diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index 0a33c14..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,10 +0,0 @@
-# ignore tex compilation files (created by emacs and latex)
-*.aux
-*.log
-*.gz
-index.html
-sheet.html
-template.html
-github.css
-auto/*
-
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index c508a99..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,17 +0,0 @@
-language: python
-
-before_install:
- - sudo apt-get install pandoc
-
-python:
- - "2.7"
-
-install:
- - pip install markdown
- - pip install beautifulsoup4
-
-script:
- - python create-index-html.py
-
-after_success:
- - bash deploy.sh
\ No newline at end of file
diff --git a/LICENSE b/LICENSE
deleted file mode 100644
index 1eea43a..0000000
--- a/LICENSE
+++ /dev/null
@@ -1,395 +0,0 @@
-Attribution 4.0 International
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diff --git a/README.md b/README.md
deleted file mode 100644
index 3ba0fe8..0000000
--- a/README.md
+++ /dev/null
@@ -1,48 +0,0 @@
-[](https://travis-ci.org/IPGP/scientific_python_cheat_sheet)
-
-# Scientific Python Cheat Sheet
-
-## Overview
-This is an overview of python, numpy, scipy, matplotlib functions that are
-useful for scientific work. It tries to keep examples as compact as possible.
-
-Chose one of the following layouts:
-* [website](https://ipgp.github.io/scientific_python_cheat_sheet)
-* [markdown](sheet.md)
-
-Or the print version (without pandas until there are enough commands for a
-third page)
-
-* [high contrast pdf (2016-06-16)](https://github.com/IPGP/scientific_python_cheat_sheet/raw/master/print_version/high_contrast.pdf)
-* [low contrast pdf (2016-06-16)](https://github.com/IPGP/scientific_python_cheat_sheet/raw/master/print_version/low_contrast.pdf)
-
-## Printing
-Printing the last version is a bit complicated so far if you want to have the
-same layout as on the webpage but possible: You can save the CSS layout as an
-image in firefox:
-
-1. use `shift + f2` to open the web console.
-2. Arange the page as you want to print it. We found that two columns is
- suitable for printing on A3 pages. You can either resize your browser or use
- the built-in zoom function for this (e.g. ctrl + mousewheel on firefox).
-3. The command `screenshot out.png --fullpage` saves the current complete view
- of the page to the download folder.
-4. Print the long image on several papers or cut it in pieces with the image
- software of your choice (e.g. gimp or inkscape).
-
-Hopefully this will be simpler in the future !
-
-## Contributing
-If you wish to contribute, you only need to edit the file [sheet.md](sheet.md)
-and push it to the master branch (preferably via pull-request). The website
-updates automatically.
-
-If, beyond your knowledge of Python, you also master HTML and CSS, you can also
-contribute to the design of the website. You can submit your ideas via the
-issues section or directly via pull-request.
-
-## Reference:
-Authors: A few scientists
-
-## License:
-[Creative Commons (CC-BY-4.0)](LICENSE)
diff --git a/create-index-html.py b/create-index-html.py
deleted file mode 100644
index 835b071..0000000
--- a/create-index-html.py
+++ /dev/null
@@ -1,151 +0,0 @@
-#!/usr/bin/env python
-
-"""
-A script to generate a file named index.html from sheet.md and templace.html
-"""
-
-from bs4 import BeautifulSoup
-import markdown
-import subprocess
-
-
-top = """
-
-
-
-
-
-
- Scientific python cheat sheet by IPGP
-
-
-
-
-
-
-
-
-
-
-
-
-"""
-
-
-bottom = """
-
-
-
-
-
-
-
-"""
-
-input_file = "sheet.md"
-output_file = "sheet.html"
-
-try:
- cmd = "pandoc {} -s -o {}".format(input_file,
- output_file)
- print cmd
- subprocess.call(cmd, shell=True)
- soup_sheet = BeautifulSoup(open(output_file), "html.parser")
- list_html = map(str, list(soup_sheet.body.children))
- sheet_html = ''.join(list_html)
- print "went the pandoc way"
-except:
- print "pandoc failed, using shitty markdown"
- with open(input_file, "r") as f:
- text = f.read()
- sheet_html = markdown.markdown(text)
-
-sheet_html_lines = sheet_html.split("\n")
-f = open("index.html", "w")
-flag_first_h2 = False
-flag_first_h3 = False
-f.write(top+"\n")
-for line in sheet_html_lines:
- if "markdown-toc" in line:
- continue
-
- if "h1" in line:
- # start table of contents group after main header
- f.write(line)
- f.write('\n
\n')
- elif "h2" in line:
- if flag_first_h2:
- # ends the section AND the subsection
- f.write('
\n\n\n')
- f.write(line+"\n")
- f.write('
\n')
- flag_first_h3 = False
- else:
- # end table of contents and begin first group
- f.write('
\n\n')
- f.write(line+"\n")
- f.write('
\n')
- flag_first_h2 = True
- elif "h3" in line:
- if flag_first_h3:
- # ends only a subsection
- f.write('
d = [nu**2for nu in b if nu < 3] # conditioned list comprehension
e = c[0] # access element
f = c[1:2] # access a slice of the list
-g = ['re', 'bl'] + ['gr'] # list concatenation
-h = ['re'] * 5# repeat a list
+g = c[-1] # access last element
+h = ['re', 'bl'] + ['gr'] # list concatenation
+i = ['re'] * 5# repeat a list
['re', 'bl'].index('re') # returns index of 're'
+a.append('yellow') # add new element to end of list
+a.extend(b) # add elements from list `b` to end of list `a`
+a.insert(1, 'yellow') # insert element in specified position're' in ['re', 'bl'] # true if 're' in list
-sorted([3, 2, 1]) # returns sorted list
+'fi' not in ['re', 'bl'] # true if 'fi' not in list
+sorted([3, 2, 1]) # returns sorted list
+a.pop(2) # remove and return item at index (default last)
Dictionaries
a = {'red': 'rouge', 'blue': 'bleu'} # dictionary
b = a['red'] # translate item
+'red' in a # true if dictionary a contains key 'red'
c = [value for key, value in a.items()] # loop through contents
-d = a.get('yellow', 'no translation found') # return default
+d = a.get('yellow', 'no translation found') # return default
+a.setdefault('extra', []).append('cyan') # init key with default
+a.update({'green': 'vert', 'brown': 'brun'}) # update dictionary by data from another one
+a.keys() # get list of keys
+a.values() # get list of values
+a.items() # get list of key-value pairs
+del a['red'] # delete key and associated with it value
+a.pop('blue') # remove specified key and return the corresponding value
+
+
+
Sets
+
a = {1, 2, 3} # initialize manually
+b = set(range(5)) # initialize from iteratable
+a.add(13) # add new element to set
+a.discard(13) # discard element from set
+a.update([21, 22, 23]) # update set with elements from iterable
+a.pop() # remove and return an arbitrary set element
+2 in {1, 2, 3} # true if 2 in set
+5 not in {1, 2, 3} # true if 5 not in set
+a.issubset(b) # test whether every element in a is in b
+a <= b # issubset in operator form
+a.issuperset(b) # test whether every element in b is in a
+a >= b # issuperset in operator form
+a.intersection(b) # return the intersection of two sets as a new set
+a.difference(b) # return the difference of two or more sets as a new set
+a - b # difference in operator form
+a.symmetric_difference(b) # return the symmetric difference of two sets as a new set
+a.union(b) # return the union of sets as a new set
+c = frozenset() # the same as set but immutable
Strings
@@ -225,7 +265,7 @@
Functions, Classes, Generators,
x = Point(3)
# Generator iterates without
-# creating all values at ones
+# creating all values at oncedef firstn(n):
num = 0while num < n:
@@ -254,22 +294,23 @@
Functions, Classes, Generators,
IPython
-
Python console
-
<object>? # Information about the object
-<object>.<TAB> # tab completion
+
console
+
<object>? # Information about the object
+<object>.<TAB> # tab completion
-# measure runtime of a function:
-%timeit range(1000)
-100000 loops, best of 3: 7.76 us per loop
+# run scripts / profile / debug
+%run myscript.py
-# run scripts and debug
-%run
-%run -d # run in debug mode
-%run -t # measures execution time
-%run -p # runs a profiler
-%debug # jumps to the debugger after an exception
+%timeit range(1000) # measure runtime of statement
+%run -t myscript.py # measure script execution time
-%pdb # run debugger automatically on exception
+%prun <statement> # run statement with profiler
+%prun -s <key> <statement> # sort by key, e.g. "cumulative" or "calls"
+%run -p myfile.py # profile script
+
+%run -d myscript.py # run script in debug mode
+%debug # jumps to the debugger after an exception
+%pdb # run debugger automatically on exception# examine history
%history
@@ -279,10 +320,13 @@
Python console
!make # prefix command with "!"# clean namespace
-%reset
+%reset
+
+# run code from clipboard
+%paste
-
Debugger commands
+
debugger
n # execute next line
b 42# set breakpoint in the main file at line 42
b myfile.py:42# set breakpoint in 'myfile.py' at line 42
@@ -295,6 +339,11 @@
Debugger commands
pp locals() # show all variables in local scope
pp globals() # show all variables in global scope
+
+
command line
+
ipython --pdb -- myscript.py argument1 --option1 # debug after exception
+ipython -i -- myscript.py argument1 --option1 # console after finish
+
NumPy (import numpy as np)
@@ -317,6 +366,7 @@
indexing
a = np.arange(100) # initialization with 0 - 99
a[:3] = 0# set the first three indices to zero
a[2:5] = 1# set indices 2-4 to 1
+a[:-3] = 2# set all but last three elements to 2
a[start:stop:step] # general form of indexing/slicing
a[None, :] # transform to column vector
a[[1, 1, 3, 8]] # return array with values of the indices
@@ -334,11 +384,14 @@
array properties and operations
a.flatten() # collapse array to one dimension
a.conj() # return complex conjugate
a.astype(np.int16) # cast to integer
+a.tolist() # convert (possibly multidimensional) array to list
np.argmax(a, axis=1) # return index of maximum along a given axis
np.cumsum(a) # return cumulative sum
np.any(a) # True if any element is True
np.all(a) # True if all elements are True
-np.argsort(a, axis=1) # return sorted index array along axis
+np.argsort(a, axis=1) # return sorted index array along axis
+np.where(cond) # return indices where cond is True
+np.where(cond, x, y) # return elements from x or y depending on cond
boolean arrays
@@ -365,7 +418,7 @@
elementwise operations and ma
np.std(a, axis=1) # standard deviation
-
inner / outer products
+
inner/ outer products
np.dot(a, b) # inner product: a_mi b_in
np.einsum('ij,kj->ik', a, b) # einstein summation convention
np.sum(a, axis=1) # sum over axis 1
@@ -376,12 +429,19 @@
inner / outer products
np.sum(a * a.T) # matrix norm
+
linear algebra/ matrix math
+
evals, evecs = np.linalg.eig(a) # Find eigenvalues and eigenvectors
+evals, evecs = np.linalg.eigh(a) # np.linalg.eig for hermitian matrix
+
+
reading/ writing files
-np.fromfile(fname/fobject, dtype=np.float32, count=5) # binary data from file
np.loadtxt(fname/fobject, skiprows=2, delimiter=',') # ascii data from file
np.savetxt(fname/fobject, array, fmt='%.5f') # write ascii data
-np.tofile(fname/fobject) # write (C) binary data
+np.fromfile(fname/fobject, dtype=np.float32, count=5) # binary data from file
+np.tofile(fname/fobject) # write (C) binary data
+np.save(fname/fobject, array) # save as numpy binary (.npy)
+np.load(fname/fobject, mmap_mode='c') # load .npy file (memory mapped)
interpolation, integration, optimization
@@ -419,9 +479,11 @@
Matplotlib (import mat
figures and axes
fig = plt.figure(figsize=(5, 2)) # initialize figure
-ax = fig.add_subplot(3, 2, 2) # add second subplot in a 3 x 2 grid
+fig.savefig('out.png') # save png image
fig, axes = plt.subplots(5, 2, figsize=(5, 5)) # fig and 5 x 2 nparray of axes
-ax = fig.add_axes([left, bottom, width, height]) # add custom axis
+ax = fig.add_subplot(3, 2, 2) # add second subplot in a 3 x 2 grid
+ax = plt.subplot2grid((2, 2), (0, 0), colspan=2) # multi column/row axis
+ax = fig.add_axes([left, bottom, width, height]) # add custom axis
figures and axes properties
@@ -453,7 +515,8 @@
plotting routines
ax.imshow(matrix, origin='lower',
extent=(x1, x2, y1, y2)) # show image
ax.specgram(y, FS=0.1, noverlap=128,
- scale='linear') # plot a spectrogram
+ scale='linear') # plot a spectrogram
+ax.text(x, y, string, fontsize=12, color='m') # write text
@@ -461,15 +524,28 @@
Scipy (import scipy as sci)
interpolation
-
from scipy.ndimage import map_coordinates # interpolates data
-pts_new = map_coordinates(data, float_indices, # at index positions
- order=3)
+
# interpolate data at index positions:
+from scipy.ndimage import map_coordinates
+pts_new = map_coordinates(data, float_indices, order=3)
+
+# simple 1d interpolator with axis argument:
+from scipy.interpolate import interp1d
+interpolator = interp1d(x, y, axis=2, fill_value=0., bounds_error=False)
+y_new = interpolator(x_new)
Integration
from scipy.integrate import quad # definite integral of python
value = quad(func, low_lim, up_lim) # function/method
df = pd.read_csv("filename.csv") # read and load CSV file in a DataFrame
-print(df[:2]) # print first 2 lines of the DataFrame
-raw = df.values # get raw data out of DataFrame object
-cols = df.columns # get list of columns headers
+
df = pd.read_csv("filename.csv") # read and load CSV file in a DataFrame
+raw = df.values # get raw data out of DataFrame object
+cols = df.columns # get list of columns headers
+df.dtypes # get data types of all columns
+df.head(5) # get first 5 rows
+df.describe() # get basic statisitics for all columns
+df.index # get index column range
+
+#column slicin
+# (.loc[] and .ix[] are inclusive of the range of values selected)
+df.col_name # select column values as a series by column name (not optimized)
+df[['col_name']] # select column values as a dataframe by column name (not optimized)
+df.loc[:, 'col_name'] # select column values as a series by column name
+df.loc[:, ['col_name']] # select column values as a dataframe by column name
+df.iloc[:, 0] # select by column index
+df.iloc[:, [0]] # select by column index, but as a dataframe
+df.ix[:, 'col_name'] # hybrid approach with column name
+df.ix[:, 0] # hybrid approach with column index
+
+# row slicin
+print(df[:2]) # print first 2 rows of the dataframe
+df.iloc[0:2, :] # select first 2 rows of the dataframe
+df.loc[0:2,'col_name'] # select first 3 rows of the dataframe
+df.loc[0:2, ['col_name1', 'col_name3', 'col_name6']] # select first 3 rows of the 3 different columns
+df.iloc[0:2,0:2] # select fisrt 3 rows and first 3 columns
+# Again, .loc[] and .ix[] are inclusive
+
+# Dicin
+df[ df.col_name < 7 ] # select all rows where col_name < 7
+df[ (df.col_name1 < 7) & (df.col_name2 == 0) ] # combine multiple boolean indexing conditionals using bit-wise logical operators.
+ # Regular Python boolean operators (and, or) cannot be used here.
+ # Be sure to encapsulate each conditional in parenthesis to make this work.
+df[df.recency < 7] = -100# writing to slice
diff --git a/_site/params.json b/params.json
similarity index 100%
rename from _site/params.json
rename to params.json
diff --git a/print_version/generate_pdf.sh b/print_version/generate_pdf.sh
deleted file mode 100755
index 266575d..0000000
--- a/print_version/generate_pdf.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-convert page1.png page2.png -page a3 -level 50%,93% -colors 64 high_contrast.pdf
-
-convert page1.png page2.png -page a3 -colors 64 low_contrast.pdf
diff --git a/print_version/high_contrast.pdf b/print_version/high_contrast.pdf
deleted file mode 100644
index 27a24f6..0000000
Binary files a/print_version/high_contrast.pdf and /dev/null differ
diff --git a/print_version/low_contrast.pdf b/print_version/low_contrast.pdf
deleted file mode 100644
index 7489818..0000000
Binary files a/print_version/low_contrast.pdf and /dev/null differ
diff --git a/print_version/page1.png b/print_version/page1.png
deleted file mode 100644
index 88b9f0f..0000000
Binary files a/print_version/page1.png and /dev/null differ
diff --git a/print_version/page2.png b/print_version/page2.png
deleted file mode 100644
index f04f186..0000000
Binary files a/print_version/page2.png and /dev/null differ
diff --git a/sheet.md b/sheet.md
deleted file mode 100644
index efc36c6..0000000
--- a/sheet.md
+++ /dev/null
@@ -1,575 +0,0 @@
-Scientific Python Cheatsheet
-============================
-
-**Table of Contents**
-
-- [Scientific Python Cheatsheet](#scientific-python-cheatsheet)
- - [Pure Python](#pure-python)
- - [Types](#types)
- - [Lists](#lists)
- - [Dictionaries](#dictionaries)
- - [Sets](#sets)
- - [Strings](#strings)
- - [Operators](#operators)
- - [Control Flow](#control-flow)
- - [Functions, Classes, Generators, Decorators](#functions-classes-generators-decorators)
- - [IPython](#ipython)
- - [console](#console)
- - [debugger](#debugger)
- - [command line](#command-line)
- - [NumPy](#numpy-import-numpy-as-np)
- - [array initialization](#array-initialization)
- - [indexing](#indexing)
- - [array properties and operations](#array-properties-and-operations)
- - [boolean arrays](#boolean-arrays)
- - [elementwise operations and math functions](#elementwise-operations-and-math-functions)
- - [inner/ outer products](#inner-outer-products)
- - [linear algebra/ matrix math](#linear-algebra-matrix-math)
- - [reading/ writing files](#reading-writing-files)
- - [interpolation, integration, optimization](#interpolation-integration-optimization)
- - [fft](#fft)
- - [rounding](#rounding)
- - [random variables](#random-variables)
- - [Matplotlib](#matplotlib-import-matplotlib.pyplot-as-plt)
- - [figures and axes](#figures-and-axes)
- - [figures and axes properties](#figures-and-axes-properties)
- - [plotting routines](#plotting-routines)
- - [Scipy](#scipy-import-scipy-as-sci)
- - [interpolation](#interpolation)
- - [linear algebra](#linear-algebra)
- - [integration](#integration)
- - [Pandas](#pandas-import-pandas-as-pd)
- - [data structures](#data-structures)
- - [DataFrame](#dataframe)
-
-
-
-## Pure Python
-
-### Types
-```python
-a = 2 # integer
-b = 5.0 # float
-c = 8.3e5 # exponential
-d = 1.5 + 0.5j # complex
-e = 4 > 5 # boolean
-f = 'word' # string
-```
-
-### Lists
-
-```python
-a = ['red', 'blue', 'green'] # manually initialization
-b = list(range(5)) # initialize from iteratable
-c = [nu**2 for nu in b] # list comprehension
-d = [nu**2 for nu in b if nu < 3] # conditioned list comprehension
-e = c[0] # access element
-f = c[1:2] # access a slice of the list
-g = c[-1] # access last element
-h = ['re', 'bl'] + ['gr'] # list concatenation
-i = ['re'] * 5 # repeat a list
-['re', 'bl'].index('re') # returns index of 're'
-a.append('yellow') # add new element to end of list
-a.extend(b) # add elements from list `b` to end of list `a`
-a.insert(1, 'yellow') # insert element in specified position
-'re' in ['re', 'bl'] # true if 're' in list
-'fi' not in ['re', 'bl'] # true if 'fi' not in list
-sorted([3, 2, 1]) # returns sorted list
-a.pop(2) # remove and return item at index (default last)
-```
-
-### Dictionaries
-
-```python
-a = {'red': 'rouge', 'blue': 'bleu'} # dictionary
-b = a['red'] # translate item
-'red' in a # true if dictionary a contains key 'red'
-c = [value for key, value in a.items()] # loop through contents
-d = a.get('yellow', 'no translation found') # return default
-a.setdefault('extra', []).append('cyan') # init key with default
-a.update({'green': 'vert', 'brown': 'brun'}) # update dictionary by data from another one
-a.keys() # get list of keys
-a.values() # get list of values
-a.items() # get list of key-value pairs
-del a['red'] # delete key and associated with it value
-a.pop('blue') # remove specified key and return the corresponding value
-```
-
-
-### Sets
-
-```python
-a = {1, 2, 3} # initialize manually
-b = set(range(5)) # initialize from iteratable
-a.add(13) # add new element to set
-a.discard(13) # discard element from set
-a.update([21, 22, 23]) # update set with elements from iterable
-a.pop() # remove and return an arbitrary set element
-2 in {1, 2, 3} # true if 2 in set
-5 not in {1, 2, 3} # true if 5 not in set
-a.issubset(b) # test whether every element in a is in b
-a <= b # issubset in operator form
-a.issuperset(b) # test whether every element in b is in a
-a >= b # issuperset in operator form
-a.intersection(b) # return the intersection of two sets as a new set
-a.difference(b) # return the difference of two or more sets as a new set
-a - b # difference in operator form
-a.symmetric_difference(b) # return the symmetric difference of two sets as a new set
-a.union(b) # return the union of sets as a new set
-c = frozenset() # the same as set but immutable
-```
-
-### Strings
-
-```python
-a = 'red' # assignment
-char = a[2] # access individual characters
-'red ' + 'blue' # string concatenation
-'1, 2, three'.split(',') # split string into list
-'.'.join(['1', '2', 'three']) # concatenate list into string
-```
-
-### Operators
-
-```python
-a = 2 # assignment
-a += 1 (*=, /=) # change and assign
-3 + 2 # addition
-3 / 2 # integer (python2) or float (python3) division
-3 // 2 # integer division
-3 * 2 # multiplication
-3 ** 2 # exponent
-3 % 2 # remainder
-abs(a) # absolute value
-1 == 1 # equal
-2 > 1 # larger
-2 < 1 # smaller
-1 != 2 # not equal
-1 != 2 and 2 < 3 # logical AND
-1 != 2 or 2 < 3 # logical OR
-not 1 == 2 # logical NOT
-'a' in b # test if a is in b
-a is b # test if objects point to the same memory (id)
-```
-
-### Control Flow
-
-```python
-# if/elif/else
-a, b = 1, 2
-if a + b == 3:
- print('True')
-elif a + b == 1:
- print('False')
-else:
- print('?')
-
-# for
-a = ['red', 'blue', 'green']
-for color in a:
- print(color)
-
-# while
-number = 1
-while number < 10:
- print(number)
- number += 1
-
-# break
-number = 1
-while True:
- print(number)
- number += 1
- if number > 10:
- break
-
-# continue
-for i in range(20):
- if i % 2 == 0:
- continue
- print(i)
-```
-
-### Functions, Classes, Generators, Decorators
-
-```python
-# Function groups code statements and possibly
-# returns a derived value
-def myfunc(a1, a2):
- return a1 + a2
-
-x = myfunc(a1, a2)
-
-# Class groups attributes (data)
-# and associated methods (functions)
-class Point(object):
- def __init__(self, x):
- self.x = x
- def __call__(self):
- print(self.x)
-
-x = Point(3)
-
-# Generator iterates without
-# creating all values at once
-def firstn(n):
- num = 0
- while num < n:
- yield num
- num += 1
-
-x = [i for i in firstn(10)]
-
-# Decorator can be used to modify
-# the behaviour of a function
-class myDecorator(object):
- def __init__(self, f):
- self.f = f
- def __call__(self):
- print("call")
- self.f()
-
-@myDecorator
-def my_funct():
- print('func')
-
-my_funct()
-```
-
-## IPython
-
-### console
-```python
-
