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  • Jan 24 2021 17:35

    Islast on master

    Update CONTRIBUTING.md Update CODE_OF_CONDUCT.md Merge pull request #155 from sh… (compare)

  • Jan 24 2021 17:35
    Islast closed #155
  • Jan 24 2021 17:34
    Islast commented #155
  • Jan 24 2021 17:34
    Islast commented #156
  • Jan 24 2021 17:33
    Islast closed #156
  • Dec 20 2020 05:11
    kadambinipanda commented #156
  • Dec 16 2020 11:39
    kadambinipanda edited #156
  • Dec 16 2020 11:39
    kadambinipanda opened #156
  • Oct 06 2020 20:44
    shruti1421 commented #155
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  • Oct 06 2020 20:37
    shruti1421 opened #155
  • Oct 02 2020 15:11
    shruti1421 commented #4
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    shruti1421 commented #4
  • Aug 09 2020 13:00

    KirstieJane on gh-pages

    [ci skip] Autodoc commit for . (compare)

  • Aug 09 2020 12:57

    Islast on master

    replace deprecated networkx att… Revert "replace deprecated netw… replace deprecated networkx .no… and 8 more (compare)

  • Aug 09 2020 12:57
    Islast closed #154
  • Aug 09 2020 12:51
    Islast synchronize #154
  • Aug 09 2020 12:48
    Islast opened #154
  • Jan 27 2020 16:09
    Islast synchronize #153
  • Jan 15 2020 20:35
    Islast synchronize #153
Kirstie Whitaker
@KirstieJane
Amaaaazing!
Let me get that merged now
Ruslan Yermakov
@wingedRuslan
:blush:
Kirstie Whitaker
@KirstieJane
Done!! Should appear online soon
Ruslan Yermakov
@wingedRuslan
Fantastic! Thank you :relieved:
Ruslan Yermakov
@wingedRuslan
ps. it is already there
Kirstie Whitaker
@KirstieJane
Ready to submit! Great job!
Ruslan Yermakov
@wingedRuslan
:innocent:
Ruslan Yermakov
@wingedRuslan

@KirstieJane, by permanent link, you mean the link I have to submit while filling in the final evaluation?

You can navigate to the .md file that is your report in the GitHub repository and if you press y the url in the browser will change to the specific commit. That’s the most specific and permanent link.

image.png
Ruslan Yermakov
@wingedRuslan
I want to make sure that the link I am going to submit is okay
@KirstieJane , which one should I use?
Ruslan Yermakov
@wingedRuslan
I actually thought about the 1st one
and according to the google guide (link above), I am not 100% sure that the link to .md file is acceptable (maybe I am wrong here). In this case, I think I need to create a link to the public GitHub gist
Ruslan Yermakov
@wingedRuslan
@KirstieJane, what do you think?
Kirstie Whitaker
@KirstieJane
I think they’re both fine and Google will accept them both. Personally I’d put in the 1st and then if there’s anywhere to write a free text comment add that that blog is built from 2 (add the url)
Ruslan Yermakov
@wingedRuslan
okay, gotcha :smile:
and no, there is no other field or place where to include the 2nd link
so, I will just submit the 1st link (the one to my blog post on the whitakerlab website)
@KirstieJane, thanks!
Have a nice weekend :relaxed:
Kirstie Whitaker
@KirstieJane
Great stuff! You too!
Ruslan Yermakov
@wingedRuslan
@KirstieJane, did I miss the meeting??
Kirstie Whitaker
@KirstieJane
Oh no!!
That's me not being able to type in 24 hour clock
It's supposed to be 17:00
Ruslan Yermakov
@wingedRuslan
ohhh, good :)
Kirstie Whitaker
@KirstieJane
:relieved:
Ruslan Yermakov
@wingedRuslan
Hi team!
I am really really determined to merge these 2 PRs #140 and #151 into master in the next 2 weeks
Ruslan Yermakov
@wingedRuslan
last 3 weeks I was kinda offline as I was visiting my grandparents and spent some time with family before starting my master degree
@KirstieJane is there anything I can help with the review of #140 ?
Kirstie Whitaker
@KirstieJane
Hi @wingedRuslan! This week is kind of a write off for me - I have a big deadline on 24 September. But I should be able to find some time after that! Can you ping me on Wed 25??
Ruslan Yermakov
@wingedRuslan
@KirstieJane, yep, I will! Good luck with the deadline ;)
Isla
@Islast
@KirstieJane do you think command line tools should run on relative or absolute paths?
eg if i'm passing a correlation matrix file cormat.txt to network_analysis_from_corrmat, would I rather be passing the relative or the absolute path to cormat.txt
Isla
@Islast
i have them set as relative paths right now
Kirstie Whitaker
@KirstieJane
@islaist - I think relative paths are the most intuitive to use
Should make the commands more interoperable across machines, right?
Whoops - @islast! Sorry for the typo 🌺
Isla
@Islast
okay, perfect we'll keep it relative
0I24N63
@congzhaoyang
Hello everyone, I put my data into datasets, and pip re installed scona, but it reported this error. What should I do

`

AttributeError Traceback (most recent call last)
in
----> 1 G = scn.BrainNetwork(network=M, parcellation=names, centroids=centroids)

D:\conda\lib\site-packages\scona\classes.py in init(self, network, parcellation, centroids)
64 if parcellation is not None:
65 # assign parcellation names to nodes
---> 66 self.set_parcellation(parcellation)
67 if centroids is not None:
68 # assign centroids to nodes

D:\conda\lib\site-packages\scona\classes.py in set_parcellation(self, parcellation)
153 :func:BrainNetwork.set_centroids
154 '''
--> 155 assign_node_names(self, parcellation)
156
157 def set_centroids(self, centroids):

D:\conda\lib\site-packages\scona\make_graphs.py in assign_node_names(G, parcellation)
54 # Assign anatomical names to the nodes
55 for i, node in enumerate(G.nodes()):
---> 56 G.node[i]['name'] = parcellation[i]
57 #
58 G.graph['parcellation'] = True

AttributeError: 'BrainNetwork' object has no attribute 'node'
`

hello
flammert
@flammert
I have the same issue. Probably because of some recent updates. More specifically, G.node got depricated, and is now G.nodes. see https://networkx.github.io/documentation/stable/release/release_2.4.html. Could this be changed in scona?
Isla
@Islast
Hi! I believe @flammert has it right, replacing references to .node with .nodes has been on the to do list for a while. I should be able to fix this over the weekend and also get back to you on some of your questions about how to arrange your data