Merge branch 'development' into osbv2-dev

Author: pgleeson

.github/workflows/ebrains-mirror.yml

@@ -0,0 +1,33 @@
+name: Mirror to Ebrains
+
+# Configure the events that are going to trigger tha automated update of the mirror
+on:
+  push:
+    branches: [ master ]
+
+# Configure what will be updated
+jobs:
+  # set the job name
+  to_ebrains:
+    runs-on: ubuntu-latest
+    steps:
+      # this task will push the master branch of the source_repo (github) to the
+      # destination_repo (ebrains gitlab)
+      - name: syncmaster
+        uses: wei/git-sync@v3
+        # component owners need to set their own variables
+        # the destination_repo format is
+        # https://gitlab_service_account_name:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/name_of_mirror.git
+        with:
+          source_repo: "suny-downstate-medical-center/netpyne"
+          source_branch: "master"
+          destination_repo: "https://github-pusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/vbragin/netpyne.git"
+          destination_branch: "master"
+      # this task will push all tags from the source_repo to the destination_repo
+      - name: synctags
+        uses: wei/git-sync@v3
+        with:
+          source_repo: "suny-downstate-medical-center/netpyne"
+          source_branch: "refs/tags/*"
+          destination_repo: "https://github-pusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/vbragin/netpyne.git"
+          destination_branch: "refs/tags/*"

.github/workflows/tests.yml

@@ -7,23 +7,23 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        #python-version: [2.7, 3.7]
-        python-version: [3.7]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+      fail-fast: false
 
     steps:
       - name: Check out repository code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Update apt-get
         run: sudo apt-get update
 
       - name: Install packages
-        run: sudo apt-get install python-tk python3-tables
+        run: sudo apt-get install python3-tables
 
       - name: Install dependencies
         run: |

.gitignore

@@ -1,4 +1,5 @@
-/doc/source/*.rst
+/doc/source/netpyne.*.rst
+doc/source/package_reference.rst
 
 /examples/sandbox/LEMS_sandbox.xml
 /examples/M1/LEMS_M1.xml

CHANGES.md

@@ -1,46 +1,214 @@
-# Version in development
+# Version 1.1.0
 
 **New features**
 
-- Added 'linewidth' as argument of plotting.plotSpikeHist()
+- Added extracellular stimulation with a supporting xtra.mod (which includes a global variable defining the temporal modulation and a pointer to link the extracellular mechanism in NEURON). Useful for large networks
+
+- Improved netParams validation (mechs validation, improved error messages)
+
+- added ability to save transmembrane current for each segment
+
+- Updated options for batch communication (see netpyne documentation: "running a batch job (beta)")
 
 **Bug fixes**
 
-- fixed handling filenames with multiple dots in `MetaFigure.saveFig()`
+- Solve minor bug in the uniform field for extracelular stimulation (sign). Deposited the xtra.mod in support module.
 
-# Version 1.0.3.1
+- Fixed batch SGE example (credit: Adam Newton)
 
-- Hotfix to support new GUI functionality (fixes in grid parameter optimization)
+- Solved small bug when plotting colorbar in the raster plot colored by the LFP phase 
 
-- Removed redundant warnings
+- Solved conflict between diversity and segment coordinates (per population), used in LFP setups
 
-# Version 1.0.3
+- Added extracellular stimulation (option: without compiling an additional .mod file - large memory requirements-)
+
+- Update of documentation (stimSourceParams and stimTargetParams) incorporating how to define extracellular stimulations
+
+- Fixed ODict in examples/batchCell (credit: Hyunsu Lee)
+
+- Fix in RxD to support NEURON 9 (credit: Adam Newton)
+
+- Fixed recording from variables of Point process
+
+- Fixed time slicing on pre-loaded data in plotCSD() (credit: Nikita Novikov)
+
+- Fixed sbi deprecation error. Fixes in docs formatting
+
+- Fixes, refactoring and fail-fast checks in multisinaptic connections
+
+- Fix verbatim function defs in mod files (credit: Ankur Sinha)
+
+# Version 1.0.7
 
 **New features**
 
-- Added ability to load PointCell from saved network
+- Introducing `batchtools` subpackage for parameters exploration and optimization
+
+- Added progress-bar indicating network creation progress. Toggle the progress bar with cfg.progressBar
+
+- cfg.connRandomSecFromList and cfg.distributeSynsUniformly can now be overriden in individual conn rule
+
+- Added ability to use `sec`, `loc`, `preSec` and `preLoc` from list in connList-type connParams
+
+- Updated tests.examples.utils to allow for dynamic pathing
+
+- Dropped python2 support
+
+**Bug fixes**
+
+- Better handling of exceptions in `importCellParams()` (incl. `h.load_file()` - issue 782)
+
+- Pandas deprecated parameter fix
+
+- Fixed pointer id overflow on MPI (e.g. for gap junctions)
+
+- preSec and preLoc are no longer lost for inverse pointer connection
+
+- Fixed crash due to use of matplotlib.TextArea deprecated param (credit: Christian O'Reilly)
+
+- syncLines in rasterPlot restored
+
+- Fixed a bug in `gatherDataFromFiles()` where cellGids for node 0 were lost
+
+- Fixed generating rhythmic spiking pattern with 'uniform' option
+
+- Fixed misleading console output when cfg.recordStims is On
+
+- The colors in CSD plots are now properly aligned vertically with the CSD time-series overlays (credit: Sam Neymotin)
+
+- Update mkdir to makedirs (credit: Jacob Sprouse)
+
+# Version 1.0.6
+
+**New features**
+
+- Raster plot colored by phase
+
+- Examples based on the CA3 model using the 'colorbyPhase' option in the plotRaster
+
+- API for loading .mod files selectively
+
+- Ability to specify custom executor to run batch with (defaults to `sh`)
+
+**Bug fixes**
+
+- Fixed loading point cell params from legacy models (issue 607)
+
+- Fix voltage movie tutorial
+
+- Fix to automatically include netstims in the sim.allSimData object when plotRaster 'include' selects 'all'
+
+- Fixed loading netParams in some scenarios (bug caused by srting functions pre-processing)
+
+- Fix of `plotRaster` pops coloring if ordered not by gid
+
+- Made cells diversity work with popParams based on `cellsList` and `gridSpacing`
+
+- Fixed handling of output of `sim.create()` - was wrong order (credit: Kate Doxey)
+
+- Fixed undeclared var `dpi` in `plotShape()`
 
-- Added MultiPlotter class to allow plotting line data on multiple axes
+- Fixes in batch utils
 
-- Added option to use separate axis for each PSD trace (set axis='multi')
+- Added some missing math functions to use with 'Functions as string' functionality
 
-- Added new Batch method named SBI (Simulation Based Inference) with example folder (sbiOptim)
+- Switch file copying method to shutil to be compatible over all operating systems (credit: Henrik Podeus)
 
-- Added support for string functions in properties of cell mechanism, in cell geometry (in netParams.cellParams)
+# Version 1.0.5
 
-- Added support for string functions in synMech parameters
+**New features**
+
+- Time series and PSD plots for current source density (CSD)
+
+- Added colorbar to CSD plot
+
+- Support for Sun Grid Engine HPC
+
+- Extended sim.gatherData() with more optional arguments for flexibility
+
+- Specify linear/log scale in `plotRatePSD()`
+
+- Print more info about exceptions in plotting functions
+
+- Check RxD specification for potential syntax issues
+
+- Prevent zero population size in scaled-down models
+
+- Better messages for validation errors
+
+**Bug fixes**
+
+- Fixed errors in plotting with sim.cfg.gatherOnlySimData=True
+
+- Support saving and loading data in .mat and .hdf5 formats
+
+- Multiple fixes in `plotRatePSD()` - popColors, fft, minFreq
+
+- Fixed sync lines in `plotRaster()`
+
+- Fixed performance issue in `plotConn()` with `groupBy='pop'` (default)
+
+- Fixed `recordTraces` to not require more presicion than segment size (for stim and synMech)
+
+# Version 1.0.4.2
+
+**Bug fixes**
+
+- Unpin matplotlib version (params copying issue fixed)
+
+# Version 1.0.4.1
+
+**New features**
+
+- Added env variable to define head model placement
+
+# Version 1.0.4
 
-- Massive update of schemas (validator.py and setup.py) 
+**New features**
+
+- Added 'linewidth' as argument of plotting.plotSpikeHist()
+
+- More detailed validation of netParams
+
+- Save and load model in native NetPyNE format
+
+- Converted most of examples to new NetPyNE model structure
+
+- Complex stimulation ('rhythmic', 'evoked', 'poisson' and 'gauss') for VecStim created as pointCell (as a population rule)
+
+- Codebase brought into compliance with PEP8 conventions
+
+- Updates in NeuroML examples and tests
+
+**Bug fixes**
+
+- fixed handling filenames with multiple dots in `MetaFigure.saveFig()`
+
+- Fixed readCmdLimeArgs() default arguments for backward-compatibility
 
-- More control over POINTER variables through synMechParams (e.g. for gap junctions)
+- Cleaned up example models to drop some legacy/irrelevant params
 
-- Introduced cell variables in cellParams
+- RxD module: Parameters defined before reactions + names given by default when missing (by the key)
 
-- Added plotRateSpectrogram to utils.py
+- Analysis: try ... except call in plotDipole
 
-- Functions prepareCSD() and plotCSD() are now available
+- Save hObj of gap junction to connParams
 
-- Updated documentation on install and about
+- Removed duplicated or unused code from gridSearch()
+
+- Fixes in batch utilities to make OS-agnostic
+
+# Version 1.0.3.1
+
+- Hotfix to support new GUI functionality (fixes in grid parameter optimization)
+
+- Removed redundant warnings
+
+# Version 1.0.3
+
+**New features**
+
+- Added ability to load PointCell from saved network
 
 **Bug fixes**
 
@@ -60,9 +228,9 @@
 
 - Fixed some misinformation in reference.rst about the subconn
 
-- Fixed bug in dipole calculation units - changed from mA to uA 
+- Fixed bug in dipole calculation units - changed from mA to uA
 
-- Fixed bug in conditional logic when gathering LFP / dipoles 
+- Fixed bug in conditional logic when gathering LFP / dipoles
 
 - Allow tuples to specify population's cells in 'include' for plotSpike
 

README.md

@@ -7,3 +7,14 @@ For more details, installation instructions, documentation, tutorials, forums, v
 This package is developed and maintained by Dura-Bernal lab (http://dura-bernal.org) and the Neurosim lab (www.neurosimlab.org).
 
 [![Build](https://github.com/Neurosim-lab/netpyne/actions/workflows/tests.yml/badge.svg)](https://github.com/Neurosim-lab/netpyne/actions/workflows/tests.yml)
+
+## Acknowledgements
+This work was funded by grants from the NIH, NSF, NYS SCIRB, UK Welcome Trust and Australian Research Council. We are thankful to all the contributors that have collaborated in the development of this open source tool via GitHub.
+
+This project was supported by:
+- HBP Brain Simulation Platform funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 785907 (Human Brain Project SGA2).
+- EBRAINS research infrastructure, funded from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 945539 (Human Brain Project SGA3).
+
+This project has received a Voucher "Integration of NetPyNE into EBRAINS Platform (EBRnetpyne)" from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement:
+- No. 785907 (Human Brain Project SGA2).
+- No. 945539 (Human Brain Project SGA3).