install problem

[tallishpaul]

Hi,

Sorry but I am new to github, python etc, hope I don't annoy anyone too much. I am trying to install cite2c using jupyer notebook on sagemathcloud. In my ignorance:

1. I copied all the cite2c files, folders into a seperate empty folder
2. .gitignore wouldn't copy over for some reason, so I carried on anyway
3. whilst in this new folder I typed python install.py into a box which said 'terminal command' and hit the 'play' button
4. the 'terminal command' box output the following:

Traceback (most recent call last):
File "install.py", line 3, in
from IPython.html.nbextensions import install_nbextension
ImportError: No module named html.nbextensions

I am running Windows 7 in case that has anything to do with it (can't see how as it is in the cloud). From this description it'll be clear I don't know much.

I attach a screenshot in case it helps.

Is the problem that I am using sagemathcloud instead of installing Jupyter locally?

Any chance of some help or advice?
Kind regards, Paul

[takluyver]

You're doing the right thing, I don't know why it wouldn't work. Maybe SMC is on an old version of IPython, although I thought they tended to update quickly. Can you see what the output from this is:

python -c 'import IPython; print(IPython.__version__)'

[tallishpaul]

2.3.0 is the o/p, which confuses me. Once you are viewing a .ipynb it
allows you to select the python 3 kernel (so if I open the sample.ipynb it
already says Python 3 in the top right hand of the screen-probably because
I did that whilst in a different .ipynb earlier in the day)

?

On 9 October 2015 at 16:57, Thomas Kluyver [email protected] wrote:

You're doing the right thing, I don't know why it wouldn't work. Maybe SMC
is on an old version of IPython, although I thought they tended to update
quickly. Can you see what the output from this is:

python -c 'import IPython; print(IPython.version)'

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[takluyver]

It's possible that the copy of IPython that gets imported from the command line is different from the copy the server is using. The kernel-switching features require at least version 3 (this is the IPython version, separate from the Python version numbers).

I suggest you ask in a SMC forum - why is Python at the command line finding an old copy of IPython, and is it possible to install notebook extensions for your own user.

[tallishpaul]

OK, now I know what to ask, I will do that, thanks very much.

On 9 October 2015 at 19:03, Thomas Kluyver [email protected] wrote:

It's possible that the copy of IPython that gets imported from the
command line is different from the copy the server is using. The
kernel-switching features require at least version 3 (this is the IPython
version, separate from the Python version numbers).

I suggest you ask in a SMC forum - why is Python at the command line
finding an old copy of IPython, and is it possible to install notebook
extensions for your own user.

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[tallishpaul]

I contacted SMC about this, posed the questions. They tried to install
cite2c system wide and failed.

I also intalled Jupyter locally OK, but not cite2c, I get errors. This
seems a bit of a rabbit hole for someone like myself with almost no
experience. Command window output says something about My Documents not
existing. There might be something odd going on with file locations because
it is a uni PC and support have in the past mentioned how these personal
folders are not actually on the machine, they are on a uni server somewhere
for backup/recovery reasons. If I get to use a standard PC at home I will
try again. Until now I will have to do without.

Thanks for your help with this.

Kind regards
Paul

On 9 October 2015 at 19:34, Paul Gordon [email protected] wrote:

OK, now I know what to ask, I will do that, thanks very much.

On 9 October 2015 at 19:03, Thomas Kluyver [email protected]
wrote:

It's possible that the copy of IPython that gets imported from the
command line is different from the copy the server is using. The
kernel-switching features require at least version 3 (this is the IPython
version, separate from the Python version numbers).

I suggest you ask in a SMC forum - why is Python at the command line
finding an old copy of IPython, and is it possible to install notebook
extensions for your own user.

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#23 (comment).

[takluyver]

Hmm, sorry about that. If it's convenient to try again locally, can you paste the errors that you get?

The install script does two separate steps in one - it copies the files into place (installing) and sets a config option to load cite2c when you open a notebook (enabling). The enabling step probably can't be done systemwide, as it changes the user's config. With Jupyter, you should be able to do the enabling step separately like this:

jupyter nbextension enable cite2c/main

[tallishpaul]

Hi Thomas,

I've got Jupyter installed locally on a non-Uni PC. Now cite2c has
installed, and I have given it my Zotero UserID. That's the good news.

But...when I click the citation button I get the pop up 'start typing to
search Zotero', but it doesn't find anything at all. Eek.

I can't think what I am doing wrong. I have setup synching on my Firefox
Zotero plugin - I can see my two dummy references there and also in my
Zotero.org server library.

I haven't made any changes to Zotero preferences, nor installed additional
plugins. Should I have?

I don't have any private keys, is this anything to do with it?

Hoping you can help.

BTW, William Stein has got cite2c installed on SageMathCloud for everyone,
sounds promising, but it is also not finding my stuff.

Kind regards,
Paul

On 12 October 2015 at 08:51, Thomas Kluyver [email protected]
wrote:

Hmm, sorry about that. If it's convenient to try again locally, can you
paste the errors that you get?

The install script does two separate steps in one - it copies the files
into place (installing) and sets a config option to load cite2c when you
open a notebook (enabling). The enabling step probably can't be done
systemwide, as it changes the user's config. With Jupyter, you should be
able to do the enabling step separately like this:

jupyter nbextension enable cite2c/main

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[takluyver]

Hi Paul,

Have you enabled the option on Zotero to make your library public? It's on the privacy page in settings.

Eventually it should be possible to use Oauth to get access to your library without making it public - see issue #9. But that sounds tricky, so for now you need to publish your Zotero library for cite2c to search it.

Best wishes,
Thomas

[tallishpaul]

Hi Thomas,

OK, that was the problem. It'd be good for it not to be public though, that
might not really matter to me. It's still not quite working on SMC, I got
back to William, copied here at the bottom.

I have just realised that I can't get a pdf output from Jupyter (or SMC),
which seems to be a general current issue, something you've been helping
with. It seems a really important issue, it makes it tricky to communicate
with my colleagues who don't use Jupyter.

Thanks for all your help with this.

Kind regards
Paul

copy of what happens in SMC presently
It's good that the install seems to have worked, but when I use the
citation button to choose a reference, it inserts this:

when I do what appears to be exactly the same thing on a local Jupyter
install I get

(I've changed the numbers in case that identifies me on Zotero-such is my
ignorance!)

On 14 October 2015 at 14:37, Thomas Kluyver [email protected]
wrote:

Hi Paul,

Have you enabled the option on Zotero to make your library public? It's on
the privacy page in settings https://www.zotero.org/settings/privacy.

Eventually it should be possible to use Oauth to get access to your
library without making it public - see issue #9
#9. But that sounds tricky,
so for now you need to publish your Zotero library for cite2c to search it.

Best wishes,
Thomas

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