Merge branch 'development' into neuroml_updates

* development: (49 commits)
  Extracellular stimulation via .mod
  small correction in plotter.py
  Conflict diversity and LFP
  Conflict between diversity and LFP
  for unit tests, rolled back to 3.12 so far
  test with python 3.9-3.13
  drop python 3.7 for unit-tests
  plotCSD: time slicing on pre-loaded data (credit: Nikita Novikov)
  extracellular stimulation
  quick fix to `update` method that allows for working with lists. (#837)
  d/w expanse setup, moved {env} {res} {custom} (#834)
  hot fix (submits.py) (#833)
  code adjustments to internal sim.clearAll(), added sim.close() (#832)
  file cleanup, slurm scripts and timeout added to batchtools submit templates (#831)
  updated upload instructions to exclude downtime
  fixed sbi deprecation error. fixes in docs formatting
  minor correction to CHANGES.md
  VERSION 1.0.7
  Revert "Exlude tests from discovery / installation" - due to issue that has emerged with spack installation (EBRAINS platform). Will re-visit later..
  merge of batchtools into the development repository. (#829)
  ...

.github/workflows/tests.yml

@@ -7,16 +7,15 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        #python-version: [2.7, 3.7]
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
       fail-fast: false
 
     steps:
       - name: Check out repository code
         uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 

CHANGES.md

@@ -1,3 +1,54 @@
+- 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
+
+- 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
+
+- 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
+
+
+# Version 1.0.7
+
+**New features**
+
+- 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**

doc/build.py

@@ -38,20 +38,23 @@
     10d) It will fix the Package Index file
     10e) It will build the html files
 11) Post the documentation
-    11a) ssh [email protected] "rm -r ~/public_html"
+    11a) ssh [email protected] "cp -r ~/public_html ~/public_html_backup"
         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 [email protected]:///home/gkaue9v7ctjf/public_html
+    11b) scp -r build [email protected]:///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)
-    11c) ssh [email protected] "cp -r ~/redirect_html/. ~/public_html/"
+    11c) ssh [email protected] "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 [email protected] "rm -r ~/public_html_backup/"
 12) Update PYPI (pip) with the latest release
     12a) cd netpyne
     12b) python3 setup.py bdist_wheel --universal
     12c) python setup.py upload_via_twine
-         Username: salvadord
+        (outdated) Username: salvadord
+        Enter the token (https://dura-bernallab.slack.com/archives/D02A30N4Z50/p1707862380181609)
 13) Announce the new release
     13a) New release announcement text:
          NetPyNE v#.#.# is now available. For a complete list of changes and bug fixes see: https://github.com/suny-downstate-medical-center/netpyne/releases/tag/v#.#.#
-         See here for instructions to install or update to the latest version: http://www.netpyne.org/install.html
+         See here for instructions to install or update to the latest version: https://www.netpyne.org/documentation/installation
     13b) Announce on NEURON forum:
          https://www.neuron.yale.edu/phpBB/viewtopic.php?f=45&t=3685&sid=9c380fe3a835babd47148c81ae71343e
     13c) Announce to Google group:

doc/source/conf.py

@@ -67,9 +67,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.0.6'
+version = '1.0.7'
 # The full version, including alpha/beta/rc tags.
-release = '1.0.6'
+release = '1.0.7'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.