Merge branch 'neuroml_updates' into osbv2

.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/*"

.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

@@ -1,3 +1,63 @@
+# Version in development
+
+**New features**
+
+- Raster plot colored by phase
+
+- Examples based on the CA3 model using the 'colorbyPhase' option in the plotRaster
+
+**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)
+
+# Version 1.0.5
+
+**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**
@@ -52,28 +112,6 @@
 
 - Added ability to load PointCell from saved network
 
-- Added MultiPlotter class to allow plotting line data on multiple axes
-
-- Added option to use separate axis for each PSD trace (set axis='multi')
-
-- Added new Batch method named SBI (Simulation Based Inference) with example folder (sbiOptim)
-
-- Added support for string functions in properties of cell mechanism, in cell geometry (in netParams.cellParams)
-
-- Added support for string functions in synMech parameters
-
-- Massive update of schemas (validator.py and setup.py) 
-
-- More control over POINTER variables through synMechParams (e.g. for gap junctions)
-
-- Introduced cell variables in cellParams
-
-- Added plotRateSpectrogram to utils.py
-
-- Functions prepareCSD() and plotCSD() are now available
-
-- Updated documentation on install and about
-
 **Bug fixes**
 
 - Fixed bug with loading CompartCell with custom mechanisms from saved network
@@ -92,9 +130,9 @@
 
 - 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).

doc/build.py

@@ -74,7 +74,7 @@
 shutil.rmtree('build', ignore_errors=True)
 
 # All .rst files but those listed here will be deleted during this process
-keep = ['about.rst', 'advanced.rst', 'index.rst', 'install.rst', 'reference.rst', 'tutorial.rst', 'contrib.rst', 'modeling-specification-v1.0.rst']
+keep = ['about.rst', 'index.rst', 'install.rst', 'user_documentation.rst', 'tutorial.rst', 'contrib.rst', 'modeling-specification-v1.0.rst']
 
 print('Deleting old .rst files.')
 for file in os.listdir('source'):
@@ -94,12 +94,12 @@
 
 # sphinx-apidoc produces a file called "netpyne" that we want to call "Package Index"
 print('Fixing Package Index file.')
-os.system('mv source/netpyne.rst source/package_index.rst')
-with open('source/package_index.rst') as f:
+os.system('mv source/netpyne.rst source/package_reference.rst')
+with open('source/package_reference.rst') as f:
     lines = f.readlines()
-    lines[0] = 'Package Index\n'
+    lines[0] = 'Package Reference\n'
     lines[1] = '=============\n'
-with open('source/package_index.rst', 'w') as f:
+with open('source/package_reference.rst', 'w') as f:
     f.writelines(lines)
 
 # Generate the html files