyne): include model files in NSG zip also by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/280

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.1.7...v1.1.8

- Python
Published by sanjayankur31 over 2 years ago

pyneuroml - v1.1.7

What's Changed

  • Testing sbml by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/267
  • feat(graph-generator): allow passing kwargs to GraphVizHandler by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/270
  • feat(plotter): use matplotlib rcparams defaults for missing options by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/271
  • Test sbml by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/274
  • added -validate-sbml option by @robertvi in https://github.com/NeuroML/pyNeuroML/pull/266
  • Tweaks to sbml; fix generate_plot() in pynml; to v1.1.7 by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/275
  • Expose meta in LEMSSimulation by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/262

New Contributors

  • @robertvi made their first contribution in https://github.com/NeuroML/pyNeuroML/pull/266

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.1.5...v1.1.7

- Python
Published by pgleeson over 2 years ago

pyneuroml - v1.1.5

What's Changed

  • feat(pynml): do not import plotters if mpl is not already imported by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/269

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.1.4...v1.1.5

- Python
Published by sanjayankur31 over 2 years ago

pyneuroml - v1.1.4

What's Changed

  • Close cylindrical meshes for vispy viewer by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/264

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.1.3...v1.1.4

- Python
Published by sanjayankur31 over 2 years ago

pyneuroml - v1.1.3

What's Changed

  • chore(deps): remove unused pandas by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/261
  • Improve performance of vispy plotter using meshes and their instances by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/260
  • For 1.1.3 release by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/263

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.1.2...v1.1.3

- Python
Published by sanjayankur31 over 2 years ago

pyneuroml - v1.1.2

What's Changed

  • Reduce memory usage when generating morph plots and a few minor fixes by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/258
  • To 1.1.2 by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/259

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.1.1...v1.1.2

- Python
Published by sanjayankur31 over 2 years ago

pyneuroml - v1.1.1

What's Changed

  • To v1.1.0; uses jnml jar 0.12.4 by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/256
  • feat(write): include HDF5 writing by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/255
  • Feat/hybrid plots: allow users to specify how they want various cells in networks to be plotted by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/253
  • Changes for NML v2.3 release by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/257

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.1.0...v1.1.1

- Python
Published by pgleeson over 2 years ago

pyneuroml - v1.1.0

What's Changed

  • fix(plots): provide axis for colorbar by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/252
  • fix(vispy-morph): get title from cell object if no network is found by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/251
  • feat(morph-plots): improve colouring of cells/groups in schematic plot by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/248
  • feat(pynml): include more info in version by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/249
  • Feat/chan den analysis by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/242
  • Feat/nsgr integration by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/243
  • To v1.1.0; Update to jnml v0.12.3 jar by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/254

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.0.10...v1.1.0

- Python
Published by pgleeson over 2 years ago

pyneuroml - v1.0.10

What's Changed

  • feat(generate-if-curve): allow specifying segment and fraction along by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/235
  • Chore/remove deprecated setup.py by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/234
  • chore: remove deprecated setup.py by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/233
  • Feat/add all contributors by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/240
  • Remove argparse dependency by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/244
  • To v1.0.9 by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/245
  • feat: add method to rotate cell by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/218
  • feat(if-curve): save spike threshold current value also by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/237
  • Feat: extend morphology plotting methods to accept a file path and objects; move vispy bits to separate module to reduce import errors (breaking) by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/238
  • allow netpyne runner to also return command output by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/246
  • feat(pynml-netpyne): allow netpyne runner to also return command output by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/239
  • To v1.0.10; removed 'experimental' build config, uses 'dev' as development env/dependencies by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/247

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.0.8...v1.0.10

- Python
Published by pgleeson over 2 years ago

pyneuroml - v1.0.9

What's Changed

  • feat(generate-if-curve): allow specifying segment and fraction along by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/235
  • Chore/remove deprecated setup.py by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/234
  • chore: remove deprecated setup.py by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/233
  • Feat/add all contributors by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/240
  • Remove argparse dependency by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/244
  • To v1.0.9 by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/245
  • feat: add method to rotate cell by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/218
  • feat(if-curve): save spike threshold current value also by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/237
  • Feat: extend morphology plotting methods to accept a file path and objects; move vispy bits to separate module to reduce import errors (breaking) by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/238
  • allow netpyne runner to also return command output by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/246
  • feat(pynml-netpyne): allow netpyne runner to also return command output by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/239

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v1.0.8...v1.0.9

- Python
Published by pgleeson over 2 years ago

pyneuroml - v1.0.8

Intermediate release pre NMLv2.3

What's Changed

  • Feature: add functions to create a combine archive from a provided "root" file by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/208
  • ci(py311): add py311 to ci and setup.py by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/211
  • feat: improve installation of extra deps by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/212
  • Adding logic for one-shot validation of multiple input files by @borismarin in https://github.com/NeuroML/pyNeuroML/pull/215
  • test(modchananalysis): test to check that nrnivmodl is run when required by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/217
  • pynml-modchananalysis excepting on division by zero by @borismarin in https://github.com/NeuroML/pyNeuroML/pull/216
  • Feat/more morphplots -> exp by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/219
  • Feat/more morphplots by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/213
  • A few minor changes and bugfix for 2d plotting by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/221
  • Plotting fixes related to #220, and regenerates man pages by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/222
  • Fix for reloading saved spike data by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/223
  • chore: regenerate man pages by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/226
  • Update to v1.0.1 with jnml jar v0.12.2 by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/227
  • To v1.0.2 & fix for pypi by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/228
  • Install pyelectro & neurotune from pypi by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/229
  • To v1.0.6 & remove inspyred req by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/230
  • To v1.0.7; remove inspyred from setup.py all reqs by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/231
  • To v1.0.8; Catches import of vispy so won't fail if not installed. by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/232

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v0.7.5...v1.0.8

- Python
Published by pgleeson almost 3 years ago

pyneuroml - v1.0.7

What's Changed

  • Feature: add functions to create a combine archive from a provided "root" file by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/208
  • ci(py311): add py311 to ci and setup.py by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/211
  • feat: improve installation of extra deps by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/212
  • Adding logic for one-shot validation of multiple input files by @borismarin in https://github.com/NeuroML/pyNeuroML/pull/215
  • test(modchananalysis): test to check that nrnivmodl is run when required by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/217
  • pynml-modchananalysis excepting on division by zero by @borismarin in https://github.com/NeuroML/pyNeuroML/pull/216
  • Feat/more morphplots -> exp by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/219
  • Feat/more morphplots by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/213
  • A few minor changes and bugfix for 2d plotting by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/221
  • Plotting fixes related to #220, and regenerates man pages by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/222
  • Fix for reloading saved spike data by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/223
  • chore: regenerate man pages by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/226
  • Update to v1.0.1 with jnml jar v0.12.2 by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/227
  • To v1.0.2 & fix for pypi by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/228
  • Install pyelectro & neurotune from pypi by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/229
  • To v1.0.6 & remove inspyred req by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/230
  • To v1.0.7; remove inspyred from setup.py all reqs by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/231

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v0.7.5...v1.0.7

- Python
Published by pgleeson almost 3 years ago

pyneuroml - v1.0.6

Intermediate release pre NMLv2.3

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v0.7.5...v1.0.6

- Python
Published by pgleeson almost 3 years ago

pyneuroml - v1.0.5

Intermediate release pre NMLv2.3

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v0.7.5...v1.0.5

- Python
Published by pgleeson almost 3 years ago

pyneuroml - v1.0.3

Intermediate release pre NMLv2.3

What's Changed

  • Feature: add functions to create a combine archive from a provided "root" file by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/208
  • ci(py311): add py311 to ci and setup.py by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/211
  • feat: improve installation of extra deps by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/212
  • Adding logic for one-shot validation of multiple input files by @borismarin in https://github.com/NeuroML/pyNeuroML/pull/215
  • test(modchananalysis): test to check that nrnivmodl is run when required by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/217
  • pynml-modchananalysis excepting on division by zero by @borismarin in https://github.com/NeuroML/pyNeuroML/pull/216
  • Feat/more morphplots -> exp by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/219
  • Feat/more morphplots by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/213
  • A few minor changes and bugfix for 2d plotting by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/221
  • Plotting fixes related to #220, and regenerates man pages by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/222
  • Fix for reloading saved spike data by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/223
  • chore: regenerate man pages by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/226
  • Update to v1.0.1 with jnml jar v0.12.2 by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/227
  • To v1.0.2 & fix for pypi by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/228

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v0.7.5...v1.0.3

- Python
Published by pgleeson almost 3 years ago

pyneuroml - v1.0.1

Intermediate release pre NeuroMLv2.3

What's Changed

  • Feature: add functions to create a combine archive from a provided "root" file by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/208
  • ci(py311): add py311 to ci and setup.py by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/211
  • feat: improve installation of extra deps by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/212
  • Adding logic for one-shot validation of multiple input files by @borismarin in https://github.com/NeuroML/pyNeuroML/pull/215
  • test(modchananalysis): test to check that nrnivmodl is run when required by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/217
  • pynml-modchananalysis excepting on division by zero by @borismarin in https://github.com/NeuroML/pyNeuroML/pull/216
  • Feat/more morphplots -> exp by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/219
  • Feat/more morphplots by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/213
  • A few minor changes and bugfix for 2d plotting by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/221
  • Plotting fixes related to #220, and regenerates man pages by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/222
  • Fix for reloading saved spike data by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/223
  • chore: regenerate man pages by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/226
  • Update to v1.0.1 with jnml jar v0.12.2 by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/227

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v0.7.5...v1.0.1

- Python
Published by pgleeson almost 3 years ago

pyneuroml - v0.7.5

What's Changed

  • Feat/document channelanalysis by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/206
  • To v0.7.5 and jnml 0.12.1 by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/209

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v0.7.3...v0.7.5

- Python
Published by sanjayankur31 about 3 years ago

pyneuroml - v0.7.3

What's Changed

  • Mainly new jar for jnml by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/195
  • Move mod2nml script to neuron utilities by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/193
  • Document cell analysis function, add test by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/200
  • Improved error code generation; To v0.7.3 by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/203
  • Adding latest jnml jar by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/205

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v0.7.2...v0.7.3

- Python
Published by sanjayankur31 over 3 years ago

pyneuroml - v0.7.2

What's Changed

  • Update channel export by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/177
  • Latest experimental branch incl chan analysis updates by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/179
  • update changes to the template file by @shayan823 in https://github.com/NeuroML/pyNeuroML/pull/174
  • Plotly features to dev by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/180
  • Feat/plotly plotting by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/176
  • Feat/use webgl interactive plot by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/181
  • For 2d plots by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/182
  • Add morphology plotter util by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/178
  • Add cell builder utility functions by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/107
  • Feat/channelml2nml2 by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/185
  • Fix/libneuroml 139 by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/187
  • feat(utils): validate component on creation by factory by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/188
  • Feat/add neuron cell info utils by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/184
  • feat: migrate factory functions to libNeuroML by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/189
  • Feat/cell builder updates: migrated to libNeuroML! by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/191

New Contributors

  • @shayan823 made their first contribution in https://github.com/NeuroML/pyNeuroML/pull/174

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v0.7.1...v0.7.2

- Python
Published by sanjayankur31 over 3 years ago

pyneuroml - v0.7.1

What's Changed

  • Fixes display of realtime output by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/171
  • Test netpyne json by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/175

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v0.7.0...v0.7.1

- Python
Published by sanjayankur31 over 3 years ago

pyneuroml - v0.7.0

What's Changed

  • BREAKING CHANGE: drop py2 support by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/162
  • Document neuron export functions by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/164
  • To v0.7.0 using jnml jar v0.12.0 & initial EDEN support by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/168
  • More EDEN functions by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/169

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v0.5.20...v0.7.0

- Python
Published by sanjayankur31 over 3 years ago

pyneuroml - v0.5.20

pyNeuroML v0.5.20 for NeuroML release 2.2

- Python
Published by pgleeson about 4 years ago

pyneuroml - v0.5.18

v0.5.18 release

What's Changed

  • feat: update matplotlib usage to remove deprecated methods by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/96
  • enh(pynml): add -netpyne option by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/94
  • feat: add function to validate NeuroML2 LEMS file by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/108
  • Enable documentation on RTD by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/111
  • Consolidate logging (and other minor tweaks) by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/112
  • Feat/document pynml by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/115
  • ci: make ci install deps from necessary branches by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/119
  • Finish consolidating logging by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/116
  • PR: list recordables by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/121
  • improvement: add typing as requirements for py<3.5 by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/123
  • feat: format with black by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/124
  • To v0.5.18 by @pgleeson in https://github.com/NeuroML/pyNeuroML/pull/128
  • Feat/issue 126: allow programmatic access to output of jnml from validation by @sanjayankur31 in https://github.com/NeuroML/pyNeuroML/pull/127

Full Changelog: https://github.com/NeuroML/pyNeuroML/compare/v0.5.11...v0.5.18

- Python
Published by sanjayankur31 over 4 years ago

pyneuroml - v0.3.15

v0.3.15 release

- Python
Published by pgleeson about 7 years ago