What's Changed

PyPi.org push action not working by @espenhgn in https://github.com/LFPy/LFPy/pull/469

Full Changelog: https://github.com/LFPy/LFPy/compare/v2.3.4...v2.3.5

- Python
Published by espenhgn about 1 year ago

lfpy - LFPy-v2.3.5rc2

Full Changelog: https://github.com/LFPy/LFPy/compare/v2.3.5rc1...v2.3.5rc2

- Python
Published by espenhgn about 1 year ago

lfpy - LFPy-v2.3.5rc1

Full Changelog: https://github.com/LFPy/LFPy/compare/v2.3.4...v2.3.5rc1

- Python
Published by espenhgn about 1 year ago

What's Changed

Allowing multiple templateargs in LFPy/templatecell.py and updating modeldb example links by @darshanmandge in https://github.com/LFPy/LFPy/pull/466

New Contributors

@darshanmandge made their first contribution in https://github.com/LFPy/LFPy/pull/466

Full Changelog: https://github.com/LFPy/LFPy/compare/v2.3.3...v2.3.4

- Python
Published by espenhgn about 1 year ago

What's Changed

More efficient calculation of axial currents by @torbjone in https://github.com/LFPy/LFPy/pull/460

Full Changelog: https://github.com/LFPy/LFPy/compare/v2.3.2...v2.3.3

- Python
Published by espenhgn about 1 year ago

What's Changed

Fixed readthedocs build
Fixed DeprecationWarning and other minor issues

Full Changelog: https://github.com/LFPy/LFPy/compare/v2.3.1...v2.3.2

- Python
Published by torbjone over 2 years ago

What's Changed

NEURON is pip installable for Python 3.11 by @espenhgn in https://github.com/LFPy/LFPy/pull/442
Method for calculating membrane currents from membrane potentials by @torbjone in https://github.com/LFPy/LFPy/pull/446
Ebrains mirror by @torbjone in https://github.com/LFPy/LFPy/pull/447
Update README.md by @torbjone in https://github.com/LFPy/LFPy/pull/451
Documentation fixes by @torbjone in https://github.com/LFPy/LFPy/pull/455

Full Changelog: https://github.com/LFPy/LFPy/compare/v2.3...v2.3.1

- Python
Published by torbjone over 2 years ago

What's Changed

Python 3.7-3.10; updated citation by @espenhgn in https://github.com/LFPy/LFPy/pull/407
Update tests for LFPykit@master, bump version to 2.3.dev, by @espenhgn in https://github.com/LFPy/LFPy/pull/408
Minor example fixes by @espenhgn in https://github.com/LFPy/LFPy/pull/409
Fix Network MPI issue by @espenhgn in https://github.com/LFPy/LFPy/pull/411
Fix crash with Neuron 8.1; improved Cell.getidxparent_children method by @espenhgn in https://github.com/LFPy/LFPy/pull/415
set Cell.arc3d if pt3d==True by @espenhgn in https://github.com/LFPy/LFPy/pull/419
New LFPy logo, some docstring fixes by @espenhgn in https://github.com/LFPy/LFPy/pull/421
removed deprecated MEG class by @espenhgn in https://github.com/LFPy/LFPy/pull/422
fixed set*_recorders use of dt by @espenhgn in https://github.com/LFPy/LFPy/pull/425
runtime compile of NMODL files by @espenhgn in https://github.com/LFPy/LFPy/pull/427
never close stale issues/PRs by @espenhgn in https://github.com/LFPy/LFPy/pull/432
Get rid of package dependency on mpi4py by @espenhgn in https://github.com/LFPy/LFPy/pull/433
faster InfiniteHomogeneousVolCondMEG.calculate_H_from_iaxial method by @espenhgn in https://github.com/LFPy/LFPy/pull/437
Prep LFPy-2.3 release by @espenhgn in https://github.com/LFPy/LFPy/pull/439
bump LFPy-2.3rc0 -> 2.3 by @espenhgn in https://github.com/LFPy/LFPy/pull/441

Full Changelog: https://github.com/LFPy/LFPy/compare/v2.2.5...v2.3

- Python
Published by espenhgn about 3 years ago

What's Changed

Python 3.7-3.10; updated citation by @espenhgn in https://github.com/LFPy/LFPy/pull/407
Update tests for LFPykit@master, bump version to 2.3.dev, by @espenhgn in https://github.com/LFPy/LFPy/pull/408
Minor example fixes by @espenhgn in https://github.com/LFPy/LFPy/pull/409
Fix Network MPI issue by @espenhgn in https://github.com/LFPy/LFPy/pull/411
Fix crash with Neuron 8.1; improved Cell.getidxparent_children method by @espenhgn in https://github.com/LFPy/LFPy/pull/415
set Cell.arc3d if pt3d==True by @espenhgn in https://github.com/LFPy/LFPy/pull/419
New LFPy logo, some docstring fixes by @espenhgn in https://github.com/LFPy/LFPy/pull/421
removed deprecated MEG class by @espenhgn in https://github.com/LFPy/LFPy/pull/422
fixed set*_recorders use of dt by @espenhgn in https://github.com/LFPy/LFPy/pull/425
runtime compile of NMODL files by @espenhgn in https://github.com/LFPy/LFPy/pull/427
never close stale issues/PRs by @espenhgn in https://github.com/LFPy/LFPy/pull/432
Get rid of package dependency on mpi4py by @espenhgn in https://github.com/LFPy/LFPy/pull/433
faster InfiniteHomogeneousVolCondMEG.calculate_H_from_iaxial method by @espenhgn in https://github.com/LFPy/LFPy/pull/437
Prep LFPy-2.3 release by @espenhgn in https://github.com/LFPy/LFPy/pull/439

Full Changelog: https://github.com/LFPy/LFPy/compare/v2.2.5...v2.3rc0

- Python
Published by espenhgn about 3 years ago

Release notes

This is the 6th maintenance release for LFPy-2.2

What's Changed

Python 3.7-3.10; updated citation by @espenhgn in https://github.com/LFPy/LFPy/pull/407
fix Neuron 8.1 issue, version bump by @espenhgn in https://github.com/LFPy/LFPy/pull/417

Full Changelog: https://github.com/LFPy/LFPy/compare/v2.2.5...v2.2.6

- Python
Published by espenhgn almost 4 years ago

Release notes

This is the 5th maintenance release for LFPy-2.2. This version expects LFPykit>=0.4,<0.5

What's Changed

Replace Lintly action by @espenhgn in https://github.com/LFPy/LFPy/pull/399
fix download of Hay2011 model codes by @espenhgn in https://github.com/LFPy/LFPy/pull/403
bump version to 2.2.5 by @espenhgn in https://github.com/LFPy/LFPy/pull/405

Full Changelog: https://github.com/LFPy/LFPy/compare/v2.2.4...v2.2.5

- Python
Published by espenhgn almost 4 years ago

Release notes

This is the 4th maintenance release for LFPy-2.2.

What's Changed

Implementation of Network.enableextracellularstimulation() by @Alexis-Melot in https://github.com/LFPy/LFPy/pull/373
Updated Dockerfile, pinning versions, linting by @espenhgn in https://github.com/LFPy/LFPy/pull/376
add CITATION.cff file by @espenhgn in https://github.com/LFPy/LFPy/pull/377
Update CITATION.cff by @espenhgn in https://github.com/LFPy/LFPy/pull/379
fix MEG.calculateHfrom_iaxial method and docstring by @espenhgn in https://github.com/LFPy/LFPy/pull/381
add py=3.10 to build matrix by @espenhgn in https://github.com/LFPy/LFPy/pull/382
Incorporate InfiniteHomogeneousVolCondMEG and SphericallySymmetricVolCondMEG by @espenhgn in https://github.com/LFPy/LFPy/pull/383
remove NSG example files by @espenhgn in https://github.com/LFPy/LFPy/pull/384
Remove mazzoni example files by @espenhgn in https://github.com/LFPy/LFPy/pull/385
remove use of .rot files by @espenhgn in https://github.com/LFPy/LFPy/pull/387
Require LFPykit>=0.4 by @espenhgn in https://github.com/LFPy/LFPy/pull/390
%pylab inline no longer an option by @espenhgn in https://github.com/LFPy/LFPy/pull/391
fix test function by @espenhgn in https://github.com/LFPy/LFPy/pull/395
use st.truncnorm for delays and multapses. formatting by @espenhgn in https://github.com/LFPy/LFPy/pull/392
bump version to 2.2.4 by @espenhgn in https://github.com/LFPy/LFPy/pull/393

New Contributors

@Alexis-Melot made their first contribution in https://github.com/LFPy/LFPy/pull/373

Full Changelog: https://github.com/LFPy/LFPy/compare/v2.2.3...v2.2.4

- Python
Published by espenhgn about 4 years ago

Release notes

This is the 3rd maintenance release for LFPy-2.2.

What's Changed

add support for scipy.stats.rvcontinuous and rvdiscrete delayfun by @espenhgn in https://github.com/LFPy/LFPy/pull/356
Fix readthedocs builds by @espenhgn in https://github.com/LFPy/LFPy/pull/361
modified Dockerfile for Singularity on JUSUF by @espenhgn in https://github.com/LFPy/LFPy/pull/362
filter warnings for existing sections with networks by @espenhgn in https://github.com/LFPy/LFPy/pull/365
Some minor fixes to example scripts by @espenhgn in https://github.com/LFPy/LFPy/pull/369
bump version to 2.2.3 by @espenhgn in https://github.com/LFPy/LFPy/pull/371

Full Changelog: https://github.com/LFPy/LFPy/compare/v2.2.2...v2.2.3

- Python
Published by espenhgn over 4 years ago

Release notes

This is the 2nd maintenance release for LFPy-2.2.

Changesets

This bugfix release contains the following changesets since https://github.com/LFPy/LFPy/releases/tag/v2.2: 5986b4f (HEAD -> master, tag: v2.2.2, origin/master, origin/HEAD) bump version to 2.2.2 (#351) 8c92ac2 lintly must be happy ea6d09b updated Dockerfile recipe (#349) 5f2b8db add platform aarch64 (#347) 5ca29ad Add missing length attribute to DummyCell class (#344) 6a6d7d3 Fix DeprecationWarning w. neuron.run() (#336) e2019bc Remove mocked packages mpi4py and neuron (#334) 14a9ab7 formatting b38146f Better support for platform osx-arm64 (#329) 23449af remove MEAutility from dependencies (#327) 669967e (tag: v2.2.1) prep 2.2.1 release (#324) 9eb9fba fixed gathering of somavs if number of cells < MPI::Size (#323) aa0a3ba pick random connections using np.random.binomial (#321) b49e726 Fix 315 317 (#320) 6d77e21 fix DeprecationWarnings (#314) 3812f63 fix for h5py < 3 (#313) f419c92 pass weightFunction to network.connect (#309) 78634c4 customfun(cell) must be assumed (#308) 977b507 convert _create_sectionlists method to protected (#307) 7aaf9df Update README.md

- Python
Published by espenhgn over 4 years ago

lfpy - LFPy-2.2.1

Release notes

This is the first maintenance release for LFPy-2.2.

Changesets

This bugfix release contains the following changesets since https://github.com/LFPy/LFPy/releases/tag/v2.2: 669967e (HEAD -> master, tag: v2.2.1, origin/master, origin/HEAD) prep 2.2.1 release (#324) 9eb9fba fixed gathering of somavs if number of cells < MPI::Size (#323) aa0a3ba pick random connections using np.random.binomial (#321) b49e726 Fix 315 317 (#320) 6d77e21 fix DeprecationWarnings (#314) 3812f63 fix for h5py < 3 (#313) f419c92 pass weightFunction to network.connect (#309) 78634c4 customfun(cell) must be assumed (#308) 977b507 convert _create_sectionlists method to protected (#307) 7aaf9df Update README.md

- Python
Published by espenhgn almost 5 years ago

lfpy - LFPy-2.2

LFPy-2.2

Release notes:

This release incorporates LFPykit (https://github.com/LFPy/LFPykit), and breaks backwards compatibility in certain cases as detalied here: (from https://github.com/LFPy/LFPy/pull/226#issue-496068806)

This release breaks backwards compatibility in some cases. Major changes including API changes:

Built in forward-model codes are being replaced by those in LFPykit (https://github.com/LFPy/LFPykit, https://LFPykit.rtfd.io)
new linear forward model classes from LFPykit.models:

- `PointSourcePotential`

- `LineSourcePotential`

- `CurrentDipoleMoment`

- `LaminarCurrentSourceDensity`

- `VolumetricCurrentSourceDensity`

LFPy.Cell.simulate() and LFPy.Network.simulate() now accepts probes=[<LFPykit.models.* like instance>, ...] representing extracellular recording devices, current dipole moment calculations.
Cell/Network.simulate() arguments electrode, dotprodcoeffs and rec_current_dipole_moment have been replaced with single parameter probes.
if Cell/Network.simulate(probes=[<instance>], to_memory=True), the simulated measurement is set as <instance>.data
Network.simulate now calls hidden class methods Network._run_simulation or Network._run_simulation_with_probes internally.
File format for simulating to file (Cell/Network.simulate(probes=[<instance>], to_file=True)) has been revised, each element in probes results it's own group named according to <instance>.__class__.__name__<number>
Cell attributes ustart, umid, uend; u in {x, y, z} has been replaced with ndarrays {x, y, z} of shape (totnsegs, 2). To get to the mid point simply issue u.mean(axis=-1).
Cell attribute diam is now renamed d (same as in LFPykit.GeometryCell)
Tests and examples have been adapted to accommodate above changes.
Much better agreement with the pep8 style guide.
lintly flake8 check is running for each PR.
Adds the eegmegcalc.NYHeadModel class from LFPykit
All forward models from either transmembrane currents or dipole moments are defined as part of LFPykit - class methods that depend on LFPy.Cell methods are added as part of LFPy (as not to introduce a circular dependency)

Changesets

This feature/bugfix release contains the following changesets since https://github.com/LFPy/LFPy/releases/tag/v2.1.2: 47ebf98 (HEAD -> master, tag: v2.2, origin/master, origin/HEAD) Prep release 2.2 (#303) 4262d6d Found fix for segfault11. Removed use of finalizer. (#301) b7ffcf6 Delete Synapses onto Cell object after simulate call (#298) 0d96868 Turn hoc list attributes into protected (#297) 2dacb9b (HEAD -> master, tag: v2.2rc5, origin/master, origin/HEAD) prep 2.2rc5 release (#294) 4a474a4 extended Network.connect() saveconnections feature to include all synaptic info (#293) 540f094 (origin/master, origin/HEAD) Add macOS to build recipe (#291) 61441f5 stale after 90 days, close after 30 (#290) 3d2c34e run builds on python3.9, removed 3.6 (#288) 334688f call mknrndll on Windows if it is available (#284) b0f8207 extended conda install instructions (#282) 4620e8c removed print statement (#281) c8c7ff4 run coveralls after tests (#279) 536ae73 goodbye travis-ci and thanks for all the fish (#277) 71d1a1b missed commit (#275) f954772 bump version (#274) 7a3b612 (tag: v2.2rc3) bump version (again) df1f553 added some test files to MANIFEST, bump version df4658e (tag: v2.2rc2) added longdescriptioncontenttype for PyPI fd65dbc don't build wheels (#272) 7ca094b test travisCI.com (#271) 018168b bump version (need to test pythonpublish action) (#270) 19bc95d (tag: v2.2rc1) Merge pull request #226 from LFPy/2.2.dev0 0993e1b (origin/2.2.dev0) fixed merge conflicts b82bc92 Merge branch '2.2.dev0' of github.com:LFPy/LFPy into 2.2.dev0 c1252eb added some missing tests to LFPy.runtests function (#269) 9ebd40b call destructor f4e870e Bump version to 2.2rc1 etc (#267) b9ef180 add class VolumetricCurrentSourceDensity (#265) 296ad04 more appropriate assert patterns (#263) 9ddb76d Prep merge with master (#262) 6de0526 Removed DeprecationWarnings (#260) 15482b8 Replaced exec calls by setattr (#255) df422c4 add python wheels to python publish action (#258) 46324de Example fixes (#259) 0f76be2 use neuron from pipy for ci (#257) ee6939b Replaced static default parameters with more suited pattern. closes #253 (#254) 5077d53 avoid multistage build (singularity) 10405c7 point docker badge to hub.docker.com/r/lfpy/lfpy 04c5451 moving docker hub Dockerfile here (#256) 645f1b4 (Helveg/2.2.dev0) set different seeds for each external input (#245) ac64d80 Docker (#243) 49bbff1 fixed parameter dependent namespace cleanup (#240) 9caaced Fixed import of parameterset.ParameterSet which caused MPI hangs (#239) a8fc6fe fix freeze on multinode jobs 321864f added funding info from master branch 0f97ed4 include NYHeadModel class from LFPykit (#237) 5a88faf imports lfpykit.LaminarCurrentSourceDensity. Updated documentation (#236) 829cdf3 Update python-app.yml b7eeacd Update python-app.yml 47041ff Documentation overhaul (#233) d0df0bc monkeypatches LFPykit classes with LFPy-specific methods (#231) 064b993 Update python-app.yml 84e6289 More example fixes (#230) c0f8c7c fix EOF 9faa120 should stop lintly complaining 99ab4df Update python-app.yml 0c6160c Merge pull request #228 from LFPy/espenhgn-patch-1 147eb1a Update python-app.yml ea4d700 Merge pull request #227 from LFPy/espenhgn-patch-1 f1b021b Update python-app.yml b0a6a62 use LFPykit@master b01d798 Merge pull request #225 from LFPy/fix-222-2 f1c62d6 fixed examples 67da39b Incorporate LFPykit into LFPy (#220) 29de022 converted runsimulation.runsimulation to Cell class method (#217) 4b405dd removed python 3.6 from travisCI builds 5949319 adds misc. files for workflows and Issue automation 68394cf add LFPykit to travisCI build e7ec1a0 adds LFPykit as dependency, starts v2.2 development

- Python
Published by espenhgn about 5 years ago

lfpy - LFPy-2.2rc5

LFPy-2.2rc5

Release notes:

This release incorporates LFPykit (https://github.com/LFPy/LFPykit), and breaks backwards compatibility in certain cases as detalied here: https://github.com/LFPy/LFPy/pull/226#issue-496068806

Changesets

This feature/bugfix Release Candidate contains the following changesets since https://github.com/LFPy/LFPy/releases/tag/v2.1.2:

2dacb9b (HEAD -> master, tag: v2.2rc5, origin/master, origin/HEAD) prep 2.2rc5 release (#294) 4a474a4 extended Network.connect() saveconnections feature to include all synaptic info (#293) 540f094 (origin/master, origin/HEAD) Add macOS to build recipe (#291) 61441f5 stale after 90 days, close after 30 (#290) 3d2c34e run builds on python3.9, removed 3.6 (#288) 334688f call mknrndll on Windows if it is available (#284) b0f8207 extended conda install instructions (#282) 4620e8c removed print statement (#281) c8c7ff4 run coveralls after tests (#279) 536ae73 goodbye travis-ci and thanks for all the fish (#277) 71d1a1b missed commit (#275) f954772 bump version (#274) 7a3b612 (tag: v2.2rc3) bump version (again) df1f553 added some test files to MANIFEST, bump version df4658e (tag: v2.2rc2) added longdescriptioncontenttype for PyPI fd65dbc don't build wheels (#272) 7ca094b test travisCI.com (#271) 018168b bump version (need to test pythonpublish action) (#270) 19bc95d (tag: v2.2rc1) Merge pull request #226 from LFPy/2.2.dev0 0993e1b (origin/2.2.dev0) fixed merge conflicts b82bc92 Merge branch '2.2.dev0' of github.com:LFPy/LFPy into 2.2.dev0 c1252eb added some missing tests to LFPy.runtests function (#269) 9ebd40b call destructor f4e870e Bump version to 2.2rc1 etc (#267) b9ef180 add class VolumetricCurrentSourceDensity (#265) 296ad04 more appropriate assert patterns (#263) 9ddb76d Prep merge with master (#262) 6de0526 Removed DeprecationWarnings (#260) 15482b8 Replaced exec calls by setattr (#255) df422c4 add python wheels to python publish action (#258) 46324de Example fixes (#259) 0f76be2 use neuron from pipy for ci (#257) ee6939b Replaced static default parameters with more suited pattern. closes #253 (#254) 5077d53 avoid multistage build (singularity) 10405c7 point docker badge to hub.docker.com/r/lfpy/lfpy 04c5451 moving docker hub Dockerfile here (#256) 645f1b4 (Helveg/2.2.dev0) set different seeds for each external input (#245) ac64d80 Docker (#243) 49bbff1 fixed parameter dependent namespace cleanup (#240) 9caaced Fixed import of parameterset.ParameterSet which caused MPI hangs (#239) a8fc6fe fix freeze on multinode jobs 321864f added funding info from master branch 0f97ed4 include NYHeadModel class from LFPykit (#237) 5a88faf imports lfpykit.LaminarCurrentSourceDensity. Updated documentation (#236) 829cdf3 Update python-app.yml b7eeacd Update python-app.yml 47041ff Documentation overhaul (#233) d0df0bc monkeypatches LFPykit classes with LFPy-specific methods (#231) 064b993 Update python-app.yml 84e6289 More example fixes (#230) c0f8c7c fix EOF 9faa120 should stop lintly complaining 99ab4df Update python-app.yml 0c6160c Merge pull request #228 from LFPy/espenhgn-patch-1 147eb1a Update python-app.yml ea4d700 Merge pull request #227 from LFPy/espenhgn-patch-1 f1b021b Update python-app.yml b0a6a62 use LFPykit@master b01d798 Merge pull request #225 from LFPy/fix-222-2 f1c62d6 fixed examples 67da39b Incorporate LFPykit into LFPy (#220) 29de022 converted runsimulation.runsimulation to Cell class method (#217) 4b405dd removed python 3.6 from travisCI builds 5949319 adds misc. files for workflows and Issue automation 68394cf add LFPykit to travisCI build e7ec1a0 adds LFPykit as dependency, starts v2.2 development

- Python
Published by espenhgn about 5 years ago

lfpy - LFPy-2.2rc3

LFPy-2.2rc3

Release notes:

This release incorporates LFPykit (https://github.com/LFPy/LFPykit), and breaks backwards compatibility in certain cases as detalied here: https://github.com/LFPy/LFPy/pull/226#issue-496068806

Changesets

This feature/bugfix Release Candidate contains the following changesets since https://github.com/LFPy/LFPy/releases/tag/v2.1.1:

7a3b612 (HEAD -> master, tag: v2.2rc3, origin/master, origin/HEAD) bump version (again) df1f553 added some test files to MANIFEST, bump version df4658e (tag: v2.2rc2) added longdescriptioncontenttype for PyPI fd65dbc don't build wheels (#272) 7ca094b test travisCI.com (#271) 018168b bump version (need to test pythonpublish action) (#270) 19bc95d (tag: v2.2rc1) Merge pull request #226 from LFPy/2.2.dev0 0993e1b (origin/2.2.dev0, 2.2.dev0) fixed merge conflicts b82bc92 Merge branch '2.2.dev0' of github.com:LFPy/LFPy into 2.2.dev0 c1252eb added some missing tests to LFPy.runtests function (#269) 9ebd40b call destructor f4e870e Bump version to 2.2rc1 etc (#267) b9ef180 add class VolumetricCurrentSourceDensity (#265) 296ad04 more appropriate assert patterns (#263) 9ddb76d Prep merge with master (#262) 6de0526 Removed DeprecationWarnings (#260) 15482b8 Replaced exec calls by setattr (#255) df422c4 add python wheels to python publish action (#258) 46324de Example fixes (#259) 0f76be2 use neuron from pipy for ci (#257) ee6939b Replaced static default parameters with more suited pattern. closes #253 (#254) 5077d53 avoid multistage build (singularity) 10405c7 point docker badge to hub.docker.com/r/lfpy/lfpy 04c5451 moving docker hub Dockerfile here (#256) 645f1b4 (Helveg/2.2.dev0) set different seeds for each external input (#245) ac64d80 Docker (#243) 49bbff1 fixed parameter dependent namespace cleanup (#240) 9caaced Fixed import of parameterset.ParameterSet which caused MPI hangs (#239) a8fc6fe fix freeze on multinode jobs 321864f added funding info from master branch 0f97ed4 include NYHeadModel class from LFPykit (#237) 5a88faf imports lfpykit.LaminarCurrentSourceDensity. Updated documentation (#236) 829cdf3 Update python-app.yml b7eeacd Update python-app.yml 47041ff Documentation overhaul (#233) d0df0bc monkeypatches LFPykit classes with LFPy-specific methods (#231) 064b993 Update python-app.yml 84e6289 More example fixes (#230) c0f8c7c fix EOF 9faa120 should stop lintly complaining 99ab4df Update python-app.yml 0c6160c Merge pull request #228 from LFPy/espenhgn-patch-1 147eb1a Update python-app.yml ea4d700 Merge pull request #227 from LFPy/espenhgn-patch-1 f1b021b Update python-app.yml b0a6a62 use LFPykit@master b01d798 Merge pull request #225 from LFPy/fix-222-2 f1c62d6 fixed examples 67da39b Incorporate LFPykit into LFPy (#220) 29de022 converted runsimulation.run_simulation to Cell class method (#217) 4b405dd removed python 3.6 from travisCI builds 5949319 adds misc. files for workflows and Issue automation 68394cf add LFPykit to travisCI build e7ec1a0 adds LFPykit as dependency, starts v2.2 development

- Python
Published by espenhgn over 5 years ago

lfpy - LFPy-2.2rc2

- Python
Published by espenhgn over 5 years ago

lfpy - LFPy-2.2rc1

LFPy-2.2rc1

Release notes:

This release incorporates LFPykit (https://github.com/LFPy/LFPykit), and breaks backwards compatibility in certain cases as detalied here: https://github.com/LFPy/LFPy/pull/226#issue-496068806

Changesets

This feature/bugfix Release Candidate contains the following changesets since https://github.com/LFPy/LFPy/releases/tag/v2.1.1 19bc95d (HEAD -> master, tag: v2.2rc1, origin/master, origin/HEAD) Merge pull request #226 from LFPy/2.2.dev0 0993e1b (origin/2.2.dev0, 2.2.dev0) fixed merge conflicts b82bc92 Merge branch '2.2.dev0' of github.com:LFPy/LFPy into 2.2.dev0 c1252eb added some missing tests to LFPy.runtests function (#269) 9ebd40b call destructor f4e870e Bump version to 2.2rc1 etc (#267) b9ef180 add class VolumetricCurrentSourceDensity (#265) 296ad04 more appropriate assert patterns (#263) 9ddb76d Prep merge with master (#262) 6de0526 Removed DeprecationWarnings (#260) 15482b8 Replaced exec calls by setattr (#255) df422c4 add python wheels to python publish action (#258) 46324de Example fixes (#259) 0f76be2 use neuron from pipy for ci (#257) ee6939b Replaced static default parameters with more suited pattern. closes #253 (#254) 5077d53 avoid multistage build (singularity) 10405c7 point docker badge to hub.docker.com/r/lfpy/lfpy 04c5451 moving docker hub Dockerfile here (#256) 645f1b4 (Helveg/2.2.dev0) set different seeds for each external input (#245) ac64d80 Docker (#243) 49bbff1 fixed parameter dependent namespace cleanup (#240) 9caaced Fixed import of parameterset.ParameterSet which caused MPI hangs (#239) a8fc6fe fix freeze on multinode jobs 321864f added funding info from master branch 0f97ed4 include NYHeadModel class from LFPykit (#237) 5a88faf imports lfpykit.LaminarCurrentSourceDensity. Updated documentation (#236) 829cdf3 Update python-app.yml b7eeacd Update python-app.yml 47041ff Documentation overhaul (#233) d0df0bc monkeypatches LFPykit classes with LFPy-specific methods (#231) 064b993 Update python-app.yml 84e6289 More example fixes (#230) c0f8c7c fix EOF 9faa120 should stop lintly complaining 99ab4df Update python-app.yml 0c6160c Merge pull request #228 from LFPy/espenhgn-patch-1 147eb1a Update python-app.yml ea4d700 Merge pull request #227 from LFPy/espenhgn-patch-1 f1b021b Update python-app.yml b0a6a62 use LFPykit@master b01d798 Merge pull request #225 from LFPy/fix-222-2 f1c62d6 fixed examples 67da39b Incorporate LFPykit into LFPy (#220) 29de022 converted runsimulation.runsimulation to Cell class method (#217) 4b405dd removed python 3.6 from travisCI builds 5949319 adds misc. files for workflows and Issue automation 68394cf add LFPykit to travisCI build e7ec1a0 adds LFPykit as dependency, starts v2.2 development

- Python
Published by espenhgn over 5 years ago

lfpy - LFPy-2.1.2

Maintenance release.

Commits since previous release (https://github.com/LFPy/LFPy/releases/tag/v2.1.1): 133f901 (HEAD -> master, tag: v2.1.2, origin/master, origin/HEAD) bump version to 2.1.2 before 2.2rc1 (#268) 031ccc2 use buildpack-deps:focal as base 49f819f (Helveg/master) set different seeds for each external input (#244) 5b1ced9 Update README.md d60dc91 (origin/lfpykit) removed createrotationfile.py (#215) 3660710 give default values to 4-sphere radius and sigmas. Some cleanup (#188) e2b2a3d Merge pull request #212 from espenhgn/rel_v2.1.1

- Python
Published by espenhgn over 5 years ago

lfpy - LFPy-2.1.1

Feature and bugfix release. Main changes:

Supports NEURON>7.7.2
LFPy.Cell keyword arguments cm and Ra defaults to None (used to be equal to neuron.h.Section() defaults)
Improved LFPy.Cell.__del__() destructor method that can be called to ensure safer execution of multiple independent cell simulations in succession (using NEURON>=7.8.x in particular)
Additional unittests

Commits since previous release https://github.com/LFPy/LFPy/releases/tag/v2.1: e2b2a3dda0d880b503eb269368cbbfeb04724972 (HEAD -> master, origin/master, origin/HEAD) Merge pull request #212 from espenhgn/relv2.1.1 1ebdae178425020f5b5be7ab9e454c74a99c4488 (tag: v2.1.1, origin/relv2.1.1, relv2.1.1) changed version to 2.1.1 743c71016e2b12fad302577585de666346d4017c (HEAD -> master, tag: v2.1.1rc1, origin/master, origin/HEAD) Formatting/future proofing (#210) df8d15b58e77999752d586069b684e60c5799ee7 Set Ra and cm only if not None (#211) 0452c48b4d240ef6a2801bc7bff0a193158ff1d6 fix morphology issue with NEURON>7.7.2 (#206) 394d085835e6e8ba589dd4b6e732876d10d560f2 Tests that currents sum to approximately zero (#207) 797ee1c38209ce871ad6c1653e59bd5b7cb9c659 Merge pull request #190 from espenhgn/hmin 4597315fea19d6bf2822c9cd68fc7925ebaa986b (origin/hmin) Merge branch 'master' into hmin 9db86367a5e77cc3e9edd796b9245b1c6e984df5 Merge pull request #204 from espenhgn/rel2.1.1 7da0d5567a9ef4f77b9d7d24f028bd90de9746a3 (origin/rel2.1.1) v2.1.1rc1 96d52432e9fce4ab0a545febed984aeaf84a723b v2.1.1.rc1 f49a768092496ef41b88e27b298cd5a48466d38d prefer mpich neuron build on travisCI a857b6847e0a6b43baa0603c1b2de9c570f0eff7 figure out which gcc is used by TravisCI 3cda48dbabba6d0ccf2d13720aa437ff8588e7b2 list packages in test environment for debugging 5a100025ff81dc91eb93faef085a3c04df66a96a add gcclinux-64 to test environment 3436b90a2ca75992d1c8ec13fabc994860a8df03 add gxxlinux-64 to test env 0bc95c3d19fadf303e31b5035751976860f11757 Merge branch 'master' into rel2.1.1 d90c207b91fe914c786f2142f90f2afb6525f99f remove --quiet flag c8e7134e821116b1134bf97395239084a4ff0c37 prep 2.1.1 bugfix release 82e18886961e40d52a2ff86c980acae7328e343d Merge pull request #201 from espenhgn/fix-199 0054091f7d4462d8d81f3dd1129ae0109df91c08 (origin/fix-199) renamed folder 211b175cea554c04c99facd894f9c1abc314d180 switch to conda on travisCI 2da2cee06be25613aa446160a8897a49accd63c7 Merge pull request #200 from espenhgn/fix-197 c41c1241e7d3945cbc891e477a684b96e8784835 (origin/fix-197) fix docstring example 056c30c9a421e71ade1ec992537c6a026da8cfcd Merge pull request #198 from espenhgn/dotprodresults 85b4a7b732e053fb68282d6a78758405fb29ac2b (origin/dotprodresults) added missing tests for Cell.simulate(dotprodcoeffs=[..]) parameter 56611c53ce27b6bafdc76d0d08b9490ff8601acf Merge pull request #193 from espenhgn/fix-192 8504c51906a47f9e5e552bff9a5efd779f8f132b (origin/fix-192) fixed conda install info 5705441baac90494a7266e12a45c1aca93fee79d add cvode.rtol(rtol) control option to Cell.simulate df592e2230981fdd7778232605cbe403fcc3e445 Merge pull request #189 from espenhgn/master 518628acf1af6d89038b0e068926f5e9ad42c50d add calculation of extracellular potential to example bfa2973d89019a1685469cab4fc6ef5f979a5004 Merge pull request #182 from lobertrand/minorfixdeleted_sections 06a1831766d204cf15522b6600ded868871613dd Minor fix 1d329a35e17e08f53840bad241f7be2d2b3963c4 Merge pull request #181 from espenhgn/2.1.0 154c8a53d828147c688c10c56bff9dc34431b34a (origin/2.1.0) prep 2.1.0 release

- Python
Published by espenhgn over 5 years ago

lfpy - LFPy-2.1.1rc1

Feature and bugfix release candidate. Main changes:

Supports NEURON>7.7.2
LFPy.Cell keyword arguments cm and Ra defaults to None (used to be equal to neuron.h.Section() defaults)
Improved LFPy.Cell.__del__() destructor method that can be called to ensure safer execution of multiple independent cell simulations in succession (using NEURON>=7.8.x in particular)
Additional unittests

Commits since previous release https://github.com/LFPy/LFPy/releases/tag/v2.1: 743c71016e2b12fad302577585de666346d4017c (HEAD -> master, tag: v2.1.1rc1, origin/master, origin/HEAD) Formatting/future proofing (#210) df8d15b58e77999752d586069b684e60c5799ee7 Set Ra and cm only if not None (#211) 0452c48b4d240ef6a2801bc7bff0a193158ff1d6 fix morphology issue with NEURON>7.7.2 (#206) 394d085835e6e8ba589dd4b6e732876d10d560f2 Tests that currents sum to approximately zero (#207) 797ee1c38209ce871ad6c1653e59bd5b7cb9c659 Merge pull request #190 from espenhgn/hmin 4597315fea19d6bf2822c9cd68fc7925ebaa986b (origin/hmin) Merge branch 'master' into hmin 9db86367a5e77cc3e9edd796b9245b1c6e984df5 Merge pull request #204 from espenhgn/rel2.1.1 7da0d5567a9ef4f77b9d7d24f028bd90de9746a3 (origin/rel2.1.1) v2.1.1rc1 96d52432e9fce4ab0a545febed984aeaf84a723b v2.1.1.rc1 f49a768092496ef41b88e27b298cd5a48466d38d prefer mpich neuron build on travisCI a857b6847e0a6b43baa0603c1b2de9c570f0eff7 figure out which gcc is used by TravisCI 3cda48dbabba6d0ccf2d13720aa437ff8588e7b2 list packages in test environment for debugging 5a100025ff81dc91eb93faef085a3c04df66a96a add gcclinux-64 to test environment 3436b90a2ca75992d1c8ec13fabc994860a8df03 add gxxlinux-64 to test env 0bc95c3d19fadf303e31b5035751976860f11757 Merge branch 'master' into rel2.1.1 d90c207b91fe914c786f2142f90f2afb6525f99f remove --quiet flag c8e7134e821116b1134bf97395239084a4ff0c37 prep 2.1.1 bugfix release 82e18886961e40d52a2ff86c980acae7328e343d Merge pull request #201 from espenhgn/fix-199 0054091f7d4462d8d81f3dd1129ae0109df91c08 (origin/fix-199) renamed folder 211b175cea554c04c99facd894f9c1abc314d180 switch to conda on travisCI 2da2cee06be25613aa446160a8897a49accd63c7 Merge pull request #200 from espenhgn/fix-197 c41c1241e7d3945cbc891e477a684b96e8784835 (origin/fix-197) fix docstring example 056c30c9a421e71ade1ec992537c6a026da8cfcd Merge pull request #198 from espenhgn/dotprodresults 85b4a7b732e053fb68282d6a78758405fb29ac2b (origin/dotprodresults) added missing tests for Cell.simulate(dotprodcoeffs=[..]) parameter 56611c53ce27b6bafdc76d0d08b9490ff8601acf Merge pull request #193 from espenhgn/fix-192 8504c51906a47f9e5e552bff9a5efd779f8f132b (origin/fix-192) fixed conda install info 5705441baac90494a7266e12a45c1aca93fee79d add cvode.rtol(rtol) control option to Cell.simulate df592e2230981fdd7778232605cbe403fcc3e445 Merge pull request #189 from espenhgn/master 518628acf1af6d89038b0e068926f5e9ad42c50d add calculation of extracellular potential to example bfa2973d89019a1685469cab4fc6ef5f979a5004 Merge pull request #182 from lobertrand/minorfixdeletedsections 06a1831766d204cf15522b6600ded868871613dd Minor fix 1d329a35e17e08f53840bad241f7be2d2b3963c4 Merge pull request #181 from espenhgn/2.1.0 154c8a53d828147c688c10c56bff9dc34431b34a (origin/2.1.0) prep 2.1.0 release

- Python
Published by espenhgn over 5 years ago

lfpy - LFPy-2.1

Feature and bugfix release. Main features are the addition of MEAutility (https://github.com/alejoe91/MEAutility) functionality for configuring electrode geometries and improved use of variable time step methods.

Merges/commits since LFPy-2.0.7: 7141fbab23c2a172e4301e655fbee2fd0dc50e79 (HEAD -> master, tag: v2.1, origin/master, origin/HEAD) v2.1 (#180) 2cffc136fca99218f839826abe99eb69d4e7e89c (tag: v2.1rc1) V2.1rc1 (#179) de95b0420550cbdf234ecd4bf605e0c4b4c97bb6 Merge pull request #177 from espenhgn/master 6280b14f5d640e00ec10b0ca596e883de720528a refactoring 4be60a3c3bedaffbf5882e46831a5b951843dc30 Merge pull request #176 from LFPy/racm 8c96bbeb66fde5e9131f04164767cc3bc1de3359 (origin/racm) Set ra and cm even when passive=False 207095689106914e97e12653d680596c710b9b0d Cvode fixes (#172) 1d6447c1b2d69881f4734fb7a4d78317dc0929e5 (alejoe91/master) made use of variable_dt consistent across simulate methods (#171) 5c172558929e5455a370f66a69b412487b732bfc Use MEAutility as backend for electrodes (#159)

- Python
Published by espenhgn over 5 years ago

lfpy - LFPy-2.1rc1

Feature and bugfix release. Main features are the addition of MEAutility (https://github.com/alejoe91/MEAutility) functionality for configuring electrode geometries and improved use of variable time step methods.

Commits since LFPy-2.0.7: 2cffc136fca99218f839826abe99eb69d4e7e89c (HEAD -> master, tag: v2.1rc1, origin/master, origin/HEAD) V2.1rc1 (#179) de95b0420550cbdf234ecd4bf605e0c4b4c97bb6 Merge pull request #177 from espenhgn/master 6280b14f5d640e00ec10b0ca596e883de720528a refactoring 4be60a3c3bedaffbf5882e46831a5b951843dc30 Merge pull request #176 from LFPy/racm 8c96bbeb66fde5e9131f04164767cc3bc1de3359 (origin/racm) Set ra and cm even when passive=False 207095689106914e97e12653d680596c710b9b0d Cvode fixes (#172) 1d6447c1b2d69881f4734fb7a4d78317dc0929e5 (alejoe91/master) made use of variable_dt consistent across simulate methods (#171) 5c172558929e5455a370f66a69b412487b732bfc Use MEAutility as backend for electrodes (#159)

- Python
Published by espenhgn over 5 years ago

lfpy - LFPy-2.0.7

Bugfix release.

Fixes since LFPy-2.0.4: 9cbe65f (HEAD -> master, tag: v2.0.7, origin/master, origin/HEAD) v2.0.7 (#169) 9e25ca6 (tag: v2.0.7.rc1) V2.0.7.rc1 (#168) ee96839 (tag: v2.0.6) Merge pull request #167 from espenhgn/v2.0.6 b4af4e0 Merge pull request #166 from espenhgn/cythonfix 530c532 (origin/v2.0.6) trying to fix pipy build, upped minorminor version 2bd53b1 (origin/cythonfix) fix Cython FutureWarning cfeeb04 (tag: v2.0.5) fix github pythonpublish.yml a432934 Merge pull request #165 from espenhgn/v2.0.5 34fdba7 Merge pull request #164 from espenhgn/rz c76e2e2 Merge pull request #163 from espenhgn/fixnumpydoc 1881bcb Merge pull request #154 from LFPy/espenhgn-patch-1 800eee4 (origin/rz) remove unuzed rz param (thanks alejoe91) 669f1f4 (origin/v2.0.5) prep v2.0.5 release 67257d7 Readthedocs (#2) 2c7ae1a (origin/fixnumpydoc) Merge pull request #157 from solveignaess/cellparamfix 774fe64 (solveig/cellparamfix) minor documentation fix cell parameters ae91cbd (solveig/master) added symmetry test and simplified decompose function (#156) 3817e0f fixed bug in decomposedipole, eegmegcalc.py (#155) f081468 (origin/espenhgn-patch-1) Add upload to Test PYPI 657d9bb Create pythonpublish.yml

- Python
Published by espenhgn almost 6 years ago

lfpy - LFPy-2.0.7.rc1

Test PyPi github build action

- Python
Published by espenhgn almost 6 years ago

lfpy - LFPy-2.0.6

Fix broken PyPI package.

Commits since v2.0.5: ee96839 (HEAD -> master, tag: v2.0.6, origin/master, origin/HEAD) Merge pull request #167 from espenhgn/v2.0.6 b4af4e0 Merge pull request #166 from espenhgn/cythonfix 530c532 (origin/v2.0.6) trying to fix pipy build, upped minorminor version 2bd53b1 (origin/cythonfix) fix Cython FutureWarning

- Python
Published by espenhgn almost 6 years ago

lfpy - LFPy-2.0.5

Changes since LFPy-2.0.4: cfeeb04 (HEAD -> master, tag: v2.0.5, origin/master, origin/HEAD) fix github pythonpublish.yml a432934 Merge pull request #165 from espenhgn/v2.0.5 34fdba7 Merge pull request #164 from espenhgn/rz c76e2e2 Merge pull request #163 from espenhgn/fixnumpydoc 1881bcb Merge pull request #154 from LFPy/espenhgn-patch-1 800eee4 (origin/rz) remove unuzed rz param (thanks alejoe91) 669f1f4 (origin/v2.0.5, v2.0.5) prep v2.0.5 release 67257d7 Readthedocs (#2) 2c7ae1a (origin/fixnumpydoc) Merge pull request #157 from solveignaess/cellparamfix 774fe64 minor documentation fix cell parameters ae91cbd added symmetry test and simplified decompose function (#156) 3817e0f fixed bug in decomposedipole, eegmegcalc.py (#155) f081468 (origin/espenhgn-patch-1) Add upload to Test PYPI 657d9bb Create pythonpublish.yml

- Python
Published by espenhgn almost 6 years ago

lfpy - LFPy-2.0.4

Fixes since v2.0.3: 159f583 Added fix for small bug in Cell.get_closest_idx (#151) 7c50a4b checkout LFPy source in /opt (#149) 34f855d added Docker container build files + instructions + minor fixes (#147) f0923c2 Found and fixed problem with parent segment having more than two children (#145) b2554a5 Merge pull request #144 from espenhgn/h5pyfix 1a80c96 (origin/h5pyfix) fix h5py DeprecationWarning 1af46ce Update README.md 7333545 Update README.md 24294cf Update README.md 134129f Changed way of computing p_rad to avoid roundoff errors (#142)

- Python
Published by espenhgn about 6 years ago

lfpy - LFPy-2.0.3

Fixes since v2.0.2: 73b4f33 (HEAD -> master, tag: v2.0.3, origin/master, origin/HEAD) v2.0.3 release (#141) 0d822e8 Cleanup of FourSphereVolumeConductor (#140) 10ec644 Adds some conda-related information and conda environment files (#138) e48a158 Merge pull request #137 from espenhgn/execfix a757c52 (origin/execfix) fixes Cell.get_rand_idx_area_and_distribution_norm if fun arg is str 50f43c6 Merge pull request #136 from minrk/patch-1 20b7568 remove setuptools runtime dependency 9eaaa5a Fixes #137 (#135) 0f94de0 fixed windows neuron install url, fixed typo 9e18dc9 Turned example*.py into jupyter notebooks (#133) 5690679 render content 7b7e219 fixed citations f7a5157 Update README.md 61dc02c update readthedocs environment file (#132) 3b314f0 replace nose with py.test. Fixed DeprecationWarnings (#131) ada2a3b Merge pull request #130 from espenhgn/fix_126 bfade3c (origin/fix_126) fixes issue 126

- Python
Published by espenhgn over 6 years ago

lfpy - LFPy-2.0.2

Contains the following updates since v2.0: afd5ea9 (HEAD -> master, tag: v2.0.2, origin/master, origin/HEAD) semantic changes to network examples (#124) 8a4eb45 Removed dependence on CSA (#123) 2f49577 Merge pull request #122 from LFPy/EEG_example_fix 08bbd63 Passive parameters was not set in EEG example, causing unphysiological behaviour. f50ba73 tuned network example (#121) 124c2b9 Synapse bug (#120) 6f3be2c (torbjone/synapse_fix, torbjone/master) Issue117 fixes (#119) 2e0db05 (tag: v2.0.1) Issue #113 fixes (#114) 2e5797a Misc Formatting (#111) 5f959ff allow arg fun as str type in Cell.get_rand_idx_area_and_distribution_… (#110) 1058b3d Add missing file examples/bioRxiv281717/figure_7_8/example_parallel_network.py (#108) 3e62ac0 add DOI badge 3d7a459 adds explanation of figure_7_8 folder e426b42 Merge pull request #104 from espenhgn/benchmarks 08c73bb (origin/benchmarks) adding benchmark scripts 0a055fa Merge pull request #103 from torbjone/loop_over_points_fix 4970b2f Testing new way to sum points on electrode surface. 7aff01f Merge pull request #102 from espenhgn/master 76e997a doc fix, removed unused imports fb6df8a Merge pull request #101 from espenhgn/pep8 257ff06 (origin/pep8) PEP-8 fixes 8606e2a adds link to CNS2018 tutorial slides ab7809f (tag: v2.0.0) v2.0.0

- Python
Published by espenhgn about 7 years ago

lfpy - LFPy-2.0.1

What's Changed

PEP-8 fixes by @espenhgn in https://github.com/LFPy/LFPy/pull/101
doc fix, removed unused imports by @espenhgn in https://github.com/LFPy/LFPy/pull/102
Testing new way to sum points on electrode surface. by @torbjone in https://github.com/LFPy/LFPy/pull/103
adding benchmark scripts by @espenhgn in https://github.com/LFPy/LFPy/pull/104
Add missing file examples/bioRxiv281717/figure78/exampleparallelnetwork.py by @espenhgn in https://github.com/LFPy/LFPy/pull/108
allow arg fun as str type in Cell.getrandidxareaanddistribution… by @espenhgn in https://github.com/LFPy/LFPy/pull/110
Misc Formatting by @espenhgn in https://github.com/LFPy/LFPy/pull/111
Issue #113 fixes by @espenhgn in https://github.com/LFPy/LFPy/pull/114

Full Changelog: https://github.com/LFPy/LFPy/compare/v2.0.0...v2.0.1

- Python
Published by espenhgn about 7 years ago

lfpy - LFPy-2.0.0

Full Changelog: https://github.com/LFPy/LFPy/compare/v2.0...v2.0.0

- Python
Published by espenhgn over 7 years ago

lfpy - v1.1.3

LFPy release v1.1.3.

What's Changed

square contact added by @alejoe91 in https://github.com/LFPy/LFPy/pull/2
Set pos 3d fixed by @alejoe91 in https://github.com/LFPy/LFPy/pull/4
fixed implementation of linesource method by @espenhgn in https://github.com/LFPy/LFPy/pull/5
Mostly trivial cosmetic changes and updates by @torbjone in https://github.com/LFPy/LFPy/pull/12
Set pos 3d new by @alejoe91 in https://github.com/LFPy/LFPy/pull/17

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

- Python
Published by espenhgn about 9 years ago

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lfpy - LFPy-2.0.0

lfpy - v1.1.3

What's Changed