Feat/swc loaderfile Adding SWC loader to load SWC file

NeuroML / pyNeuroML

A single package in Python unifying scripts and modules for reading, writing, simulating and analysing NeuroML2/LEMS models.

https://docs.neuroml.org/Userdocs/Software/pyNeuroML.html

GNU Lesser General Public License v3.0

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Feat/swc loaderfile Adding SWC loader to load SWC file #384

Open AdityaBITMESRA opened 4 weeks ago

AdityaBITMESRA commented 4 weeks ago

This pull request adds a new module for loading and parsing SWC files

sanjayankur31 commented 3 weeks ago

Converted to a draft @AdityaBITMESRA. We'll mark it as "ready for review" once the various bits have come in.

sanjayankur31 commented 3 weeks ago

add docstrings
docstrings should contain references to information on SWC standard and so on
later: consider using something like networkx so that we take advantage of efficient under the hood representations: https://networkx.org/documentation/stable/#

sanjayankur31 commented 3 weeks ago

add unit tests cases for each method

sanjayankur31 commented 3 weeks ago

https://github.com/pgleeson/Cvapp-NeuroMorpho.org/blob/master/caseExamples/SomaFormat-NMOv5.3.pdf

github-actions[bot] commented 3 weeks ago

Package	Line Rate	Health
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analysis	37%	❌
archive	72%	➖
channelml	55%	➖
lems	46%	❌
neuron	31%	❌
neuron.analysis	0%	❌
plot	47%	❌
povray	0%	❌
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sanjayankur31 commented 2 weeks ago

Looking good! Notes from the meeting:

let's leave the optimisation (networkx etc. bits) for the moment
rather, let's focus on implementing the functions we'll need so that we have a "public API": get_parent, get_children, get_branch_points, and so on---a bunch of "getters"
lets test these out and confirm that they work correctly
later, we can optimise these under the hood

AdityaBITMESRA commented 2 weeks ago

Thankyou for the instructions

AdityaBITMESRA commented 2 weeks ago

Hi @sanjayankur31 , can you have a look to see if I am going correctly?

sanjayankur31 commented 1 week ago

Sure, will try to do it today, otherwise it may have to wait for Friday---we have a full day conf/symposium tomorrow so wont' be able to get a lot of time at my desk

AdityaBITMESRA commented 1 week ago

Thankyou for the comments.I will look into it

AdityaBITMESRA commented 1 week ago

Hi @sanjayankur31. I have addressed all the comments. Please take a look when time permits

sanjayankur31 commented 6 days ago

Cool, I'll try to do that today. Could you check and fix the issue ruff is pointing out? (If you set up pre-commit, ruff should run on your system and fix things each time you commit---see the contributing.md file)

AdityaBITMESRA commented 6 days ago

I have already setup pre-commit hooks but I think the ruff is pointing out to an error in PlotMorphologyVispy.py file(unused imports) which is not the file I was working on. So what should I do?

sanjayankur31 commented 6 days ago

Hrm, that must've been fixed in develop. Let me update your branch here on GitHub and that should fix it.

sanjayankur31 commented 6 days ago

OK, that fixes it. Do remember to pull on your local machine so you get the updates to your branch too.

AdityaBITMESRA commented 6 days ago

sure...thankyou