migrating repository

Author: rafaelfsilva

docs/source/analyzing_traces.rst

@@ -8,14 +8,14 @@ workflow executions, and to build distributions of workflow execution behaviors,
 which are used to evaluate methods and techniques in simulation or in real
 conditions.
 
-The first axis of the WorkflowHub project targets the analysis of actual workflow
+The first axis of the WfCommons project targets the analysis of actual workflow
 execution traces (i.e., the workflow execution profile data and characterizations)
 in order to build **recipes** of workflow applications. These recipes contain
 the necessary information for generating synthetic, yet realistic, workflow
 traces that resemble the structure and distribution of the original workflow
 executions.
 
-A `list of workflow execution traces <https://workflowhub.org/traces.html>`_
+A `list of workflow execution traces <https://wfcommons.org/traces.html>`_
 that are compatible with :ref:`json-format-label` is kept constantly updated
 in our project website.
 
@@ -24,45 +24,45 @@ Workflow Execution Traces
 
 A workflow execution trace represents an actual execution of a scientific
 workflow on a distributed platform (e.g., clouds, grids, HPC, etc.). In the
-WorkflowHub project, a trace is represented in a JSON file following the
+WfCommons project, a trace is represented in a JSON file following the
 schema described in :ref:`json-format-label` section. This Python package
 provides a *trace loader* tool for importing workflow execution traces
 for analysis. For instance, the code snippet below shows how a trace can
-be loaded using the :class:`~workflowhub.trace.trace.Trace` class: ::
+be loaded using the :class:`~wfcommons.trace.trace.Trace` class: ::
 
-    from workflowhub import Trace
+    from wfcommons import Trace
     trace = Trace(input_trace='/path/to/trace/file.json')
 
-The :class:`~workflowhub.trace.trace.Trace` class provides a number of
+The :class:`~wfcommons.trace.trace.Trace` class provides a number of
 methods for interacting with the workflow trace, including:
 
-- :meth:`~workflowhub.trace.trace.Trace.draw`: produces an image or a pdf file representing the trace.
-- :meth:`~workflowhub.trace.trace.Trace.leaves`: gets the leaves of the workflow (i.e., the tasks without any successors).
-- :meth:`~workflowhub.trace.trace.Trace.roots`: gets the roots of the workflow (i.e., the tasks without any predecessors).
-- :meth:`~workflowhub.trace.trace.Trace.write_dot`: writes a dot file of the trace.
+- :meth:`~wfcommons.trace.trace.Trace.draw`: produces an image or a pdf file representing the trace.
+- :meth:`~wfcommons.trace.trace.Trace.leaves`: gets the leaves of the workflow (i.e., the tasks without any successors).
+- :meth:`~wfcommons.trace.trace.Trace.roots`: gets the roots of the workflow (i.e., the tasks without any predecessors).
+- :meth:`~wfcommons.trace.trace.Trace.write_dot`: writes a dot file of the trace.
 
 The Trace Analyzer
 ------------------
 
-The :class:`~workflowhub.trace.trace_analyzer.TraceAnalyzer` class provides
+The :class:`~wfcommons.trace.trace_analyzer.TraceAnalyzer` class provides
 a number of tools for analyzing collection of workflow execution traces. The
-goal of the :class:`~workflowhub.trace.trace_analyzer.TraceAnalyzer` is to
+goal of the :class:`~wfcommons.trace.trace_analyzer.TraceAnalyzer` is to
 perform analyzes of one or multiple workflow execution traces, and build
 summaries of the analyzes per workflow' task type prefix.
 
 .. note::
 
     Although any workflow execution trace represented as a
-    :class:`~workflowhub.trace.trace.Trace` object (i.e., compatible with
+    :class:`~wfcommons.trace.trace.Trace` object (i.e., compatible with
     :ref:`json-format-label`) can be appended to the
-    :class:`~workflowhub.trace.trace_analyzer.TraceAnalyzer`, we strongly
+    :class:`~wfcommons.trace.trace_analyzer.TraceAnalyzer`, we strongly
     recommend that only traces of a single workflow application type be
     appended to an analyzer object. You may though create several analyzer
     objects per workflow application.
 
-The :meth:`~workflowhub.trace.trace_analyzer.TraceAnalyzer.append_trace` method
+The :meth:`~wfcommons.trace.trace_analyzer.TraceAnalyzer.append_trace` method
 allows you to include traces for analysis. The
-:meth:`~workflowhub.trace.trace_analyzer.TraceAnalyzer.build_summary` method
+:meth:`~wfcommons.trace.trace_analyzer.TraceAnalyzer.build_summary` method
 processes all appended traces. The method applies probability distributions fitting
 to a series of data to find the *best* (i.e., minimizes the mean square error)
 probability distribution that represents the analyzed data. The method returns
@@ -94,8 +94,8 @@ in which themselves are used to :ref:`generate realistic synthetic workflow trac
 <generating-workflows-label>`.
 
 Probability distribution fits can also be plotted by using the
-:meth:`~workflowhub.trace.trace_analyzer.TraceAnalyzer.generate_fit_plots` or
-:meth:`~workflowhub.trace.trace_analyzer.TraceAnalyzer.generate_all_fit_plots`
+:meth:`~wfcommons.trace.trace_analyzer.TraceAnalyzer.generate_fit_plots` or
+:meth:`~wfcommons.trace.trace_analyzer.TraceAnalyzer.generate_all_fit_plots`
 methods -- plots will be saved as :code:`png` files.
 
 Examples
@@ -108,7 +108,7 @@ distribution fitting for task *prefixes* of the Seismology workflow
 plots (runtime, and input and output files) into the :code:`fits` folder using
 :code:`seismology` as a prefix for each generated plot: ::
 
-    from workflowhub import Trace, TraceAnalyzer
+    from wfcommons import Trace, TraceAnalyzer
     from os import listdir
     from os.path import isfile, join
 

docs/source/dev_api_generator.rst

@@ -1,113 +1,113 @@
-workflowhub.generator
+wfcommons.generator
 =====================
 
 .. toctree::
    :maxdepth: 4
 
-workflowhub.generator.generator
+wfcommons.generator.generator
 -------------------------------
 
-.. automodule:: workflowhub.generator.generator
+.. automodule:: wfcommons.generator.generator
    :members:
    :undoc-members:
    :show-inheritance:
    :private-members:
    :noindex:
 
 
-workflowhub.generator.workflow.abstract\_recipe
+wfcommons.generator.workflow.abstract\_recipe
 -----------------------------------------------
 
-.. automodule:: workflowhub.generator.workflow.abstract_recipe
+.. automodule:: wfcommons.generator.workflow.abstract_recipe
    :members:
    :undoc-members:
    :show-inheritance:
    :private-members:
 
-workflowhub.generator.workflow.blast\_recipe
+wfcommons.generator.workflow.blast\_recipe
 --------------------------------------------
 
-.. automodule:: workflowhub.generator.workflow.blast_recipe
+.. automodule:: wfcommons.generator.workflow.blast_recipe
    :members:
    :undoc-members:
    :show-inheritance:
    :private-members:
    :noindex:
 
-workflowhub.generator.workflow.bwa\_recipe
+wfcommons.generator.workflow.bwa\_recipe
 ------------------------------------------
 
-.. automodule:: workflowhub.generator.workflow.bwa_recipe
+.. automodule:: wfcommons.generator.workflow.bwa_recipe
    :members:
    :undoc-members:
    :show-inheritance:
    :private-members:
    :noindex:
 
-workflowhub.generator.workflow.cycles\_recipe
+wfcommons.generator.workflow.cycles\_recipe
 ---------------------------------------------
 
-.. automodule:: workflowhub.generator.workflow.cycles_recipe
+.. automodule:: wfcommons.generator.workflow.cycles_recipe
    :members:
    :undoc-members:
    :show-inheritance:
    :private-members:
    :noindex:
 
-workflowhub.generator.workflow.epigenomics\_recipe
+wfcommons.generator.workflow.epigenomics\_recipe
 --------------------------------------------------
 
-.. automodule:: workflowhub.generator.workflow.epigenomics_recipe
+.. automodule:: wfcommons.generator.workflow.epigenomics_recipe
    :members:
    :undoc-members:
    :show-inheritance:
    :private-members:
    :noindex:
 
-workflowhub.generator.workflow.genome\_recipe
+wfcommons.generator.workflow.genome\_recipe
 ---------------------------------------------
 
-.. automodule:: workflowhub.generator.workflow.genome_recipe
+.. automodule:: wfcommons.generator.workflow.genome_recipe
    :members:
    :undoc-members:
    :show-inheritance:
    :private-members:
    :noindex:
 
-workflowhub.generator.workflow.montage\_recipe
+wfcommons.generator.workflow.montage\_recipe
 ----------------------------------------------
 
-.. automodule:: workflowhub.generator.workflow.montage_recipe
+.. automodule:: wfcommons.generator.workflow.montage_recipe
    :members:
    :undoc-members:
    :show-inheritance:
    :private-members:
    :noindex:
 
-workflowhub.generator.workflow.seismology\_recipe
+wfcommons.generator.workflow.seismology\_recipe
 -------------------------------------------------
 
-.. automodule:: workflowhub.generator.workflow.seismology_recipe
+.. automodule:: wfcommons.generator.workflow.seismology_recipe
    :members:
    :undoc-members:
    :show-inheritance:
    :private-members:
    :noindex:
 
-workflowhub.generator.workflow.soykb\_recipe
+wfcommons.generator.workflow.soykb\_recipe
 --------------------------------------------
 
-.. automodule:: workflowhub.generator.workflow.soykb_recipe
+.. automodule:: wfcommons.generator.workflow.soykb_recipe
    :members:
    :undoc-members:
    :show-inheritance:
    :private-members:
    :noindex:
 
-workflowhub.generator.workflow.srasearch\_recipe
+wfcommons.generator.workflow.srasearch\_recipe
 ------------------------------------------------
 
-.. automodule:: workflowhub.generator.workflow.srasearch_recipe
+.. automodule:: wfcommons.generator.workflow.srasearch_recipe
    :members:
    :undoc-members:
    :show-inheritance:

docs/source/dev_api_reference.rst

@@ -2,7 +2,7 @@ Developer API Reference
 ***********************
 
 The developer API reference targets developers and researchers who
-want to contribute to the WorkflowHub project by, for example,
+want to contribute to the WfCommons project by, for example,
 developing novel techniques for trace analysis, developing new
 :ref:`workflow recipes <workflow-recipe-label>`, etc.
 The developer API reference documentation includes detailed information
@@ -13,6 +13,6 @@ Python package.
     :caption: Developer API Reference
     :maxdepth: 1
 
-    dev_api_workflowhub.rst
+    dev_api_wfcommons.rst
     dev_api_generator.rst
     dev_api_trace.rst

docs/source/dev_api_trace.rst

@@ -1,59 +1,59 @@
-workflowhub.trace
+wfcommons.trace
 =================
 
-workflowhub.trace.schema
+wfcommons.trace.schema
 ------------------------
 
-.. automodule:: workflowhub.trace.schema
+.. automodule:: wfcommons.trace.schema
    :members:
    :undoc-members:
    :show-inheritance:
    :private-members:
 
-workflowhub.trace.trace
+wfcommons.trace.trace
 -----------------------
 
-.. automodule:: workflowhub.trace.trace
+.. automodule:: wfcommons.trace.trace
    :members:
    :undoc-members:
    :show-inheritance:
    :private-members:
    :noindex:
 
-workflowhub.trace.trace\_analyzer
+wfcommons.trace.trace\_analyzer
 ---------------------------------
 
-.. automodule:: workflowhub.trace.trace_analyzer
+.. automodule:: wfcommons.trace.trace_analyzer
    :members:
    :undoc-members:
    :show-inheritance:
    :private-members:
    :noindex:
 
-workflowhub.trace.logs.abstract\_logs\_parser
+wfcommons.trace.logs.abstract\_logs\_parser
 ---------------------------------------------
 
-.. automodule:: workflowhub.trace.logs.abstract_logs_parser
+.. automodule:: wfcommons.trace.logs.abstract_logs_parser
    :members:
    :undoc-members:
    :show-inheritance:
    :private-members:
    :noindex:
 
-workflowhub.trace.logs.makeflow
+wfcommons.trace.logs.makeflow
 -------------------------------
 
-.. automodule:: workflowhub.trace.logs.makeflow
+.. automodule:: wfcommons.trace.logs.makeflow
    :members:
    :undoc-members:
    :show-inheritance:
    :private-members:
    :noindex:
 
-workflowhub.trace.logs.pegasus
+wfcommons.trace.logs.pegasus
 ------------------------------
 
-.. automodule:: workflowhub.trace.logs.pegasus
+.. automodule:: wfcommons.trace.logs.pegasus
    :members:
    :undoc-members:
    :show-inheritance:

docs/source/dev_api_workflowhub.rst docs/source/dev_api_wfcommons.rstdocs/source/dev_api_workflowhub.rst renamed to docs/source/dev_api_wfcommons.rst

@@ -1,7 +1,7 @@
-workflowhub.utils
+wfcommons.utils
 -----------------
 
-.. automodule:: workflowhub.utils
+.. automodule:: wfcommons.utils
    :members:
    :undoc-members:
    :show-inheritance: