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: References: Message-ID: 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 ? -------------- next part -------------- An HTML attachment was scrubbed... URL: 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: References: Message-ID: > 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: References: Message-ID: 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: 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: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: 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: References: Message-ID: 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 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: 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: References: Message-ID: 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 : > 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 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* -------------- next part -------------- An HTML attachment was scrubbed... URL: 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: References: Message-ID: 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 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 : > >> 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 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: 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: References: Message-ID: On 3 August 2016 at 16:07, Alan 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: 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: 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) in () ----> 1 from IPython.html.widgets import * 2 from IPython.display import display /sw/lib/python3.5/site-packages/IPython/html/widgets/__init__.py in () 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 () 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: 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: References: Message-ID: 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 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) > in () > ----> 1 from IPython.html.widgets import * > 2 from IPython.display import display > > /sw/lib/python3.5/site-packages/IPython/html/widgets/__init__.py in > () > 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 > () > 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: 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: References: Message-ID: 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 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 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) >> in () >> ----> 1 from IPython.html.widgets import * >> 2 from IPython.display import display >> >> /sw/lib/python3.5/site-packages/IPython/html/widgets/__init__.py in >> () >> 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 >> () >> 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: 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: References: Message-ID: 2016-08-03 12:07 GMT-03:00 Alan : > 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 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 : >> >>> 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 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* -------------- next part -------------- An HTML attachment was scrubbed... URL: 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 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: 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: 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 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: 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: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: 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: References: Message-ID: Thanks Thomas ! Awesome work ! -- M On Sat, Aug 13, 2016 at 6:12 AM, Thomas Kluyver 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: References: <48bdd739-be2f-4e31-bc8e-7e1c10213ed1@broadinstitute.org> Message-ID: 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 > > > 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 > > 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 > > > _______________________________________________ > IPython-dev mailing list > IPython-dev at scipy.org > https://mail.scipy.org/mailman/listinfo/ipython-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: 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: 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 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: References: Message-ID: On 21 August 2016 at 15:09, Piet van Oostrum 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? -------------- next part -------------- An HTML attachment was scrubbed... URL: 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: (Thomas Kluyver's message of "Sun, 21 Aug 2016 15:20:36 +0100") References: Message-ID: Thomas Kluyver writes: > On 21 August 2016 at 15:09, Piet van Oostrum 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 WWW: http://pietvanoostrum.com/ PGP key: [8DAE142BE17999C4]