Dependencies #1
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So yes matplotlib for visualizations in the examples. Numba and pathos are
really optional. I use seaborn for the last correlation plots in the
AxCaliber example, should that be added too?
…On 3 Feb 2018 12:55, "Demian Wassermann" ***@***.***> wrote:
https://github.com/AthenaEPI/dmipy/blob/3942f6e9c6b15372fd74ff6b941512
5811bb080b/dmipy/version.py#L60
@rutgerfick <https://github.com/rutgerfick> I think that the dependencies
are too lax. We need to add *everything* that the tool needs to import to
run. Boto is just needed for the examples so I added it but is there
something missing? I think, for instance, that you are calling matplotlib
from within the modules.
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I dunno. We should at some point reduce the amount of needed dependencies. Can we do something nice w/o seaborn?
--
Demian Wassermann, PhD
[email protected]
Associate Research Professor (CRN)
Parietal Team
INRIA Saclay Ile-de-France
1 Rue Honoré d'Estienne d'Orves, 91120 Palaiseau
… On 3 Feb 2018, at 13:03, Rutger Fick ***@***.***> wrote:
So yes matplotlib for visualizations in the examples. Numba and pathos are
really optional. I use seaborn for the last correlation plots in the
AxCaliber example, should that be added too?
On 3 Feb 2018 12:55, "Demian Wassermann" ***@***.***> wrote:
> https://github.com/AthenaEPI/dmipy/blob/3942f6e9c6b15372fd74ff6b941512
> 5811bb080b/dmipy/version.py#L60
>
> @rutgerfick <https://github.com/rutgerfick> I think that the dependencies
> are too lax. We need to add *everything* that the tool needs to import to
> run. Boto is just needed for the examples so I added it but is there
> something missing? I think, for instance, that you are calling matplotlib
> from within the modules.
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#1>, or mute the thread
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> .
>
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Not AS nice but scipy can do correlations and you can somehow make a plot
showing it with matplotlib.
It just takes 7 hours to run the example (fit AxCaliber using mix) so it
can be done for tomorrow. Is it a priority?
…On 3 Feb 2018 13:07, "Demian Wassermann" ***@***.***> wrote:
I dunno. We should at some point reduce the amount of needed dependencies.
Can we do something nice w/o seaborn?
--
Demian Wassermann, PhD
***@***.***
Associate Research Professor (CRN)
Parietal Team
INRIA Saclay Ile-de-France
1 Rue Honoré d
<https://maps.google.com/?q=1+Rue+Honor%C3%A9+d'Estienne+d'Orves,+91120+Palaiseau&entry=gmail&source=g>
'Estienne d
<https://maps.google.com/?q=1+Rue+Honor%C3%A9+d'Estienne+d'Orves,+91120+Palaiseau&entry=gmail&source=g>
'Orves, 91120 Palaiseau
<https://maps.google.com/?q=1+Rue+Honor%C3%A9+d'Estienne+d'Orves,+91120+Palaiseau&entry=gmail&source=g>
> On 3 Feb 2018, at 13:03, Rutger Fick ***@***.***> wrote:
>
> So yes matplotlib for visualizations in the examples. Numba and pathos
are
> really optional. I use seaborn for the last correlation plots in the
> AxCaliber example, should that be added too?
>
> On 3 Feb 2018 12:55, "Demian Wassermann" ***@***.***>
wrote:
>
> > https://github.com/AthenaEPI/dmipy/blob/3942f6e9c6b15372fd74ff6b941512
> > 5811bb080b/dmipy/version.py#L60
> >
> > @rutgerfick <https://github.com/rutgerfick> I think that the
dependencies
> > are too lax. We need to add *everything* that the tool needs to import
to
> > run. Boto is just needed for the examples so I added it but is there
> > something missing? I think, for instance, that you are calling
matplotlib
> > from within the modules.
> >
> > —
> > You are receiving this because you were mentioned.
> > Reply to this email directly, view it on GitHub
> > <#1>, or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/AI-
37MMmxni1H7LxsgoSYhPKV-cuY2_xks5tREkygaJpZM4R4JMl>
> > .
> >
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub, or mute the thread.
>
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Not a priority
…--
Demian Wassermann, PhD
[email protected]
Associate Research Professor (CRN)
Parietal Team
INRIA Saclay Ile-de-France
1 Rue Honoré d'Estienne d'Orves, 91120 Palaiseau
On 3 Feb 2018, at 13:09, Rutger Fick ***@***.***> wrote:
Not AS nice but scipy can do correlations and you can somehow make a plot
showing it with matplotlib.
It just takes 7 hours to run the example (fit AxCaliber using mix) so it
can be done for tomorrow. Is it a priority?
On 3 Feb 2018 13:07, "Demian Wassermann" ***@***.***> wrote:
> I dunno. We should at some point reduce the amount of needed dependencies.
> Can we do something nice w/o seaborn?
> --
> Demian Wassermann, PhD
> ***@***.***
> Associate Research Professor (CRN)
> Parietal Team
> INRIA Saclay Ile-de-France
> 1 Rue Honoré d
> <https://maps.google.com/?q=1+Rue+Honor%C3%A9+d'Estienne+d'Orves,+91120+Palaiseau&entry=gmail&source=g>
> 'Estienne d
> <https://maps.google.com/?q=1+Rue+Honor%C3%A9+d'Estienne+d'Orves,+91120+Palaiseau&entry=gmail&source=g>
> 'Orves, 91120 Palaiseau
> <https://maps.google.com/?q=1+Rue+Honor%C3%A9+d'Estienne+d'Orves,+91120+Palaiseau&entry=gmail&source=g>
>
>
>
> > On 3 Feb 2018, at 13:03, Rutger Fick ***@***.***> wrote:
> >
> > So yes matplotlib for visualizations in the examples. Numba and pathos
> are
> > really optional. I use seaborn for the last correlation plots in the
> > AxCaliber example, should that be added too?
> >
> > On 3 Feb 2018 12:55, "Demian Wassermann" ***@***.***>
> wrote:
> >
> > > https://github.com/AthenaEPI/dmipy/blob/3942f6e9c6b15372fd74ff6b941512
> > > 5811bb080b/dmipy/version.py#L60
> > >
> > > @rutgerfick <https://github.com/rutgerfick> I think that the
> dependencies
> > > are too lax. We need to add *everything* that the tool needs to import
> to
> > > run. Boto is just needed for the examples so I added it but is there
> > > something missing? I think, for instance, that you are calling
> matplotlib
> > > from within the modules.
> > >
> > > —
> > > You are receiving this because you were mentioned.
> > > Reply to this email directly, view it on GitHub
> > > <#1>, or mute the thread
> > > <https://github.com/notifications/unsubscribe-auth/AI-
> 37MMmxni1H7LxsgoSYhPKV-cuY2_xks5tREkygaJpZM4R4JMl>
> > > .
> > >
> > —
> > You are receiving this because you authored the thread.
> > Reply to this email directly, view it on GitHub, or mute the thread.
> >
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#1 (comment)>, or mute
> the thread
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> .
>
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Also 7 hours to run a notebook example seems unreasonable. Maybe at add a warning on top of it?
…--
Demian Wassermann, PhD
[email protected]
Associate Research Professor (CRN)
Parietal Team
INRIA Saclay Ile-de-France
1 Rue Honoré d'Estienne d'Orves, 91120 Palaiseau
On 3 Feb 2018, at 13:09, Rutger Fick ***@***.***> wrote:
Not AS nice but scipy can do correlations and you can somehow make a plot
showing it with matplotlib.
It just takes 7 hours to run the example (fit AxCaliber using mix) so it
can be done for tomorrow. Is it a priority?
On 3 Feb 2018 13:07, "Demian Wassermann" ***@***.***> wrote:
> I dunno. We should at some point reduce the amount of needed dependencies.
> Can we do something nice w/o seaborn?
> --
> Demian Wassermann, PhD
> ***@***.***
> Associate Research Professor (CRN)
> Parietal Team
> INRIA Saclay Ile-de-France
> 1 Rue Honoré d
> <https://maps.google.com/?q=1+Rue+Honor%C3%A9+d'Estienne+d'Orves,+91120+Palaiseau&entry=gmail&source=g>
> 'Estienne d
> <https://maps.google.com/?q=1+Rue+Honor%C3%A9+d'Estienne+d'Orves,+91120+Palaiseau&entry=gmail&source=g>
> 'Orves, 91120 Palaiseau
> <https://maps.google.com/?q=1+Rue+Honor%C3%A9+d'Estienne+d'Orves,+91120+Palaiseau&entry=gmail&source=g>
>
>
>
> > On 3 Feb 2018, at 13:03, Rutger Fick ***@***.***> wrote:
> >
> > So yes matplotlib for visualizations in the examples. Numba and pathos
> are
> > really optional. I use seaborn for the last correlation plots in the
> > AxCaliber example, should that be added too?
> >
> > On 3 Feb 2018 12:55, "Demian Wassermann" ***@***.***>
> wrote:
> >
> > > https://github.com/AthenaEPI/dmipy/blob/3942f6e9c6b15372fd74ff6b941512
> > > 5811bb080b/dmipy/version.py#L60
> > >
> > > @rutgerfick <https://github.com/rutgerfick> I think that the
> dependencies
> > > are too lax. We need to add *everything* that the tool needs to import
> to
> > > run. Boto is just needed for the examples so I added it but is there
> > > something missing? I think, for instance, that you are calling
> matplotlib
> > > from within the modules.
> > >
> > > —
> > > You are receiving this because you were mentioned.
> > > Reply to this email directly, view it on GitHub
> > > <#1>, or mute the thread
> > > <https://github.com/notifications/unsubscribe-auth/AI-
> 37MMmxni1H7LxsgoSYhPKV-cuY2_xks5tREkygaJpZM4R4JMl>
> > > .
> > >
> > —
> > You are receiving this because you authored the thread.
> > Reply to this email directly, view it on GitHub, or mute the thread.
> >
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <#1 (comment)>, or mute
> the thread
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> .
>
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I'll change it over the next days then.
…On 3 Feb 2018 13:11, "Demian Wassermann" ***@***.***> wrote:
Not a priority
--
Demian Wassermann, PhD
***@***.***
Associate Research Professor (CRN)
Parietal Team
INRIA Saclay Ile-de-France
1 Rue Honoré d
<https://maps.google.com/?q=1+Rue+Honor%C3%A9+d'Estienne+d'Orves,+91120+Palaiseau&entry=gmail&source=g>
'Estienne d
<https://maps.google.com/?q=1+Rue+Honor%C3%A9+d'Estienne+d'Orves,+91120+Palaiseau&entry=gmail&source=g>
'Orves, 91120 Palaiseau
<https://maps.google.com/?q=1+Rue+Honor%C3%A9+d'Estienne+d'Orves,+91120+Palaiseau&entry=gmail&source=g>
> On 3 Feb 2018, at 13:09, Rutger Fick ***@***.***> wrote:
>
> Not AS nice but scipy can do correlations and you can somehow make a plot
> showing it with matplotlib.
>
> It just takes 7 hours to run the example (fit AxCaliber using mix) so it
> can be done for tomorrow. Is it a priority?
>
> On 3 Feb 2018 13:07, "Demian Wassermann" ***@***.***>
wrote:
>
> > I dunno. We should at some point reduce the amount of needed
dependencies.
> > Can we do something nice w/o seaborn?
> > --
> > Demian Wassermann, PhD
> > ***@***.***
> > Associate Research Professor (CRN)
> > Parietal Team
> > INRIA Saclay Ile-de-France
<https://maps.google.com/?q=Ile-de-France+%0D+%3E+%3E+1+Rue+Honor%C3%A9&entry=gmail&source=g>
> > 1 Rue Honoré
<https://maps.google.com/?q=Ile-de-France+%0D+%3E+%3E+1+Rue+Honor%C3%A9&entry=gmail&source=g>
d
> > <https://maps.google.com/?q=1+Rue+Honor%C3%A9+d'Estienne+d'
Orves,+91120+Palaiseau&entry=gmail&source=g>
> > 'Estienne d
> > <https://maps.google.com/?q=1+Rue+Honor%C3%A9+d'Estienne+d'
Orves,+91120+Palaiseau&entry=gmail&source=g>
> > 'Orves, 91120 Palaiseau
> > <https://maps.google.com/?q=1+Rue+Honor%C3%A9+d'Estienne+d'
Orves,+91120+Palaiseau&entry=gmail&source=g>
> >
> >
> >
> > > On 3 Feb 2018, at 13:03, Rutger Fick ***@***.***>
wrote:
> > >
> > > So yes matplotlib for visualizations in the examples. Numba and
pathos
> > are
> > > really optional. I use seaborn for the last correlation plots in the
> > > AxCaliber example, should that be added too?
> > >
> > > On 3 Feb 2018 12:55, "Demian Wassermann" ***@***.***>
> > wrote:
> > >
> > > > https://github.com/AthenaEPI/dmipy/blob/
3942f6e
> > > > 5811bb080b/dmipy/version.py#L60
> > > >
> > > > @rutgerfick <https://github.com/rutgerfick> I think that the
> > dependencies
> > > > are too lax. We need to add *everything* that the tool needs to
import
> > to
> > > > run. Boto is just needed for the examples so I added it but is
there
> > > > something missing? I think, for instance, that you are calling
> > matplotlib
> > > > from within the modules.
> > > >
> > > > —
> > > > You are receiving this because you were mentioned.
> > > > Reply to this email directly, view it on GitHub
> > > > <#1>, or mute the thread
> > > > <https://github.com/notifications/unsubscribe-auth/AI-
> > 37MMmxni1H7LxsgoSYhPKV-cuY2_xks5tREkygaJpZM4R4JMl>
> > > > .
> > > >
> > > —
> > > You are receiving this because you authored the thread.
> > > Reply to this email directly, view it on GitHub, or mute the thread.
> > >
> >
> > —
> > You are receiving this because you were mentioned.
> > Reply to this email directly, view it on GitHub
> > <#1 (comment)>,
or mute
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auth/AI-37Hl2rnyQglxCcKVYpN5W-iQxylC7ks5tREvjgaJpZM4R4JMl>
> > .
> >
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub, or mute the thread.
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Added timing estimates for fitting data in the notebooks for every example. Will take care of the seaborn dependency later. |
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dmipy/dmipy/version.py
Line 60 in 3942f6e
@rutgerfick I think that the dependencies are too lax. We need to add everything that the tool needs to import to run. Boto is just needed for the examples so I added it but is there something missing? I think, for instance, that you are calling
matplotlibfrom within the modules.The text was updated successfully, but these errors were encountered: