Without it tests/ will be installed as a top level Python module.

…ate-medical-center/development

PR from development to master - VERSION 1.0.5

Included in python 3.12+
https://docs.python.org/3.12/library/typing.html#typing.override

More readable, and IDE friendly

I seem to be able to run NetPyNE sims fine with MPI, so this comment
does not seem to apply any more.

See, override decoration helps :)

[skip ci]

It's a warning that the user should be aware of.

erev is not required in Nernst or GHK2

Since NEURON's hoc only uses 10 decimal digits, to match it, we must
limit our Python value to 10 decimal digits

…ate-medical-center/development

PR from development to master - VERSION 1.0.6

… into feat/neuroml-ankur

If we want it to be verbose, we toggle the verbosity in the module like
this:

```
logger = logging.getLogger("name of module").setLevel(..)
```

We approximate if it *isnt* close to the value

To fix this annoying note:

"Node.js 16 actions are deprecated. Please update the following actions
to use Node.js 20: actions/setup-python@v4.."

This reverts commit 15e66bb.

To ensure we get the complete value, and not the string converted one.

Because sometimes NetPyNE's internal format stores floats as strings,
and so using `%r` results in invalid NeuroML.

Eg:
https://github.com/sanjayankur31/netpyne/actions/runs/8008676196/job/21875614690

```
<membraneProperties>
    <channelDensity id="leak_soma_group" ionChannel="leak_hh" condDensity="0.003 S_per_cm2" erev="-70 mV" ion="non_specific"/>
    <channelDensity id="k_soma_group" ionChannel="k_hh" condDensity="0.036 S_per_cm2" erev="'-77' mV" ion="k"/>
    <channelDensity id="na_soma_group" ionChannel="na_hh" condDensity="0.12 S_per_cm2" erev="'50' mV" ion="na"/>
    <spikeThresh value="10 mV"/>
    <specificCapacitance value="1 uF_per_cm2" segmentGroup="soma_group"/>
    <initMembPotential value="-71 mV"/>
</membraneProperties>
```

Notice how values for membrane potential are correct but erevs for the
two channels are not.

This reverts commit 169d5fe.

…acts in color plots

The `imp` module has been removed in Python 3.12:
https://docs.python.org/3/whatsnew/3.12.html#imp

The inplace=True keyword was removed from newer Pandas versions, thus the inplace option is replaced by re-assigning the variable, following Pandas recs (pandas-dev/pandas#57104)
Changing df['popInd'].cat.set_categories(sim.net.pops.keys(), inplace=True) by df['popInd'] = df['popInd'].cat.set_categories(sim.net.pops.keys()) in analysis/spikes.py

…e-medical-center/development

fixed pointer id overflow on MPI (e.g. for gap junctions)

…overriden in individual conn rule

…List`-type connParams (but so far, only if `synsPerConn == 1` - need to elaborate more general approach)

Adding loading bar for cell and connectivity creation using tqdm package

Fixing double printing of Creating network sentence

hotfix, PR?

…evelopment

define `cellInds` before reference in `syncLines` logic

…31/feat/update-setup-py

ci: update setup-python action

…31/feat/dev-imp

fix(py312): remove `imp`

…ate-medical-center/python2dropped

dropped python 2 support

…velopment

Pandas deprecated parameter fix + Loading Bar

…Institute/development

add default padding (==1) for plotCSD, to avoid top/bottom edge artifacts in color plots

… lost

…ny-downstate-medical-center#817)

* fixed bug in conn, updated test/examples/* to use dynamic pathing

* update CHANGES.md

…(beta version) (suny-downstate-medical-center#819)

* fixed bug in conn, updated test/examples/* to use dynamic pathing

* update CHANGES.md

* updated documentation with new batchtools (beta)

… loading bar. (suny-downstate-medical-center#821)

* Updated logic, bug fix

cfg.progressBar = 2 will display all progress bars
cfg.progressBar = 1 will call tqdm with progress bars w/ leave = 0
cfg.progressBar = 0 will disable the progress bar.

…ater PR

…cumentation

Removing the minimumdescent=False from the call to TextArea

…medical-center#829)

* batch tools subpackage merge into dev,

see PR suny-downstate-medical-center#818 suny-downstate-medical-center#822 suny-downstate-medical-center#826 suny-downstate-medical-center#827 

see documentation

…move-saveFileStep

Remove saveFileStep

…reilly/patch-1

Bug fix in scalebar - removing the use of the minimumdescent argument in the call to TextArea

…development

Exlude tests from discovery / installation

…at has emerged with spack installation (EBRAINS platform). Will re-visit later..

This reverts commit e5aa9e8.

…mplates (suny-downstate-medical-center#831)

see netpyne.batchtools esp. submits.py and search.py

slurm job submission:
search() now supports job_type='slurm' with associated 'ifs' and 'socket' communication modes

the run_config for these submission scripts should specify the following arguments:
'allocation' (allocation for the job)
'walltime' (time limit before job termination)
'nodes' (# nodes for job)
'coresPerNode' (number of cores per job--i.e. the mpiexec -n value)
'email' (user email)
'custom' (any custom commands to execute prior to sourcing ~/.bashrc)
'command' (execution of script, command to be run from the project directory to run the script)

update to see submission:
run_config for the submission now includes the following argument 
'realtime' (time limit before job termination)