Fwd: PyData Community Cookbook - August Update

[Stefan van der Walt]

Hi everyone

Is anyone interested in writing a scikit-image chapter for the
following book?

Stéfan

- Original message -
From: Andy Ray Terrel 
Subject: PyData Community Cookbook - August Update
Date: Sat, 20 Aug 2016 07:14:58 -0500

Hello everyone,

You are receiving this email because you were either invited and
committed to join our project. Please feel free to forward this message
to a more appropriate list or person. For questions please email pydata-
cookb...@numfocus.org.

Katy Huff and myself are starting a project to build a cookbook of
advanced material for the PyData community. The cookbook will be
published by Addison-Wesley. We have invited a number of contributors to
see if such a project would have some interest and received
overwhelmingly positive feedback.

The book will cover several major topics, organized as such, with some
sample packages:

- IDE: IPython/Jupyter
- Data Structures / Numerics: NumPy, Pandas, Xray, PyTables
- Viz: Matplotlib, Bokeh, Seaborn, yt
- Algorithms / Science: SciPy, Scikit-learn, Scikit-image, statsmodels,
  sympy, gensim
- Performance / Scale: Cython, Numexpr, Numba, Dask, pyspark


We expect each submission to be about 15 - 20 pages describing an
example of the power of each library. While we have reached out to the
projects about putting each submission together we are happy to accept
chapters for libraries we did not initially identify.

To facilitate the book we have put together a repository for
collecting and reviewing submissions at
https://github.com/pydata/pydata-cookbook . We are asking for
submissions in rst but would appreciate any other files, such as
jupyter notebooks or code, for a digital appendix as well.

If you read this far and are interested in contributing.  The proposed
schedule is the following:

Sept 1: Submit a pull request with a title, abstract and author list for
the submission.
Nov 15: Submit a completed chapter.
Dec 31: Reviews for chapters finished.
Jan 31: All chapter revisions due.

Thanks for you time!


--
Andy R. Terrel, PhD
President, NumFOCUS
a...@numfocus.org

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Task board

[Stefan van der Walt]

Hi, everyone

As Juan mentioned recently, it's becoming harder to keep track of the
motion of the project as a whole.  Sometimes, tickets lounge unattended
for an unacceptable long time.

I can think of two main routes for improving the situation:

1) Improve our team structure, so that individuals take responsibility
for moving certain aspects of the project forward. 
2) Processes / systems to help us get a grasp on the current state of
things

I have some ideas around (1) that need fleshing out, but in the mean
time I was looking at http://zube.io to address part of (2).

Do you have any experience with this system?  Zube can be compared
against HuBoard, gh-board, and ZenHub.  A test scikit-image board is
here: https://zube.io/projects/4670/kanban  (it's vanilla, I haven't
done anything with it yet)

Let me hear your thoughts.

Stéfan

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Re: Fwd: PyData Community Cookbook - August Update

[Emmanuelle Gouillart]

Hi Stéfan,

is it something that we could re-use for the documentation of
scikit-image, in the user guide for example?

Best
Emma

On Mon, Aug 29, 2016 at 01:13:33PM -0700, Stefan van der Walt wrote:
> Hi everyone

> Is anyone interested in writing a scikit-image chapter for the following book?

> Stéfan

> - Original message -
> From: Andy Ray Terrel 
> Subject: PyData Community Cookbook - August Update
> Date: Sat, 20 Aug 2016 07:14:58 -0500

> Hello everyone,

> You are receiving this email because you were either invited and committed to
> join our project. Please feel free to forward this message to a more
> appropriate list or person. For questions please email
> pydata-cookb...@numfocus.org.

> Katy Huff and myself are starting a project to build a cookbook of advanced
> material for the PyData community. The cookbook will be published by
> Addison-Wesley. We have invited a number of contributors to see if such a
> project would have some interest and received overwhelmingly positive
> feedback. 

> The book will cover several major topics, organized as such, with some sample
> packages:

> - IDE: IPython/Jupyter
> - Data Structures / Numerics: NumPy, Pandas, Xray, PyTables
> - Viz: Matplotlib, Bokeh, Seaborn, yt
> - Algorithms / Science: SciPy, Scikit-learn, Scikit-image, statsmodels, sympy,
> gensim
> - Performance / Scale: Cython, Numexpr, Numba, Dask, pyspark


> We expect each submission to be about 15 - 20 pages describing an example of
> the power of each library. While we have reached out to the projects about
> putting each submission together we are happy to accept chapters for libraries
> we did not initially identify.

> To facilitate the book we have put together a repository for collecting and
> reviewing submissions at https://github.com/pydata/pydata-cookbook . We are
> asking for submissions in rst but would appreciate any other files, such as
> jupyter notebooks or code, for a digital appendix as well.

> If you read this far and are interested in contributing.  The proposed 
> schedule
> is the following:

> Sept 1: Submit a pull request with a title, abstract and author list for the
> submission.
> Nov 15: Submit a completed chapter.
> Dec 31: Reviews for chapters finished.
> Jan 31: All chapter revisions due.

> Thanks for you time!

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Re: Task board

[Emmanuelle Gouillart]

Hi Stéfan,

thanks for continuing the discussion on this important subject. I would
reformulate your two points as 1) social aspects/community management and
2) technical tools and processes. 

In my opinion, we need a little bit of both. Dashboards can be useful if
they save time and provide meaningful information that would be painful
to retrieve otherwise. One should nevertheless be wary of too many
metrics and quantitative indices (a problem that cripples the
creativity of scientific research!): it is sometimes very tempting to
merge two small PRs instead of spending time on a single difficult one.

I don't have much to say about the 2nd point since I don't know the tool.
For the 1st point, here are some ideas and suggestions from the top of my
head
- assigning / self-assigning PRs might be a good idea, as Juan suggested
- when a PR is stalling and the contributor is not responding, we should
  either take over if possible, or close it after some warnings.
- keeping a good balance between the number of active contributors and
active reviewers is hard. Recently several people have contributed
several PRs, demonstrating an expertise in some domain of image
processing. Maybe we should ask them whether they would be willing to
review PRs and be more active in including these persons. 
- in the core team, maybe we should say more explicitely when we are or
  are not available (announce it somewhere? have a google calendar?). I
know that there are periods of time where I can't spend any time on
scikit-image, it can be weeks or even months. If the rest of the team
had such information for every core member, it would save time
because someone else could try to take over. We could also have pairs of
people with similar expertise (segmentation, computer vision,
architecture, etc.), who could work in pairs and replace the other person
when one is not available.
- we could take turns to be in charge of checking the global advance of
PRs. It's a pain of a job, but if it's one week every two months it's
not so bad.

Here are my 2 cents. I think it's a question of focussing our resources
better, and maybe empowering new people, because I'm not sure we can
spend much more time on the reviewing process.

Cheers,
Emma

On Mon, Aug 29, 2016 at 01:17:48PM -0700, Stefan van der Walt wrote:
> Hi, everyone

> As Juan mentioned recently, it's becoming harder to keep track of the
> motion of the project as a whole.  Sometimes, tickets lounge unattended
> for an unacceptable long time.

> I can think of two main routes for improving the situation:

> 1) Improve our team structure, so that individuals take responsibility
> for moving certain aspects of the project forward. 
> 2) Processes / systems to help us get a grasp on the current state of
> things

> I have some ideas around (1) that need fleshing out, but in the mean
> time I was looking at http://zube.io to address part of (2).

> Do you have any experience with this system?  Zube can be compared
> against HuBoard, gh-board, and ZenHub.  A test scikit-image board is
> here: https://zube.io/projects/4670/kanban  (it's vanilla, I haven't
> done anything with it yet)

> Let me hear your thoughts.

> Stéfan

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Inclusive community statement

[Stefan van der Walt]

Dear contributors and users

You may know that I am not very fond of Codes of Conduct in general.  I
think they are well intentioned, but they are also often aggressive, use
words more commonly associated with law enforcement, and may leave one
feeling a tad scared and unenthusiastic.

At the same time, I do think it is important to be inviting to newcomers
of all groups, and to make that clear on our website.

What would you say to a "Community Guidelines" or "How We Work
(together)" statement on the scikit-image front page?

Something along the lines of:

"We welcome each and every contributor to scikit-image.  Our aim is
enthusiastic and productive collaboration, to build an excellent
software library, and to have a ton of fun doing it.  We encourage one
another to be gentle in criticism of others' work, humble in
acknowledging our own mistakes, and generous in our praise.

If you ever feel like you are not being treated as well as you should,
please get in touch with one of the project leads.  We are committed to
making this community a safe and welcome space."

Best regards
Stéfan

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Re: Image edge detection

[Dipankar “Dipu” Ganguly]

Hi:

I have ImageJ installed on the same Mac that I am using to develop IPython 
Image Processing algorithms under Anaconda Navigator’s Jupyter. Can I load 
ImageJ as a package in my Image Processing environment and call its functions 
as I do with Scikit-image?

Thanks

Dipu

Dipankar “Dipu” Ganguly
dipu...@gmail.com
Cell: 408-203-8814







> On Aug 8, 2016, at 5:24 PM, Stéfan van der Walt  wrote:
> 
> Hi Dipu
> 
> Please try one of the examples from the gallery:
> 
> http://scikit-image.org/docs/dev/auto_examples/ 
> 
> 
> Stéfan
> 
> On 8 August 2016 at 17:09, Dipankar Ganguly  > wrote:
> I am trying to do an image edge detection project using Python 3.5 under 
> Jupyter on Anaconda's Navigator on my Mac running OS 10.11.6. I have verified 
> that  the Envirnoment does have scikit-image installed   I have run into this 
> at the very outset.
> 
> _
>  File "", line 1
> import scikit-image as image
>  ^
> SyntaxError: invalid syntax
> __
> 
> How do I solve this? Is there a more recent package I should be using?
> 
> Thanks.
> 
> Dipu
> 
> 
> 
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