Merge branch 'development' into neuroml_updates

Author: pgleeson

.github/workflows/tests.yml

@@ -23,7 +23,7 @@ jobs:
         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: |

CHANGES.md

@@ -1,5 +1,21 @@
+# Version 1.1.0
+
+**New features**
+
 - 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**
+
+- Solve minor bug in the uniform field for extracelular stimulation (sign). Deposited the xtra.mod in support module.
+
+- Fixed batch SGE example (credit: Adam Newton)
+
 - Solved small bug when plotting colorbar in the raster plot colored by the LFP phase 
 
 - Solved conflict between diversity and segment coordinates (per population), used in LFP setups
@@ -8,6 +24,19 @@
 
 - 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
 

doc/build.py

@@ -42,6 +42,8 @@
         NOTE: it may give the error "... no matching host key type found ...". In this case, try using the "-oHostKeyAlgorithms=+ssh-rsa" argument in ssh command and in scp command below (as well as in 11c)
     11b) scp -r build gkaue9v7ctjf@107.180.3.236:///home/gkaue9v7ctjf/public_html_new
         NOTE: it may give the error "path canonocalization failed", then use the argument "-O" in scp call - it rolls back to legacy mode (see also NOTE in 11a)
+        NOTE: faster command?::
+        NOTE: rsync -r --progress build/ gkaue9v7ctjf@107.180.3.236:/home/gkaue9v7ctjf/public_html_new
     11c) ssh gkaue9v7ctjf@107.180.3.236 "cp -r ~/redirect_html/. ~/public_html_new/ && rm -r ~/public_html && mv ~/public_html_new ~/public_html"
     11d) Make sure new documentation is up and running
     11e) ssh gkaue9v7ctjf@107.180.3.236 "rm -r ~/public_html_backup/"

doc/source/conf.py

@@ -67,9 +67,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.0.7'
+version = '1.1.0'
 # The full version, including alpha/beta/rc tags.
-release = '1.0.7'
+release = '1.1.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.