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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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    shruti1421 opened #155
  • Oct 02 2020 15:11
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  • 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
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
Very excited to see some new users of scona :sparkles: