[WIP] Reorg and adding SC13 content

.gitignore

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+*~
+*.pyc
+node_modules/*

Gruntfile.js

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+/* global module:false */
+module.exports = function(grunt) {
+
+	// Project configuration
+	grunt.initConfig({
+		pkg: grunt.file.readJSON('package.json'),
+		meta: {
+			banner:
+				'/*!\n' +
+				' * reveal.js <%= pkg.version %> (<%= grunt.template.today("yyyy-mm-dd, HH:MM") %>)\n' +
+				' * http://lab.hakim.se/reveal-js\n' +
+				' * MIT licensed\n' +
+				' *\n' +
+				' * Copyright (C) 2013 Hakim El Hattab, http://hakim.se\n' +
+				' */'
+		},
+
+		// Tests will be added soon
+		qunit: {
+			files: [ 'test/**/*.html' ]
+		},
+
+		uglify: {
+			options: {
+				banner: '<%= meta.banner %>\n'
+			},
+			build: {
+				src: 'js/reveal.js',
+				dest: 'js/reveal.min.js'
+			}
+		},
+
+		cssmin: {
+			compress: {
+				files: {
+					'css/reveal.min.css': [ 'css/reveal.css' ]
+				}
+			}
+		},
+
+		sass: {
+			main: {
+				files: {
+					'css/theme/default.css': 'css/theme/source/default.scss',
+					'css/theme/beige.css': 'css/theme/source/beige.scss',
+					'css/theme/night.css': 'css/theme/source/night.scss',
+					'css/theme/serif.css': 'css/theme/source/serif.scss',
+					'css/theme/simple.css': 'css/theme/source/simple.scss',
+					'css/theme/sky.css': 'css/theme/source/sky.scss',
+					'css/theme/moon.css': 'css/theme/source/moon.scss',
+					'css/theme/solarized.css': 'css/theme/source/solarized.scss'
+				}
+			}
+		},
+
+		jshint: {
+			options: {
+				curly: false,
+				eqeqeq: true,
+				immed: true,
+				latedef: true,
+				newcap: true,
+				noarg: true,
+				sub: true,
+				undef: true,
+				eqnull: true,
+				browser: true,
+				expr: true,
+				globals: {
+					head: false,
+					module: false,
+					console: false
+				}
+			},
+			files: [ 'Gruntfile.js', 'js/reveal.js' ]
+		},
+
+		connect: {
+			server: {
+				options: {
+					port: 8000,
+					base: '.'
+				}
+			}
+		},
+
+		zip: {
+			'reveal-js-presentation.zip': [
+				'index.html',
+				'css/**',
+				'js/**',
+				'lib/**',
+				'images/**',
+				'plugin/**'
+			]
+		},
+
+		watch: {
+			main: {
+				files: [ 'Gruntfile.js', 'js/reveal.js', 'css/reveal.css' ],
+				tasks: 'default'
+			},
+			theme: {
+				files: [ 'css/theme/source/*.scss', 'css/theme/template/*.scss' ],
+				tasks: 'themes'
+			}
+		}
+
+	});
+
+	// Dependencies
+	grunt.loadNpmTasks( 'grunt-contrib-jshint' );
+	grunt.loadNpmTasks( 'grunt-contrib-cssmin' );
+	grunt.loadNpmTasks( 'grunt-contrib-uglify' );
+	grunt.loadNpmTasks( 'grunt-contrib-watch' );
+	grunt.loadNpmTasks( 'grunt-contrib-sass' );
+	grunt.loadNpmTasks( 'grunt-contrib-connect' );
+	grunt.loadNpmTasks( 'grunt-zip' );
+
+	// Default task
+	grunt.registerTask( 'default', [ 'jshint', 'cssmin', 'uglify' ] );
+
+	// Theme task
+	grunt.registerTask( 'themes', [ 'sass' ] );
+
+	// Package presentation to archive
+	grunt.registerTask( 'package', [ 'default', 'zip' ] );
+
+	// Serve presentation locally
+	grunt.registerTask( 'serve', [ 'connect', 'watch' ] );
+
+};

examples/data/numbers

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+1 2 
+3 4 
+5 6
+7 8
+9 10

examples/intro/01_hello_world.py

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+#!/usr/bin/env python
+
+import math
+r = math.pi / 2.0
+s = math.sin(r)
+print "Hello world, sin(%f)=%f" % (r,s)

examples/intro/02_write_numbers.py

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+#!/usr/bin/env python
+
+import math
+import os
+
+data_dir = os.path.join(os.path.dirname(__file__), "..", "data")
+infile = os.path.join(data_dir, "numbers")
+outfile = os.path.join(data_dir, "f_numbers")
+
+f = open(infile, 'r')
+g = open(outfile, 'w')
+
+def func(y):
+    if y >= 0.0:
+        return y**5.0*math.exp(-y)
+    else:
+        return 0.0
+
+
+print "Read from", infile
+
+for line in f:
+    line = line.split()
+    x, y = float(line[0]), float(line[1])
+    g.write("%g %12.5e\n" % (x,func(y)))
+
+print "Wrote to", outfile
+f.close(); g.close()

examples/intro/03_call_sys_commands.py

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+#!/usr/bin/env python
+
+import sys
+import os
+
+cmd = 'date'
+output = os.popen(cmd)
+lines = output.readlines()
+fail = output.close()
+
+if fail: print 'You do not have the date command'; sys.exit()
+
+for line in lines:
+    line = line.split()
+    print "The current time is %s on %s %s, %s" %  (line[3],line[2],line[1],line[-1])   

examples/intro/04_regular_expressions.py

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+#!/usr/bin/env python
+
+import os
+import re
+
+data_dir = os.path.join(os.path.dirname(__file__), "..", "data")
+infile = os.path.join(data_dir, "python.bib")
+
+pattern1 = "@Book{(.*),"
+pattern2 = "\s+title\s+=\s+{(.*)},"
+
+print "Reading from", infile
+for line in file(infile):
+    match = re.search(pattern1, line)
+    if match: 
+        print "Found a book with the tag '%s'" % match.group(1)
+
+    match = re.search(pattern2, line)
+    if match:
+        print "The title is '%s'" % match.group(1)

examples/intro/05_debug.py

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+l = range(10)
+
+l[10] = 5

examples/intro/06_simple_plot.py

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+import pylab as pl
+import numpy as np
+
+X = np.linspace(-np.pi, np.pi, 256, endpoint=True)
+C, S = np.cos(X), np.sin(X)
+
+pl.plot(X, C)
+pl.plot(X, S)
+
+#pl.show()
+pl.savefig("foo.png")

examples/intro/07_simple_plot_customize.py

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+import pylab as pl
+import numpy as np
+# Create a figure of size 8x6 points, 80 dots per inch
+pl.figure(figsize=(8, 6), dpi=80)
+# Create a new subplot from a grid of 1x1
+pl.subplot(1, 1, 1)
+X = np.linspace(-np.pi, np.pi, 256, endpoint=True)
+C, S = np.cos(X), np.sin(X)
+# Plot cosine with a blue continuous line of width 1 (pixels)
+pl.plot(X, C, color="blue", linewidth=2.5, linestyle="-")
+# Plot sine with a green continuous line of width 1 (pixels)
+pl.plot(X, S, color="green", linewidth=2.5, linestyle="--") # Set x limits
+pl.xlim(-4.0, 4.0) # Set x ticks
+pl.xticks(np.linspace(-4, 4, 9, endpoint=True)) # Set y limits
+pl.ylim(-1.0, 1.0) # Set y ticks
+pl.yticks(np.linspace(-1, 1, 5, endpoint=True)) # Save figure using 72 dots per inch
+# savefig("exercice_2.png", dpi=72)
+# Show result on screen
+pl.show()

examples/intro/08_simple_plot_legend.py

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+import pylab as pl
+import numpy as np
+# Create a figure of size 8x6 points, 80 dots per inch
+pl.figure(figsize=(8, 6), dpi=80)
+# Create a new subplot from a grid of 1x1
+pl.subplot(1, 1, 1)
+X = np.linspace(-np.pi, np.pi, 256, endpoint=True)
+C, S = np.cos(X), np.sin(X)
+# Plot cosine with a blue continuous line of width 1 (pixels)
+pl.plot(X, C, color="blue", linewidth=2.5, linestyle="-", label="cosine")
+# Plot sine with a green continuous line of width 1 (pixels)
+pl.plot(X, S, color="green", linewidth=2.5, linestyle="--", label="sine") # Set x limits
+pl.xlim(-4.0, 4.0) # Set x ticks
+pl.xticks(np.linspace(-4, 4, 9, endpoint=True)) # Set y limits
+pl.ylim(-1.0, 1.0) # Set y ticks
+pl.yticks(np.linspace(-1, 1, 5, endpoint=True)) # Save figure using 72 dots per inch
+
+pl.legend(loc='upper left')
+
+
+# savefig("exercice_2.png", dpi=72)
+# Show result on screen
+pl.show()

examples/intro/09_simple_plot_spline.py

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+import pylab as pl
+import numpy as np
+# Create a figure of size 8x6 points, 80 dots per inch
+pl.figure(figsize=(8, 6), dpi=80)
+# Create a new subplot from a grid of 1x1
+pl.subplot(1, 1, 1)
+X = np.linspace(-np.pi, np.pi, 256, endpoint=True)
+C, S = np.cos(X), np.sin(X)
+# Plot cosine with a blue continuous line of width 1 (pixels)
+pl.plot(X, C, color="blue", linewidth=2.5, linestyle="-", label="cosine")
+# Plot sine with a green continuous line of width 1 (pixels)
+pl.plot(X, S, color="green", linewidth=2.5, linestyle="--", label="sine") # Set x limits
+pl.xlim(-4.0, 4.0) # Set x ticks
+pl.xticks(np.linspace(-4, 4, 9, endpoint=True)) # Set y limits
+pl.ylim(-1.0, 1.0) # Set y ticks
+pl.yticks(np.linspace(-1, 1, 5, endpoint=True)) # Save figure using 72 dots per inch
+
+
+
+ax = pl.gca() # gca stands for 'get current axis'
+ax.spines['right'].set_color('none') 
+ax.spines['top'].set_color('none') 
+ax.xaxis.set_ticks_position('bottom') 
+ax.spines['bottom'].set_position(('data',0)) 
+ax.yaxis.set_ticks_position('left') 
+ax.spines['left'].set_position(('data',0))
+
+
+pl.legend(loc='upper left')
+
+
+# savefig("exercice_2.png", dpi=72)
+# Show result on screen
+pl.show()

examples/intro/10_histogram.py

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+import pylab
+from numpy import random
+
+pylab.plot(random.randn(10000), 100)
+pylab.show()

examples/intro/11_histogram_2.py

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+import pylab
+
+n, bins, patches = pylab.hist(pylab.randn(1000), 40, normed=1)
+l, = pylab.plot(bins, pylab.normpdf(bins, 0.0, 1.0), 'r--', label='fit', linewidth=3)
+pylab.legend([l, patches[0]], ['fit', 'hist'])
+
+pylab.show()

examples/scale/Bratu3D.pyx

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+from petsc4py.PETSc cimport Vec,  PetscVec
+from petsc4py.PETSc cimport Mat,  PetscMat
+from petsc4py.PETSc cimport DA,   PetscDM
+from petsc4py.PETSc cimport SNES, PetscSNES
+
+from petsc4py.PETSc import Error
+
+cdef extern from "Bratu3Dimpl.h":
+    ctypedef struct Params:
+        double lambda_
+    int FormInitGuess(PetscDM da, PetscVec x, Params *p)
+    int FormFunction (PetscDM da, PetscVec x, PetscVec F, Params *p)
+    int FormJacobian (PetscDM da, PetscVec x, PetscMat J, Params *p)
+
+def formInitGuess(Vec x, DA da, double lambda_):
+    cdef int ierr
+    cdef Params p = {"lambda_" : lambda_}
+    ierr = FormInitGuess(da.dm, x.vec, &p)
+    if ierr != 0: raise Error(ierr)
+
+def formFunction(SNES snes, Vec x, Vec f, DA da, double lambda_):
+    cdef int ierr
+    cdef Params p = {"lambda_" : lambda_}
+    ierr = FormFunction(da.dm, x.vec, f.vec, &p)
+    if ierr != 0: raise Error(ierr)
+
+def formJacobian(SNES snes, Vec x, Mat J, Mat P, DA da, double lambda_):
+    cdef int ierr
+    cdef Params p = {"lambda_" : lambda_}
+    ierr = FormJacobian(da.dm, x.vec, P.mat, &p)
+    if ierr != 0: raise Error(ierr)
+    if J != P: J.assemble() # for matrix-free operator
+    return Mat.Structure.SAME_NONZERO_PATTERN