fixing package installation

Author: rafaelfsilva

docs/source/generating_workflows.rst

@@ -12,8 +12,26 @@ WfCommons JSON format (WfFormat), which is already supported by simulation frame
 `WRENCH <https://wrench-project.org>`_.
 
 
-The Workflow Generator
-----------------------
+.. _recipes-list:
+
+WfCommons Workflows Recipes
+---------------------------
+
+The current list of available workflow recipes include:
+
+- :class:`~wfcommons.wfchef.recipes.blast_recipe.BlastRecipe`: :code:`from wfcommons.wfchef.recipes import BlastWorkflowRecipe`
+- :class:`~wfcommons.wfchef.recipes.bwa_recipe.BwaRecipe`: :code:`from wfcommons.wfchef.recipes import BwaRecipe`
+- :class:`~wfcommons.wfchef.recipes.cycles_recipe.CyclesRecipe`: :code:`from wfcommons.wfchef.recipes import CyclesRecipe`
+- :class:`~wfcommons.wfchef.recipes.epigenomics_recipe.EpigenomicsRecipe`: :code:`from wfcommons.wfchef.recipes import EpigenomicsRecipe`
+- :class:`~wfcommons.wfchef.recipes.genome_recipe.GenomeRecipe`: :code:`from wfcommons.wfchef.recipes import GenomeRecipe`
+- :class:`~wfcommons.wfchef.recipes.montage_recipe.MontageRecipe`: :code:`from wfcommons.wfchef.recipes import MontageRecipe`
+- :class:`~wfcommons.wfchef.recipes.seismology_recipe.SeismologyRecipe`: :code:`from wfcommons.wfchef.recipes import SeismologyRecipe`
+- :class:`~wfcommons.wfchef.recipes.soykb_recipe.SoykbRecipe`: :code:`from wfcommons.wfchef.recipes import SoykbRecipe`
+- :class:`~wfcommons.wfchef.recipes.srasearch_recipe.SrasearchRecipe`: :code:`from wfcommons.wfchef.recipes import SrasearchRecipe`
+
+
+The Workflow Instances Generator
+--------------------------------
 
 Synthetic workflow instances are generated using the
 :class:`~wfcommons.generator.generator.WorkflowGenerator` class. This
@@ -41,6 +59,9 @@ methods for writing the generated workflow instance into files:
 - :meth:`~wfcommons.common.workflow.Workflow.write_dot`: write a DOT file of a workflow instance.
 - :meth:`~wfcommons.common.workflow.Workflow.write_json`: write a JSON file of a workflow instance.
 
+All workflow recipes provide a common method, :code:`from_num_tasks`, that defines the lower
+bound for the total number of tasks in the synthetic workflow.
+
 Increasing/Reducing Runtime and File Sizes
 ******************************************
 

docs/source/generating_workflows_recipe.rst

@@ -6,7 +6,7 @@ Generating Workflows Recipes
 **WfChef** is the WfCommons component that automates the construction of
 synthetic workflow generators for any given workflow application. The input
 to this component is a set of real workflow instances described in the
-:ref:`json-format-label` (e.g., instances available in **WfInstances**).
+:ref:`json-format-label` (e.g., instances available in :ref:`wfinstances-label`).
 WfChef automatically analyzes a set of real workflow instances for
 two purposes. First, it discovers workflow subgraphs that represent
 fundamental task dependency patterns. Second, it derives
@@ -21,47 +21,49 @@ workflow instances with any arbitrary number of tasks.
 Workflow Recipes
 ----------------
 
-A **workflow recipe** is a data structure that encodes the discovered pattern occurrences
-as well as the statistical models of workflow task characteristics.
-The WfCommons package provides a number of *workflow recipes* for generating realistic 
-synthetic workflow instances. 
-
-All workflow recipes provide a common method, :code:`from_num_tasks`, that defines the lower
-bound for the total number of tasks in the synthetic workflow.
+A **workflow recipe** is a data structure that encodes the discovered
+pattern occurrences as well as the statistical models of workflow task
+characteristics. More precisely, a recipe embodies results from statistical
+analysis and distribution fitting performed for each workflow task type
+so as to characterize task runtime and input/output data sizes. The
+recipes also incorporates information regarding the graph structure of
+the workflows (tasks dependencies and frequency of occurrences), which are
+automatically derived from the analysis of the workflow instances.
 
+This Python package provides several *workflow recipes* (see :ref:`recipes-list`)
+for generating realistic synthetic workflow instances.
 
 .. _workflow-recipe-generator-label:
 
 Workflow Recipe Generator
 --------------------------
 
-To create a recipe the method :meth:`find_patterns` analyzes the real workflow graphs 
-in order to identify subgraphs that represent fundamental task dependency patterns. 
+To create a recipe, WfChef analyzes the real workflow graphs in order to
+identify subgraphs that represent fundamental task dependency patterns.
 Based on the identified subgraphs and on measured task type frequencies in the real
 workflows, WfChef outputs a generator that can generate realistic synthetic
-workflow instances with an arbitrary numbers of tasks. The code snippet below shows 
-how to create a recipe for the Epigenomics application: ::
-
-    $ wfchef create path/to/real/instances -o ./epigenomics -v --name Epigenomics
+workflow instances with an arbitrary numbers of tasks (see :ref:`generating-workflows-label`).
 
-The flags that can be used with this command are:
+The code snippet below shows an example of how to create a recipe for the
+Epigenomics application: ::
 
-:code:`-o` or :code:`--out` is a required flag that stands for the name of the directory to be created that is going to 
-contain the recipe.
+    $ wfchef create /path/to/real/instances -o ./epigenomics -v --name Epigenomics
 
-:code:`-n` or :code:`--name` is a required flag that stands for the name of the recipe. Tipically, the format used is 
-*ApplicationName*. 
+The following flags can be used with this command:
 
-:code:`-v` or :code:`--verbose` if set, activates status messages.
+- :code:`-o` or :code:`--out` is a required flag that stands for the name of the directory to be created that is going to contain the recipe.
+- :code:`-n` or :code:`--name` is a required flag that stands for the name of the recipe. Tipically, the format used is *ApplicationName*.
+- :code:`-v` or :code:`--verbose` if set, activates status messages.
+- :code:`--no-install` if set, does not install the recipe automatically.
+- :code:`-c` or :code:`--cutoff` takes a number of tasks in the samples the user wants to consider to create the recipe.
 
-:code:`--no-install` if set, does not install the recipe automatically.
+*Example*: :code:`--cutoff 4000`, it means that all real world instances
+that will be consider for the creation of the recipe will have 4000 or
+less tasks. This is a useful flag to use when there is trust that all
+possible patterns present in this application can be already found in the
+smaller instances.
 
-:code:`-c` or :code:`--cutoff` takes a number of tasks in the samples the user wants to consider to create the recipe. 
-Example: :code:`--cutoff 4000`, it means that all real world instances that will be consider for the creation of the 
-recipe have 4000 or less tasks. This is a useful flag to use when there is trust that all possible patterns present
-in this application can be already found in the smaller instances. 
-
-The recipes are automatically installed and can be used throughout the system. WfCommons creates a Python package in the directory 
+Workflow recipes are automatically installed and can be used throughout the system. WfCommons creates a Python package in the directory
 specified by the flag :code:`--out` in which the :file:`setup.py` and :file:`recipe.py` files are stored. If the flag :code:`--no-install` is set 
 when creating a package for a specific application, the user will need to install the package before using it. The code 
 bellow is an example of how to install/uninstall a package for an application in WfCommons: ::
@@ -85,17 +87,6 @@ To check which recipes are installed in a system and how to import them use: ::
     $ wfchef ls
 
 
-The current list of available workflow recipes include:
-
-- :class:`~wfcommons.wfchef.recipes.blast_recipe.BlastRecipe`: :code:`from wfcommons.wfchef.recipes import BlastWorkflowRecipe`
-- :class:`~wfcommons.wfchef.recipes.bwa_recipe.BwaRecipe`: :code:`from wfcommons.wfchef.recipes import BwaRecipe`
-- :class:`~wfcommons.wfchef.recipes.cycles_recipe.CyclesRecipe`: :code:`from wfcommons.wfchef.recipes import CyclesRecipe`
-- :class:`~wfcommons.wfchef.recipes.epigenomics_recipe.EpigenomicsRecipe`: :code:`from wfcommons.wfchef.recipes import EpigenomicsRecipe`
-- :class:`~wfcommons.wfchef.recipes.genome_recipe.GenomeRecipe`: :code:`from wfcommons.wfchef.recipes import GenomeRecipe`
-- :class:`~wfcommons.wfchef.recipes.montage_recipe.MontageRecipe`: :code:`from wfcommons.wfchef.recipes import MontageRecipe`
-- :class:`~wfcommons.wfchef.recipes.seismology_recipe.SeismologyRecipe`: :code:`from wfcommons.wfchef.recipes import SeismologyRecipe`
-- :class:`~wfcommons.wfchef.recipes.soykb_recipe.SoykbRecipe`: :code:`from wfcommons.wfchef.recipes import SoykbRecipe`
-- :class:`~wfcommons.wfchef.recipes.srasearch_recipe.SrasearchRecipe`: :code:`from wfcommons.wfchef.recipes import SrasearchRecipe`
 
 
 

wfcommons/wfchef/recipes/__init__.py

@@ -1,3 +1,13 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# Copyright (c) 2021 The WfCommons Team.
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+
 from .epigenomics import EpigenomicsRecipe
 from .montage import MontageRecipe
 from .cycles import CyclesRecipe

wfcommons/wfchef/skeletons/__init__.py

@@ -0,0 +1,11 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# Copyright (c) 2021 The WfCommons Team.
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+
+