From klonuo at gmail.com  Mon Aug  1 12:40:45 2016
From: klonuo at gmail.com (klo uo)
Date: Mon, 1 Aug 2016 18:40:45 +0200
Subject: [IPython-dev] [ANN] tutormagic v0.2.0
In-Reply-To: <CAB-sx631fCe9NzuyfFArhgNfa6KY+a=x4rtSAH0B4oF=dDV_1A@mail.gmail.com>
References: <CAB-sx631fCe9NzuyfFArhgNfa6KY+a=x4rtSAH0B4oF=dDV_1A@mail.gmail.com>
Message-ID: <CAA-8Ld9YEff_Y=zjq=MY8eb0dWZRsHAH4E-oDBimc7+AxrYKvQ@mail.gmail.com>

Nice too see this in extensions list. I made something similar for console
and qtconsole here: https://github.com/klonuo/opt-ipy

I was planning to do notebook extension, but then I saw that someone
already did that - you ;)

BTW OT, I recently released that `%install_ext` was removed from IPython,
and wonder why could this be


Cheers
?
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From bussonniermatthias at gmail.com  Mon Aug  1 14:11:41 2016
From: bussonniermatthias at gmail.com (Matthias Bussonnier)
Date: Mon, 1 Aug 2016 11:11:41 -0700
Subject: [IPython-dev] [ANN] tutormagic v0.2.0
In-Reply-To: <CAA-8Ld9YEff_Y=zjq=MY8eb0dWZRsHAH4E-oDBimc7+AxrYKvQ@mail.gmail.com>
References: <CAB-sx631fCe9NzuyfFArhgNfa6KY+a=x4rtSAH0B4oF=dDV_1A@mail.gmail.com>
 <CAA-8Ld9YEff_Y=zjq=MY8eb0dWZRsHAH4E-oDBimc7+AxrYKvQ@mail.gmail.com>
Message-ID: <CANJQusXx6X6PrwFes_hoYAtODoth3kG9eH_bJAbU6Zt7PUDVdA@mail.gmail.com>

> BTW OT, I recently released that `%install_ext` was removed from IPython,
> and wonder why could this be


All the use case of install_ext are covered by pip.
Install_ext has also a lot of issues:
 - less secure than pip [can of euphemism to say gigantic potential
security nightmare]
 - no way to "uninstall_ext"
 - no way to "upgrade ext"
 - no way to express versions
 - no way to list extensions.
 - no way to express dependencies.

I think you see the pattern... improving install_ext was reinventing
managing packages.
And as an IPython extension is "just" a python module that define some
magics methods, we now recommend
that extension should just be packages on PyPI.

If you find that publishing a package is too hard, I would suggest
having a look at flit[1]

-- 
M
1: https://pypi.python.org/pypi/flit


From klonuo at gmail.com  Mon Aug  1 19:17:39 2016
From: klonuo at gmail.com (klo uo)
Date: Tue, 2 Aug 2016 01:17:39 +0200
Subject: [IPython-dev] [ANN] tutormagic v0.2.0
In-Reply-To: <CANJQusXx6X6PrwFes_hoYAtODoth3kG9eH_bJAbU6Zt7PUDVdA@mail.gmail.com>
References: <CAB-sx631fCe9NzuyfFArhgNfa6KY+a=x4rtSAH0B4oF=dDV_1A@mail.gmail.com>
 <CAA-8Ld9YEff_Y=zjq=MY8eb0dWZRsHAH4E-oDBimc7+AxrYKvQ@mail.gmail.com>
 <CANJQusXx6X6PrwFes_hoYAtODoth3kG9eH_bJAbU6Zt7PUDVdA@mail.gmail.com>
Message-ID: <CAA-8Ld9LAsd5Hs=PsdT16ixq9C29H40Np_TgsJW13dOu84HXag@mail.gmail.com>

Thanks Matthias for your guidance. What you wrote makes perfect sense to me.


Cheers

On Mon, Aug 1, 2016 at 8:11 PM, Matthias Bussonnier <
bussonniermatthias at gmail.com> wrote:

> > BTW OT, I recently released that `%install_ext` was removed from IPython,
> > and wonder why could this be
>
>
> All the use case of install_ext are covered by pip.
> Install_ext has also a lot of issues:
>  - less secure than pip [can of euphemism to say gigantic potential
> security nightmare]
>  - no way to "uninstall_ext"
>  - no way to "upgrade ext"
>  - no way to express versions
>  - no way to list extensions.
>  - no way to express dependencies.
>
> I think you see the pattern... improving install_ext was reinventing
> managing packages.
> And as an IPython extension is "just" a python module that define some
> magics methods, we now recommend
> that extension should just be packages on PyPI.
>
> If you find that publishing a package is too hard, I would suggest
> having a look at flit[1]
>
> --
> M
> 1: https://pypi.python.org/pypi/flit
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev
>
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From alanwilter at gmail.com  Tue Aug  2 11:00:46 2016
From: alanwilter at gmail.com (Alan)
Date: Tue, 2 Aug 2016 16:00:46 +0100
Subject: [IPython-dev] IPython 5.0 and ConfigManager issue
Message-ID: <CAEznbzm6zN=SWtrWHshg+Od+fcfqESY=w+1BCBEP8ur3tWj-NQ@mail.gmail.com>

Hi there,

This is not working for me:

from IPython.html.services.config import ConfigManagerfrom
IPython.utils.path import locate_profilecm =
ConfigManager(profile_dir=locate_profile(get_ipython().profile))cm.update('livereveal',
{
              'theme': 'serif',
              'transition': 'zoom',
              'start_slideshow_at': 'selected',})

TraitError: The 'parent' trait of a ConfigManager instance must be a
Configurable, but a value of class 'NoneType' (i.e. None) was
specified.

It looks like IPY 5 changed the way it handles the configuration?

I have these warning in my prompt:

/sw/lib/python3.5/site-packages/IPython/utils/traitlets.py:5: UserWarning:
IPython.utils.traitlets has moved to a top-level traitlets package.

  warn("IPython.utils.traitlets has moved to a top-level traitlets
package.")

/sw/lib/python3.5/site-packages/IPython/utils/path.py:283: UserWarning:
locate_profile has moved to the IPython.paths module

  warn("locate_profile has moved to the IPython.paths module")

But I don't know how to fix it. I am using ipython/jupyter + RISE and I
want to customise my presentations.

Thanks,

Alan

-- 
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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From takowl at gmail.com  Tue Aug  2 11:18:33 2016
From: takowl at gmail.com (Thomas Kluyver)
Date: Tue, 2 Aug 2016 16:18:33 +0100
Subject: [IPython-dev] IPython 5.0 and ConfigManager issue
In-Reply-To: <CAEznbzm6zN=SWtrWHshg+Od+fcfqESY=w+1BCBEP8ur3tWj-NQ@mail.gmail.com>
References: <CAEznbzm6zN=SWtrWHshg+Od+fcfqESY=w+1BCBEP8ur3tWj-NQ@mail.gmail.com>
Message-ID: <CAOvn4qgvw5-w+ABbgmYQRFuTcg0hvy7mOZShrUbRH=q6Fce_qg@mail.gmail.com>

Hi Alan,

The import for ConfigManager is now:

from notebook.services.config import ConfigManager

And you don't need any of the profile stuff - Jupyter, which includes all
of the notebook frontend machinery, doesn't have profiles.

Thomas

On 2 August 2016 at 16:00, Alan <alanwilter at gmail.com> wrote:

> Hi there,
>
> This is not working for me:
>
> from IPython.html.services.config import ConfigManagerfrom IPython.utils.path import locate_profilecm = ConfigManager(profile_dir=locate_profile(get_ipython().profile))cm.update('livereveal', {
>               'theme': 'serif',
>               'transition': 'zoom',
>               'start_slideshow_at': 'selected',})
>
> TraitError: The 'parent' trait of a ConfigManager instance must be a Configurable, but a value of class 'NoneType' (i.e. None) was specified.
>
> It looks like IPY 5 changed the way it handles the configuration?
>
> I have these warning in my prompt:
>
> /sw/lib/python3.5/site-packages/IPython/utils/traitlets.py:5: UserWarning:
> IPython.utils.traitlets has moved to a top-level traitlets package.
>
>   warn("IPython.utils.traitlets has moved to a top-level traitlets
> package.")
>
> /sw/lib/python3.5/site-packages/IPython/utils/path.py:283: UserWarning:
> locate_profile has moved to the IPython.paths module
>
>   warn("locate_profile has moved to the IPython.paths module")
>
> But I don't know how to fix it. I am using ipython/jupyter + RISE and I
> want to customise my presentations.
>
> Thanks,
>
> Alan
>
> --
> Alan Wilter SOUSA da SILVA, DSc
> Senior Bioinformatician, UniProt
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> Tel: +44 (0)1223 494588
>
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev
>
>
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From damianavila at gmail.com  Tue Aug  2 13:33:05 2016
From: damianavila at gmail.com (=?UTF-8?Q?Dami=C3=A1n_Avila?=)
Date: Tue, 2 Aug 2016 14:33:05 -0300
Subject: [IPython-dev] IPython 5.0 and ConfigManager issue
In-Reply-To: <CAOvn4qgvw5-w+ABbgmYQRFuTcg0hvy7mOZShrUbRH=q6Fce_qg@mail.gmail.com>
References: <CAEznbzm6zN=SWtrWHshg+Od+fcfqESY=w+1BCBEP8ur3tWj-NQ@mail.gmail.com>
 <CAOvn4qgvw5-w+ABbgmYQRFuTcg0hvy7mOZShrUbRH=q6Fce_qg@mail.gmail.com>
Message-ID: <CAH+mRR2cFkA+yWPqo5baCmXjL1SZ5KvS2-3ek2vPppv5jRWK3Q@mail.gmail.com>

Just to add a little bit more of info... if you are using RISE master and
notebook 4.2.1, you probably need something like this if you have them
installed in an environment:

from traitlets.config.manager import BaseJSONConfigManager
path = "/home/damian/miniconda3/envs/rise_latest/etc/jupyter/nbconfig"
cm = BaseJSONConfigManager(config_dir=path)
cm.update('livereveal', {
    stuff...
})

where rise_latest is the environment where you have RISE + notebook
installed...

Alternative, to customize the presentation you can also use the notebook
metadata... I will be releasing a RISE 4.0.0 beta soon... where some issues
loading customization from the metadata are solved.
So you can try customization on the fly... without restarting the notebook
server nor reloading the page.

2016-08-02 12:18 GMT-03:00 Thomas Kluyver <takowl at gmail.com>:

> Hi Alan,
>
> The import for ConfigManager is now:
>
> from notebook.services.config import ConfigManager
>
> And you don't need any of the profile stuff - Jupyter, which includes all
> of the notebook frontend machinery, doesn't have profiles.
>
> Thomas
>
> On 2 August 2016 at 16:00, Alan <alanwilter at gmail.com> wrote:
>
>> Hi there,
>>
>> This is not working for me:
>>
>> from IPython.html.services.config import ConfigManagerfrom IPython.utils.path import locate_profilecm = ConfigManager(profile_dir=locate_profile(get_ipython().profile))cm.update('livereveal', {
>>               'theme': 'serif',
>>               'transition': 'zoom',
>>               'start_slideshow_at': 'selected',})
>>
>> TraitError: The 'parent' trait of a ConfigManager instance must be a Configurable, but a value of class 'NoneType' (i.e. None) was specified.
>>
>> It looks like IPY 5 changed the way it handles the configuration?
>>
>> I have these warning in my prompt:
>>
>> /sw/lib/python3.5/site-packages/IPython/utils/traitlets.py:5:
>> UserWarning: IPython.utils.traitlets has moved to a top-level traitlets
>> package.
>>
>>   warn("IPython.utils.traitlets has moved to a top-level traitlets
>> package.")
>>
>> /sw/lib/python3.5/site-packages/IPython/utils/path.py:283: UserWarning:
>> locate_profile has moved to the IPython.paths module
>>
>>   warn("locate_profile has moved to the IPython.paths module")
>>
>> But I don't know how to fix it. I am using ipython/jupyter + RISE and I
>> want to customise my presentations.
>>
>> Thanks,
>>
>> Alan
>>
>> --
>> Alan Wilter SOUSA da SILVA, DSc
>> Senior Bioinformatician, UniProt
>> European Bioinformatics Institute (EMBL-EBI)
>> European Molecular Biology Laboratory
>> Wellcome Trust Genome Campus
>> Hinxton
>> Cambridge CB10 1SD
>> United Kingdom
>> Tel: +44 (0)1223 494588
>>
>> _______________________________________________
>> IPython-dev mailing list
>> IPython-dev at scipy.org
>> https://mail.scipy.org/mailman/listinfo/ipython-dev
>>
>>
>
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev
>
>


-- 
*Dami?n*
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From alanwilter at gmail.com  Wed Aug  3 11:07:42 2016
From: alanwilter at gmail.com (Alan)
Date: Wed, 3 Aug 2016 16:07:42 +0100
Subject: [IPython-dev] IPython 5.0 and ConfigManager issue
In-Reply-To: <CAH+mRR2cFkA+yWPqo5baCmXjL1SZ5KvS2-3ek2vPppv5jRWK3Q@mail.gmail.com>
References: <CAEznbzm6zN=SWtrWHshg+Od+fcfqESY=w+1BCBEP8ur3tWj-NQ@mail.gmail.com>
 <CAOvn4qgvw5-w+ABbgmYQRFuTcg0hvy7mOZShrUbRH=q6Fce_qg@mail.gmail.com>
 <CAH+mRR2cFkA+yWPqo5baCmXjL1SZ5KvS2-3ek2vPppv5jRWK3Q@mail.gmail.com>
Message-ID: <CAEznbzmwBUj=jmMnZ_AnPP52c7tOFwXX7h8_oh6B_aAGRNqvWQ@mail.gmail.com>

Many thanks for the replies.

Indeed, based on Thomas', I did:

(slide type: skip)
from notebook.services.config import ConfigManager
from IPython.utils.path import locate_profile
cm = ConfigManager(profile_dir=locate_profile(get_ipython().profile))
cm.update('livereveal', {
              'theme': 'sky',
              'transition': 'cube', # zoom
              'start_slideshow_at': 'selected',
})

I am fine with restarting the kernel. Yet I don't get what Thomas says by
"And you don't need any of the profile stuff - Jupiter".

Well, I am happy with what I got so far.

And for Damian, I am using notebook 4.2.1 an RISE master indeed, but not
using (conda?) environment (I use Fink on my Mac + pip). And how to "you
can also use the notebook metadata..." ?

Many thanks and Many more Thanks for these incredible IPython, Jupyter and
RISE.

Alan

On 2 August 2016 at 18:33, Dami?n Avila <damianavila at gmail.com> wrote:

> Just to add a little bit more of info... if you are using RISE master and
> notebook 4.2.1, you probably need something like this if you have them
> installed in an environment:
>
> from traitlets.config.manager import BaseJSONConfigManager
> path = "/home/damian/miniconda3/envs/rise_latest/etc/jupyter/nbconfig"
> cm = BaseJSONConfigManager(config_dir=path)
> cm.update('livereveal', {
>     stuff...
> })
>
> where rise_latest is the environment where you have RISE + notebook
> installed...
>
> Alternative, to customize the presentation you can also use the notebook
> metadata... I will be releasing a RISE 4.0.0 beta soon... where some issues
> loading customization from the metadata are solved.
> So you can try customization on the fly... without restarting the notebook
> server nor reloading the page.
>
> 2016-08-02 12:18 GMT-03:00 Thomas Kluyver <takowl at gmail.com>:
>
>> Hi Alan,
>>
>> The import for ConfigManager is now:
>>
>> from notebook.services.config import ConfigManager
>>
>> And you don't need any of the profile stuff - Jupyter, which includes all
>> of the notebook frontend machinery, doesn't have profiles.
>>
>> Thomas
>>
>> On 2 August 2016 at 16:00, Alan <alanwilter at gmail.com> wrote:
>>
>>> Hi there,
>>>
>>> This is not working for me:
>>>
>>> from IPython.html.services.config import ConfigManagerfrom IPython.utils.path import locate_profilecm = ConfigManager(profile_dir=locate_profile(get_ipython().profile))cm.update('livereveal', {
>>>               'theme': 'serif',
>>>               'transition': 'zoom',
>>>               'start_slideshow_at': 'selected',})
>>>
>>> TraitError: The 'parent' trait of a ConfigManager instance must be a Configurable, but a value of class 'NoneType' (i.e. None) was specified.
>>>
>>> It looks like IPY 5 changed the way it handles the configuration?
>>>
>>> I have these warning in my prompt:
>>>
>>> /sw/lib/python3.5/site-packages/IPython/utils/traitlets.py:5:
>>> UserWarning: IPython.utils.traitlets has moved to a top-level traitlets
>>> package.
>>>
>>>   warn("IPython.utils.traitlets has moved to a top-level traitlets
>>> package.")
>>>
>>> /sw/lib/python3.5/site-packages/IPython/utils/path.py:283: UserWarning:
>>> locate_profile has moved to the IPython.paths module
>>>
>>>   warn("locate_profile has moved to the IPython.paths module")
>>>
>>> But I don't know how to fix it. I am using ipython/jupyter + RISE and I
>>> want to customise my presentations.
>>>
>>> Thanks,
>>>
>>> Alan
>>>
>>> --
>>> Alan Wilter SOUSA da SILVA, DSc
>>> Senior Bioinformatician, UniProt
>>> European Bioinformatics Institute (EMBL-EBI)
>>> European Molecular Biology Laboratory
>>> Wellcome Trust Genome Campus
>>> Hinxton
>>> Cambridge CB10 1SD
>>> United Kingdom
>>> Tel: +44 (0)1223 494588
>>>
>>> _______________________________________________
>>> IPython-dev mailing list
>>> IPython-dev at scipy.org
>>> https://mail.scipy.org/mailman/listinfo/ipython-dev
>>>
>>>
>>
>> _______________________________________________
>> IPython-dev mailing list
>> IPython-dev at scipy.org
>> https://mail.scipy.org/mailman/listinfo/ipython-dev
>>
>>
>
>
> --
> *Dami?n*
>
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev
>
>


-- 
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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From takowl at gmail.com  Wed Aug  3 11:14:31 2016
From: takowl at gmail.com (Thomas Kluyver)
Date: Wed, 3 Aug 2016 16:14:31 +0100
Subject: [IPython-dev] IPython 5.0 and ConfigManager issue
In-Reply-To: <CAEznbzmwBUj=jmMnZ_AnPP52c7tOFwXX7h8_oh6B_aAGRNqvWQ@mail.gmail.com>
References: <CAEznbzm6zN=SWtrWHshg+Od+fcfqESY=w+1BCBEP8ur3tWj-NQ@mail.gmail.com>
 <CAOvn4qgvw5-w+ABbgmYQRFuTcg0hvy7mOZShrUbRH=q6Fce_qg@mail.gmail.com>
 <CAH+mRR2cFkA+yWPqo5baCmXjL1SZ5KvS2-3ek2vPppv5jRWK3Q@mail.gmail.com>
 <CAEznbzmwBUj=jmMnZ_AnPP52c7tOFwXX7h8_oh6B_aAGRNqvWQ@mail.gmail.com>
Message-ID: <CAOvn4qjT+dcYFiDHsX14RYpef+pye_SCrdjzbwVvgotmvs5ZTw@mail.gmail.com>

On 3 August 2016 at 16:07, Alan <alanwilter at gmail.com> wrote:

> Yet I don't get what Thomas says by "And you don't need any of the profile
> stuff - Jupiter".


The lines:

from IPython.utils.path import locate_profile
cm = ConfigManager(profile_dir=locate_profile(get_ipython().profile))

Can become:

cm = ConfigManager()

IPython has a notion of 'profiles', separate sets of configurations that
you can switch between at launch. We didn't carry this notion over to
Jupyter, and since the notebook interface is part of Jupyter, it's ignoring
the IPython profile that code finds for it.

Thomas
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From alanwilter at gmail.com  Wed Aug  3 12:05:09 2016
From: alanwilter at gmail.com (Alan)
Date: Wed, 3 Aug 2016 17:05:09 +0100
Subject: [IPython-dev] How to use ipykernel for replace deprecated modules?
Message-ID: <CAEznbznF7FrkA58toJKXYuAaE=LWn6RE5Fv8DWOjgw+VtdE4hw@mail.gmail.com>

I am using

Server Information:

You are using Jupyter notebook.

The version of the notebook server is *4.2.2* and is running on:

Python 3.5.2 (default, Jun 30 2016, 18:10:25)
[GCC 4.2.1 Compatible Apple LLVM 7.0.2 (clang-700.1.81)]

Current Kernel Information:

Python 3.5.2 (default, Jun 30 2016, 18:10:25)
Type "copyright", "credits" or "license" for more information.

IPython 5.0.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.


My basic problem as follow:

from IPython.html.widgets import *
from IPython.display import display

/sw/lib/python3.5/site-packages/IPython/utils/traitlets.py:5: UserWarning:
IPython.utils.traitlets has moved to a top-level traitlets package.
  warn("IPython.utils.traitlets has moved to a top-level traitlets
package.")
/sw/lib/python3.5/site-packages/IPython/kernel/__init__.py:13: ShimWarning:
The `IPython.kernel` package has been deprecated. You should import from
ipykernel or jupyter_client instead.
  "You should import from ipykernel or jupyter_client instead.",
ShimWarning)
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-3-d4f1ddbc099e> in <module>()
----> 1 from IPython.html.widgets import *
      2 from IPython.display import display

/sw/lib/python3.5/site-packages/IPython/html/widgets/__init__.py in
<module>()
      3 from .trait_types import Color
      4
----> 5 from .widget_bool import Checkbox, ToggleButton
      6 from .widget_button import Button
      7 from .widget_box import Box, FlexBox, HBox, VBox

/sw/lib/python3.5/site-packages/IPython/html/widgets/widget_bool.py in
<module>()
     16 from .widget import DOMWidget, register
     17 from IPython.utils.traitlets import Unicode, Bool, CaselessStrEnum
---> 18 from IPython.utils.warn import DeprecatedClass
     19
     20
#-----------------------------------------------------------------------------

ImportError: cannot import name 'DeprecatedClass'

Many thanks in advance,

Alan
-- 
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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From takowl at gmail.com  Wed Aug  3 12:14:19 2016
From: takowl at gmail.com (Thomas Kluyver)
Date: Wed, 3 Aug 2016 17:14:19 +0100
Subject: [IPython-dev] How to use ipykernel for replace deprecated
	modules?
In-Reply-To: <CAEznbznF7FrkA58toJKXYuAaE=LWn6RE5Fv8DWOjgw+VtdE4hw@mail.gmail.com>
References: <CAEznbznF7FrkA58toJKXYuAaE=LWn6RE5Fv8DWOjgw+VtdE4hw@mail.gmail.com>
Message-ID: <CAOvn4qjHL1EyfihnwEo0LXasatpNeHKbFevTJPKwM7JsAMiLOQ@mail.gmail.com>

Hi Alan,

I think an upgrade has gone wrong or something, because there are files in
that traceback that shouldn't exist in IPython 5.0. I'd try removing
ipython entirely and installing it again.

Thomas

On 3 August 2016 at 17:05, Alan <alanwilter at gmail.com> wrote:

> I am using
>
> Server Information:
>
> You are using Jupyter notebook.
>
> The version of the notebook server is *4.2.2* and is running on:
>
> Python 3.5.2 (default, Jun 30 2016, 18:10:25)
> [GCC 4.2.1 Compatible Apple LLVM 7.0.2 (clang-700.1.81)]
>
> Current Kernel Information:
>
> Python 3.5.2 (default, Jun 30 2016, 18:10:25)
> Type "copyright", "credits" or "license" for more information.
>
> IPython 5.0.0 -- An enhanced Interactive Python.
> ?         -> Introduction and overview of IPython's features.
> %quickref -> Quick reference.
> help      -> Python's own help system.
> object?   -> Details about 'object', use 'object??' for extra details.
>
>
> My basic problem as follow:
>
> from IPython.html.widgets import *
> from IPython.display import display
>
> /sw/lib/python3.5/site-packages/IPython/utils/traitlets.py:5: UserWarning:
> IPython.utils.traitlets has moved to a top-level traitlets package.
>   warn("IPython.utils.traitlets has moved to a top-level traitlets
> package.")
> /sw/lib/python3.5/site-packages/IPython/kernel/__init__.py:13:
> ShimWarning: The `IPython.kernel` package has been deprecated. You should
> import from ipykernel or jupyter_client instead.
>   "You should import from ipykernel or jupyter_client instead.",
> ShimWarning)
> ---------------------------------------------------------------------------
> ImportError                               Traceback (most recent call last)
> <ipython-input-3-d4f1ddbc099e> in <module>()
> ----> 1 from IPython.html.widgets import *
>       2 from IPython.display import display
>
> /sw/lib/python3.5/site-packages/IPython/html/widgets/__init__.py in
> <module>()
>       3 from .trait_types import Color
>       4
> ----> 5 from .widget_bool import Checkbox, ToggleButton
>       6 from .widget_button import Button
>       7 from .widget_box import Box, FlexBox, HBox, VBox
>
> /sw/lib/python3.5/site-packages/IPython/html/widgets/widget_bool.py in
> <module>()
>      16 from .widget import DOMWidget, register
>      17 from IPython.utils.traitlets import Unicode, Bool, CaselessStrEnum
> ---> 18 from IPython.utils.warn import DeprecatedClass
>      19
>      20
> #-----------------------------------------------------------------------------
>
> ImportError: cannot import name 'DeprecatedClass'
>
> Many thanks in advance,
>
> Alan
> --
> Alan Wilter SOUSA da SILVA, DSc
> Senior Bioinformatician, UniProt
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> Tel: +44 (0)1223 494588
>
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev
>
>
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From alanwilter at gmail.com  Wed Aug  3 12:37:38 2016
From: alanwilter at gmail.com (Alan)
Date: Wed, 3 Aug 2016 17:37:38 +0100
Subject: [IPython-dev] How to use ipykernel for replace deprecated
	modules?
In-Reply-To: <CAOvn4qjHL1EyfihnwEo0LXasatpNeHKbFevTJPKwM7JsAMiLOQ@mail.gmail.com>
References: <CAEznbznF7FrkA58toJKXYuAaE=LWn6RE5Fv8DWOjgw+VtdE4hw@mail.gmail.com>
 <CAOvn4qjHL1EyfihnwEo0LXasatpNeHKbFevTJPKwM7JsAMiLOQ@mail.gmail.com>
Message-ID: <CAEznbznXOaTdVsGS-=dDp-v+-q0nTmmj1xxQnDaF2w4EOmWP+A@mail.gmail.com>

Many thanks Thomas!

It was my mess of mixing Fink with Pip. All fixed now.

Cheers,

Alan

On 3 August 2016 at 17:14, Thomas Kluyver <takowl at gmail.com> wrote:

> Hi Alan,
>
> I think an upgrade has gone wrong or something, because there are files in
> that traceback that shouldn't exist in IPython 5.0. I'd try removing
> ipython entirely and installing it again.
>
> Thomas
>
> On 3 August 2016 at 17:05, Alan <alanwilter at gmail.com> wrote:
>
>> I am using
>>
>> Server Information:
>>
>> You are using Jupyter notebook.
>>
>> The version of the notebook server is *4.2.2* and is running on:
>>
>> Python 3.5.2 (default, Jun 30 2016, 18:10:25)
>> [GCC 4.2.1 Compatible Apple LLVM 7.0.2 (clang-700.1.81)]
>>
>> Current Kernel Information:
>>
>> Python 3.5.2 (default, Jun 30 2016, 18:10:25)
>> Type "copyright", "credits" or "license" for more information.
>>
>> IPython 5.0.0 -- An enhanced Interactive Python.
>> ?         -> Introduction and overview of IPython's features.
>> %quickref -> Quick reference.
>> help      -> Python's own help system.
>> object?   -> Details about 'object', use 'object??' for extra details.
>>
>>
>> My basic problem as follow:
>>
>> from IPython.html.widgets import *
>> from IPython.display import display
>>
>> /sw/lib/python3.5/site-packages/IPython/utils/traitlets.py:5:
>> UserWarning: IPython.utils.traitlets has moved to a top-level traitlets
>> package.
>>   warn("IPython.utils.traitlets has moved to a top-level traitlets
>> package.")
>> /sw/lib/python3.5/site-packages/IPython/kernel/__init__.py:13:
>> ShimWarning: The `IPython.kernel` package has been deprecated. You should
>> import from ipykernel or jupyter_client instead.
>>   "You should import from ipykernel or jupyter_client instead.",
>> ShimWarning)
>>
>> ---------------------------------------------------------------------------
>> ImportError                               Traceback (most recent call
>> last)
>> <ipython-input-3-d4f1ddbc099e> in <module>()
>> ----> 1 from IPython.html.widgets import *
>>       2 from IPython.display import display
>>
>> /sw/lib/python3.5/site-packages/IPython/html/widgets/__init__.py in
>> <module>()
>>       3 from .trait_types import Color
>>       4
>> ----> 5 from .widget_bool import Checkbox, ToggleButton
>>       6 from .widget_button import Button
>>       7 from .widget_box import Box, FlexBox, HBox, VBox
>>
>> /sw/lib/python3.5/site-packages/IPython/html/widgets/widget_bool.py in
>> <module>()
>>      16 from .widget import DOMWidget, register
>>      17 from IPython.utils.traitlets import Unicode, Bool, CaselessStrEnum
>> ---> 18 from IPython.utils.warn import DeprecatedClass
>>      19
>>      20
>> #-----------------------------------------------------------------------------
>>
>> ImportError: cannot import name 'DeprecatedClass'
>>
>> Many thanks in advance,
>>
>> Alan
>> --
>> Alan Wilter SOUSA da SILVA, DSc
>> Senior Bioinformatician, UniProt
>> European Bioinformatics Institute (EMBL-EBI)
>> European Molecular Biology Laboratory
>> Wellcome Trust Genome Campus
>> Hinxton
>> Cambridge CB10 1SD
>> United Kingdom
>> Tel: +44 (0)1223 494588
>>
>> _______________________________________________
>> IPython-dev mailing list
>> IPython-dev at scipy.org
>> https://mail.scipy.org/mailman/listinfo/ipython-dev
>>
>>
>
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev
>
>


-- 
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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From damianavila at gmail.com  Wed Aug  3 15:36:41 2016
From: damianavila at gmail.com (=?UTF-8?Q?Dami=C3=A1n_Avila?=)
Date: Wed, 3 Aug 2016 16:36:41 -0300
Subject: [IPython-dev] IPython 5.0 and ConfigManager issue
In-Reply-To: <CAEznbzmwBUj=jmMnZ_AnPP52c7tOFwXX7h8_oh6B_aAGRNqvWQ@mail.gmail.com>
References: <CAEznbzm6zN=SWtrWHshg+Od+fcfqESY=w+1BCBEP8ur3tWj-NQ@mail.gmail.com>
 <CAOvn4qgvw5-w+ABbgmYQRFuTcg0hvy7mOZShrUbRH=q6Fce_qg@mail.gmail.com>
 <CAH+mRR2cFkA+yWPqo5baCmXjL1SZ5KvS2-3ek2vPppv5jRWK3Q@mail.gmail.com>
 <CAEznbzmwBUj=jmMnZ_AnPP52c7tOFwXX7h8_oh6B_aAGRNqvWQ@mail.gmail.com>
Message-ID: <CAH+mRR2adgkq9jXLzTU-s=KY9Esqm3N5bjzZJhB+S5UYWnoWZQ@mail.gmail.com>

2016-08-03 12:07 GMT-03:00 Alan <alanwilter at gmail.com>:

> Many thanks for the replies.
>
> Indeed, based on Thomas', I did:
>
> (slide type: skip)
> from notebook.services.config import ConfigManager
> from IPython.utils.path import locate_profile
> cm = ConfigManager(profile_dir=locate_profile(get_ipython().profile))
> cm.update('livereveal', {
>               'theme': 'sky',
>               'transition': 'cube', # zoom
>               'start_slideshow_at': 'selected',
> })
>
> I am fine with restarting the kernel. Yet I don't get what Thomas says by
> "And you don't need any of the profile stuff - Jupiter".
>
> Well, I am happy with what I got so far.
>
> And for Damian, I am using notebook 4.2.1 an RISE master indeed, but not
> using (conda?) environment (I use Fink on my Mac + pip).
>

OK ;-)


> And how to "you can also use the notebook metadata..." ?
>

https://github.com/damianavila/RISE#alternative-configuration-method


>
> Many thanks and Many more Thanks for these incredible IPython, Jupyter and
> RISE.
>
> Alan
>
> On 2 August 2016 at 18:33, Dami?n Avila <damianavila at gmail.com> wrote:
>
>> Just to add a little bit more of info... if you are using RISE master and
>> notebook 4.2.1, you probably need something like this if you have them
>> installed in an environment:
>>
>> from traitlets.config.manager import BaseJSONConfigManager
>> path = "/home/damian/miniconda3/envs/rise_latest/etc/jupyter/nbconfig"
>> cm = BaseJSONConfigManager(config_dir=path)
>> cm.update('livereveal', {
>>     stuff...
>> })
>>
>> where rise_latest is the environment where you have RISE + notebook
>> installed...
>>
>> Alternative, to customize the presentation you can also use the notebook
>> metadata... I will be releasing a RISE 4.0.0 beta soon... where some issues
>> loading customization from the metadata are solved.
>> So you can try customization on the fly... without restarting the
>> notebook server nor reloading the page.
>>
>> 2016-08-02 12:18 GMT-03:00 Thomas Kluyver <takowl at gmail.com>:
>>
>>> Hi Alan,
>>>
>>> The import for ConfigManager is now:
>>>
>>> from notebook.services.config import ConfigManager
>>>
>>> And you don't need any of the profile stuff - Jupyter, which includes
>>> all of the notebook frontend machinery, doesn't have profiles.
>>>
>>> Thomas
>>>
>>> On 2 August 2016 at 16:00, Alan <alanwilter at gmail.com> wrote:
>>>
>>>> Hi there,
>>>>
>>>> This is not working for me:
>>>>
>>>> from IPython.html.services.config import ConfigManagerfrom IPython.utils.path import locate_profilecm = ConfigManager(profile_dir=locate_profile(get_ipython().profile))cm.update('livereveal', {
>>>>               'theme': 'serif',
>>>>               'transition': 'zoom',
>>>>               'start_slideshow_at': 'selected',})
>>>>
>>>> TraitError: The 'parent' trait of a ConfigManager instance must be a Configurable, but a value of class 'NoneType' (i.e. None) was specified.
>>>>
>>>> It looks like IPY 5 changed the way it handles the configuration?
>>>>
>>>> I have these warning in my prompt:
>>>>
>>>> /sw/lib/python3.5/site-packages/IPython/utils/traitlets.py:5:
>>>> UserWarning: IPython.utils.traitlets has moved to a top-level traitlets
>>>> package.
>>>>
>>>>   warn("IPython.utils.traitlets has moved to a top-level traitlets
>>>> package.")
>>>>
>>>> /sw/lib/python3.5/site-packages/IPython/utils/path.py:283: UserWarning:
>>>> locate_profile has moved to the IPython.paths module
>>>>
>>>>   warn("locate_profile has moved to the IPython.paths module")
>>>>
>>>> But I don't know how to fix it. I am using ipython/jupyter + RISE and I
>>>> want to customise my presentations.
>>>>
>>>> Thanks,
>>>>
>>>> Alan
>>>>
>>>> --
>>>> Alan Wilter SOUSA da SILVA, DSc
>>>> Senior Bioinformatician, UniProt
>>>> European Bioinformatics Institute (EMBL-EBI)
>>>> European Molecular Biology Laboratory
>>>> Wellcome Trust Genome Campus
>>>> Hinxton
>>>> Cambridge CB10 1SD
>>>> United Kingdom
>>>> Tel: +44 (0)1223 494588
>>>>
>>>> _______________________________________________
>>>> IPython-dev mailing list
>>>> IPython-dev at scipy.org
>>>> https://mail.scipy.org/mailman/listinfo/ipython-dev
>>>>
>>>>
>>>
>>> _______________________________________________
>>> IPython-dev mailing list
>>> IPython-dev at scipy.org
>>> https://mail.scipy.org/mailman/listinfo/ipython-dev
>>>
>>>
>>
>>
>> --
>> *Dami?n*
>>
>> _______________________________________________
>> IPython-dev mailing list
>> IPython-dev at scipy.org
>> https://mail.scipy.org/mailman/listinfo/ipython-dev
>>
>>
>
>
> --
> Alan Wilter SOUSA da SILVA, DSc
> Senior Bioinformatician, UniProt
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> Tel: +44 (0)1223 494588
>
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev
>
>


-- 
*Dami?n*
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From thorin at broadinstitute.org  Fri Aug  5 16:16:10 2016
From: thorin at broadinstitute.org (Thorin Tabor)
Date: Fri, 5 Aug 2016 13:16:10 -0700
Subject: [IPython-dev] ANN: GenePattern Notebook released
Message-ID: <48bdd739-be2f-4e31-bc8e-7e1c10213ed1@broadinstitute.org>

We are pleased to announce the release of GenePattern Notebook, an 
extension for Jupyter which provides access to hundreds of different 
bioinformatic analyses through the GenePattern web service.

http://genepattern.org/genepattern-notebooks 
<http://genepattern.org/genepattern-notebooks>
https://github.com/genepattern/genepattern-notebook 
<https://github.com/genepattern/genepattern-notebook>

Supported analyses include machine learning algorithms (clustering, 
classification, dimension reduction), tools for working with gene 
expression data (both RNA-seq and microarray), sequence variation and 
copy number analysis, proteomics, flow cytometry and network analysis.

Included in the extension are visual widgets for running analyses, tools 
for sending results to downstream steps in a bioinformatic workflow, 
Jupyter magics for creating GenePattern widgets and a Python library for 
programmatically working with your results.

To get started after installing the extension, just open a notebook and 
change a cell to the new GenePattern cell type. A full walk-through of 
using the extension is available on our website:

http://genepattern.org/using-the-genepattern-notebook-environment 
<http://genepattern.org/using-the-genepattern-notebook-environment>

An early version of the GenePattern Notebook Repository, a service 
providing access to GenePattern Notebook functionality as well as a 
variety of example notebooks, is available at the address below.

https://notebook.genepattern.org <https://notebook.genepattern.org>

The GenePattern Notebook extension can also be easily installed from pip 
or conda:

     pip install genepattern-notebook

or

     conda install -c genepattern genepattern-notebook

Once installed, you will need to install and enable the accompanying 
server and nbextensions. The ipywidgets nbextension must also be enabled:

     jupyter nbextension enable --py widgetsnbextension
     jupyter nbextension install --py genepattern
     jupyter nbextension enable --py genepattern
     jupyter serverextension enable --py genepattern

The GenePattern Notebook extension supports both Python 3.3+ and Python 2.7.

Cheers!
The GenePattern Team

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From fperez.net at gmail.com  Tue Aug  9 22:07:53 2016
From: fperez.net at gmail.com (Fernando Perez)
Date: Tue, 9 Aug 2016 19:07:53 -0700
Subject: [IPython-dev] ANN: GenePattern Notebook released
In-Reply-To: <48bdd739-be2f-4e31-bc8e-7e1c10213ed1@broadinstitute.org>
References: <48bdd739-be2f-4e31-bc8e-7e1c10213ed1@broadinstitute.org>
Message-ID: <CAHAreOoRLzd94mtGyzraqc+1U4nZ2VskikK_nM5SqDGC9bDrFQ@mail.gmail.com>

Congrats, and thanks for letting us know!

BTW, I didn't see your post on the general Jupyter list:

https://groups.google.com/forum/#!forum/jupyter

I'd recommend reposting there, as most of Jupyter-general discussion has
moved over to that forum, leaving the IPython list for topics that are more
specific to that kernel and terminal shell.  Obviously it's quite OK to
post there too, I'm just thinking of having better reach for your message.

Best

f

On Fri, Aug 5, 2016 at 1:16 PM, Thorin Tabor <thorin at broadinstitute.org>
wrote:

> We are pleased to announce the release of GenePattern Notebook, an
> extension for Jupyter which provides access to hundreds of different
> bioinformatic analyses through the GenePattern web service.
>
>     http://genepattern.org/genepattern-notebooks
>     https://github.com/genepattern/genepattern-notebook
>
> Supported analyses include machine learning algorithms (clustering,
> classification, dimension reduction), tools for working with gene
> expression data (both RNA-seq and microarray), sequence variation and copy
> number analysis, proteomics, flow cytometry and network analysis.
>
> Included in the extension are visual widgets for running analyses, tools
> for sending results to downstream steps in a bioinformatic workflow,
> Jupyter magics for creating GenePattern widgets and a Python library for
> programmatically working with your results.
>
> To get started after installing the extension, just open a notebook and
> change a cell to the new GenePattern cell type. A full walk-through of
> using the extension is available on our website:
>
>      http://genepattern.org/using-the-genepattern-notebook-environment
>
> An early version of the GenePattern Notebook Repository, a service
> providing access to GenePattern Notebook functionality as well as a variety
> of example notebooks, is available at the address below.
>
>     https://notebook.genepattern.org
>
> The GenePattern Notebook extension can also be easily installed from pip
> or conda:
>
>     pip install genepattern-notebook
>
> or
>
>     conda install -c genepattern genepattern-notebook
>
> Once installed, you will need to install and enable the accompanying
> server and nbextensions. The ipywidgets nbextension must also be enabled:
>
>     jupyter nbextension enable --py widgetsnbextension
>     jupyter nbextension install --py genepattern
>     jupyter nbextension enable --py genepattern
>     jupyter serverextension enable --py genepattern
>
> The GenePattern Notebook extension supports both Python 3.3+ and Python
> 2.7.
>
> Cheers!
> The GenePattern Team
>
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev
>
>


-- 
Fernando Perez (@fperez_org; http://fperez.org)
fperez.net-at-gmail: mailing lists only (I ignore this when swamped!)
fernando.perez-at-berkeley: contact me here for any direct mail
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From takowl at gmail.com  Sat Aug 13 09:12:28 2016
From: takowl at gmail.com (Thomas Kluyver)
Date: Sat, 13 Aug 2016 14:12:28 +0100
Subject: [IPython-dev] IPython 5.1.0 released
Message-ID: <CAOvn4qgiP2vXY2eUkw4QFQVkcTa1WLeEawAOY0x_zdEck5nvqA@mail.gmail.com>

IPython 5.1.0 is now available from PyPI:
https://pypi.python.org/pypi/ipython

This is primarily a roll-up of various bugfixes following the 5.0 release,
with a couple of new features. You can see details on what has changed here:
http://ipython.readthedocs.io/en/stable/whatsnew/version5.html#ipython-5-1

Best wishes,
Thomas
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From bussonniermatthias at gmail.com  Sat Aug 13 20:09:28 2016
From: bussonniermatthias at gmail.com (Matthias Bussonnier)
Date: Sat, 13 Aug 2016 17:09:28 -0700
Subject: [IPython-dev] IPython 5.1.0 released
In-Reply-To: <CAOvn4qgiP2vXY2eUkw4QFQVkcTa1WLeEawAOY0x_zdEck5nvqA@mail.gmail.com>
References: <CAOvn4qgiP2vXY2eUkw4QFQVkcTa1WLeEawAOY0x_zdEck5nvqA@mail.gmail.com>
Message-ID: <CANJQusVp9POg9iuGpkvWhm1CSb==sV7NRp4AyVetC4WGaA6eMw@mail.gmail.com>

Thanks Thomas ! Awesome work !

-- 
M

On Sat, Aug 13, 2016 at 6:12 AM, Thomas Kluyver <takowl at gmail.com> wrote:
> IPython 5.1.0 is now available from PyPI:
> https://pypi.python.org/pypi/ipython
>
> This is primarily a roll-up of various bugfixes following the 5.0 release,
> with a couple of new features. You can see details on what has changed here:
> http://ipython.readthedocs.io/en/stable/whatsnew/version5.html#ipython-5-1
>
> Best wishes,
> Thomas
>
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev
>


From thorin at broadinstitute.org  Mon Aug 15 19:43:27 2016
From: thorin at broadinstitute.org (Thorin Tabor)
Date: Mon, 15 Aug 2016 16:43:27 -0700
Subject: [IPython-dev] ANN: GenePattern Notebook released
In-Reply-To: <CAHAreOoRLzd94mtGyzraqc+1U4nZ2VskikK_nM5SqDGC9bDrFQ@mail.gmail.com>
References: <48bdd739-be2f-4e31-bc8e-7e1c10213ed1@broadinstitute.org>
 <CAHAreOoRLzd94mtGyzraqc+1U4nZ2VskikK_nM5SqDGC9bDrFQ@mail.gmail.com>
Message-ID: <baee67c9-3e17-e443-2e82-7cd3643c386a@broadinstitute.org>

I didn't think to post there. Thanks for the suggestion!

Thorin


On 8/9/16 19:07, Fernando Perez wrote:
> Congrats, and thanks for letting us know!
>
> BTW, I didn't see your post on the general Jupyter list:
>
> https://groups.google.com/forum/#!forum/jupyter 
> <https://groups.google.com/forum/#%21forum/jupyter>
>
> I'd recommend reposting there, as most of Jupyter-general discussion 
> has moved over to that forum, leaving the IPython list for topics that 
> are more specific to that kernel and terminal shell.  Obviously it's 
> quite OK to post there too, I'm just thinking of having better reach 
> for your message.
>
> Best
>
> f
>
> On Fri, Aug 5, 2016 at 1:16 PM, Thorin Tabor 
> <thorin at broadinstitute.org <mailto:thorin at broadinstitute.org>> wrote:
>
>     We are pleased to announce the release of GenePattern Notebook, an
>     extension for Jupyter which provides access to hundreds of
>     different bioinformatic analyses through the GenePattern web service.
>
>     http://genepattern.org/genepattern-notebooks
>     <http://genepattern.org/genepattern-notebooks>
>     https://github.com/genepattern/genepattern-notebook
>     <https://github.com/genepattern/genepattern-notebook>
>
>     Supported analyses include machine learning algorithms
>     (clustering, classification, dimension reduction), tools for
>     working with gene expression data (both RNA-seq and microarray),
>     sequence variation and copy number analysis, proteomics, flow
>     cytometry and network analysis.
>
>     Included in the extension are visual widgets for running analyses,
>     tools for sending results to downstream steps in a bioinformatic
>     workflow, Jupyter magics for creating GenePattern widgets and a
>     Python library for programmatically working with your results.
>
>     To get started after installing the extension, just open a
>     notebook and change a cell to the new GenePattern cell type. A
>     full walk-through of using the extension is available on our website:
>
>     http://genepattern.org/using-the-genepattern-notebook-environment
>     <http://genepattern.org/using-the-genepattern-notebook-environment>
>
>     An early version of the GenePattern Notebook Repository, a service
>     providing access to GenePattern Notebook functionality as well as
>     a variety of example notebooks, is available at the address below.
>
>     https://notebook.genepattern.org <https://notebook.genepattern.org>
>
>     The GenePattern Notebook extension can also be easily installed
>     from pip or conda:
>
>         pip install genepattern-notebook
>
>     or
>
>         conda install -c genepattern genepattern-notebook
>
>     Once installed, you will need to install and enable the
>     accompanying server and nbextensions. The ipywidgets nbextension
>     must also be enabled:
>
>         jupyter nbextension enable --py widgetsnbextension
>         jupyter nbextension install --py genepattern
>         jupyter nbextension enable --py genepattern
>         jupyter serverextension enable --py genepattern
>
>     The GenePattern Notebook extension supports both Python 3.3+ and
>     Python 2.7.
>
>     Cheers!
>     The GenePattern Team
>
>
>     _______________________________________________
>     IPython-dev mailing list
>     IPython-dev at scipy.org <mailto:IPython-dev at scipy.org>
>     https://mail.scipy.org/mailman/listinfo/ipython-dev
>     <https://mail.scipy.org/mailman/listinfo/ipython-dev>
>
>
>
>
> -- 
> Fernando Perez (@fperez_org; http://fperez.org)
> fperez.net-at-gmail: mailing lists only (I ignore this when swamped!)
> fernando.perez-at-berkeley: contact me here for any direct mail
>
>
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> https://mail.scipy.org/mailman/listinfo/ipython-dev

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From piet-l at pietvanoostrum.com  Sun Aug 21 10:09:08 2016
From: piet-l at pietvanoostrum.com (Piet van Oostrum)
Date: Sun, 21 Aug 2016 16:09:08 +0200
Subject: [IPython-dev] Spurious newline with ipython in Emacs
Message-ID: <lxbn0m2ozf.fsf@cochabamba.vanoostrum.org>

I get spurious newlines when running ipython in Emacs (Aquamacs on Mac
OS X). I use python-mode.el and its ipython command. There is a newline
after the output prompt. The newline is not there when running in a
Terminal window.

In [2]: 2+3
Out[2]: 
5

In [3]:

You see the newline after Out[2]:

I traced this behaviour to the method write_output_prompt in the class
RichPromptDisplayHook in IPython/terminal/prompts.py.
The last line is
                print(*(s for t, s in tokens), sep='')
and this prints a newline after the output prompt.
Changing this to
                print(*(s for t, s in tokens), sep='', end='')
solves the problem.

An alternative would be to use a write in
IPython/terminal/prompts.py

                sys.stdout.write(''.join(s for t, s in tokens))

The reason that ipython in Terminal does not print the newline, is that
in such an ipython sys.displayhook.shell.pt_cli is set to a
promp_toolkit.interface.CommandLineInterface instance and its
print_tokens() method is used, and that one use write to print the
output. In ipython within Emacs sys.displayhook.shell.pt_cli = None. I
don't know why. Probably because the power of prompt_toolkit is not
needed as Emacs does the work.

Anyway, printing a newline after the output prompt is just wrong, IMHO.
-- 
Piet van Oostrum <piet-l at pietvanoostrum.com>
WWW: http://pietvanoostrum.com/
PGP key: [8DAE142BE17999C4]


From takowl at gmail.com  Sun Aug 21 10:20:36 2016
From: takowl at gmail.com (Thomas Kluyver)
Date: Sun, 21 Aug 2016 15:20:36 +0100
Subject: [IPython-dev] Spurious newline with ipython in Emacs
In-Reply-To: <lxbn0m2ozf.fsf@cochabamba.vanoostrum.org>
References: <lxbn0m2ozf.fsf@cochabamba.vanoostrum.org>
Message-ID: <CAOvn4qhTrtFVDDpNB29EzVAtAckFfXeJo=a4ecvXZ=yKxN98vA@mail.gmail.com>

On 21 August 2016 at 15:09, Piet van Oostrum <piet-l at pietvanoostrum.com>
wrote:

> The last line is
>                 print(*(s for t, s in tokens), sep='')
> and this prints a newline after the output prompt.
> Changing this to
>                 print(*(s for t, s in tokens), sep='', end='')
> solves the problem.
>


Thanks Piet, I think this was just overlooked. Do you want to make a pull
request with that change?
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From piet-l at pietvanoostrum.com  Sun Aug 21 13:29:14 2016
From: piet-l at pietvanoostrum.com (Piet van Oostrum)
Date: Sun, 21 Aug 2016 19:29:14 +0200
Subject: [IPython-dev] Spurious newline with ipython in Emacs
In-Reply-To: <CAOvn4qhTrtFVDDpNB29EzVAtAckFfXeJo=a4ecvXZ=yKxN98vA@mail.gmail.com>
 (Thomas Kluyver's message of "Sun, 21 Aug 2016 15:20:36 +0100")
References: <lxbn0m2ozf.fsf@cochabamba.vanoostrum.org>
 <CAOvn4qhTrtFVDDpNB29EzVAtAckFfXeJo=a4ecvXZ=yKxN98vA@mail.gmail.com>
Message-ID: <lx4m6e2fpx.fsf@cochabamba.vanoostrum.org>

Thomas Kluyver <takowl at gmail.com> writes:

> On 21 August 2016 at 15:09, Piet van Oostrum <piet-l at pietvanoostrum.com> wrote:
>
>     The last line is
>     ? ? ? ? ? ? ? ? print(*(s for t, s in tokens), sep='')
>     and this prints a newline after the output prompt.
>     Changing this to
>     ? ? ? ? ? ? ? ? print(*(s for t, s in tokens), sep='', end='')
>     solves the problem.
>
> Thanks Piet, I think this was just overlooked. Do you want to make a pull request with that
> change?
>
I don't have the repository cloned, so a pull request doesn't make sense for me, I think. Can someone else do it? Or should I just file a bug report?
-- 
Piet van Oostrum <piet-l at pietvanoostrum.com>
WWW: http://pietvanoostrum.com/
PGP key: [8DAE142BE17999C4]