├── LICENSE ├── README.md ├── doc ├── api │ ├── Makefile │ ├── _build │ │ ├── doctrees │ │ │ ├── environment.pickle │ │ │ ├── index.doctree │ │ │ └── pythoncyc.doctree │ │ └── html │ │ │ ├── .buildinfo │ │ │ ├── _modules │ │ │ ├── index.html │ │ │ ├── pythoncyc.html │ │ │ └── pythoncyc │ │ │ │ ├── PGDB.html │ │ │ │ ├── PTools.html │ │ │ │ ├── PToolsFrame.html │ │ │ │ └── config.html │ │ │ ├── _sources │ │ │ ├── index.txt │ │ │ └── pythoncyc.txt │ │ │ ├── _static │ │ │ ├── ajax-loader.gif │ │ │ ├── basic.css │ │ │ ├── comment-bright.png │ │ │ ├── comment-close.png │ │ │ ├── comment.png │ │ │ ├── default.css │ │ │ ├── doctools.js │ │ │ ├── down-pressed.png │ │ │ ├── down.png │ │ │ ├── file.png │ │ │ ├── jquery.js │ │ │ ├── minus.png │ │ │ ├── plus.png │ │ │ ├── pygments.css │ │ │ ├── searchtools.js │ │ │ ├── sidebar.js │ │ │ ├── underscore.js │ │ │ ├── up-pressed.png │ │ │ ├── up.png │ │ │ └── websupport.js │ │ │ ├── genindex.html │ │ │ ├── index.html │ │ │ ├── objects.inv │ │ │ ├── py-modindex.html │ │ │ ├── pythoncyc.html │ │ │ ├── search.html │ │ │ └── searchindex.js │ ├── conf.py │ ├── index.rst │ ├── make.bat │ └── pythoncyc.rst ├── tutorial.html └── tutorial.md ├── pythoncyc ├── PGDB.py ├── PTools.py ├── PToolsFrame.py ├── __init__.py └── config.py └── setup.py /LICENSE: -------------------------------------------------------------------------------- 1 | Copyright (c) 2014-2020, SRI International 2 | 3 | Permission is hereby granted, free of charge, to any person obtaining 4 | a copy of this software and associated documentation files (the 5 | "Software"), to deal in the Software without restriction, including 6 | without limitation the rights to use, copy, modify, merge, publish, 7 | distribute, sublicense, and/or sell copies of the Software, and to 8 | permit persons to whom the Software is furnished to do so, subject to 9 | the following conditions: 10 | 11 | The above copyright notice and this permission notice shall be 12 | included in all copies or substantial portions of the Software. 13 | 14 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 15 | EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 16 | MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND 17 | NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE 18 | LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION 19 | OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION 20 | WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 21 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | Copyright (c) 2014-2024, SRI International 2 | 3 | Permission is hereby granted, free of charge, to any person obtaining 4 | a copy of this software and associated documentation files (the 5 | "Software"), to deal in the Software without restriction, including 6 | without limitation the rights to use, copy, modify, merge, publish, 7 | distribute, sublicense, and/or sell copies of the Software, and to 8 | permit persons to whom the Software is furnished to do so, subject to 9 | the following conditions: 10 | 11 | The above copyright notice and this permission notice shall be 12 | included in all copies or substantial portions of the Software. 13 | 14 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 15 | EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 16 | MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND 17 | NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE 18 | LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION 19 | OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION 20 | WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 21 | 22 | 23 | PythonCyc 1.1, April 2020 24 | ============================ 25 | 26 | Overview 27 | -------- 28 | 29 | The PythonCyc module provides a Python 3.5+ interface to a Pathway Tools 30 | application running either locally or remotely. This module has been 31 | designed to work on the three platforms supported by Pathway Tools: 32 | Linux, Mac OS X, and Windows. Pathway Tools version 18.5 or 33 | above is needed to use this module. 34 | 35 | This release has been tested under Python 3.5 and 3.7 under Linux and 36 | Mac OSX. It has not been tested under Windows, or with IPython 37 | or Jupyter. 38 | 39 | The original PythonCyc 1.0 for Python 2.6-2.7 40 | [is still available](https://github.com/latendre/PythonCyc) 41 | 42 | 43 | Installation 44 | ------------ 45 | 46 | Please, consult the HTML file tutorial.html under the doc directory of this 47 | package for the installation instruction of PythonCyc and how to start 48 | Pathway Tools to be able to use PythonCyc. 49 | 50 | Documentation 51 | ------------- 52 | 53 | 1) For a tutorial on how to use PythonCyc, please consult the HTML file 54 | tutorial.html under the doc directory of this package, or [go directly 55 | to the tutorial](https://github.com/ecocyc/PythonCyc/blob/master/doc/tutorial.md) 56 | 57 | 2) API documentation for PythonCyc is available [here](http://pythoncyc.readthedocs.org). 58 | Note that there have not been any changes to the API documentation in this release. 59 | 60 | 3) The latest news about PythonCyc is available [here](http://bioinformatics.ai.sri.com/ptools/pythoncyc.html). 61 | 62 | Author 63 | ------ 64 | 65 | PythonCyc 1.0 was developed by Mario Latendresse, latendre@AI.SRI.COM 66 | The Python 3 update (aka PythonCyc 1.1) was developed by Peter Midford, midford@ai.sri.com 67 | 68 | License 69 | ------- 70 | 71 | See file LICENSE. 72 | 73 | Support 74 | ------- 75 | 76 | For comments and/or bug reports, send an email to ptools-support@ai.sri.com. 77 | 78 | Acknowledgments 79 | --------------- 80 | 81 | Thanks to Eli Bogart to have inspired some implementation details of 82 | PythonCyc via PyCyc, Tomer Altman for the Pathway Tools API 83 | documentation, and Daniel Weaver for suggesting to implement some 84 | specific functions and his design, with Kai Chen, of the beautiful PythonCyc logo. 85 | -------------------------------------------------------------------------------- /doc/api/Makefile: -------------------------------------------------------------------------------- 1 | # Makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line. 5 | SPHINXOPTS = 6 | SPHINXBUILD = sphinx-build 7 | PAPER = 8 | BUILDDIR = _build 9 | 10 | # User-friendly check for sphinx-build 11 | ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) 12 | $(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) 13 | endif 14 | 15 | # Internal variables. 16 | PAPEROPT_a4 = -D latex_paper_size=a4 17 | PAPEROPT_letter = -D latex_paper_size=letter 18 | ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . 19 | # the i18n builder cannot share the environment and doctrees with the others 20 | I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . 21 | 22 | .PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext 23 | 24 | help: 25 | @echo "Please use \`make ' where is one of" 26 | @echo " html to make standalone HTML files" 27 | @echo " dirhtml to make HTML files named index.html in directories" 28 | @echo " singlehtml to make a single large HTML file" 29 | @echo " pickle to make pickle files" 30 | @echo " json to make JSON files" 31 | @echo " htmlhelp to make HTML files and a HTML help project" 32 | @echo " qthelp to make HTML files and a qthelp project" 33 | @echo " devhelp to make HTML files and a Devhelp project" 34 | @echo " epub to make an epub" 35 | @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" 36 | @echo " latexpdf to make LaTeX files and run them through pdflatex" 37 | @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" 38 | @echo " text to make text files" 39 | @echo " man to make manual pages" 40 | @echo " texinfo to make Texinfo files" 41 | @echo " info to make Texinfo files and run them through makeinfo" 42 | @echo " gettext to make PO message catalogs" 43 | @echo " changes to make an overview of all changed/added/deprecated items" 44 | @echo " xml to make Docutils-native XML files" 45 | @echo " pseudoxml to make pseudoxml-XML files for display purposes" 46 | @echo " linkcheck to check all external links for integrity" 47 | @echo " doctest to run all doctests embedded in the documentation (if enabled)" 48 | 49 | clean: 50 | rm -rf $(BUILDDIR)/* 51 | 52 | html: 53 | $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html 54 | @echo 55 | @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." 56 | 57 | dirhtml: 58 | $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml 59 | @echo 60 | @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." 61 | 62 | singlehtml: 63 | $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml 64 | @echo 65 | @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." 66 | 67 | pickle: 68 | $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle 69 | @echo 70 | @echo "Build finished; now you can process the pickle files." 71 | 72 | json: 73 | $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json 74 | @echo 75 | @echo "Build finished; now you can process the JSON files." 76 | 77 | htmlhelp: 78 | $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp 79 | @echo 80 | @echo "Build finished; now you can run HTML Help Workshop with the" \ 81 | ".hhp project file in $(BUILDDIR)/htmlhelp." 82 | 83 | qthelp: 84 | $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp 85 | @echo 86 | @echo "Build finished; now you can run "qcollectiongenerator" with the" \ 87 | ".qhcp project file in $(BUILDDIR)/qthelp, like this:" 88 | @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/pythoncyc.qhcp" 89 | @echo "To view the help file:" 90 | @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pythoncyc.qhc" 91 | 92 | devhelp: 93 | $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp 94 | @echo 95 | @echo "Build finished." 96 | @echo "To view the help file:" 97 | @echo "# mkdir -p $$HOME/.local/share/devhelp/pythoncyc" 98 | @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pythoncyc" 99 | @echo "# devhelp" 100 | 101 | epub: 102 | $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub 103 | @echo 104 | @echo "Build finished. The epub file is in $(BUILDDIR)/epub." 105 | 106 | latex: 107 | $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex 108 | @echo 109 | @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." 110 | @echo "Run \`make' in that directory to run these through (pdf)latex" \ 111 | "(use \`make latexpdf' here to do that automatically)." 112 | 113 | latexpdf: 114 | $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex 115 | @echo "Running LaTeX files through pdflatex..." 116 | $(MAKE) -C $(BUILDDIR)/latex all-pdf 117 | @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." 118 | 119 | latexpdfja: 120 | $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex 121 | @echo "Running LaTeX files through platex and dvipdfmx..." 122 | $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja 123 | @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." 124 | 125 | text: 126 | $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text 127 | @echo 128 | @echo "Build finished. The text files are in $(BUILDDIR)/text." 129 | 130 | man: 131 | $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man 132 | @echo 133 | @echo "Build finished. The manual pages are in $(BUILDDIR)/man." 134 | 135 | texinfo: 136 | $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo 137 | @echo 138 | @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." 139 | @echo "Run \`make' in that directory to run these through makeinfo" \ 140 | "(use \`make info' here to do that automatically)." 141 | 142 | info: 143 | $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo 144 | @echo "Running Texinfo files through makeinfo..." 145 | make -C $(BUILDDIR)/texinfo info 146 | @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." 147 | 148 | gettext: 149 | $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale 150 | @echo 151 | @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." 152 | 153 | changes: 154 | $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes 155 | @echo 156 | @echo "The overview file is in $(BUILDDIR)/changes." 157 | 158 | linkcheck: 159 | $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck 160 | @echo 161 | @echo "Link check complete; look for any errors in the above output " \ 162 | "or in $(BUILDDIR)/linkcheck/output.txt." 163 | 164 | doctest: 165 | $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest 166 | @echo "Testing of doctests in the sources finished, look at the " \ 167 | "results in $(BUILDDIR)/doctest/output.txt." 168 | 169 | xml: 170 | $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml 171 | @echo 172 | @echo "Build finished. The XML files are in $(BUILDDIR)/xml." 173 | 174 | pseudoxml: 175 | $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml 176 | @echo 177 | @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." 178 | -------------------------------------------------------------------------------- /doc/api/_build/doctrees/environment.pickle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ecocyc/PythonCyc/5b843aaed0ec3759ef3c550bea4b7f9908702dc6/doc/api/_build/doctrees/environment.pickle -------------------------------------------------------------------------------- /doc/api/_build/doctrees/index.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ecocyc/PythonCyc/5b843aaed0ec3759ef3c550bea4b7f9908702dc6/doc/api/_build/doctrees/index.doctree -------------------------------------------------------------------------------- /doc/api/_build/doctrees/pythoncyc.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ecocyc/PythonCyc/5b843aaed0ec3759ef3c550bea4b7f9908702dc6/doc/api/_build/doctrees/pythoncyc.doctree -------------------------------------------------------------------------------- /doc/api/_build/html/.buildinfo: -------------------------------------------------------------------------------- 1 | # Sphinx build info version 1 2 | # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. 3 | config: 23752e97421a09ec70847c6daf5541a8 4 | tags: 645f666f9bcd5a90fca523b33c5a78b7 5 | -------------------------------------------------------------------------------- /doc/api/_build/html/_modules/index.html: -------------------------------------------------------------------------------- 1 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | Overview: module code — pythoncyc documentation 10 | 11 | 12 | 13 | 14 | 23 | 24 | 25 | 26 | 27 | 28 | 29 |
30 |

Navigation

31 | 40 |
41 | 42 |
43 |
44 |
45 |
46 | 47 |

All modules for which code is available

48 | 54 | 55 |
56 |
57 |
58 |
59 |
60 | 72 | 73 |
74 |
75 |
76 |
77 |
78 |

Navigation

79 | 88 |
89 |
90 | © Copyright 2014, Mario Latendresse. 91 | Created using Sphinx 1.2.2. 92 |
93 | 94 | -------------------------------------------------------------------------------- /doc/api/_build/html/_modules/pythoncyc.html: -------------------------------------------------------------------------------- 1 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | pythoncyc — pythoncyc documentation 10 | 11 | 12 | 13 | 14 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 |
31 |

Navigation

32 | 42 |
43 | 44 |
45 |
46 |
47 |
48 | 49 |

Source code for pythoncyc

 50 | # Copyright (c) 2014, SRI International
 51 | # 
 52 | # Permission is hereby granted, free of charge, to any person obtaining
 53 | # a copy of this software and associated documentation files (the
 54 | # "Software"), to deal in the Software without restriction, including
 55 | # without limitation the rights to use, copy, modify, merge, publish,
 56 | # distribute, sublicense, and/or sell copies of the Software, and to
 57 | # permit persons to whom the Software is furnished to do so, subject to
 58 | # the following conditions:
 59 | # 
 60 | # The above copyright notice and this permission notice shall be
 61 | # included in all copies or substantial portions of the Software.
 62 | # 
 63 | # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 64 | # EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 65 | # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 66 | # NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
 67 | # LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
 68 | # OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 69 | # WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 70 | # ----------------------------------------------------------------------
 71 | 
 72 | """
 73 | This module is part of PythonCyc, a Python interface module to Pathway Tools.
 74 | This code has been tested with Python 2.6.
 75 | 
 76 | Pathway Tools (version 18.5 and up) must be running on some machine
 77 | with at least the option '-python'. It is also recommended
 78 | to start Pathway Tools with the option -lisp, so that the
 79 | connection can be monitored:
 80 | 
 81 | ./pathway-tools -lisp -python
 82 | 
 83 | The global functions defined in this init file can be called before any
 84 | PGDB (an organism database in Pathway Tools) has been selected.
 85 | In fact, two of these functions, select_organism and
 86 | its synonym so, are needed to "select" a PGDB by creating a PGDB object.
 87 | See class PGDB in PGDB.py for information about how to use a PGDB object.
 88 | 
 89 | Please consult the tutorial.html file, under directory doc, for more information
 90 | about how to use PythonCyc.
 91 | """
 92 | 
 93 | from PGDB import PGDB
 94 | from PTools import sendQueryToPTools
 95 | 
 96 | 
[docs]def select_organism(orgid):
 97 |     """
 98 |     Select an organism PGDB based on its unique organism id.
 99 |        orgid: string, the unique organism id in Pathway Tools (e.g., ecoli, meta).
100 |     """
101 |     return PGDB(orgid)
102 | 

103 | 
[docs]def so(orgid):
104 |     """ A synonym of method select_organism. """
105 |     return select_organism(orgid)
106 | 

107 | 
[docs]def all_orgids():
108 |     """ 
109 |     Returns all organism unique ids (orgids) available 
110 |     from the current running Pathway Tools. 
111 |     """
112 |     orgids = sendQueryToPTools('(all-orgids)')
113 |     return orgids
114 | 

115 | 
[docs]def biovelo(query):
116 |     """
117 |     Execute a BioVelo query and return the result.
118 |     
119 |     Parameters
120 |       query: a string, which is a BioVelo query.
121 |     Returns 
122 |        Whatever the BioVelo query computes.
123 |     
124 |     Example
125 |        bv('[(p, reactions-of-pathway(p)): p<-ecoli^^pathways]')
126 |     """
127 |     return sendQueryToPTools('(biovelo "'+query+'")')
128 | 

129 | 
[docs]def bv(query):
130 |     """
131 |     A synonym of method biovelo.
132 |     """
133 |     return biovelo(query)
134 | 

135 | 
[docs]def run_fba(fileName):
136 |     """
137 |     The function run_fba does not need to have an organism selected before
138 |     being used because the FBA input file provided as input can specify
139 |     the organism.
140 | 
141 |     For the documentation of this function, see method run_fba
142 |     in file PGDB.py.
143 |     """
144 |     return sendQueryToPTools('(python-run-fba "'+fileName+'")')
145 |
146 | 147 |
148 |
149 |
150 |
151 |
152 | 164 | 165 |
166 |
167 |
168 | 169 |
170 |

Navigation

171 | 181 |
182 |
183 | © Copyright 2014, Mario Latendresse. 184 | Created using Sphinx 1.2.2. 185 |
186 | 187 | -------------------------------------------------------------------------------- /doc/api/_build/html/_modules/pythoncyc/PTools.html: -------------------------------------------------------------------------------- 1 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | pythoncyc.PTools — pythoncyc documentation 10 | 11 | 12 | 13 | 14 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 |
31 |

Navigation

32 | 43 |
44 | 45 |
46 |
47 |
48 |
49 | 50 |

Source code for pythoncyc.PTools

 51 | # Copyright (c) 2014, SRI International
 52 | # 
 53 | # Permission is hereby granted, free of charge, to any person obtaining
 54 | # a copy of this software and associated documentation files (the
 55 | # "Software"), to deal in the Software without restriction, including
 56 | # without limitation the rights to use, copy, modify, merge, publish,
 57 | # distribute, sublicense, and/or sell copies of the Software, and to
 58 | # permit persons to whom the Software is furnished to do so, subject to
 59 | # the following conditions:
 60 | # 
 61 | # The above copyright notice and this permission notice shall be
 62 | # included in all copies or substantial portions of the Software.
 63 | # 
 64 | # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 65 | # EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 66 | # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 67 | # NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
 68 | # LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
 69 | # OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 70 | # WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 71 | # ----------------------------------------------------------------------
 72 | 
 73 | """
 74 | This module handles basic operations for receiving and sending messages via a
 75 | network socket to Pathway Tools.
 76 | 
 77 | No major class is defined in this file, but only toplevel functions and
 78 | some simple classes for errors handling.
 79 | 
 80 | """
 81 | 
 82 | import os
 83 | import sys
 84 | import socket as so
 85 | import json
 86 | import time
 87 | import config
 88 | 
 89 | 
[docs]def recvAll(s):
 90 |     """
 91 |     Receive the entire message sent by Pathway Tools on socket s.
 92 |     The message starts with a single character type, which is either 'A'
 93 |     or 'L'. The 'A' time is used without providing a length but can take
 94 |     longer to receive because it uses a timeout technique to read the entire
 95 |     message. The 'L' type assumes that the length of the message, in characters,
 96 |     is given on the next 10 characters as an integer. The message length is the
 97 |     number of characters after these 10 characters.
 98 | 
 99 |     Parm
100 |        s, an open network socket.
101 |     Return
102 |        the message received on socket s as a string.
103 |     """
104 | 
105 |     if config._debug:
106 |         print 'recvAll ...'
107 |     # Get the type of message which is one character long.
108 |     type = s.recv(1)
109 |     # print "type ", type
110 |     if type == 'A':
111 |         # The length of the message is not given, use time out approach.
112 |         return recvTimeOut(s)
113 |     elif type == 'L':
114 |         # The next 10 characters give the length.
115 |         lengthMsg = int(recvFixedLength(s, 10))
116 |         if config._debug:
117 |             print "lengthMsg ", lengthMsg
118 |         return recvFixedLength(s, lengthMsg)            
119 |     else:
120 |         # Something is broken on the server side, so
121 |         # use recv with a long timeout to try flushing
122 |         # the sent message.
123 |         return recvTimeOut(s, timeOut=5)
124 | 

125 | 
[docs]def sendAll(s, query):
126 |     sent_len  = 0
127 |     query_len = len(query)
128 |     while sent_len < query_len:
129 |         nb_chars = s.send(query[sent_len:])
130 |         if nb_chars == 0:
131 |             raise PythonCycError("Connection to Pathway Tools broke while sending query %s." % query)
132 |         sent_len = sent_len + nb_chars
133 | 

134 | 
[docs]def recvFixedLength(s, lengthMsg):
135 |     """
136 |     Receive a fixed length message on socket s.
137 |     Parm
138 |         lengthMsg, an integer, which is the length in characters of the 
139 |                    message to receive.
140 |     Return
141 |         the message received as a string.
142 |     """
143 |     pieces = []
144 |     nbBytesRecv = 0
145 |     while nbBytesRecv < lengthMsg:
146 |         piece = s.recv(min(lengthMsg - nbBytesRecv, 4096))
147 |         if piece == '':
148 |             # Give up now because nothing was received.
149 |             return ''.join(pieces)
150 |         pieces.append(piece)
151 |         nbBytesRecv = nbBytesRecv + len(piece)
152 |     # print 'Fixed receive: ',  ''.join(pieces)
153 |     return ''.join(pieces)
154 | 

155 | 
[docs]def recvTimeOut(socket, timeOut=2):
156 |     """
157 |     Receive a message of unknown length on socket. While receiving a message, if no
158 |     more characters are sent on socket after timeOut seconds, it is
159 |     assumed that the message has ended. Therefore, it will always, whatever the lenght
160 |     of the message, take at least timeOut seconds to execute this method. If no character
161 |     is received after 60 seconds, this method returns with an empty message.
162 | 
163 |     Parms
164 |          socket, an open network socket.
165 |          timeOut, number of seconds before timing out between fragments of the received
166 |                   message.
167 |     Return
168 |          The received message, as a string, on socket.
169 |     """
170 |     # Keep each received packet in an array.
171 |     pieces = []
172 |     # Keep track of time between recvs.
173 |     begin = time.time()
174 |     while 1:
175 |         # If we started to get data and the timeOut occurs,
176 |         # we assume that Pathway Tools sent everything.
177 |         if pieces and time.time() - begin > timeOut:
178 |             break
179 |         elif time.time() - begin > 60:
180 |             break
181 |         # Try to receive some text.
182 |         try:
183 |             data = socket.recv(4096)
184 |             if data:
185 |                 pieces.append(data)
186 |                 # Reset beginning time for next recv.
187 |                 begin = time.time()
188 |             else:
189 |                 # Slow down in case timeOut is small.
190 |                 time.sleep(0.1)
191 |         except so.error:
192 |             pass
193 |     
194 |     # Join all the pieces together.
195 |     if pieces == []:
196 |         return None
197 |     else:
198 |         return ''.join(pieces)
199 | 
200 | # Call a PTools function synchronously for any PGDB.

201 | 
[docs]def sendQueryToPTools(query):
202 |     """ 
203 |     Send a query to a running Pathway Tools application via a socket.
204 |     
205 |     Parm
206 |       query, a string that the Python server in Pathway Tools can evaluate. 
207 |     Returns
208 |       The result of the query, as a Python object, decoded by Json.
209 |     """
210 |     if config._debug:
211 |         print 'Sending query '+query
212 |     if config._hostname == '':
213 |        raise PToolsError('The hostname to connect to a running Pathway Tools has not been set. Use function config.set_hostname() to set the host name of your running Pathway Tools.') 
214 |     try:
215 |         s = so.socket(so.AF_INET, so.SOCK_STREAM)
216 |         # Make socket non blocking.
217 |         s.setblocking(0)
218 |         s.settimeout(360)  # The query may take a long time in some cases.
219 |         s.connect((config._hostname,config._hostport))
220 |     except so.error, msg:
221 |         raise PToolsError('Failed to create a connection to a running Pathway Tools at '+ config._hostname+ ' on port '+ str(config._hostport)+'. Make sure Pathway Tools is running with option -python. Error code: '+str(msg[0])+', error message: '+ msg[1])
222 |     # Send, receive and close socket.
223 |     sendAll(s,query)
224 |     if config._debug:
225 |         print 'Sent '+query+' to Pathway Tools.'
226 |     response = recvAll(s)
227 |     if config._debug and len(response) < 4000:
228 |         print 'JSON Received: ', response
229 |     r = json.loads(response)
230 |     s.close()
231 |     if isinstance(r,basestring) and r.startswith(':error'):
232 |         raise PToolsError('An internal error occurred in the running Pathway Tools application: %s' % r)
233 |     else:
234 |         # Return some result.
235 |         return r
236 | 

237 | 
[docs]class PythonCycError(Exception):
238 |     """Error generated by one of the module of PythonCyc due to an incorrect
239 |        use of its methods or functions.
240 |     """
241 |     pass
242 | 

243 | 
[docs]class PToolsError(Exception):
244 |     """Error generated when Pathway Tools send an error due to its own Lisp execution."""
245 |     pass
246 |
247 | 248 |
249 |
250 |
251 |
252 |
253 | 265 | 266 |
267 |
268 |
269 | 270 |
271 |

Navigation

272 | 283 |
284 |
285 | © Copyright 2014, Mario Latendresse. 286 | Created using Sphinx 1.2.2. 287 |
288 | 289 | -------------------------------------------------------------------------------- /doc/api/_build/html/_modules/pythoncyc/config.html: -------------------------------------------------------------------------------- 1 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | pythoncyc.config — pythoncyc documentation 10 | 11 | 12 | 13 | 14 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 |
31 |

Navigation

32 | 43 |
44 | 45 |
46 |
47 |
48 |
49 | 50 |

Source code for pythoncyc.config

 51 | # Copyright (c) 2014, SRI International
 52 | # 
 53 | # Permission is hereby granted, free of charge, to any person obtaining
 54 | # a copy of this software and associated documentation files (the
 55 | # "Software"), to deal in the Software without restriction, including
 56 | # without limitation the rights to use, copy, modify, merge, publish,
 57 | # distribute, sublicense, and/or sell copies of the Software, and to
 58 | # permit persons to whom the Software is furnished to do so, subject to
 59 | # the following conditions:
 60 | # 
 61 | # The above copyright notice and this permission notice shall be
 62 | # included in all copies or substantial portions of the Software.
 63 | # 
 64 | # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 65 | # EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
 66 | # MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 67 | # NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
 68 | # LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
 69 | # OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 70 | # WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 71 | # ----------------------------------------------------------------------
 72 | 
 73 | """
 74 | This module can be used to set various parameters for PythonCyc,
 75 | in particular to set debug on or off, the host name and port number
 76 | of the running Pathway Tools' Python server. By default, the Pathway Tools
 77 | Python server is running locally on port 5008.
 78 | """
 79 | 
 80 | _debug = False
 81 | _hostname = "localhost"
 82 | _hostport = 5008
 83 | 
 84 | 
[docs]def set_debug_on():
 85 |     """
 86 |      Turn on debug mode for PythonCyc.
 87 |      Turning on debugging should turn on output tracings of the communications between PythonCyc and Pathway Tools.
 88 |     """
 89 |     global _debug
 90 |     _debug = True
 91 |     print 'Debug on.'
 92 |     

 93 | 
[docs]def set_debug_off():
 94 |     """
 95 |      Turn off debug mode for PythonCyc.
 96 |      Turning off debugging should turn off all output tracings of the communications between PythonCyc and Pathway Tools.
 97 | 
 98 |     """
 99 |     global _debug
100 |     _debug = False
101 |     print 'Debug off.'
102 | 

103 | 
[docs]def set_host_name(hostname):
104 |     global _hostname
105 |     _hostname = hostname
106 |     print 'PythonCyc will communicate with Pathway Tools running on host name ',_hostname
107 | 

108 | 
[docs]def set_host_port(hostport):
109 |     global _hostport
110 |     _hostport = hostport
111 |     print 'PythonCyc will communicate with Pathway Tools running on host port ',_hostport

112 |
113 | 114 |
115 |
116 |
117 |
118 |
119 | 131 | 132 |
133 |
134 |
135 |
136 |
137 |

Navigation

138 | 149 |
150 |
151 | © Copyright 2014, Mario Latendresse. 152 | Created using Sphinx 1.2.2. 153 |
154 | 155 | -------------------------------------------------------------------------------- /doc/api/_build/html/_sources/index.txt: -------------------------------------------------------------------------------- 1 | .. pythoncyc documentation master file, created by 2 | sphinx-quickstart on Tue Nov 4 08:47:50 2014. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | Welcome to pythoncyc's documentation! 7 | ===================================== 8 | 9 | Contents: 10 | 11 | .. toctree:: 12 | :maxdepth: 4 13 | 14 | pythoncyc 15 | 16 | 17 | Indices and tables 18 | ================== 19 | 20 | * :ref:`genindex` 21 | * :ref:`modindex` 22 | * :ref:`search` 23 | 24 | -------------------------------------------------------------------------------- /doc/api/_build/html/_sources/pythoncyc.txt: -------------------------------------------------------------------------------- 1 | pythoncyc package 2 | ================= 3 | 4 | Submodules 5 | ---------- 6 | 7 | pythoncyc.PGDB module 8 | --------------------- 9 | 10 | .. automodule:: pythoncyc.PGDB 11 | :members: 12 | :undoc-members: 13 | :show-inheritance: 14 | 15 | pythoncyc.PTools module 16 | ----------------------- 17 | 18 | .. automodule:: pythoncyc.PTools 19 | :members: 20 | :undoc-members: 21 | :show-inheritance: 22 | 23 | pythoncyc.PToolsFrame module 24 | ---------------------------- 25 | 26 | .. automodule:: pythoncyc.PToolsFrame 27 | :members: 28 | :undoc-members: 29 | :show-inheritance: 30 | 31 | pythoncyc.config module 32 | ----------------------- 33 | 34 | .. automodule:: pythoncyc.config 35 | :members: 36 | :undoc-members: 37 | :show-inheritance: 38 | 39 | 40 | Module contents 41 | --------------- 42 | 43 | .. automodule:: pythoncyc 44 | :members: 45 | :undoc-members: 46 | :show-inheritance: 47 | -------------------------------------------------------------------------------- /doc/api/_build/html/_static/ajax-loader.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ecocyc/PythonCyc/5b843aaed0ec3759ef3c550bea4b7f9908702dc6/doc/api/_build/html/_static/ajax-loader.gif -------------------------------------------------------------------------------- /doc/api/_build/html/_static/basic.css: -------------------------------------------------------------------------------- 1 | /* 2 | * basic.css 3 | * ~~~~~~~~~ 4 | * 5 | * Sphinx stylesheet -- basic theme. 6 | * 7 | * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS. 8 | * :license: BSD, see LICENSE for details. 9 | * 10 | */ 11 | 12 | /* -- main layout ----------------------------------------------------------- */ 13 | 14 | div.clearer { 15 | clear: both; 16 | } 17 | 18 | /* -- relbar ---------------------------------------------------------------- */ 19 | 20 | div.related { 21 | width: 100%; 22 | font-size: 90%; 23 | } 24 | 25 | div.related h3 { 26 | display: none; 27 | } 28 | 29 | div.related ul { 30 | margin: 0; 31 | padding: 0 0 0 10px; 32 | list-style: none; 33 | } 34 | 35 | div.related li { 36 | display: inline; 37 | } 38 | 39 | div.related li.right { 40 | float: right; 41 | margin-right: 5px; 42 | } 43 | 44 | /* -- sidebar --------------------------------------------------------------- */ 45 | 46 | div.sphinxsidebarwrapper { 47 | padding: 10px 5px 0 10px; 48 | } 49 | 50 | div.sphinxsidebar { 51 | float: left; 52 | width: 230px; 53 | margin-left: -100%; 54 | font-size: 90%; 55 | } 56 | 57 | div.sphinxsidebar ul { 58 | list-style: none; 59 | } 60 | 61 | div.sphinxsidebar ul ul, 62 | div.sphinxsidebar ul.want-points { 63 | margin-left: 20px; 64 | list-style: square; 65 | } 66 | 67 | div.sphinxsidebar ul ul { 68 | margin-top: 0; 69 | margin-bottom: 0; 70 | } 71 | 72 | div.sphinxsidebar form { 73 | margin-top: 10px; 74 | } 75 | 76 | div.sphinxsidebar input { 77 | border: 1px solid #98dbcc; 78 | font-family: sans-serif; 79 | font-size: 1em; 80 | } 81 | 82 | div.sphinxsidebar #searchbox input[type="text"] { 83 | width: 170px; 84 | } 85 | 86 | div.sphinxsidebar #searchbox input[type="submit"] { 87 | width: 30px; 88 | } 89 | 90 | img { 91 | border: 0; 92 | max-width: 100%; 93 | } 94 | 95 | /* -- search page ----------------------------------------------------------- */ 96 | 97 | ul.search { 98 | margin: 10px 0 0 20px; 99 | padding: 0; 100 | } 101 | 102 | ul.search li { 103 | padding: 5px 0 5px 20px; 104 | background-image: url(file.png); 105 | background-repeat: no-repeat; 106 | background-position: 0 7px; 107 | } 108 | 109 | ul.search li a { 110 | font-weight: bold; 111 | } 112 | 113 | ul.search li div.context { 114 | color: #888; 115 | margin: 2px 0 0 30px; 116 | text-align: left; 117 | } 118 | 119 | ul.keywordmatches li.goodmatch a { 120 | font-weight: bold; 121 | } 122 | 123 | /* -- index page ------------------------------------------------------------ */ 124 | 125 | table.contentstable { 126 | width: 90%; 127 | } 128 | 129 | table.contentstable p.biglink { 130 | line-height: 150%; 131 | } 132 | 133 | a.biglink { 134 | font-size: 1.3em; 135 | } 136 | 137 | span.linkdescr { 138 | font-style: italic; 139 | padding-top: 5px; 140 | font-size: 90%; 141 | } 142 | 143 | /* -- general index --------------------------------------------------------- */ 144 | 145 | table.indextable { 146 | width: 100%; 147 | } 148 | 149 | table.indextable td { 150 | text-align: left; 151 | vertical-align: top; 152 | } 153 | 154 | table.indextable dl, table.indextable dd { 155 | margin-top: 0; 156 | margin-bottom: 0; 157 | } 158 | 159 | table.indextable tr.pcap { 160 | height: 10px; 161 | } 162 | 163 | table.indextable tr.cap { 164 | margin-top: 10px; 165 | background-color: #f2f2f2; 166 | } 167 | 168 | img.toggler { 169 | margin-right: 3px; 170 | margin-top: 3px; 171 | cursor: pointer; 172 | } 173 | 174 | div.modindex-jumpbox { 175 | border-top: 1px solid #ddd; 176 | border-bottom: 1px solid #ddd; 177 | margin: 1em 0 1em 0; 178 | padding: 0.4em; 179 | } 180 | 181 | div.genindex-jumpbox { 182 | border-top: 1px solid #ddd; 183 | border-bottom: 1px solid #ddd; 184 | margin: 1em 0 1em 0; 185 | padding: 0.4em; 186 | } 187 | 188 | /* -- general body styles --------------------------------------------------- */ 189 | 190 | a.headerlink { 191 | visibility: hidden; 192 | } 193 | 194 | h1:hover > a.headerlink, 195 | h2:hover > a.headerlink, 196 | h3:hover > a.headerlink, 197 | h4:hover > a.headerlink, 198 | h5:hover > a.headerlink, 199 | h6:hover > a.headerlink, 200 | dt:hover > a.headerlink { 201 | visibility: visible; 202 | } 203 | 204 | div.body p.caption { 205 | text-align: inherit; 206 | } 207 | 208 | div.body td { 209 | text-align: left; 210 | } 211 | 212 | .field-list ul { 213 | padding-left: 1em; 214 | } 215 | 216 | .first { 217 | margin-top: 0 !important; 218 | } 219 | 220 | p.rubric { 221 | margin-top: 30px; 222 | font-weight: bold; 223 | } 224 | 225 | img.align-left, .figure.align-left, object.align-left { 226 | clear: left; 227 | float: left; 228 | margin-right: 1em; 229 | } 230 | 231 | img.align-right, .figure.align-right, object.align-right { 232 | clear: right; 233 | float: right; 234 | margin-left: 1em; 235 | } 236 | 237 | img.align-center, .figure.align-center, object.align-center { 238 | display: block; 239 | margin-left: auto; 240 | margin-right: auto; 241 | } 242 | 243 | .align-left { 244 | text-align: left; 245 | } 246 | 247 | .align-center { 248 | text-align: center; 249 | } 250 | 251 | .align-right { 252 | text-align: right; 253 | } 254 | 255 | /* -- sidebars -------------------------------------------------------------- */ 256 | 257 | div.sidebar { 258 | margin: 0 0 0.5em 1em; 259 | border: 1px solid #ddb; 260 | padding: 7px 7px 0 7px; 261 | background-color: #ffe; 262 | width: 40%; 263 | float: right; 264 | } 265 | 266 | p.sidebar-title { 267 | font-weight: bold; 268 | } 269 | 270 | /* -- topics ---------------------------------------------------------------- */ 271 | 272 | div.topic { 273 | border: 1px solid #ccc; 274 | padding: 7px 7px 0 7px; 275 | margin: 10px 0 10px 0; 276 | } 277 | 278 | p.topic-title { 279 | font-size: 1.1em; 280 | font-weight: bold; 281 | margin-top: 10px; 282 | } 283 | 284 | /* -- admonitions ----------------------------------------------------------- */ 285 | 286 | div.admonition { 287 | margin-top: 10px; 288 | margin-bottom: 10px; 289 | padding: 7px; 290 | } 291 | 292 | div.admonition dt { 293 | font-weight: bold; 294 | } 295 | 296 | div.admonition dl { 297 | margin-bottom: 0; 298 | } 299 | 300 | p.admonition-title { 301 | margin: 0px 10px 5px 0px; 302 | font-weight: bold; 303 | } 304 | 305 | div.body p.centered { 306 | text-align: center; 307 | margin-top: 25px; 308 | } 309 | 310 | /* -- tables ---------------------------------------------------------------- */ 311 | 312 | table.docutils { 313 | border: 0; 314 | border-collapse: collapse; 315 | } 316 | 317 | table.docutils td, table.docutils th { 318 | padding: 1px 8px 1px 5px; 319 | border-top: 0; 320 | border-left: 0; 321 | border-right: 0; 322 | border-bottom: 1px solid #aaa; 323 | } 324 | 325 | table.field-list td, table.field-list th { 326 | border: 0 !important; 327 | } 328 | 329 | table.footnote td, table.footnote th { 330 | border: 0 !important; 331 | } 332 | 333 | th { 334 | text-align: left; 335 | padding-right: 5px; 336 | } 337 | 338 | table.citation { 339 | border-left: solid 1px gray; 340 | margin-left: 1px; 341 | } 342 | 343 | table.citation td { 344 | border-bottom: none; 345 | } 346 | 347 | /* -- other body styles ----------------------------------------------------- */ 348 | 349 | ol.arabic { 350 | list-style: decimal; 351 | } 352 | 353 | ol.loweralpha { 354 | list-style: lower-alpha; 355 | } 356 | 357 | ol.upperalpha { 358 | list-style: upper-alpha; 359 | } 360 | 361 | ol.lowerroman { 362 | list-style: lower-roman; 363 | } 364 | 365 | ol.upperroman { 366 | list-style: upper-roman; 367 | } 368 | 369 | dl { 370 | margin-bottom: 15px; 371 | } 372 | 373 | dd p { 374 | margin-top: 0px; 375 | } 376 | 377 | dd ul, dd table { 378 | margin-bottom: 10px; 379 | } 380 | 381 | dd { 382 | margin-top: 3px; 383 | margin-bottom: 10px; 384 | margin-left: 30px; 385 | } 386 | 387 | dt:target, .highlighted { 388 | background-color: #fbe54e; 389 | } 390 | 391 | dl.glossary dt { 392 | font-weight: bold; 393 | font-size: 1.1em; 394 | } 395 | 396 | .field-list ul { 397 | margin: 0; 398 | padding-left: 1em; 399 | } 400 | 401 | .field-list p { 402 | margin: 0; 403 | } 404 | 405 | .optional { 406 | font-size: 1.3em; 407 | } 408 | 409 | .versionmodified { 410 | font-style: italic; 411 | } 412 | 413 | .system-message { 414 | background-color: #fda; 415 | padding: 5px; 416 | border: 3px solid red; 417 | } 418 | 419 | .footnote:target { 420 | background-color: #ffa; 421 | } 422 | 423 | .line-block { 424 | display: block; 425 | margin-top: 1em; 426 | margin-bottom: 1em; 427 | } 428 | 429 | .line-block .line-block { 430 | margin-top: 0; 431 | margin-bottom: 0; 432 | margin-left: 1.5em; 433 | } 434 | 435 | .guilabel, .menuselection { 436 | font-family: sans-serif; 437 | } 438 | 439 | .accelerator { 440 | text-decoration: underline; 441 | } 442 | 443 | .classifier { 444 | font-style: oblique; 445 | } 446 | 447 | abbr, acronym { 448 | border-bottom: dotted 1px; 449 | cursor: help; 450 | } 451 | 452 | /* -- code displays --------------------------------------------------------- */ 453 | 454 | pre { 455 | overflow: auto; 456 | overflow-y: hidden; /* fixes display issues on Chrome browsers */ 457 | } 458 | 459 | td.linenos pre { 460 | padding: 5px 0px; 461 | border: 0; 462 | background-color: transparent; 463 | color: #aaa; 464 | } 465 | 466 | table.highlighttable { 467 | margin-left: 0.5em; 468 | } 469 | 470 | table.highlighttable td { 471 | padding: 0 0.5em 0 0.5em; 472 | } 473 | 474 | tt.descname { 475 | background-color: transparent; 476 | font-weight: bold; 477 | font-size: 1.2em; 478 | } 479 | 480 | tt.descclassname { 481 | background-color: transparent; 482 | } 483 | 484 | tt.xref, a tt { 485 | background-color: transparent; 486 | font-weight: bold; 487 | } 488 | 489 | h1 tt, h2 tt, h3 tt, h4 tt, h5 tt, h6 tt { 490 | background-color: transparent; 491 | } 492 | 493 | .viewcode-link { 494 | float: right; 495 | } 496 | 497 | .viewcode-back { 498 | float: right; 499 | font-family: sans-serif; 500 | } 501 | 502 | div.viewcode-block:target { 503 | margin: -1px -10px; 504 | padding: 0 10px; 505 | } 506 | 507 | /* -- math display ---------------------------------------------------------- */ 508 | 509 | img.math { 510 | vertical-align: middle; 511 | } 512 | 513 | div.body div.math p { 514 | text-align: center; 515 | } 516 | 517 | span.eqno { 518 | float: right; 519 | } 520 | 521 | /* -- printout stylesheet --------------------------------------------------- */ 522 | 523 | @media print { 524 | div.document, 525 | div.documentwrapper, 526 | div.bodywrapper { 527 | margin: 0 !important; 528 | width: 100%; 529 | } 530 | 531 | div.sphinxsidebar, 532 | div.related, 533 | div.footer, 534 | #top-link { 535 | display: none; 536 | } 537 | } -------------------------------------------------------------------------------- /doc/api/_build/html/_static/comment-bright.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ecocyc/PythonCyc/5b843aaed0ec3759ef3c550bea4b7f9908702dc6/doc/api/_build/html/_static/comment-bright.png -------------------------------------------------------------------------------- /doc/api/_build/html/_static/comment-close.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ecocyc/PythonCyc/5b843aaed0ec3759ef3c550bea4b7f9908702dc6/doc/api/_build/html/_static/comment-close.png -------------------------------------------------------------------------------- /doc/api/_build/html/_static/comment.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ecocyc/PythonCyc/5b843aaed0ec3759ef3c550bea4b7f9908702dc6/doc/api/_build/html/_static/comment.png -------------------------------------------------------------------------------- /doc/api/_build/html/_static/default.css: -------------------------------------------------------------------------------- 1 | /* 2 | * default.css_t 3 | * ~~~~~~~~~~~~~ 4 | * 5 | * Sphinx stylesheet -- default theme. 6 | * 7 | * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS. 8 | * :license: BSD, see LICENSE for details. 9 | * 10 | */ 11 | 12 | @import url("basic.css"); 13 | 14 | /* -- page layout ----------------------------------------------------------- */ 15 | 16 | body { 17 | font-family: sans-serif; 18 | font-size: 100%; 19 | background-color: #11303d; 20 | color: #000; 21 | margin: 0; 22 | padding: 0; 23 | } 24 | 25 | div.document { 26 | background-color: #1c4e63; 27 | } 28 | 29 | div.documentwrapper { 30 | float: left; 31 | width: 100%; 32 | } 33 | 34 | div.bodywrapper { 35 | margin: 0 0 0 230px; 36 | } 37 | 38 | div.body { 39 | background-color: #ffffff; 40 | color: #000000; 41 | padding: 0 20px 30px 20px; 42 | } 43 | 44 | div.footer { 45 | color: #ffffff; 46 | width: 100%; 47 | padding: 9px 0 9px 0; 48 | text-align: center; 49 | font-size: 75%; 50 | } 51 | 52 | div.footer a { 53 | color: #ffffff; 54 | text-decoration: underline; 55 | } 56 | 57 | div.related { 58 | background-color: #133f52; 59 | line-height: 30px; 60 | color: #ffffff; 61 | } 62 | 63 | div.related a { 64 | color: #ffffff; 65 | } 66 | 67 | div.sphinxsidebar { 68 | } 69 | 70 | div.sphinxsidebar h3 { 71 | font-family: 'Trebuchet MS', sans-serif; 72 | color: #ffffff; 73 | font-size: 1.4em; 74 | font-weight: normal; 75 | margin: 0; 76 | padding: 0; 77 | } 78 | 79 | div.sphinxsidebar h3 a { 80 | color: #ffffff; 81 | } 82 | 83 | div.sphinxsidebar h4 { 84 | font-family: 'Trebuchet MS', sans-serif; 85 | color: #ffffff; 86 | font-size: 1.3em; 87 | font-weight: normal; 88 | margin: 5px 0 0 0; 89 | padding: 0; 90 | } 91 | 92 | div.sphinxsidebar p { 93 | color: #ffffff; 94 | } 95 | 96 | div.sphinxsidebar p.topless { 97 | margin: 5px 10px 10px 10px; 98 | } 99 | 100 | div.sphinxsidebar ul { 101 | margin: 10px; 102 | padding: 0; 103 | color: #ffffff; 104 | } 105 | 106 | div.sphinxsidebar a { 107 | color: #98dbcc; 108 | } 109 | 110 | div.sphinxsidebar input { 111 | border: 1px solid #98dbcc; 112 | font-family: sans-serif; 113 | font-size: 1em; 114 | } 115 | 116 | 117 | 118 | /* -- hyperlink styles ------------------------------------------------------ */ 119 | 120 | a { 121 | color: #355f7c; 122 | text-decoration: none; 123 | } 124 | 125 | a:visited { 126 | color: #355f7c; 127 | text-decoration: none; 128 | } 129 | 130 | a:hover { 131 | text-decoration: underline; 132 | } 133 | 134 | 135 | 136 | /* -- body styles ----------------------------------------------------------- */ 137 | 138 | div.body h1, 139 | div.body h2, 140 | div.body h3, 141 | div.body h4, 142 | div.body h5, 143 | div.body h6 { 144 | font-family: 'Trebuchet MS', sans-serif; 145 | background-color: #f2f2f2; 146 | font-weight: normal; 147 | color: #20435c; 148 | border-bottom: 1px solid #ccc; 149 | margin: 20px -20px 10px -20px; 150 | padding: 3px 0 3px 10px; 151 | } 152 | 153 | div.body h1 { margin-top: 0; font-size: 200%; } 154 | div.body h2 { font-size: 160%; } 155 | div.body h3 { font-size: 140%; } 156 | div.body h4 { font-size: 120%; } 157 | div.body h5 { font-size: 110%; } 158 | div.body h6 { font-size: 100%; } 159 | 160 | a.headerlink { 161 | color: #c60f0f; 162 | font-size: 0.8em; 163 | padding: 0 4px 0 4px; 164 | text-decoration: none; 165 | } 166 | 167 | a.headerlink:hover { 168 | background-color: #c60f0f; 169 | color: white; 170 | } 171 | 172 | div.body p, div.body dd, div.body li { 173 | text-align: justify; 174 | line-height: 130%; 175 | } 176 | 177 | div.admonition p.admonition-title + p { 178 | display: inline; 179 | } 180 | 181 | div.admonition p { 182 | margin-bottom: 5px; 183 | } 184 | 185 | div.admonition pre { 186 | margin-bottom: 5px; 187 | } 188 | 189 | div.admonition ul, div.admonition ol { 190 | margin-bottom: 5px; 191 | } 192 | 193 | div.note { 194 | background-color: #eee; 195 | border: 1px solid #ccc; 196 | } 197 | 198 | div.seealso { 199 | background-color: #ffc; 200 | border: 1px solid #ff6; 201 | } 202 | 203 | div.topic { 204 | background-color: #eee; 205 | } 206 | 207 | div.warning { 208 | background-color: #ffe4e4; 209 | border: 1px solid #f66; 210 | } 211 | 212 | p.admonition-title { 213 | display: inline; 214 | } 215 | 216 | p.admonition-title:after { 217 | content: ":"; 218 | } 219 | 220 | pre { 221 | padding: 5px; 222 | background-color: #eeffcc; 223 | color: #333333; 224 | line-height: 120%; 225 | border: 1px solid #ac9; 226 | border-left: none; 227 | border-right: none; 228 | } 229 | 230 | tt { 231 | background-color: #ecf0f3; 232 | padding: 0 1px 0 1px; 233 | font-size: 0.95em; 234 | } 235 | 236 | th { 237 | background-color: #ede; 238 | } 239 | 240 | .warning tt { 241 | background: #efc2c2; 242 | } 243 | 244 | .note tt { 245 | background: #d6d6d6; 246 | } 247 | 248 | .viewcode-back { 249 | font-family: sans-serif; 250 | } 251 | 252 | div.viewcode-block:target { 253 | background-color: #f4debf; 254 | border-top: 1px solid #ac9; 255 | border-bottom: 1px solid #ac9; 256 | } -------------------------------------------------------------------------------- /doc/api/_build/html/_static/doctools.js: -------------------------------------------------------------------------------- 1 | /* 2 | * doctools.js 3 | * ~~~~~~~~~~~ 4 | * 5 | * Sphinx JavaScript utilities for all documentation. 6 | * 7 | * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS. 8 | * :license: BSD, see LICENSE for details. 9 | * 10 | */ 11 | 12 | /** 13 | * select a different prefix for underscore 14 | */ 15 | $u = _.noConflict(); 16 | 17 | /** 18 | * make the code below compatible with browsers without 19 | * an installed firebug like debugger 20 | if (!window.console || !console.firebug) { 21 | var names = ["log", "debug", "info", "warn", "error", "assert", "dir", 22 | "dirxml", "group", "groupEnd", "time", "timeEnd", "count", "trace", 23 | "profile", "profileEnd"]; 24 | window.console = {}; 25 | for (var i = 0; i < names.length; ++i) 26 | window.console[names[i]] = function() {}; 27 | } 28 | */ 29 | 30 | /** 31 | * small helper function to urldecode strings 32 | */ 33 | jQuery.urldecode = function(x) { 34 | return decodeURIComponent(x).replace(/\+/g, ' '); 35 | }; 36 | 37 | /** 38 | * small helper function to urlencode strings 39 | */ 40 | jQuery.urlencode = encodeURIComponent; 41 | 42 | /** 43 | * This function returns the parsed url parameters of the 44 | * current request. Multiple values per key are supported, 45 | * it will always return arrays of strings for the value parts. 46 | */ 47 | jQuery.getQueryParameters = function(s) { 48 | if (typeof s == 'undefined') 49 | s = document.location.search; 50 | var parts = s.substr(s.indexOf('?') + 1).split('&'); 51 | var result = {}; 52 | for (var i = 0; i < parts.length; i++) { 53 | var tmp = parts[i].split('=', 2); 54 | var key = jQuery.urldecode(tmp[0]); 55 | var value = jQuery.urldecode(tmp[1]); 56 | if (key in result) 57 | result[key].push(value); 58 | else 59 | result[key] = [value]; 60 | } 61 | return result; 62 | }; 63 | 64 | /** 65 | * highlight a given string on a jquery object by wrapping it in 66 | * span elements with the given class name. 67 | */ 68 | jQuery.fn.highlightText = function(text, className) { 69 | function highlight(node) { 70 | if (node.nodeType == 3) { 71 | var val = node.nodeValue; 72 | var pos = val.toLowerCase().indexOf(text); 73 | if (pos >= 0 && !jQuery(node.parentNode).hasClass(className)) { 74 | var span = document.createElement("span"); 75 | span.className = className; 76 | span.appendChild(document.createTextNode(val.substr(pos, text.length))); 77 | node.parentNode.insertBefore(span, node.parentNode.insertBefore( 78 | document.createTextNode(val.substr(pos + text.length)), 79 | node.nextSibling)); 80 | node.nodeValue = val.substr(0, pos); 81 | } 82 | } 83 | else if (!jQuery(node).is("button, select, textarea")) { 84 | jQuery.each(node.childNodes, function() { 85 | highlight(this); 86 | }); 87 | } 88 | } 89 | return this.each(function() { 90 | highlight(this); 91 | }); 92 | }; 93 | 94 | /** 95 | * Small JavaScript module for the documentation. 96 | */ 97 | var Documentation = { 98 | 99 | init : function() { 100 | this.fixFirefoxAnchorBug(); 101 | this.highlightSearchWords(); 102 | this.initIndexTable(); 103 | }, 104 | 105 | /** 106 | * i18n support 107 | */ 108 | TRANSLATIONS : {}, 109 | PLURAL_EXPR : function(n) { return n == 1 ? 0 : 1; }, 110 | LOCALE : 'unknown', 111 | 112 | // gettext and ngettext don't access this so that the functions 113 | // can safely bound to a different name (_ = Documentation.gettext) 114 | gettext : function(string) { 115 | var translated = Documentation.TRANSLATIONS[string]; 116 | if (typeof translated == 'undefined') 117 | return string; 118 | return (typeof translated == 'string') ? translated : translated[0]; 119 | }, 120 | 121 | ngettext : function(singular, plural, n) { 122 | var translated = Documentation.TRANSLATIONS[singular]; 123 | if (typeof translated == 'undefined') 124 | return (n == 1) ? singular : plural; 125 | return translated[Documentation.PLURALEXPR(n)]; 126 | }, 127 | 128 | addTranslations : function(catalog) { 129 | for (var key in catalog.messages) 130 | this.TRANSLATIONS[key] = catalog.messages[key]; 131 | this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')'); 132 | this.LOCALE = catalog.locale; 133 | }, 134 | 135 | /** 136 | * add context elements like header anchor links 137 | */ 138 | addContextElements : function() { 139 | $('div[id] > :header:first').each(function() { 140 | $('\u00B6'). 141 | attr('href', '#' + this.id). 142 | attr('title', _('Permalink to this headline')). 143 | appendTo(this); 144 | }); 145 | $('dt[id]').each(function() { 146 | $('\u00B6'). 147 | attr('href', '#' + this.id). 148 | attr('title', _('Permalink to this definition')). 149 | appendTo(this); 150 | }); 151 | }, 152 | 153 | /** 154 | * workaround a firefox stupidity 155 | */ 156 | fixFirefoxAnchorBug : function() { 157 | if (document.location.hash && $.browser.mozilla) 158 | window.setTimeout(function() { 159 | document.location.href += ''; 160 | }, 10); 161 | }, 162 | 163 | /** 164 | * highlight the search words provided in the url in the text 165 | */ 166 | highlightSearchWords : function() { 167 | var params = $.getQueryParameters(); 168 | var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : []; 169 | if (terms.length) { 170 | var body = $('div.body'); 171 | if (!body.length) { 172 | body = $('body'); 173 | } 174 | window.setTimeout(function() { 175 | $.each(terms, function() { 176 | body.highlightText(this.toLowerCase(), 'highlighted'); 177 | }); 178 | }, 10); 179 | $('

' + _('Hide Search Matches') + '

') 181 | .appendTo($('#searchbox')); 182 | } 183 | }, 184 | 185 | /** 186 | * init the domain index toggle buttons 187 | */ 188 | initIndexTable : function() { 189 | var togglers = $('img.toggler').click(function() { 190 | var src = $(this).attr('src'); 191 | var idnum = $(this).attr('id').substr(7); 192 | $('tr.cg-' + idnum).toggle(); 193 | if (src.substr(-9) == 'minus.png') 194 | $(this).attr('src', src.substr(0, src.length-9) + 'plus.png'); 195 | else 196 | $(this).attr('src', src.substr(0, src.length-8) + 'minus.png'); 197 | }).css('display', ''); 198 | if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) { 199 | togglers.click(); 200 | } 201 | }, 202 | 203 | /** 204 | * helper function to hide the search marks again 205 | */ 206 | hideSearchWords : function() { 207 | $('#searchbox .highlight-link').fadeOut(300); 208 | $('span.highlighted').removeClass('highlighted'); 209 | }, 210 | 211 | /** 212 | * make the url absolute 213 | */ 214 | makeURL : function(relativeURL) { 215 | return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL; 216 | }, 217 | 218 | /** 219 | * get the current relative url 220 | */ 221 | getCurrentURL : function() { 222 | var path = document.location.pathname; 223 | var parts = path.split(/\//); 224 | $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() { 225 | if (this == '..') 226 | parts.pop(); 227 | }); 228 | var url = parts.join('/'); 229 | return path.substring(url.lastIndexOf('/') + 1, path.length - 1); 230 | } 231 | }; 232 | 233 | // quick alias for translations 234 | _ = Documentation.gettext; 235 | 236 | $(document).ready(function() { 237 | Documentation.init(); 238 | }); 239 | -------------------------------------------------------------------------------- /doc/api/_build/html/_static/down-pressed.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ecocyc/PythonCyc/5b843aaed0ec3759ef3c550bea4b7f9908702dc6/doc/api/_build/html/_static/down-pressed.png -------------------------------------------------------------------------------- /doc/api/_build/html/_static/down.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ecocyc/PythonCyc/5b843aaed0ec3759ef3c550bea4b7f9908702dc6/doc/api/_build/html/_static/down.png -------------------------------------------------------------------------------- /doc/api/_build/html/_static/file.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ecocyc/PythonCyc/5b843aaed0ec3759ef3c550bea4b7f9908702dc6/doc/api/_build/html/_static/file.png -------------------------------------------------------------------------------- /doc/api/_build/html/_static/minus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ecocyc/PythonCyc/5b843aaed0ec3759ef3c550bea4b7f9908702dc6/doc/api/_build/html/_static/minus.png -------------------------------------------------------------------------------- /doc/api/_build/html/_static/plus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ecocyc/PythonCyc/5b843aaed0ec3759ef3c550bea4b7f9908702dc6/doc/api/_build/html/_static/plus.png -------------------------------------------------------------------------------- /doc/api/_build/html/_static/pygments.css: -------------------------------------------------------------------------------- 1 | .highlight .hll { background-color: #ffffcc } 2 | .highlight { background: #eeffcc; } 3 | .highlight .c { color: #408090; font-style: italic } /* Comment */ 4 | .highlight .err { border: 1px solid #FF0000 } /* Error */ 5 | .highlight .k { color: #007020; font-weight: bold } /* Keyword */ 6 | .highlight .o { color: #666666 } /* Operator */ 7 | .highlight .cm { color: #408090; font-style: italic } /* Comment.Multiline */ 8 | .highlight .cp { color: #007020 } /* Comment.Preproc */ 9 | .highlight .c1 { color: #408090; font-style: italic } /* Comment.Single */ 10 | .highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */ 11 | .highlight .gd { color: #A00000 } /* Generic.Deleted */ 12 | .highlight .ge { font-style: italic } /* Generic.Emph */ 13 | .highlight .gr { color: #FF0000 } /* Generic.Error */ 14 | .highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */ 15 | .highlight .gi { color: #00A000 } /* Generic.Inserted */ 16 | .highlight .go { color: #333333 } /* Generic.Output */ 17 | .highlight .gp { color: #c65d09; font-weight: bold } /* Generic.Prompt */ 18 | .highlight .gs { font-weight: bold } /* Generic.Strong */ 19 | .highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */ 20 | .highlight .gt { color: #0044DD } /* Generic.Traceback */ 21 | .highlight .kc { color: #007020; font-weight: bold } /* Keyword.Constant */ 22 | .highlight .kd { color: #007020; font-weight: bold } /* Keyword.Declaration */ 23 | .highlight .kn { color: #007020; font-weight: bold } /* Keyword.Namespace */ 24 | .highlight .kp { color: #007020 } /* Keyword.Pseudo */ 25 | .highlight .kr { color: #007020; font-weight: bold } /* Keyword.Reserved */ 26 | .highlight .kt { color: #902000 } /* Keyword.Type */ 27 | .highlight .m { color: #208050 } /* Literal.Number */ 28 | .highlight .s { color: #4070a0 } /* Literal.String */ 29 | .highlight .na { color: #4070a0 } /* Name.Attribute */ 30 | .highlight .nb { color: #007020 } /* Name.Builtin */ 31 | .highlight .nc { color: #0e84b5; font-weight: bold } /* Name.Class */ 32 | .highlight .no { color: #60add5 } /* Name.Constant */ 33 | .highlight .nd { color: #555555; font-weight: bold } /* Name.Decorator */ 34 | .highlight .ni { color: #d55537; font-weight: bold } /* Name.Entity */ 35 | .highlight .ne { color: #007020 } /* Name.Exception */ 36 | .highlight .nf { color: #06287e } /* Name.Function */ 37 | .highlight .nl { color: #002070; font-weight: bold } /* Name.Label */ 38 | .highlight .nn { color: #0e84b5; font-weight: bold } /* Name.Namespace */ 39 | .highlight .nt { color: #062873; font-weight: bold } /* Name.Tag */ 40 | .highlight .nv { color: #bb60d5 } /* Name.Variable */ 41 | .highlight .ow { color: #007020; font-weight: bold } /* Operator.Word */ 42 | .highlight .w { color: #bbbbbb } /* Text.Whitespace */ 43 | .highlight .mf { color: #208050 } /* Literal.Number.Float */ 44 | .highlight .mh { color: #208050 } /* Literal.Number.Hex */ 45 | .highlight .mi { color: #208050 } /* Literal.Number.Integer */ 46 | .highlight .mo { color: #208050 } /* Literal.Number.Oct */ 47 | .highlight .sb { color: #4070a0 } /* Literal.String.Backtick */ 48 | .highlight .sc { color: #4070a0 } /* Literal.String.Char */ 49 | .highlight .sd { color: #4070a0; font-style: italic } /* Literal.String.Doc */ 50 | .highlight .s2 { color: #4070a0 } /* Literal.String.Double */ 51 | .highlight .se { color: #4070a0; font-weight: bold } /* Literal.String.Escape */ 52 | .highlight .sh { color: #4070a0 } /* Literal.String.Heredoc */ 53 | .highlight .si { color: #70a0d0; font-style: italic } /* Literal.String.Interpol */ 54 | .highlight .sx { color: #c65d09 } /* Literal.String.Other */ 55 | .highlight .sr { color: #235388 } /* Literal.String.Regex */ 56 | .highlight .s1 { color: #4070a0 } /* Literal.String.Single */ 57 | .highlight .ss { color: #517918 } /* Literal.String.Symbol */ 58 | .highlight .bp { color: #007020 } /* Name.Builtin.Pseudo */ 59 | .highlight .vc { color: #bb60d5 } /* Name.Variable.Class */ 60 | .highlight .vg { color: #bb60d5 } /* Name.Variable.Global */ 61 | .highlight .vi { color: #bb60d5 } /* Name.Variable.Instance */ 62 | .highlight .il { color: #208050 } /* Literal.Number.Integer.Long */ -------------------------------------------------------------------------------- /doc/api/_build/html/_static/searchtools.js: -------------------------------------------------------------------------------- 1 | /* 2 | * searchtools.js_t 3 | * ~~~~~~~~~~~~~~~~ 4 | * 5 | * Sphinx JavaScript utilties for the full-text search. 6 | * 7 | * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS. 8 | * :license: BSD, see LICENSE for details. 9 | * 10 | */ 11 | 12 | 13 | /** 14 | * Porter Stemmer 15 | */ 16 | var Stemmer = function() { 17 | 18 | var step2list = { 19 | ational: 'ate', 20 | tional: 'tion', 21 | enci: 'ence', 22 | anci: 'ance', 23 | izer: 'ize', 24 | bli: 'ble', 25 | alli: 'al', 26 | entli: 'ent', 27 | eli: 'e', 28 | ousli: 'ous', 29 | ization: 'ize', 30 | ation: 'ate', 31 | ator: 'ate', 32 | alism: 'al', 33 | iveness: 'ive', 34 | fulness: 'ful', 35 | ousness: 'ous', 36 | aliti: 'al', 37 | iviti: 'ive', 38 | biliti: 'ble', 39 | logi: 'log' 40 | }; 41 | 42 | var step3list = { 43 | icate: 'ic', 44 | ative: '', 45 | alize: 'al', 46 | iciti: 'ic', 47 | ical: 'ic', 48 | ful: '', 49 | ness: '' 50 | }; 51 | 52 | var c = "[^aeiou]"; // consonant 53 | var v = "[aeiouy]"; // vowel 54 | var C = c + "[^aeiouy]*"; // consonant sequence 55 | var V = v + "[aeiou]*"; // vowel sequence 56 | 57 | var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 58 | var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 59 | var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 60 | var s_v = "^(" + C + ")?" + v; // vowel in stem 61 | 62 | this.stemWord = function (w) { 63 | var stem; 64 | var suffix; 65 | var firstch; 66 | var origword = w; 67 | 68 | if (w.length < 3) 69 | return w; 70 | 71 | var re; 72 | var re2; 73 | var re3; 74 | var re4; 75 | 76 | firstch = w.substr(0,1); 77 | if (firstch == "y") 78 | w = firstch.toUpperCase() + w.substr(1); 79 | 80 | // Step 1a 81 | re = /^(.+?)(ss|i)es$/; 82 | re2 = /^(.+?)([^s])s$/; 83 | 84 | if (re.test(w)) 85 | w = w.replace(re,"$1$2"); 86 | else if (re2.test(w)) 87 | w = w.replace(re2,"$1$2"); 88 | 89 | // Step 1b 90 | re = /^(.+?)eed$/; 91 | re2 = /^(.+?)(ed|ing)$/; 92 | if (re.test(w)) { 93 | var fp = re.exec(w); 94 | re = new RegExp(mgr0); 95 | if (re.test(fp[1])) { 96 | re = /.$/; 97 | w = w.replace(re,""); 98 | } 99 | } 100 | else if (re2.test(w)) { 101 | var fp = re2.exec(w); 102 | stem = fp[1]; 103 | re2 = new RegExp(s_v); 104 | if (re2.test(stem)) { 105 | w = stem; 106 | re2 = /(at|bl|iz)$/; 107 | re3 = new RegExp("([^aeiouylsz])\\1$"); 108 | re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); 109 | if (re2.test(w)) 110 | w = w + "e"; 111 | else if (re3.test(w)) { 112 | re = /.$/; 113 | w = w.replace(re,""); 114 | } 115 | else if (re4.test(w)) 116 | w = w + "e"; 117 | } 118 | } 119 | 120 | // Step 1c 121 | re = /^(.+?)y$/; 122 | if (re.test(w)) { 123 | var fp = re.exec(w); 124 | stem = fp[1]; 125 | re = new RegExp(s_v); 126 | if (re.test(stem)) 127 | w = stem + "i"; 128 | } 129 | 130 | // Step 2 131 | re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; 132 | if (re.test(w)) { 133 | var fp = re.exec(w); 134 | stem = fp[1]; 135 | suffix = fp[2]; 136 | re = new RegExp(mgr0); 137 | if (re.test(stem)) 138 | w = stem + step2list[suffix]; 139 | } 140 | 141 | // Step 3 142 | re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; 143 | if (re.test(w)) { 144 | var fp = re.exec(w); 145 | stem = fp[1]; 146 | suffix = fp[2]; 147 | re = new RegExp(mgr0); 148 | if (re.test(stem)) 149 | w = stem + step3list[suffix]; 150 | } 151 | 152 | // Step 4 153 | re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; 154 | re2 = /^(.+?)(s|t)(ion)$/; 155 | if (re.test(w)) { 156 | var fp = re.exec(w); 157 | stem = fp[1]; 158 | re = new RegExp(mgr1); 159 | if (re.test(stem)) 160 | w = stem; 161 | } 162 | else if (re2.test(w)) { 163 | var fp = re2.exec(w); 164 | stem = fp[1] + fp[2]; 165 | re2 = new RegExp(mgr1); 166 | if (re2.test(stem)) 167 | w = stem; 168 | } 169 | 170 | // Step 5 171 | re = /^(.+?)e$/; 172 | if (re.test(w)) { 173 | var fp = re.exec(w); 174 | stem = fp[1]; 175 | re = new RegExp(mgr1); 176 | re2 = new RegExp(meq1); 177 | re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); 178 | if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) 179 | w = stem; 180 | } 181 | re = /ll$/; 182 | re2 = new RegExp(mgr1); 183 | if (re.test(w) && re2.test(w)) { 184 | re = /.$/; 185 | w = w.replace(re,""); 186 | } 187 | 188 | // and turn initial Y back to y 189 | if (firstch == "y") 190 | w = firstch.toLowerCase() + w.substr(1); 191 | return w; 192 | } 193 | } 194 | 195 | 196 | 197 | /** 198 | * Simple result scoring code. 199 | */ 200 | var Scorer = { 201 | // Implement the following function to further tweak the score for each result 202 | // The function takes a result array [filename, title, anchor, descr, score] 203 | // and returns the new score. 204 | /* 205 | score: function(result) { 206 | return result[4]; 207 | }, 208 | */ 209 | 210 | // query matches the full name of an object 211 | objNameMatch: 11, 212 | // or matches in the last dotted part of the object name 213 | objPartialMatch: 6, 214 | // Additive scores depending on the priority of the object 215 | objPrio: {0: 15, // used to be importantResults 216 | 1: 5, // used to be objectResults 217 | 2: -5}, // used to be unimportantResults 218 | // Used when the priority is not in the mapping. 219 | objPrioDefault: 0, 220 | 221 | // query found in title 222 | title: 15, 223 | // query found in terms 224 | term: 5 225 | }; 226 | 227 | 228 | /** 229 | * Search Module 230 | */ 231 | var Search = { 232 | 233 | _index : null, 234 | _queued_query : null, 235 | _pulse_status : -1, 236 | 237 | init : function() { 238 | var params = $.getQueryParameters(); 239 | if (params.q) { 240 | var query = params.q[0]; 241 | $('input[name="q"]')[0].value = query; 242 | this.performSearch(query); 243 | } 244 | }, 245 | 246 | loadIndex : function(url) { 247 | $.ajax({type: "GET", url: url, data: null, 248 | dataType: "script", cache: true, 249 | complete: function(jqxhr, textstatus) { 250 | if (textstatus != "success") { 251 | document.getElementById("searchindexloader").src = url; 252 | } 253 | }}); 254 | }, 255 | 256 | setIndex : function(index) { 257 | var q; 258 | this._index = index; 259 | if ((q = this._queued_query) !== null) { 260 | this._queued_query = null; 261 | Search.query(q); 262 | } 263 | }, 264 | 265 | hasIndex : function() { 266 | return this._index !== null; 267 | }, 268 | 269 | deferQuery : function(query) { 270 | this._queued_query = query; 271 | }, 272 | 273 | stopPulse : function() { 274 | this._pulse_status = 0; 275 | }, 276 | 277 | startPulse : function() { 278 | if (this._pulse_status >= 0) 279 | return; 280 | function pulse() { 281 | var i; 282 | Search._pulse_status = (Search._pulse_status + 1) % 4; 283 | var dotString = ''; 284 | for (i = 0; i < Search._pulse_status; i++) 285 | dotString += '.'; 286 | Search.dots.text(dotString); 287 | if (Search._pulse_status > -1) 288 | window.setTimeout(pulse, 500); 289 | } 290 | pulse(); 291 | }, 292 | 293 | /** 294 | * perform a search for something (or wait until index is loaded) 295 | */ 296 | performSearch : function(query) { 297 | // create the required interface elements 298 | this.out = $('#search-results'); 299 | this.title = $('

' + _('Searching') + '

').appendTo(this.out); 300 | this.dots = $('').appendTo(this.title); 301 | this.status = $('

').appendTo(this.out); 302 | this.output = $('