From efiring at hawaii.edu  Mon Jun  5 15:56:36 2017
From: efiring at hawaii.edu (Eric Firing)
Date: Mon, 5 Jun 2017 09:56:36 -1000
Subject: [Matplotlib-devel] weekly meeting
Message-ID: <f5b875e7-c954-b46b-5156-d93b1154b5b6@hawaii.edu>

Participants were Paul Hobson and myself.  We discussed and merged one 
PR, at which point github went down, so we ended the meeting.  (The 
github outage turned out to be brief.)

Eric

From isaac.gerg at gergltd.com  Tue Jun  6 09:41:07 2017
From: isaac.gerg at gergltd.com (Isaac Gerg)
Date: Tue, 6 Jun 2017 09:41:07 -0400
Subject: [Matplotlib-devel] ylabels offset in box and whisker plots
Message-ID: <CADnN3yUKg7hgjdZP6dYx_F3Hohb9n3qGUKBijoTCPYG-2ABOkQ@mail.gmail.com>

Any idea why this is happening?


Code...
    # Boxplot
    plt.clf()
    fig = matplotlib.pyplot.gcf()
    fig.set_size_inches(9,16)
    plt.rc('lines', **{'marker':None})
    plt.grid(True)
    data = r.copy()/100
    data = np.log10(data)
    data[np.isinf(data)] = np.nan
    idx = np.nanmedian(data.T, axis=0).argsort()
    data = data[idx, :]
    newGenii = []
    z = []
    for k in idx:
        newGenii.append(genii[k])
    for k in range(data.shape[0]):
        tmp = data.T[:,k]
        tmp = tmp[np.isfinite(tmp)]
        z.append(tmp)
    plt.boxplot(z, notch = False, vert = False, whis=[5,95], sym='')
    plt.yticks(np.arange(data.shape[0]), newGenii, size='xx-small')
    plt.xlabel('Log10 Abundance')
    plt.title('Genus -- Box and Whisker')
    plt.savefig(os.path.join(baseDir, 'box and whisker.png'))
    plt.close('all')


[image: Inline image 1]
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From isaac.gerg at gergltd.com  Tue Jun  6 12:02:06 2017
From: isaac.gerg at gergltd.com (Isaac Gerg)
Date: Tue, 6 Jun 2017 12:02:06 -0400
Subject: [Matplotlib-devel] ylabels offset in box and whisker plots
In-Reply-To: <1CC22032-8AE8-47F6-8769-84AC7C232865@uvic.ca>
References: <CADnN3yUKg7hgjdZP6dYx_F3Hohb9n3qGUKBijoTCPYG-2ABOkQ@mail.gmail.com>
 <1CC22032-8AE8-47F6-8769-84AC7C232865@uvic.ca>
Message-ID: <CADnN3yXxw64zD_f3XYFUhy6U9FwXDjLv4Z8NVY8koH-UOqHYFw@mail.gmail.com>

I fixed it by adding 1 to the arange in yticks.  No idea though why i need
this.

On Tue, Jun 6, 2017 at 11:58 AM, Jody Klymak <jklymak at uvic.ca> wrote:

> On 6 Jun 2017, at 6:41, Isaac Gerg wrote:
>
> Any idea why this is happening?
>
>
> Code...
> # Boxplot
> plt.clf()
> fig = matplotlib.pyplot.gcf()
>
> Try to supply a self-contained minimal working example
> <https://en.wikipedia.org/wiki/Minimal_Working_Example>. What is
> happening that you don?t think should happen?
>
> Cheers, Jody
>
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From jklymak at uvic.ca  Tue Jun  6 11:58:37 2017
From: jklymak at uvic.ca (Jody Klymak)
Date: Tue, 06 Jun 2017 08:58:37 -0700
Subject: [Matplotlib-devel] ylabels offset in box and whisker plots
In-Reply-To: <CADnN3yUKg7hgjdZP6dYx_F3Hohb9n3qGUKBijoTCPYG-2ABOkQ@mail.gmail.com>
References: <CADnN3yUKg7hgjdZP6dYx_F3Hohb9n3qGUKBijoTCPYG-2ABOkQ@mail.gmail.com>
Message-ID: <1CC22032-8AE8-47F6-8769-84AC7C232865@uvic.ca>


On 6 Jun 2017, at 6:41, Isaac Gerg wrote:

> Any idea why this is happening?
>
>
> Code...
>     # Boxplot
>     plt.clf()
>     fig = matplotlib.pyplot.gcf()
>

Try to supply a self-contained [minimal working 
example](https://en.wikipedia.org/wiki/Minimal_Working_Example).  What 
is happening that you don?t think should happen?

Cheers,  Jody

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From tcaswell at gmail.com  Thu Jun  8 10:42:17 2017
From: tcaswell at gmail.com (Thomas Caswell)
Date: Thu, 08 Jun 2017 14:42:17 +0000
Subject: [Matplotlib-devel] added lgtm PR integration
Message-ID: <CAA48SF8zVZ_S=nOMCiMqy2kfHdmLWJMK_qGDD04VQFgJ3aX3OQ@mail.gmail.com>

Folks,

I added PR integration for
https://lgtm.com/projects/g/matplotlib/matplotlib/ .

We have had two PRs based on issues this service, lets give it a whirl as a
CI.

Tom
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From jklymak at uvic.ca  Tue Jun 13 16:16:51 2017
From: jklymak at uvic.ca (Jody Klymak)
Date: Tue, 13 Jun 2017 13:16:51 -0700
Subject: [Matplotlib-devel] Documentation: only building one tutorial...
Message-ID: <A6389C21-075A-48AE-BE75-D665837477CF@uvic.ca>

	
Hi all,

I think I asked this before last time I contributed to the tutorials, 
but is there some way to just build the docs of one tutorial at a time 
as I edit?

Thanks,   Jody

From antony.lee at berkeley.edu  Thu Jun 29 03:49:50 2017
From: antony.lee at berkeley.edu (Antony Lee)
Date: Thu, 29 Jun 2017 00:49:50 -0700
Subject: [Matplotlib-devel] A (new) cairo backend for matplotlib
Message-ID: <CAGRr6BE7nCS-zr48DedvNzTzGtQ3hj8DeJhvjF_esh00ejuT6A@mail.gmail.com>

Hi all,

Following my frustration with the somewhat incomprehensible (... to me) Agg
backend codebase, and as recently mentioned on the gitter channel, I have
hacked together a mostly complete native cairo backend for matplotlib.  See
https://github.com/anntzer/mpl_cairo (which also lists the missing features
that I can see).  It is based on pybind11 and requires a C++ compiler with
C++17 support (e.g., GCC 7.1).

One of the original motivations was to get rid of the "inaccurate marker
stamping" issue (https://github.com/matplotlib/matplotlib/issues/7262,
https://github.com/matplotlib/matplotlib/issues/7233).  Yes, I could have
tried to revert the original patch too...  The repository contains a few
examples where the new cairo backend places markers much more accurately.

Removing that optimization means that the backend is a bit slower than Agg
for drawing markers (though not more than ~1.5x); for other tasks it
appears to be nearly as fast.  It is dramatically faster than the current
(somewhat buggy) pycairo/cairocffi-based cairo backend (gtk3cairo, and
qt5cairo with https://github.com/matplotlib/matplotlib/pull/8771).

Being a native backend allows us to directly call libraries such as
freetype (bypassing -- in part -- the longstanding suggestion that ft2font
needs to be rewritten); it should likewise be possible to support complex
text layout (http://matplotlib.org/devel/MEP/MEP14.html) with the
appropriate library (from a quick search,
https://github.com/HOST-Oman/libraqm seems to be an interesting
possibility).  Additionally, cairo itself has an OpenGL (cairo-gl) backend,
which we may look into (currently, the cairo calls go into an image buffer
which is then picked up by the GUI toolkit for display; the idea would be
to instead use the cairo-gl backend to directly render to the display).

I am not making a PR out of this backend *yet* mostly due to the dependency
on a very recent compiler, which I believe would not be acceptable to many,
and would probably require delving into the build scripts.  Note that even
if I remove the C++17-isms from the codebase (which I'd rather not do --
"auto [x, y] = ..." is quite nice), pybind11 requires C++11 and suggests
using a C++14 compiler.  Additionally, the backend depends on a number of
other large (current) PRs which do not seem close to get in (as listed in
the README).  But I'd appreciate if you give it a try and give me some
feedback.

Antony
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From njs at pobox.com  Thu Jun 29 04:32:28 2017
From: njs at pobox.com (Nathaniel Smith)
Date: Thu, 29 Jun 2017 01:32:28 -0700
Subject: [Matplotlib-devel] A (new) cairo backend for matplotlib
In-Reply-To: <CAGRr6BE7nCS-zr48DedvNzTzGtQ3hj8DeJhvjF_esh00ejuT6A@mail.gmail.com>
References: <CAGRr6BE7nCS-zr48DedvNzTzGtQ3hj8DeJhvjF_esh00ejuT6A@mail.gmail.com>
Message-ID: <CAPJVwBnKSe2yuLPNsuGNCRqABSR5XbV=E=aw+oFrGVNn0kg43w@mail.gmail.com>

On Thu, Jun 29, 2017 at 12:49 AM, Antony Lee <antony.lee at berkeley.edu> wrote:
> I am not making a PR out of this backend *yet* mostly due to the dependency
> on a very recent compiler, which I believe would not be acceptable to many,
> and would probably require delving into the build scripts.  Note that even
> if I remove the C++17-isms from the codebase (which I'd rather not do --
> "auto [x, y] = ..." is quite nice), pybind11 requires C++11 and suggests
> using a C++14 compiler.

FWIW, the manylinux1 compiler (gcc 4.8.2) can only handle C++11. There
should be a manylinux2 coming along eventually (i.e., as soon as
someone steps up to do it, could be tomorrow, could be next year),
which will be able to use gcc 6.2.1. It looks like 6.2.1 has full
support for C++14 and partial support for C++17:
https://gcc.gnu.org/projects/cxx-status.html

-n

-- 
Nathaniel J. Smith -- https://vorpus.org

From jklymak at gmail.com  Tue Jun 13 09:24:08 2017
From: jklymak at gmail.com (Jody Klymak)
Date: Tue, 13 Jun 2017 13:24:08 -0000
Subject: [Matplotlib-devel] step-by-step to installling from source using
 conda?
Message-ID: <EB4704F0-3BE6-4D40-8796-E41741BD237D@gmail.com>

	
Hi all,

I?m somewhat stymied trying to understand how to install matplotlib in 
a development environment using conda.

I have MacOS, and I have brew gcc etc.  I know how to set up a env in 
conda.

I eventually want to be able to run the tests, so that I can stop 
uploading things with PEP8 errors etc.

Sorry if this is too vague.  I can start over again and send specific 
errors if that is easier, but I would bet someone has a step-by-step.

Thanks,   Jody
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