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WIP: NeuroML import and export fixes and enhancements #810
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WIP: NeuroML import and export fixes and enhancements #810
Commits on Jul 26, 2023
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Exlude tests from discovery / installation
Without it tests/ will be installed as a top level Python module.
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Commits on Sep 20, 2023
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Merge pull request suny-downstate-medical-center#777 from suny-downst…
…ate-medical-center/development PR from development to master - VERSION 1.0.5
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Commits on Nov 29, 2023
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Commits on Nov 30, 2023
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chore(requirements): use overrides for python < 3.12
Included in python 3.12+ https://docs.python.org/3.12/library/typing.html#typing.override
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chore(neuroml): convert comments to docstrings
More readable, and IDE friendly
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chore(neuroml): remove (probably) outdated comment
I seem to be able to run NetPyNE sims fine with MPI, so this comment does not seem to apply any more.
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fix(neuroml): correct override
See, override decoration helps :)
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Commits on Dec 4, 2023
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Commits on Dec 5, 2023
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chore(neuroml): use warning instead of debug
It's a warning that the user should be aware of.
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feat(neuroml): remove commented out code
erev is not required in Nernst or GHK2
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Commits on Dec 13, 2023
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Commits on Dec 21, 2023
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Commits on Dec 22, 2023
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feat(neuroml): round channel density values to 10 digits
Since NEURON's hoc only uses 10 decimal digits, to match it, we must limit our Python value to 10 decimal digits
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Commits on Jan 26, 2024
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Commits on Feb 12, 2024
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Merge pull request suny-downstate-medical-center#806 from suny-downst…
…ate-medical-center/development PR from development to master - VERSION 1.0.6
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Commits on Feb 14, 2024
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Commits on Feb 16, 2024
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Merge branch 'feat/neuroml-ankur' of github.com:sanjayankur31/netpyne…
… into feat/neuroml-ankur
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Commits on Feb 20, 2024
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chore(neuroml): make less verbose
If we want it to be verbose, we toggle the verbosity in the module like this: ``` logger = logging.getLogger("name of module").setLevel(..) ```
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fix(neuroml): correct conditional logic
We approximate if it *isnt* close to the value
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ci: update setup-python action
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.."
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Commits on Feb 21, 2024
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Revert "fix(neuroml): correct conditional logic"
This reverts commit 15e66bb.
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Commits on Feb 22, 2024
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feat(neuroml): use
%r
instead of%s
To ensure we get the complete value, and not the string converted one.
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Commits on Feb 23, 2024
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feat(neuroml-export): use float when exporting
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.
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Revert "feat(neuroml-export): use float when exporting"
This reverts commit 169d5fe.
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Commits on Mar 1, 2024
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add default padding (==1) for plotCSD, to avoid top/bottom edge artif…
…acts in color plots
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Commits on Mar 5, 2024
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Commits on Mar 17, 2024
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The `imp` module has been removed in Python 3.12: https://docs.python.org/3/whatsnew/3.12.html#imp
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Commits on Mar 27, 2024
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Pandas deprecated parameter fix
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
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Commits on Mar 28, 2024
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Commits on Apr 1, 2024
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Merge pull request suny-downstate-medical-center#1 from suny-downstat…
…e-medical-center/development fixed pointer id overflow on MPI (e.g. for gap junctions)
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Commits on Apr 5, 2024
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cfg.connRandomSecFromList and cfg.distributeSynsUniformly can now be …
…overriden in individual conn rule
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ability to use
sec
,loc
,preSec
andpreLoc
from list in `conn……List`-type connParams (but so far, only if `synsPerConn == 1` - need to elaborate more general approach)
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Commits on Apr 15, 2024
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Adding loading bar for net creation
Adding loading bar for cell and connectivity creation using tqdm package
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Commits on Apr 18, 2024
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Fixing double printing of Creating network sentence
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Commits on Apr 19, 2024
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Merge pull request suny-downstate-medical-center#814 from jchen6727/d…
…evelopment define `cellInds` before reference in `syncLines` logic
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Commits on Apr 25, 2024
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Merge pull request suny-downstate-medical-center#809 from sanjayankur…
…31/feat/update-setup-py ci: update setup-python action
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Merge pull request suny-downstate-medical-center#812 from sanjayankur…
…31/feat/dev-imp fix(py312): remove `imp`
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Merge pull request suny-downstate-medical-center#815 from suny-downst…
…ate-medical-center/python2dropped dropped python 2 support
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Commits on May 1, 2024
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Merge pull request suny-downstate-medical-center#813 from RomanB22/de…
…velopment Pandas deprecated parameter fix + Loading Bar
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Merge pull request suny-downstate-medical-center#811 from NathanKline…
…Institute/development add default padding (==1) for plotCSD, to avoid top/bottom edge artifacts in color plots
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Commits on May 3, 2024
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Commits on May 11, 2024
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fixed bug in conn, updated test/examples/* to use dynamic pathing (su…
…ny-downstate-medical-center#817) * fixed bug in conn, updated test/examples/* to use dynamic pathing * update CHANGES.md
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Commits on May 14, 2024
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updating documentation (user_documentation.rst) re: new
batchtools
……(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)
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Commits on May 16, 2024
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quick fix, adding cfg.progressBar logic, fixed another issue with the…
… 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.
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Commits on Aug 6, 2024
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Removing the minimumdescent=False from the call to TextArea
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Commits on Aug 30, 2024
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merge of batchtools into the development repository. (suny-downstate-…
…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
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Merge pull request suny-downstate-medical-center#825 from yubelyrn/re…
…move-saveFileStep Remove saveFileStep
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Merge pull request suny-downstate-medical-center#828 from christian-o…
…reilly/patch-1 Bug fix in scalebar - removing the use of the minimumdescent argument in the call to TextArea
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Merge pull request suny-downstate-medical-center#767 from penguinpee/…
…development Exlude tests from discovery / installation
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Commits on Aug 31, 2024
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Revert "Exlude tests from discovery / installation" - due to issue th…
…at has emerged with spack installation (EBRAINS platform). Will re-visit later.. This reverts commit e5aa9e8.
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Commits on Sep 10, 2024
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file cleanup, slurm scripts and timeout added to batchtools submit te…
…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)
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feat(neuroml): stop casting dict keys to list
This is only required if one modifies the keys of the dict while iterating over it, which we do not.
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feat(neuroml): simplify looking for segment parent's section
The same segment objects are used everywhere, so the segment object in `parent_seg` will also be the one used in the lists in `ordered_segs`. So, there's no need to iterate and compare ids, simply look if the object is in the list.
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Commits on Oct 15, 2024
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