Team:EPF Lausanne/Software
| Name | Description | |
|---|---|---|
| code2html | Script creating automatically HTML and CSS code from source files in Python, C++ or BASH. | Download |
| ODE Generator | Program generating automatically the ODEs governing our system from the circuit structure. | |
| ODE Solver | Class solving a system of non-linear ODEs given the initial condition. | Download |
| ODE Fit | Class fitting the parameter of a system of ODEs to experimental data. | Download |
| Human Blaster | Script blasting gRNAs versus the human genome.(Need selenium for python and FireFox) | Download |
code2html
The following Python script allows to generate HTML (and CSS) code from source files in C++ and Python languages. It is based on Pygment, a Python syntax highlighter. All code in our Wiki is formatted using this script.
This script accepts two command line arguments: the first argument is the name of the file to convert, the second one (optional) is to ask separate HTML and CSS files.
The style is hard coded, but it can be changed easily by modifying the style string. Pygment documentation lists available themes and explains how to create new ones.
"""
Copyright (C) 2015 iGEM Team EPF_Lausanne
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>
Command:
######################################
python code2html INPUTFILE [CSS]
######################################
INPUTFILE: name (with path) of the file to convert to html
CSS: write "true" (ot "t", "yes", "y") in order to obtain separate .html and .css files ("false" by default)
"""
from pygments import highlight
from pygments.lexers import PythonLexer
from pygments.lexers import CppLexer
from pygments.lexers import BashLexer
from pygments.formatters import HtmlFormatter
# Code formatting style
style = "monokai"
# C++ extensions
cpp = ["cpp","cxx","cc","h"]
# Python extensions
py = ["py"]
# Bash extensions
bash = ["sh","bash"]
def load_file_as_sting(fname):
"""
Open the file FNAME and save all its content in an unformatted string
"""
content = ""
with open(fname,'r') as f: # Open the file (read only)
content = f.read() # Read file and store it in an unformatted string
# The file is automatically closed
return content
def save_string_as_file(fname,string):
"""
Save the unformatted string STRING into the file FNAME
"""
with open(fname,'w') as f: # Open the file (write only)
f.write(string)
# The file is automatically closed
def lexer_formatter(language,css=False):
"""
Return the lexer for the appropriate language and the HTML formatter
"""
L = None
if language in py:
# Python Lexer
L = PythonLexer()
elif language in cpp:
# C++ Lexer
L = CppLexer()
elif language in bash:
# Bash Lexer
L = BashLexer()
else:
raise NameError("Invalid language.")
HF = HtmlFormatter(full=not css,style=style)
return L, HF
def code_to_htmlcss(code,language):
"""
Transform CODE into html and css (separate files)
"""
# Obtain lexer and HtmlFormatter
L, HF = lexer_formatter(language,css=True)
# Create html code
html = highlight(code,L,HF)
# Create css code
css = HF.get_style_defs('.highlight')
return html,css
def code_to_html(code,language):
"""
Transform CODE into html and css (all in the same file)
"""
# Obtain lexer and HtmlFormatter
L, HF = lexer_formatter(language)
# Create fill html code
html = highlight(code,L,HF)
return html
import sys
if __name__ == "__main__":
"""
Command:
######################################
python code2html INPUTFILE [CSS]
######################################
INPUTFILE: name (with path) of the file to convert to html
CSS: write "true" (ot "t", "yes", "y") in order to obtain separate .html and .css files ("false" by default)
"""
# Command line arguments
args = sys.argv
# Check command line arguments
ncla = len(args) # number of command line arguments
if ncla != 2 and ncla != 3 :
raise TypeError("Invalid number of command line arguments.")
css_bool = False
if ncla == 3 and args[-1].lower() in ["true",'t',"yes",'y']:
css_bool = True # Export css separately
# Input file
fname_code = sys.argv[1] # Name of the file containing the code to convert in html
# Input file extension
language = fname_code.split('.')[-1]
# Output files
fname_html = fname_code.split('.')[0] + ".html" # Name of the file where the html code will be stored
fname_css = fname_code.split('.')[0] + ".css" # Name of the file where the css code will be stored
# Save code into a unformatted string
code = load_file_as_sting(fname_code)
if css_bool == False: # Convert to standalone html
html = code_to_html(code,language)
else: # Convert to html and css separately
html,css = code_to_htmlcss(code,language)
# Save html
save_string_as_file(fname_html,html)
if css_bool == True:
# Save css
save_string_as_file(fname_css,css)
ODE Generator
ODE Solver
