JoalHeagney's profile - activity

I was hoping that list_plot's biggest memory component was just an image, not a dynamic object. I'm assuming this is not true?

I have created a python generator that yeilds a list of single values (e.g. like [1,971,15,341,..]) up to some defined length of n,and wanted to plot them in sagemath.

When I pass the generator to list_plot, I get an error as list_plot only accepts lists, tuples and dictionaries.

Is there any way to get the list_plot behaviour from a generator without converting to a list first (To memory-hungry for my purpose)?

If not, I'm planning to request an enhancement to list_plot, if at all possible.

Rdkit is conda-installed and when you use the official installation instructions, the rdkit goes into the miniconda python library rather than the sagemath python. I have been able to get them together by installing both sage and rdkit using conda, except the conda sage is 8.3, not 8.4.

This is also covered here: [https://ask.sagemath.org/question/100...]

I've also found recently that with sage version 7.6, install.packages won't work unless I specifically set method='wget'. This is using a http mirror, but I don't know if that has anything to do with it.

E.g.

install.packages('automap',method='wget')

Otherwise it complains that it doesn't have a version of that package for the version of R included with sagemath.

E.g.

package ‘automap' is not available (for R version 3.2.4 Revised)

Hi guys. Just playing around with titration curves in water, which is a remarkably difficult problem to do.

Basically I can derive an equation for volume of base versus pH of solution, and plot it.

However, I'd like to swap the x and y axes.

Or do I have to use implicit_plot? :(

Hi guys, this is a little problem I came across a week ago.

I'm trying to define a python function that accepts:
1. a callable sage function (of potentially more than one variable) as the first argument (henceforth called func), and
2. a symbolic variable as the second argument (henceforth called xsub)

My function then needs to define a dummy symbolic variable (t), and substitute xsub with t in func.
I can do this for one variable equations in current 4.8 sagemath, by ignoring the new substitution syntax, but it throws up a depreciation warning (Which I'm assuming will become an error in 5.0).

Here's what my code looks like:

def fracintegral(func,xsub,n,a=0):
    var('t')
    assume(x>a)
    assume(t>a)
    return integrate((x-t)^(n-1)*func(t),t,a,x)

The last line should look something like:

    return integrate((x-t)^(n-1)*func(x=t),t,a,x)

If I try:

    return integrate((x-t)^(n-1)*func(xsub=t),t,a,x)

then substitution of func(x=t) doesn't occur (and the integrate function effectively treats func as a constant with respect to dt).

Trying:

    return integrate((x-t)^(n-1)*func.subs(xsub==t),t,a,x)

So, any idea how a function can accept a symbolic variable, and dynamically substitute out that variable in a callable function?

Okay, finally have most of an answer.

1. Install Humor-Sans.ttf in ~/.fonts (You may have to rename it).

2. Under Linux, the .matplotlib directory lives in ~/.sage. cd into it and remove the fontList.cache

3. Currently, use of constant-value tick_formatters such as pi, e, sqrt(2) will default back to using the normal font - this is unlikely to have a quick solution as the Humor Sans font is missing several mathematical symbols any way.

Hi Antlab. Yup, that's the issue that I found. The problem is that I can't find the .matplotlib on my Linux install, either in the home directory, or in the sage directory.

Hi guys. Attempting to use the xkcd graphics feature that has been recently added to matplotlib from within sagemath.

import matplotlib.pyplot
matplotlib.pyplot.xkcd()
plot(sin(x),(x,-pi,pi),ticks=pi/4,tick_formatter=pi)

Matplotlib throws the following warning:

/home/joal/bin/sage-6.2/local/lib/python2.7/site-packages/matplotlib-1.3\ .1-py2.7-linux-x86_64.egg/matplotlib/font_manager.py:1236: UserWarning: findfont: Font family ['Humor Sans', 'Comic Sans MS'] not found. Falling back to Bitstream Vera Sans (prop.get_family(), self.defaultFamily[fontext]))

I have installed Humor Sans.ttf onto the main system, and into the directory:
/home/joal/bin/sage-6.2/local/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/mpl-data/fonts/

... but don't know how to reset the matplotlib font cache so matplotlib will pay attention to the new font.

[EDIT]

Okay, seem to have part of the solution - need to verify on a Linux machine this weekend.

EDIT of EDIT
The tricks below don't work on LinuxMint.

The font is recognised in the virtualbox image if it is dumped into:
sage-6.2/local/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/mpl-data/fonts/
and renamed Humor-Sans.ttf

Then you need to create a .matplotlib folder in the user directory.
mkdir ~/.matplotlib

The concern is that it now that Humor Sans is used for text font, but not for the numbers on the horizontal and vertical axes. Any suggestions, sagers?

[EDIT]

Which turns out to be a consequence of using the pi tick_formatter.

On the other hand, if you want to use R packages, there are a few that depend on tcl/tk themselves (not just the download gui). Ggplot2 comes to mind. Whether you will be able to use the tcl/tk interfaces within these libraries is moot, but they definitely won't compile/install without them.

Are you thinking of something like this?

def fracintegral(func,xsub,n,a=0):
    t = var('t')
    assume(x>a)
    assume(t>a)
    return integrate((x-t)^(n-1)*func.subs({xsub:t}),t,a,x)

which gives a deprecation-free

sage: var("x y")
(x, y)
sage: f1 = function("f", x)
sage: fracintegral(f1, x, 4)
-integrate((t - x)^3*f(t), t, 0, x)
sage: f2 = function("f", x, y)
sage: fracintegral(f2, y, 4)
-integrate((t - x)^3*f(x, t), t, 0, x)
sage: f3(x,y) = x^2+sin(y)
sage: fracintegral(f3, y, 4)
(x, y) |--> 1/4*x^6 + x^3 - 6*x + 6*sin(x)

I had these issues when first using the binary versions of sagemath. Installing wouldn't work, and the "include directories are empty" message would pop up in sage -R.

Solved it by using the command: sage -fr to force-rebuild the R package. Make sure you have all the build dependencies for libpng, libjpeg, cairo, etc. installed.

Then I could use install.packages("...") from sage -R, the notebook in R mode, or %r-cell mode with no issues.

Now I use a source build/updated version of sage instead.