Changes in [1659:32e069184b7d:1663:6f48078a9554] in orange-bioinformatics


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61 added
73 deleted
5 edited

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  • docs/widgets/Makefile

    r1623 r1662  
    66SPHINXBUILD   = sphinx-build 
    77PAPER         = 
     8BUILDDIR      = build 
    89 
    910# Internal variables. 
    1011PAPEROPT_a4     = -D latex_paper_size=a4 
    1112PAPEROPT_letter = -D latex_paper_size=letter 
    12 #ALLSPHINXOPTS   = -d _build/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . 
    13 ALLSPHINXOPTS   = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) rst 
     13ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) rst 
    1414 
    15 .PHONY: help clean html dirhtml pickle json htmlhelp qthelp latex changes linkcheck doctest 
     15.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest 
    1616 
    1717help: 
    1818    @echo "Please use \`make <target>' where <target> is one of" 
    19     @echo "  html      to make standalone HTML files" 
    20     @echo "  dirhtml   to make HTML files named index.html in directories" 
    21     @echo "  pickle    to make pickle files" 
    22     @echo "  json      to make JSON files" 
    23     @echo "  htmlhelp  to make HTML files and a HTML help project" 
    24     @echo "  qthelp    to make HTML files and a qthelp project" 
    25     @echo "  latex     to make LaTeX files, you can set PAPER=a4 or PAPER=letter" 
    26     @echo "  changes   to make an overview of all changed/added/deprecated items" 
    27     @echo "  linkcheck to check all external links for integrity" 
    28     @echo "  doctest   to run all doctests embedded in the documentation (if enabled)" 
     19    @echo "  html       to make standalone HTML files" 
     20    @echo "  dirhtml    to make HTML files named index.html in directories" 
     21    @echo "  singlehtml to make a single large HTML file" 
     22    @echo "  pickle     to make pickle files" 
     23    @echo "  json       to make JSON files" 
     24    @echo "  htmlhelp   to make HTML files and a HTML help project" 
     25    @echo "  qthelp     to make HTML files and a qthelp project" 
     26    @echo "  devhelp    to make HTML files and a Devhelp project" 
     27    @echo "  epub       to make an epub" 
     28    @echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter" 
     29    @echo "  latexpdf   to make LaTeX files and run them through pdflatex" 
     30    @echo "  text       to make text files" 
     31    @echo "  man        to make manual pages" 
     32    @echo "  changes    to make an overview of all changed/added/deprecated items" 
     33    @echo "  linkcheck  to check all external links for integrity" 
     34    @echo "  doctest    to run all doctests embedded in the documentation (if enabled)" 
    2935 
    3036clean: 
    31     -rm -rf _build/* 
     37    -rm -rf $(BUILDDIR)/* 
    3238 
    3339html: 
    34     $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) . 
     40    $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html 
    3541    @echo 
    36     @echo "Build finished. The HTML pages are in .. ." 
     42    @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." 
    3743 
    3844dirhtml: 
    39     $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) .dirhtml 
     45    $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml 
    4046    @echo 
    41     @echo "Build finished. The HTML pages are in .dirhtml." 
     47    @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." 
     48 
     49singlehtml: 
     50    $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml 
     51    @echo 
     52    @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." 
    4253 
    4354pickle: 
    44     $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) .pickle 
     55    $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle 
    4556    @echo 
    4657    @echo "Build finished; now you can process the pickle files." 
    4758 
    4859json: 
    49     $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) .json 
     60    $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json 
    5061    @echo 
    5162    @echo "Build finished; now you can process the JSON files." 
    5263 
    5364htmlhelp: 
    54     $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) .htmlhelp 
     65    $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp 
    5566    @echo 
    5667    @echo "Build finished; now you can run HTML Help Workshop with the" \ 
    57           ".hhp project file in .htmlhelp." 
     68          ".hhp project file in $(BUILDDIR)/htmlhelp." 
    5869 
    5970qthelp: 
    60     $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) .qthelp 
     71    $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp 
    6172    @echo 
    6273    @echo "Build finished; now you can run "qcollectiongenerator" with the" \ 
    63           ".qhcp project file in .qthelp, like this:" 
    64     @echo "# qcollectiongenerator .qthelp/OrangeWidgetCatalog.qhcp" 
     74          ".qhcp project file in $(BUILDDIR)/qthelp, like this:" 
     75    @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/OrangeX.qhcp" 
    6576    @echo "To view the help file:" 
    66     @echo "# assistant -collectionFile .qthelp/OrangeWidgetCatalog.qhc" 
     77    @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/OrangeX.qhc" 
     78 
     79devhelp: 
     80    $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp 
     81    @echo 
     82    @echo "Build finished." 
     83    @echo "To view the help file:" 
     84    @echo "# mkdir -p $$HOME/.local/share/devhelp/OrangeX" 
     85    @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/OrangeX" 
     86    @echo "# devhelp" 
     87 
     88epub: 
     89    $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub 
     90    @echo 
     91    @echo "Build finished. The epub file is in $(BUILDDIR)/epub." 
    6792 
    6893latex: 
    69     $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) .latex 
     94    $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex 
    7095    @echo 
    71     @echo "Build finished; the LaTeX files are in .latex." 
    72     @echo "Run \`make all-pdf' or \`make all-ps' in that directory to" \ 
    73           "run these through (pdf)latex." 
     96    @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." 
     97    @echo "Run \`make' in that directory to run these through (pdf)latex" \ 
     98          "(use \`make latexpdf' here to do that automatically)." 
     99 
     100latexpdf: 
     101    $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex 
     102    @echo "Running LaTeX files through pdflatex..." 
     103    make -C $(BUILDDIR)/latex all-pdf 
     104    @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." 
     105 
     106text: 
     107    $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text 
     108    @echo 
     109    @echo "Build finished. The text files are in $(BUILDDIR)/text." 
     110 
     111man: 
     112    $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man 
     113    @echo 
     114    @echo "Build finished. The manual pages are in $(BUILDDIR)/man." 
    74115 
    75116changes: 
    76     $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) .changes 
     117    $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes 
    77118    @echo 
    78     @echo "The overview file is in .changes." 
     119    @echo "The overview file is in $(BUILDDIR)/changes." 
    79120 
    80121linkcheck: 
    81     $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) .linkcheck 
     122    $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck 
    82123    @echo 
    83124    @echo "Link check complete; look for any errors in the above output " \ 
    84           "or in .linkcheck/output.txt." 
     125          "or in $(BUILDDIR)/linkcheck/output.txt." 
    85126 
    86127doctest: 
    87     $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) .doctest 
     128    $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest 
    88129    @echo "Testing of doctests in the sources finished, look at the " \ 
    89           "results in .doctest/output.txt." 
     130          "results in $(BUILDDIR)/doctest/output.txt." 
  • docs/widgets/rst/PIPA.rst

    r1623 r1662  
    22==== 
    33 
    4 .. image:: ../../../widgets/icons/PIPA.png 
    5    :alt: widget icon 
     4.. image:: ../../../_bioinformatics/widgets/icons/PIPA.png 
     5   :alt: Widget icon 
    66    
    77Signals 
     
    1818----------- 
    1919 
    20 .. image:: PIPA.* 
     20.. image:: images/PIPA.* 
    2121   :alt: PIPA widget 
    2222 
     
    3232In the schema below we connected PIPA to Data Table, GO Enrichment Analysis, and Distance Map (through Attribute Distance) widgets. 
    3333 
    34 .. image:: PIPA_schema.* 
     34.. image:: images/PIPA_schema.* 
    3535   :alt: Example schema with PIPA widget 
    3636 
    3737The Data Table widget below contains the output from the PIPA widget. Each column contains gene expressions of a single experiment. The labels are shown in the table header. 
    3838   
    39 .. image:: PIPA_datatable.* 
     39.. image:: images/PIPA_datatable.* 
    4040   :alt: Output of PIPA in a data table. 
    4141 
    4242The Distance Map widget shows distances between experiments. The distances are measured with Attribute Distance widget, which was set to compute Pearson distances (as (1-PearsonCorrelation)/2). 
    4343 
    44 .. image:: PIPA_distance.* 
     44.. image:: images/PIPA_distance.* 
    4545   :alt: Distances between experiments. 
    46   
  • docs/widgets/rst/conf.py

    r1623 r1662  
    11# -*- coding: utf-8 -*- 
    2 # 
    3 # Orange widget catalog documentation build configuration file, created by 
    4 # sphinx-quickstart on Fri Oct  8 15:09:05 2010. 
    52# 
    63# This file is execfile()d with the current directory set to its containing dir. 
     
    1310 
    1411import sys, os 
     12 
     13import imp 
     14module_setup = imp.load_source('module_setup', os.path.join(os.path.dirname(__file__), '..', '..', '..', 'setup.py')) 
     15VERSION = module_setup.VERSION 
     16AUTHOR = module_setup.AUTHOR 
     17NAME = module_setup.NAME 
     18 
     19DOCUMENTATION_TYPE = "Widgets" 
     20 
     21TITLE = "%s %s v%s documentation" % (NAME, DOCUMENTATION_TYPE, VERSION) 
    1522 
    1623# If extensions (or modules to document with autodoc) are in another directory, 
     
    2330# Add any Sphinx extension module names here, as strings. They can be extensions 
    2431# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. 
    25 extensions = ['sphinx.ext.autodoc', 'sphinx.ext.pngmath'] 
     32extensions = ['sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.pngmath'] 
    2633 
    2734# Add any paths that contain templates here, relative to this directory. 
     
    3845 
    3946# General information about the project. 
    40 project = u'Orange widget catalog' 
    41 copyright = u'Bioinformatics Laboratory, FRI UL' 
     47project = NAME 
     48copyright = AUTHOR 
    4249 
    4350# The version info for the project you're documenting, acts as replacement for 
     
    4653# 
    4754# The short X.Y version. 
    48 version = '2.0b' 
     55version = VERSION 
    4956# The full version, including alpha/beta/rc tags. 
    50 release = '2.0b' 
     57release = VERSION 
    5158 
    5259# The language for content autogenerated by Sphinx. Refer to documentation 
     
    9299# The theme to use for HTML and HTML Help pages.  Major themes that come with 
    93100# Sphinx are currently 'default' and 'sphinxdoc'. 
    94 html_theme = 'orange_theme' 
     101html_theme = 'nature' 
    95102 
    96103# Theme options are theme-specific and customize the look and feel of a theme 
    97104# further.  For a list of options available for each theme, see the 
    98105# documentation. 
    99 html_theme_options = {"collapsiblesidebar": "true"} 
    100 if html_theme == "orange_theme": 
    101     html_theme_options.update({"orangeheaderfooter": "false"}) 
    102      
     106#html_theme_options = {} 
    103107 
    104108# Add any paths that contain custom themes here, relative to this directory. 
    105 html_theme_path = ["../../sphinx-ext/themes"] 
     109#html_theme_path = [] 
    106110 
    107111# The name for this set of Sphinx documents.  If None, it defaults to 
    108112# "<project> v<release> documentation". 
    109 html_title = project 
     113html_title = TITLE 
    110114 
    111115# A shorter title for the navigation bar.  Default is the same as html_title. 
     
    135139 
    136140# Custom sidebar templates, maps document names to template names. 
    137 html_sidebars = { 
    138    '*': ['globaltoc.html', 'sourcelink.html', 'searchbox.html'], 
    139    '*/*': [], #Disable sidebar for individual widgets  
    140 } 
    141  
     141#html_sidebars = {} 
    142142 
    143143# Additional templates that should be rendered to pages, maps page names to 
     
    146146 
    147147# If false, no module index is generated. 
    148 #html_use_modindex = True 
     148#html_domain_indices = True 
    149149 
    150150# If false, no index is generated. 
     
    156156# If true, links to the reST sources are added to the pages. 
    157157#html_show_sourcelink = True 
     158 
     159# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. 
     160html_show_sphinx = False 
     161 
     162# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. 
     163html_show_copyright = False 
    158164 
    159165# If true, an OpenSearch description file will be output, and all pages will 
     
    166172 
    167173# Output file base name for HTML help builder. 
    168 htmlhelp_basename = 'Orangewidgetcatalogdoc' 
     174htmlhelp_basename = DOCUMENTATION_TYPE.lower().replace(' ', '') 
    169175 
    170176 
     
    180186# (source start file, target name, title, author, documentclass [howto/manual]). 
    181187latex_documents = [ 
    182   ('index', 'Orangewidgetcatalog.tex', u'Orange widget catalog Documentation', 
    183    u'Blaz Zupan', 'manual'), 
     188  ('index', '%s.tex' % (DOCUMENTATION_TYPE.lower().replace(' ', ''),), html_title, 
     189   copyright, 'manual'), 
    184190] 
    185191 
     
    192198#latex_use_parts = False 
    193199 
     200# If true, show page references after internal links. 
     201#latex_show_pagerefs = False 
     202 
     203# If true, show URL addresses after external links. 
     204#latex_show_urls = False 
     205 
    194206# Additional stuff for the LaTeX preamble. 
    195207#latex_preamble = '' 
     
    199211 
    200212# If false, no module index is generated. 
    201 #latex_use_modindex = True 
     213#latex_domain_indices = True 
     214 
     215# -- Options for manual page output -------------------------------------------- 
     216 
     217# One entry per manual page. List of tuples 
     218# (source start file, name, description, authors, manual section). 
     219man_pages = [ 
     220    ('index', DOCUMENTATION_TYPE.lower().replace(' ', ''), TITLE, 
     221     [AUTHOR], 1) 
     222] 
     223 
     224# Example configuration for intersphinx: refer to the Python standard library. 
     225intersphinx_mapping = { 
     226    'python': ('http://python.readthedocs.org/en/latest/', None), 
     227} 
     228 
  • docs/widgets/rst/index.rst

    r1623 r1662  
    1 .. Orange Widget Catalog documentation master file, created by 
    2    sphinx-quickstart on Mon Oct 11 17:05:09 2010. 
    3    You can adapt this file completely to your liking, but it should at least 
    4    contain the root `toctree` directive. 
     1Orange-Bioinformatics Widgets documentation 
     2=========================================== 
    53 
    6 Welcome to Orange Widget Catalog's documentation! 
    7 ================================================= 
     4Orange Bioinformatics is an add-on for Orange_ data mining software package. It 
     5extends Orange by providing common functionality for basic tasks in 
     6bioinformatics. It also provides widgets for Orange Canvas, which enable users 
     7who are not programmers to manage microarray and genomic data flow and to 
     8customize their analysis by combining common data analysis tools to fit their 
     9needs. 
    810 
    9 Contents: 
     11.. _Orange: http://orange.biolab.si/ 
     12 
     13Widgets: 
    1014 
    1115.. toctree:: 
     
    1418   PIPA.rst 
    1519 
     20Source Code and Issue Tracker 
     21----------------------------- 
     22 
     23Source code is available on Bitbucket_. For issues and wiki we use Trac_. 
     24 
     25.. _Bitbucket: https://bitbucket.org/biolab/orange-bioinformatics 
     26.. _Trac: http://orange.biolab.si/trac/ 
     27 
    1628Indices and tables 
    1729================== 
    1830 
    1931* :ref:`genindex` 
    20 * :ref:`modindex` 
    2132* :ref:`search` 
    22  
  • setup.py

    r1659 r1663  
    11#!/usr/bin/env python 
    22 
    3 import distribute_setup 
    4 distribute_setup.use_setuptools() 
     3try: 
     4    import distribute_setup 
     5    distribute_setup.use_setuptools() 
     6except ImportError: 
     7    # For documentation we load setup.py to get version 
     8    # so it does not matter if importing fails 
     9    pass 
    510 
    611import os 
     
    1015NAME = 'Orange-Bioinformatics' 
    1116 
    12 VERSION = '1.1a' 
     17VERSION = '2.5a1' 
    1318 
    1419DESCRIPTION = 'Orange Bioinformatics add-on for Orange data mining software package.' 
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