Ecosyste.ms: Issues

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GitHub / BlueBrain/BlueCelluLab issues and pull requests

#212 - CI(dependabot): Bump anothrNick/github-tag-action from 1.70.0 to 1.71.0

Pull Request - State: closed - Opened by dependabot[bot] about 2 months ago
Labels: dependencies

#211 - allow user to use custom function for simulation callback

Pull Request - State: closed - Opened by AurelienJaquier 3 months ago - 1 comment

#210 - Replace memory addresses with UUIDs to enhance the uniqueness of template_name

Pull Request - State: closed - Opened by ilkilic 3 months ago - 4 comments

#208 - Add JOSS citation

Pull Request - State: closed - Opened by ilkilic 3 months ago - 1 comment

#207 - broken link in the examples README file

Issue - State: closed - Opened by anilbey 3 months ago - 1 comment

#205 - minor improvement to sonata-network example

Pull Request - State: closed - Opened by ilkilic 3 months ago - 1 comment

#204 - Update copyright year

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

#203 - Update readme citation and add CITATION.cff file

Pull Request - State: closed - Opened by AurelienJaquier 4 months ago

#202 - Add authors to zenodo file

Pull Request - State: closed - Opened by AurelienJaquier 4 months ago - 1 comment

#201 - update mypy reference

Pull Request - State: closed - Opened by anilbey 4 months ago - 1 comment

#200 - Fix: Add missing 'units' attribute to timestamp in test HDF5 file

Pull Request - State: closed - Opened by ilkilic 4 months ago - 1 comment

#199 - add explanation for figure1

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

#198 - CI(dependabot): Bump anothrNick/github-tag-action from 1.69.0 to 1.70.0

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies

#197 - add bb5-tests

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

#196 - remove double CircuitSimulation

Pull Request - State: closed - Opened by AurelienJaquier 4 months ago - 1 comment

#195 - replace amp_cv with relative_skew

Pull Request - State: closed - Opened by ilkilic 4 months ago - 1 comment

#194 - Example 7 proposition

Pull Request - State: closed - Opened by ejayromero 5 months ago - 1 comment

#193 - Add holding current to apply_multiple_stimuli

Pull Request - State: closed - Opened by AurelienJaquier 5 months ago - 1 comment

#192 - Feat: support custom node sets defined in simulation config

Pull Request - State: closed - Opened by ilkilic 5 months ago - 1 comment

#191 - add cvode argument to apply_multiple_stimuli

Pull Request - State: closed - Opened by AurelienJaquier 5 months ago - 1 comment

#190 - add contributing guidelines

Pull Request - State: closed - Opened by anilbey 5 months ago - 1 comment

#188 - Joss paper

Pull Request - State: open - Opened by anilbey 5 months ago - 1 comment

#187 - Correct 'projections' for get_syn_descriptions

Pull Request - State: closed - Opened by ilkilic 6 months ago - 2 comments

#184 - Fix: handle edge case in synapse location calculation with syn_description

Pull Request - State: closed - Opened by ilkilic 6 months ago - 10 comments

#182 - amplitude based stimuli in apply_multiple_stimuli

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

#181 - further restrict IsolatedProcess by setting multiprocessing start method

Pull Request - State: closed - Opened by anilbey 7 months ago - 1 comment

#180 - StimulusFactory: enable amplitude based versions of the protocols

Issue - State: closed - Opened by anilbey 7 months ago - 2 comments

#179 - add cheops to list of stim docs

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

#178 - warning to log in serialized_sections #176

Pull Request - State: closed - Opened by anilbey 7 months ago - 1 comment

#177 - relax h5py to >=3.8.0, to make it easier to package in spack

Pull Request - State: closed - Opened by mgeplf 7 months ago - 1 comment

#176 - Warning needed on serialised sections?

Issue - State: closed - Opened by arnaudon 7 months ago - 3 comments

#175 - remove examples from package distribution

Pull Request - State: closed - Opened by anilbey 7 months ago - 1 comment

#174 - CI(dependabot): Bump anothrNick/github-tag-action from 1.67.0 to 1.69.0

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#173 - Update singlecell and sequence-stimuli example

Pull Request - State: closed - Opened by darshanmandge 7 months ago - 1 comment

#172 - add cheops stimuli to StimulusFactory vsc[#minor]

Pull Request - State: closed - Opened by anilbey 7 months ago - 1 comment

#171 - SONATA update: expect synapse_replay files as h5

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

#170 - update plot aesthetics in example notebooks

Pull Request - State: closed - Opened by anilbey 7 months ago - 1 comment

#169 - Fix accessing afferent_section_pos of synapse description

Pull Request - State: closed - Opened by anilbey 7 months ago - 1 comment

#168 - fetch afferent_section_pos from sonata

Pull Request - State: closed - Opened by anilbey 7 months ago - 4 comments

#167 - account for unknown section types

Pull Request - State: closed - Opened by anilbey 7 months ago - 1 comment

#166 - bug when morphology is not in a subfolder

Issue - State: open - Opened by AurelienJaquier 7 months ago

#165 - Controls the passing of NEURON global params to processes

Pull Request - State: closed - Opened by anilbey 7 months ago - 1 comment

#164 - Update stimulus factory API [vcs: #minor]

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

#163 - fix spike detection in tools

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

#162 - add macos ci tests

Pull Request - State: closed - Opened by anilbey 7 months ago - 1 comment

#161 - Improve threshold search

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

#160 - FIX: bug in setting NeuronGlobals by CircuitSim::run

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

#159 - update pyproject.toml simplify setuptools package find

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

#158 - deprecate SSim use CircuitSimulation

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

#157 - rm debugtest mark, tests are equally debuggable

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

#156 - Migrate from setup.py to pyproject.toml

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

#155 - CI(dependabot): Bump softprops/action-gh-release from 1 to 2

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#154 - decouple setting global neuron attributes from sim run [vcs: #minor]

Pull Request - State: closed - Opened by anilbey 8 months ago - 2 comments

#151 - injecting a sequence of stimuli on the same cell in isolation

Pull Request - State: closed - Opened by anilbey 9 months ago - 7 comments

#150 - add neuroglia synapses in bluecellulab

Issue - State: open - Opened by sfarina05 9 months ago - 1 comment

#149 - Refactor functions that include running isolated simulations [vcs: #minor]

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

#148 - Use CaptureOutput to forward hoc's stdout to logger.debug

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

#147 - TStim implementation in add_step and add_ramp

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

#146 - migrate pkg_resources -> importlib.resources

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

#145 - Performance: enable tox-uv in CI workflows

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

#144 - map SONATA spec's LINEAR input

Issue - State: open - Opened by anilbey 9 months ago

#143 - Run a profiler to detect performance bottlenecks

Issue - State: open - Opened by anilbey 9 months ago

#142 - Enable injecting Python generated Stimuli [vcs: #minor]

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

#141 - CI: pass CODECOV token in release->test workflow call

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

#140 - Allow custom section names in hoc files for Cell object

Issue - State: closed - Opened by darshanmandge 9 months ago - 3 comments

#139 - set logger level of importer module to debug

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

#137 - Simplify psection representation in Cell

Pull Request - State: closed - Opened by anilbey 9 months ago - 3 comments

#136 - logging info in importer

Issue - State: closed - Opened by arnaudon 9 months ago - 5 comments

#134 - fix #117 soma_scaler/AIS_scaler

Pull Request - State: closed - Opened by anilbey 10 months ago - 1 comment

#133 - reloading neuron mechanisms in _load_hoc_and_mod_files

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

#132 - apply small refactorings

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

#130 - avoid accessing private hoc attribute in core.py

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

#129 - use public_hoc_cell instead of accessing getCell in core.py

Issue - State: closed - Opened by darshanmandge 10 months ago - 1 comment

#128 - Function cell.get_psection not working

Issue - State: closed - Opened by stefanoantonel 10 months ago - 4 comments

#127 - Add default value for segx param, improve docs vcs: #minor

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

#126 - Add default segx to add_voltage_recording

Issue - State: closed - Opened by stefanoantonel 10 months ago

#125 - CI(dependabot): Bump codecov/codecov-action from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago
Labels: dependencies

#124 - Allow API functions to be used without loading hoc/mod #minor

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

#123 - libsonata has in the process of refactoring its module

Pull Request - State: closed - Opened by mgeplf 10 months ago - 1 comment

#122 - replace bluecellulab.neuron -> neuron

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

#121 - readme running tests

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

#120 - pytest-nose-test-deprecation

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

#119 - bluepysnap 3.0.0 #major

Pull Request - State: closed - Opened by edasubert 10 months ago - 1 comment

#118 - CI(dependabot): Bump actions/setup-python from 4 to 5

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago
Labels: dependencies

#117 - bug in the assignment of AIS_scaler/soma_scaler

Issue - State: closed - Opened by anilbey 11 months ago

#116 - add afferent_section_pos to common properties

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

#115 - prevent KeyError get_all_stimuli_entries

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

#114 - avoid adding extra label and population encoding to graph

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

#113 - use typing_extensions.deprecated decorator

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