.gitignore

+*.pyc
+*.egg-info
+.tox
+dist
+build
+_build
+doc/hosted_site.cmd
+.ruffus_history.sqlite
+ruffus_development.*
\ No newline at end of file

.gitmodules

+[submodule "doc/sphinx_rtd_theme"]
+	path = doc/sphinx_rtd_theme
+	url = https://github.com/bunbun/sphinx_rtd_theme.git

.hgignore

+.*\.pyc$
+^nested_dict.egg-info/.+
+^dist
+_build$
+doc/hosted_site.cmd
+^.tox
+^.ruffus_history.sqlite$

.travis.yml

+language: python
+
+# all python versions tested via pip in tox
+python:
+  - "2.7"
+  - "3.4"
+  - "3.5"
+  - "3.6"
+
+before_install:
+
+install: python setup.py install
+
+script: cd ruffus/test && /bin/bash run_all_unit_tests.cmd
+
+sudo: false

MANIFEST.in

+include *.TXT
+recursive-include doc *
+recursive-include ruffus *.py
+include ruffus/test/run_all_unit_tests.cmd 
+include ruffus/test/run_all_unit_tests3.cmd
+include README.rst

PKG-INFO

-Metadata-Version: 1.1
-Name: ruffus
-Version: 2.6.3
-Summary: Light-weight Python Computational Pipeline Management
-Home-page: http://www.ruffus.org.uk
-Author: Leo Goodstadt
-Author-email: ruffus_lib@llew.org.uk
-License: MIT
-Download-URL: https://pypi.python.org/pypi/ruffus
-Description: 
-        ***************************************
-        Overview
-        ***************************************
-        
-        
-            The Ruffus module is a lightweight way to add support
-            for running computational pipelines.
-        
-            Computational pipelines are often conceptually quite simple, especially
-            if we breakdown the process into simple stages, or separate **tasks**.
-        
-            Each stage or **task** in a computational pipeline is represented by a python function
-            Each python function can be called in parallel to run multiple **jobs**.
-        
-            Ruffus was originally designed for use in bioinformatics to analyse multiple genome
-            data sets.
-        
-        ***************************************
-        Documentation
-        ***************************************
-        
-            Ruffus documentation can be found `here <http://www.ruffus.org.uk>`__ ,
-            with `download notes <http://www.ruffus.org.uk/installation.html>`__ ,
-            a `tutorial <http://www.ruffus.org.uk/tutorials/new_tutorial/introduction.html>`__ and
-            an `in-depth manual <http://www.ruffus.org.uk/tutorials/new_tutorial/manual_contents.html>`__ .
-        
-        
-        ***************************************
-        Background
-        ***************************************
-        
-            The purpose of a pipeline is to determine automatically which parts of a multi-stage
-            process needs to be run and in what order in order to reach an objective ("targets")
-        
-            Computational pipelines, especially for analysing large scientific datasets are
-            in widespread use.
-            However, even a conceptually simple series of steps can be difficult to set up and
-            maintain.
-        
-        ***************************************
-        Design
-        ***************************************
-            The ruffus module has the following design goals:
-        
-                * Lightweight
-                * Scalable / Flexible / Powerful
-                * Standard Python
-                * Unintrusive
-                * As simple as possible
-        
-        ***************************************
-        Features
-        ***************************************
-        
-            Automatic support for
-        
-                * Managing dependencies
-                * Parallel jobs, including dispatching work to computational clusters
-                * Re-starting from arbitrary points, especially after errors (checkpointing)
-                * Display of the pipeline as a flowchart
-                * Managing complex pipeline topologies
-        
-        
-        ***************************************
-        A Simple example
-        ***************************************
-        
-                Use the **@follows(...)** python decorator before the function definitions::
-        
-                    from ruffus import *
-                    import sys
-        
-                    def first_task():
-                        print "First task"
-        
-                    @follows(first_task)
-                    def second_task():
-                        print "Second task"
-        
-                    @follows(second_task)
-                    def final_task():
-                        print "Final task"
-        
-        
-        
-        
-                the ``@follows`` decorator indicate that the ``first_task`` function precedes ``second_task`` in
-                the pipeline.
-        
-                The canonical Ruffus decorator is ``@transform`` which **transforms** data flowing down a
-                computational pipeline from one stage to teh next.
-        
-        ********
-        Usage
-        ********
-        
-            Each stage or **task** in a computational pipeline is represented by a python function
-            Each python function can be called in parallel to run multiple **jobs**.
-        
-            1. Import module::
-        
-                    import ruffus
-        
-        
-            1. Annotate functions with python decorators
-        
-            2. Print dependency graph if you necessary
-        
-                - For a graphical flowchart in ``jpg``, ``svg``, ``dot``, ``png``, ``ps``, ``gif`` formats::
-        
-                    pipeline_printout_graph ("flowchart.svg")
-        
-                This requires ``dot`` to be installed
-        
-                - For a text printout of all jobs ::
-        
-                    pipeline_printout(sys.stdout)
-        
-        
-            3. Run the pipeline::
-        
-                pipeline_run()
-        
-        
-        
-Keywords: make task pipeline parallel bioinformatics science
-Platform: UNKNOWN
-Classifier: Intended Audience :: End Users/Desktop
-Classifier: Development Status :: 5 - Production/Stable
-Classifier: Intended Audience :: Developers
-Classifier: Intended Audience :: Science/Research
-Classifier: Intended Audience :: Information Technology
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Programming Language :: Python
-Classifier: Topic :: Scientific/Engineering
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Classifier: Topic :: System :: Distributed Computing
-Classifier: Topic :: Software Development :: Build Tools
-Classifier: Topic :: Software Development :: Build Tools
-Classifier: Topic :: Software Development :: Libraries
-Classifier: Environment :: Console

debian/changelog

+python-ruffus (2.7-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+    Closes: #903531
+  * Standards-Version: 4.1.5
+  * Build-Depends: python3-sphinx-rtd-theme
+
+ -- Andreas Tille <tille@debian.org>  Wed, 11 Jul 2018 11:21:00 +0200
+
 python-ruffus (2.6.3+dfsg-5) unstable; urgency=medium
 
   * Testsuite: autopkgtest-pkg-python

debian/control

@@ -11,8 +11,9 @@ Build-Depends: debhelper (>= 11~),
                python3-all,
                python3-setuptools,
                python3-sphinx,
+               python3-sphinx-rtd-theme,
                graphviz
-Standards-Version: 4.1.4
+Standards-Version: 4.1.5
 Vcs-Browser: https://salsa.debian.org/med-team/python-ruffus
 Vcs-Git: https://salsa.debian.org/med-team/python-ruffus.git
 Homepage: http://www.ruffus.org.uk/

debian/patches/fix_test.patch

-Author: Andreas Tille <tille@debian.org>
-Last-Update: Fri, 13 Mar 2015 11:00:09 +0100
-Description: replace failed test from upstream Git where it is fixed
-
---- a/ruffus/test/test_file_name_parameters.py
-+++ b/ruffus/test/test_file_name_parameters.py
-@@ -1613,3 +1613,4 @@ class Test_product_param_factory(unittes
- 
- if __name__ == '__main__':
-     unittest.main()
-+

debian/patches/python-3.5.patch

-Author: Andreas Tille <tille@debian.org>
-Last-Update: Fri, 15 Jan 2016 10:08:16 +0100
-Bug-Debian: https://bugs.debian.org/811002
-Description: Fix issue in test suite when using Python 3.5
- See https://lists.debian.org/debian-python/2016/01/msg00060.html
-
---- a/ruffus/test/test_ruffus_utility.py
-+++ b/ruffus/test/test_ruffus_utility.py
-@@ -259,7 +259,8 @@ class Test_compile_regex (unittest.TestC
-         try:
-             compile_regex("Dummy Task", regex(".*)"), Exception, "test1")
-         except Exception as e:
--            self.assertEqual(e.args, ('Dummy Task', "test1: regular expression regex('.*)') is malformed\n[sre_constants.error: (unbalanced parenthesis)]"))
-+            self.assertEqual(e.args[0], 'Dummy Task')
-+            self.assertIn("test1: regular expression regex('.*)') is malformed\n[sre_constants.error: (unbalanced parenthesis", e.args[1])
- 
-         # bad number of items regex
-         self.assertRaises(Exception, compile_regex, "Dummy Task", regex(".*", "o"), Exception, "test1")

debian/patches/series

-fix_test.patch
-python-3.5.patch
 use_libjs-mathjax.patch
 sphinx.ext.pngmath_deprecated.patch
 use_png_instead_of_jpg.patch

debian/patches/sphinx.ext.pngmath_deprecated.patch

@@ -5,7 +5,7 @@ Description: Fix sphinx.ext.mathjax: other math package is already loaded
 
 --- a/doc/conf.py
 +++ b/doc/conf.py
-@@ -30,7 +30,7 @@ import ruffus, ruffus.task, ruffus.ruffu
+@@ -36,7 +36,7 @@ def setup(app):
  # Add any Sphinx extension module names here, as strings. They can be extensions
  # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
  extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx', 'sphinx.ext.todo',

debian/patches/use_libjs-mathjax.patch

@@ -4,7 +4,7 @@ Description: Use Debian packaged mathjax
 
 --- a/doc/conf.py
 +++ b/doc/conf.py
-@@ -32,6 +32,8 @@ import ruffus, ruffus.task, ruffus.ruffu
+@@ -38,6 +38,8 @@ def setup(app):
  extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx', 'sphinx.ext.todo',
                'sphinx.ext.coverage', 'sphinx.ext.pngmath', 'sphinx.ext.mathjax', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode']
  

debian/patches/use_png_instead_of_jpg.patch

@@ -5,7 +5,7 @@ Description: Create PNG instead of JPG to work around bug #827806
 
 --- a/doc/pipeline_functions.rst
 +++ b/doc/pipeline_functions.rst
-@@ -455,7 +455,7 @@ Pipeline functions
+@@ -460,7 +460,7 @@ Ruffus Functions
      **Example**:
          ::
  
@@ -16,7 +16,7 @@ Description: Create PNG instead of JPG to work around bug #827806
  
 --- a/ruffus/task.py
 +++ b/ruffus/task.py
-@@ -4572,7 +4572,7 @@ def pipeline_printout_graph(stream,
+@@ -4573,7 +4573,7 @@ def pipeline_printout_graph(stream,
  
      :param stream: where to print to
      :type stream: file-like object with ``write()`` function

doc/conf.py

@@ -17,6 +17,12 @@ print sys.path
 import ruffus, ruffus.task, ruffus.ruffus_version
 
 
+def setup(app):
+   #app.add_javascript("custom.js")
+   if not on_rtd:
+       app.add_stylesheet("ruffus.css")
+
+
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
@@ -46,7 +52,7 @@ master_doc = 'contents'
 
 # General information about the project.
 project = u'ruffus'
-copyright = u'2009-2013 Leo Goodstadt'
+copyright = u'2009-2015 Leo Goodstadt'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -72,7 +78,7 @@ print version, release
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['_build']
+exclude_patterns = ['_build', "sphinx_rtd_theme"]
 
 # The reST default role (used for this markup: `text`) to use for all documents.
 #default_role = None
@@ -105,36 +111,39 @@ pygments_style = 'sphinx'
 # given in html_static_path.
 import os
 on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
-if not on_rtd:
-    html_style = 'ruffus.css'
+#if not on_rtd:
+#    html_style = 'ruffus.css'
 #html_style = 'ruffus.css'
 
-# a list of builtin themes.
-html_theme = 'default'
+if not on_rtd:
+    # a list of builtin themes.
+    import sphinx_rtd_theme
+    html_theme = "sphinx_rtd_theme"
+    #html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+    html_theme_path = ["sphinx_rtd_theme"]
+
+#html_theme = 'default'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 #html_theme_options = {}
 
-# Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
-
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
 #html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
+html_short_title = "Ruffus " + version
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = None
+#html_logo = "images/logo64.png"
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-#html_favicon = None
+html_favicon = "static_data/favicon32.ico"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

doc/contents.rst

@@ -5,182 +5,53 @@
 ==========================================
 Start Here:
 ==========================================
-.. toctree::
-   :maxdepth: 2
-
-   installation.rst
-   tutorials/new_tutorial/manual_contents.rst
-   tutorials/new_tutorial/introduction.rst
-   tutorials/new_tutorial/transform.rst
-   tutorials/new_tutorial/transform_in_parallel.rst
-   tutorials/new_tutorial/originate.rst
-   tutorials/new_tutorial/pipeline_printout.rst
-   tutorials/new_tutorial/command_line.rst
-   tutorials/new_tutorial/pipeline_printout_graph.rst
-   tutorials/new_tutorial/output_file_names.rst
-   tutorials/new_tutorial/mkdir.rst
-   tutorials/new_tutorial/checkpointing.rst
-   tutorials/new_tutorial/decorators_compendium.rst
-   tutorials/new_tutorial/split.rst
-   tutorials/new_tutorial/merge.rst
-   tutorials/new_tutorial/multiprocessing.rst
-   tutorials/new_tutorial/logging.rst
-   tutorials/new_tutorial/subdivide_collate.rst
-   tutorials/new_tutorial/combinatorics.rst
-   tutorials/new_tutorial/active_if.rst
-   tutorials/new_tutorial/posttask.rst
-   tutorials/new_tutorial/inputs.rst
-   tutorials/new_tutorial/onthefly.rst
-   tutorials/new_tutorial/parallel.rst
-   tutorials/new_tutorial/check_if_uptodate.rst
-   tutorials/new_tutorial/flowchart_colours.rst
-   tutorials/new_tutorial/dependencies.rst
-   tutorials/new_tutorial/exceptions.rst
-   tutorials/new_tutorial/list_of_ruffus_names.rst
-   tutorials/new_tutorial/deprecated_files.rst
-   tutorials/new_tutorial/deprecated_files_re.rst
-
-
-Example code for:
 
 .. toctree::
+   :titlesonly:
    :maxdepth: 1
+   :caption: Introduction
+   :name: introduction_toc
 
-   tutorials/new_tutorial/introduction_code.rst
-   tutorials/new_tutorial/transform_code.rst
-   tutorials/new_tutorial/transform_in_parallel_code.rst
-   tutorials/new_tutorial/originate_code.rst
-   tutorials/new_tutorial/pipeline_printout_code.rst
-   tutorials/new_tutorial/pipeline_printout_graph_code.rst
-   tutorials/new_tutorial/output_file_names_code.rst
-   tutorials/new_tutorial/mkdir_code.rst
-   tutorials/new_tutorial/checkpointing_code.rst
-   tutorials/new_tutorial/split_code.rst
-   tutorials/new_tutorial/merge_code.rst
-   tutorials/new_tutorial/multiprocessing_code.rst
-   tutorials/new_tutorial/logging_code.rst
-   tutorials/new_tutorial/subdivide_collate_code.rst
-   tutorials/new_tutorial/combinatorics_code.rst
-   tutorials/new_tutorial/inputs_code.rst
-   tutorials/new_tutorial/onthefly_code.rst
-   tutorials/new_tutorial/flowchart_colours_code.rst
-
-
-
-=====================
-Overview:
-=====================
-.. toctree::
-   :maxdepth: 2
-
-   cheatsheet.rst
-   pipeline_functions.rst
-   drmaa_wrapper_functions.rst
    installation.rst
-   design.rst
-   Bugs and Updates <history>
+   history.rst
    tutorials/new_syntax.rst
-   tutorials/new_syntax_worked_example.rst
-   tutorials/new_syntax_worked_example_code.rst
    Future plans <todo>
-   Implementation_notes <implementation_notes.rst>
    faq.rst
-   glossary.rst
    gallery.rst
    why_ruffus.rst
-
-=====================
-Examples
-=====================
-.. toctree::
-   :maxdepth: 2
-
-   examples/bioinformatics/index.rst
-   examples/bioinformatics/part2.rst
-   examples/bioinformatics/part1_code.rst
-   examples/bioinformatics/part2_code.rst
-   examples/paired_end_data.py.rst
+   tutorials/new_tutorial/manual_contents.rst
 
 
 
 =====================
-Reference:
+Quick Reference:
 =====================
-######################
-Decorators
-######################
 .. toctree::
     :maxdepth: 1
+    :caption: Reference
+    :name: reference_toc
 
+    pipeline_functions.rst
     decorators/decorators.rst
     decorators/indicator_objects.rst
 
 
-.. topic::
-    Core
-
-    .. toctree::
-        :maxdepth: 1
-
-        decorators/originate.rst
-        decorators/split.rst
-        decorators/transform.rst
-        decorators/merge.rst
-
-.. topic::
-    For advanced users
-
-    .. toctree::
-        :maxdepth: 1
-
-        decorators/subdivide.rst
-        decorators/transform_ex.rst
-        decorators/collate.rst
-        decorators/collate_ex.rst
-        decorators/graphviz.rst
-        decorators/mkdir.rst
-        decorators/jobs_limit.rst
-        decorators/posttask.rst
-        decorators/active_if.rst
-        decorators/follows.rst
-
-.. topic::
-    Combinatorics
-
-    .. toctree::
-        :maxdepth: 1
 
-        decorators/product.rst
-        decorators/permutations.rst
-        decorators/combinations.rst
-        decorators/combinations_with_replacement.rst
-
-.. topic::
-    Esoteric
-
-    .. toctree::
-        :maxdepth: 1
-
-        decorators/files_ex.rst
-        decorators/check_if_uptodate.rst
-        decorators/parallel.rst
-
-.. topic::
-    Deprecated
+.. toctree::
+   :maxdepth: 2
+   :hidden:
 
-    .. toctree::
-        :maxdepth: 1
+   design.rst
+   Implementation_notes <implementation_notes.rst>
+   cheatsheet.rst
+   glossary.rst
 
-        decorators/files.rst
-        decorators/files_re.rst
 
 
-######################
-Modules:
-######################
 
 .. toctree::
    :maxdepth: 2
+   :hidden:
 
    task.rst
    proxy_logger.rst

doc/decorators/active_if.rst

@@ -10,7 +10,7 @@
 
 
 ############
-@active_if
+active_if
 ############
 
 .. Comment. These are parameter names
@@ -71,9 +71,10 @@
         Produces the following output:
 
             .. code-block:: pycon
-                :emphasize-lines: 1,13
+                :emphasize-lines: 1,2,14,15
 
-                >>> # @active_if switches off task "this_task_might_be_inactive" because run_if_true_2 == False
+                >>> # @active_if switches off task "this_task_might_be_inactive"
+                >>> # because run_if_true_2 == False
                 >>> pipeline_run(verbose = 3)
 
                 Task enters queue = create_files
@@ -85,7 +86,8 @@
                 Completed Task = create_files
                 Inactive Task = this_task_might_be_inactive
 
-                >>> # @active_if switches on task "this_task_might_be_inactive" because all run_if_true conditions are met
+                >>> # @active_if switches on task "this_task_might_be_inactive"
+                >>> # because all run_if_true conditions are met
                 >>> run_if_true_2 = True
                 >>> pipeline_run(verbose = 3)