Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / NeuroML/pyNeuroML issues and pull requests

#228 - To v1.0.2 & fix for pypi

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

#227 - Update to v1.0.1 with jnml jar v0.12.2

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

#226 - chore: regenerate man pages

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

#225 - reloading data uses quantity path string instead of column id

Issue - State: closed - Opened by sanjayankur31 over 1 year ago
Labels: T: bug, T: enhancement, S: ready for review, S: needs info, good first issue

#224 - Print `python -version`, neuron path etc. info in `pyneuroml -version`

Issue - State: closed - Opened by sanjayankur31 over 1 year ago
Labels: T: enhancement, Help wanted, good first issue

#223 - Fix for reloading saved spike data

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

#222 - Plotting fixes related to #220, and regenerates man pages

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

#221 - A few minor changes and bugfix for 2d plotting

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

#220 - Suggested updates to 2D plots etc

Issue - State: closed - Opened by pgleeson over 1 year ago - 1 comment
Labels: T: enhancement

#219 - Feat/more morphplots -> exp

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

#218 - feat: add method to rotate cell

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

#217 - test(modchananalysis): test to check that nrnivmodl is run when required

Pull Request - State: closed - Opened by sanjayankur31 over 1 year ago - 3 comments
Labels: S: ready for review

#216 - pynml-modchananalysis excepting on division by zero

Pull Request - State: closed - Opened by borismarin over 1 year ago - 3 comments
Labels: T: bug, S: ready for review

#215 - Adding logic for one-shot validation of multiple input files

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

#213 - Feat/more morphplots

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

#212 - feat: improve installation of extra deps

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

#211 - ci(py311): add py311 to ci and setup.py

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

#209 - To v0.7.5 and jnml 0.12.1

Pull Request - State: closed - Opened by pgleeson almost 2 years ago

#208 - Feature: add functions to create a combine archive from a provided "root" file

Pull Request - State: closed - Opened by sanjayankur31 almost 2 years ago - 1 comment
Labels: T: enhancement, S: ready for review

#207 - Implement archiving to combine archive format

Issue - State: closed - Opened by sanjayankur31 almost 2 years ago - 2 comments
Labels: T: enhancement

#206 - Feat/document channelanalysis

Pull Request - State: closed - Opened by sanjayankur31 almost 2 years ago

#205 - Adding latest jnml jar

Pull Request - State: closed - Opened by pgleeson almost 2 years ago

#204 - mview_neuroml2.hoc docs not create default soma, dendrite, axonal groups

Issue - State: closed - Opened by sanjayankur31 almost 2 years ago - 2 comments
Labels: T: bug, T: enhancement, T: question, S: needs info

#203 - Improved error code generation; To v0.7.3

Pull Request - State: closed - Opened by pgleeson almost 2 years ago

#202 - [Bug] pynml-modchananalysis: `ZeroDivisionError: float division by zero`

Issue - State: closed - Opened by sanjayankur31 almost 2 years ago - 5 comments
Labels: T: bug

#201 - pynml-modchananalysis: allow saving of plots without user intervention (for batch processing)

Issue - State: closed - Opened by sanjayankur31 almost 2 years ago - 2 comments
Labels: T: enhancement, good first issue

#200 - Document cell analysis function, add test

Pull Request - State: closed - Opened by sanjayankur31 almost 2 years ago
Labels: T: enhancement

#199 - Update LEMSSimulation to also take string parameters

Issue - State: closed - Opened by sanjayankur31 almost 2 years ago
Labels: T: enhancement

#198 - [Bug] Cannot create spike output file for class cell2CaPools

Issue - State: closed - Opened by harshagurnani almost 2 years ago - 8 comments
Labels: T: bug, S: release pending

#197 - Plotting inactivation/activation

Issue - State: closed - Opened by christian-oreilly almost 2 years ago - 4 comments

#196 - [Bug] Output export to Neuron are specific on ions, not channels

Issue - State: closed - Opened by christian-oreilly almost 2 years ago - 9 comments
Labels: T: bug

#195 - Mainly new jar for jnml

Pull Request - State: closed - Opened by pgleeson almost 2 years ago - 2 comments

#194 - Development to exp

Pull Request - State: closed - Opened by pgleeson almost 2 years ago

#193 - Move mod2nml script to neuron utilities

Pull Request - State: closed - Opened by sanjayankur31 almost 2 years ago - 4 comments
Labels: T: enhancement

#192 - Plotting: add wire diagram generator for morphologies

Issue - State: open - Opened by sanjayankur31 about 2 years ago
Labels: T: enhancement, Help wanted, P: low, good first issue

#191 - Feat/cell builder updates: migrated to libNeuroML!

Pull Request - State: closed - Opened by sanjayankur31 about 2 years ago

#190 - CellBuilder: add function to add unbranched list of segments to a cell

Issue - State: closed - Opened by sanjayankur31 about 2 years ago - 1 comment
Labels: T: enhancement

#189 - feat: migrate factory functions to libNeuroML

Pull Request - State: closed - Opened by sanjayankur31 about 2 years ago

#188 - feat(utils): validate component on creation by factory

Pull Request - State: closed - Opened by sanjayankur31 about 2 years ago

#187 - Fix/libneuroml 139

Pull Request - State: closed - Opened by sanjayankur31 about 2 years ago - 1 comment
Labels: T: enhancement, S: ready for review

#186 - Use development branch of libNML in requirements-dev

Pull Request - State: closed - Opened by pgleeson about 2 years ago - 3 comments

#185 - Feat/channelml2nml2

Pull Request - State: closed - Opened by sanjayankur31 about 2 years ago
Labels: T: enhancement, S: ready for review, P: low

#184 - Feat/add neuron cell info utils

Pull Request - State: closed - Opened by sanjayankur31 about 2 years ago - 10 comments
Labels: T: enhancement, S: ready for review

#183 - Feat/surface plots

Pull Request - State: closed - Opened by sanjayankur31 about 2 years ago

#182 - For 2d plots

Pull Request - State: closed - Opened by pgleeson about 2 years ago - 4 comments

#181 - Feat/use webgl interactive plot

Pull Request - State: closed - Opened by sanjayankur31 about 2 years ago

#180 - Plotly features to dev

Pull Request - State: closed - Opened by pgleeson about 2 years ago

#179 - Latest experimental branch incl chan analysis updates

Pull Request - State: closed - Opened by pgleeson about 2 years ago

#178 - Add morphology plotter util

Pull Request - State: closed - Opened by sanjayankur31 about 2 years ago - 4 comments
Labels: T: enhancement, S: ready for review

#177 - Update channel export

Pull Request - State: closed - Opened by pgleeson about 2 years ago - 1 comment

#176 - Feat/plotly plotting

Pull Request - State: closed - Opened by sanjayankur31 about 2 years ago - 1 comment
Labels: T: enhancement, S: ready for review

#175 - Test netpyne json

Pull Request - State: closed - Opened by pgleeson about 2 years ago

#174 - update changes to the template file

Pull Request - State: closed - Opened by shayan823 over 2 years ago - 5 comments

#173 - Update ChannelInfo_TEMPLATE.md

Pull Request - State: closed - Opened by shayan823 over 2 years ago - 4 comments

#172 - To v0.7.0

Pull Request - State: closed - Opened by pgleeson over 2 years ago - 1 comment

#171 - Fixes display of realtime output

Pull Request - State: closed - Opened by pgleeson over 2 years ago

#170 - Add CellBuilder.py to pyNeuroML

Issue - State: closed - Opened by pgleeson over 2 years ago - 1 comment

#169 - More EDEN functions

Pull Request - State: closed - Opened by pgleeson over 2 years ago

#168 - To v0.7.0 using jnml jar v0.12.0 & initial EDEN support

Pull Request - State: closed - Opened by pgleeson over 2 years ago

#167 - Add Eden support

Issue - State: closed - Opened by sanjayankur31 over 2 years ago
Labels: T: enhancement

#166 - pynml -validate *nml doesn't validate all *nml files at once

Issue - State: closed - Opened by pgleeson over 2 years ago - 2 comments
Labels: T: enhancement, Help wanted, good first issue

#165 - Add a check in pynml-modchananalysis to see whether mod files are compiled yet

Issue - State: closed - Opened by pgleeson over 2 years ago
Labels: T: enhancement, Help wanted, good first issue

#164 - Document neuron export functions

Pull Request - State: closed - Opened by sanjayankur31 over 2 years ago - 3 comments
Labels: S: ready for review, C: docs, P: low

#163 - [Bug] NetPyNe 1.0.1 doesn't work with pyNeuroML

Issue - State: closed - Opened by jonrkarr over 2 years ago - 2 comments

#162 - BREAKING CHANGE: drop py2 support

Pull Request - State: closed - Opened by sanjayankur31 over 2 years ago
Labels: T: enhancement, S: ready for review

#161 - pyNeuroML 0.5.19 breaks simulation with Brian2

Issue - State: closed - Opened by jonrkarr almost 3 years ago - 2 comments

#160 - Add swc export to pynml

Pull Request - State: closed - Opened by sanjayankur31 almost 3 years ago - 1 comment
Labels: T: enhancement, S: ready for review

#159 - Feat/document 2stage opt

Pull Request - State: closed - Opened by sanjayankur31 almost 3 years ago
Labels: T: enhancement, S: ready for review

#157 - Tweaks to tuner code

Pull Request - State: closed - Opened by sanjayankur31 almost 3 years ago
Labels: T: bug, S: ready for review

#155 - Feat/increase tuning verbosity

Pull Request - State: closed - Opened by sanjayankur31 almost 3 years ago - 1 comment

#154 - NeuroMLTuner: return fitted values as strings with units for easy consumption?

Issue - State: closed - Opened by sanjayankur31 almost 3 years ago - 1 comment
Labels: T: enhancement

#152 - NeuroML 2.2 release

Pull Request - State: closed - Opened by pgleeson almost 3 years ago - 2 comments

#150 - Generalise modification of parameters in NeuroMLController

Issue - State: open - Opened by sanjayankur31 almost 3 years ago - 2 comments
Labels: T: enhancement, Help wanted, good first issue

#146 - Add man pages for all CLI tools

Pull Request - State: closed - Opened by sanjayankur31 almost 3 years ago
Labels: T: enhancement

#145 - Add tuning example to CI

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

#143 - Feat/extra requires

Pull Request - State: closed - Opened by sanjayankur31 almost 3 years ago - 2 comments
Labels: S: ready for review

#141 - Manage or document additional requirements for other simulation tools

Issue - State: closed - Opened by jonrkarr almost 3 years ago - 4 comments
Labels: T: enhancement

#140 - [Bug] Simulation tools do not save results to consistent locations

Issue - State: open - Opened by jonrkarr almost 3 years ago - 2 comments

#139 - [Bug] jNeuroML ignores errors with NetPyNe

Issue - State: closed - Opened by jonrkarr almost 3 years ago - 1 comment

#134 - feat(pynml): add `-moose` option

Pull Request - State: closed - Opened by sanjayankur31 almost 3 years ago
Labels: T: enhancement, S: ready for review

#133 - Add `-swc` option to export NeuroML cell files to SWC format

Issue - State: closed - Opened by sanjayankur31 almost 3 years ago - 7 comments
Labels: T: enhancement, good first issue

#131 - Provide shorter aliases to `run...` methods?

Issue - State: closed - Opened by sanjayankur31 almost 3 years ago
Labels: T: enhancement, P: low

#129 - Would it be useful to add functionality to search neuromldb in `pynml`?

Issue - State: closed - Opened by sanjayankur31 almost 3 years ago
Labels: T: enhancement, T: question

#127 - Feat/issue 126: allow programmatic access to output of jnml from validation

Pull Request - State: closed - Opened by sanjayankur31 almost 3 years ago - 5 comments
Labels: T: enhancement, S: ready for review, P: low

#125 - Provide cleaner error messages

Issue - State: closed - Opened by jonrkarr almost 3 years ago - 1 comment
Labels: T: enhancement

#121 - PR: list recordables

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

#120 - Add option to generate and save simulation output plots using matplotlib when Display is used in LEMS

Issue - State: closed - Opened by sanjayankur31 about 3 years ago - 1 comment
Labels: T: enhancement

#114 - Create python-publish.yml

Pull Request - State: closed - Opened by sanjayankur31 about 3 years ago - 3 comments
Labels: T: enhancement

#108 - feat: add function to validate NeuroML2 LEMS file

Pull Request - State: closed - Opened by sanjayankur31 over 3 years ago
Labels: T: enhancement, S: ready for review

#107 - Add cell builder utility functions

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

#105 - Add helper methods to build cells

Issue - State: closed - Opened by sanjayankur31 over 3 years ago
Labels: T: enhancement, S: release pending

#98 - What is the affect of the Simulation/@method attribute?

Issue - State: open - Opened by jonrkarr over 3 years ago - 3 comments
Labels: T: question

#96 - feat: update matplotlib usage to remove deprecated methods

Pull Request - State: closed - Opened by sanjayankur31 over 3 years ago - 1 comment
Labels: S: ready for review

#94 - enh(pynml): add -netpyne option

Pull Request - State: closed - Opened by sanjayankur31 over 3 years ago

#93 - Add `-moose` option to pynml to export models to MOOSE

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

#89 - Create a pure Python SWC -> NeuroML converter

Issue - State: closed - Opened by pgleeson over 3 years ago - 18 comments
Labels: T: enhancement