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PR: list recordables #121

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Merged
merged 19 commits into from
Aug 19, 2021
Merged

PR: list recordables #121

merged 19 commits into from
Aug 19, 2021

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@sanjayankur31
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@sanjayankur31 sanjayankur31 commented Aug 4, 2021

This should pass correctly 🤞

@sanjayankur31
feat(pynml): add function to extract LEMS NeuroML2 definitions
2eb3106 
Also includes a simple unit test.
@sanjayankur31
ci: enable unit testing with pytest
b0c2bf9
@sanjayankur31
ci(flake8): move flake to run at end of CI cycle
30e9a0b
@sanjayankur31
chore(logging): set default level to INFO
ded6f11
@sanjayankur31
refactor(pynml): simplify function to only return str path of dir
8026caf 
Just simplifies it so that users don't have to worry about it being a
str or a TemporaryDirectory object.

Also updates the accompanying unit test.
@sanjayankur31
refactor(pynml): improve LEMS definition file extraction function
fbe811b
@sanjayankur31
feat(pynml): add functions to list exposures and list recording paths
7e85e40 
Should help with NeuroML/Documentation#15

TODO: the LEMS functions that this wraps around seem to be incomplete. I
don't think the exposures listed there include ones inherited from their
superclasses/ancestors.
@sanjayankur31
ci: add requirements file for development
0481af1 
This will follow the development branches of the other Python libraries.
@sanjayankur31
improvement(pynml): set the default logging level to INFO
0c40ff8
@sanjayankur31
improvement(tests): correct removal of temp dir
a072bc9
@sanjayankur31
improvement(tests): set default logging level for test
82931e8
@sanjayankur31
improvement(tests): add more assertions to test
cc468ac
@sanjayankur31
chore(tests): consolidate in one folder
c63c146
@sanjayankur31
chore: remove duplicate requirements file
4a300f5
@sanjayankur31 sanjayankur31 self-assigned this Aug 4, 2021
@sanjayankur31 sanjayankur31 added S: ready for review Status: ready for review T: enhancement Type: enhancement labels Aug 4, 2021
@sanjayankur31 sanjayankur31 requested a review from pgleeson August 4, 2021 08:44
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sanjayankur31 commented Aug 4, 2021

@pgleeson : ready now---looks like some conflicts had popped up in the other PR

@sanjayankur31 sanjayankur31 mentioned this pull request Aug 4, 2021
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pgleeson
pgleeson reviewed Aug 4, 2021
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@sanjayankur31
feat: update function name
e929f12 
Since we're only listing exposures here, we update the function name to
reflect this.
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sanjayankur31 commented Aug 10, 2021

Updated the function to clearly say that we only list paths for exposures at the moment.

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sanjayankur31 commented Aug 16, 2021

Requires LEMS/pylems#60 to be merged, since the function signature changed.

We now get this sort of output:

pytest -k test_recording_path_listing -s
============================================================== test session starts ===============================================================
platform linux -- Python 3.9.6, pytest-6.2.4, py-1.10.0, pluggy-0.13.1
rootdir: /home/asinha/Documents/02_Code/00_mine/2020-OSB/NeuroML-software/pyNeuroML
collected 5 items / 3 deselected / 2 selected

tests/test_pynml.py pyNeuroML >>> pyneuroml.pynml - INFO - NeuroML LEMS definition files extracted to: /tmp/tmpyx5boi_w/NeuroML2CoreTypes/
IzhNet/IzhPop0[0]/iMemb
IzhNet/IzhPop0[0]/iSyn
IzhNet/IzhPop0[0]/u
IzhNet/IzhPop0[0]/v
IzhNet/explicitInput/pulseGen_0/i
.pyNeuroML >>> pyneuroml.pynml - INFO - NeuroML LEMS definition files extracted to: /tmp/tmpi1nbq6hx/NeuroML2CoreTypes/
single_hh_cell_network/pop0[0]/caConc
single_hh_cell_network/pop0[0]/caConcExt
single_hh_cell_network/pop0[0]/iCa
single_hh_cell_network/pop0[0]/iChannels
single_hh_cell_network/pop0[0]/iSyn
single_hh_cell_network/pop0[0]/spiking
single_hh_cell_network/pop0[0]/surfaceArea
single_hh_cell_network/pop0[0]/totSpecCap
single_hh_cell_network/pop0[0]/v
single_hh_cell_network/pop0[1]/caConc
single_hh_cell_network/pop0[1]/caConcExt
single_hh_cell_network/pop0[1]/iCa
single_hh_cell_network/pop0[1]/iChannels
single_hh_cell_network/pop0[1]/iSyn
single_hh_cell_network/pop0[1]/spiking
single_hh_cell_network/pop0[1]/surfaceArea
single_hh_cell_network/pop0[1]/totSpecCap
single_hh_cell_network/pop0[1]/v
single_hh_cell_network/pop1/0/caConc
single_hh_cell_network/pop1/0/caConcExt
single_hh_cell_network/pop1/0/iCa
single_hh_cell_network/pop1/0/iChannels
single_hh_cell_network/pop1/0/iSyn
single_hh_cell_network/pop1/0/spiking
single_hh_cell_network/pop1/0/surfaceArea
single_hh_cell_network/pop1/0/totSpecCap
single_hh_cell_network/pop1/0/v
single_hh_cell_network/pop1/1/caConc
single_hh_cell_network/pop1/1/caConcExt
single_hh_cell_network/pop1/1/iCa
single_hh_cell_network/pop1/1/iChannels
single_hh_cell_network/pop1/1/iSyn
single_hh_cell_network/pop1/1/spiking
single_hh_cell_network/pop1/1/surfaceArea
single_hh_cell_network/pop1/1/totSpecCap
single_hh_cell_network/pop1/1/v

@sanjayankur31
chore(deps): bump pylems minimum version to 0.5.7
343f70e 
Since 0.5.7 includes the necessary API additions for the functions used
here.
@pgleeson pgleeson merged commit 6ae61ed into development Aug 19, 2021
@sanjayankur31 sanjayankur31 deleted the feat/pr-list-recordables branch July 26, 2022 09:36
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