renaming workflowhub to wfcommons

rafaelfsilva · rafaelfsilva · commit 8ad60d3aecdf · 2021-04-24T18:43:23.000-07:00
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -7,8 +7,8 @@ assignees: ''
 
 ---
 
-**WorkflowHub Information**
-- WorkflowHub version: [e.g., 0.3, master branch, etc.]
+**WfCommons Information**
+- WfCommons version: [e.g., 0.3, master branch, etc.]
 - Python Version: [e.g., 3.5]
 
 **Describe the bug**
diff --git a/README.md b/README.md
@@ -9,13 +9,13 @@
 
 This Python package provides a collection of tools for:
 
-- Analyzing traces of actual workflow executions;
+- Analyzing instances of actual workflow executions;
 - Producing recipes structures for creating workflow recipes for workflow generation; and
-- Generating synthetic realistic workflow traces.
+- Generating synthetic realistic workflow instances.
 
 ## Installation
 
-WfCommons is available on [PyPI](https://pypi.org/project/workflowhub).
+WfCommons is available on [PyPI](https://pypi.org/project/wfcommons).
 WfCommons requires Python3.6+ and has been tested on Linux and macOS.
 
 ### Requirements
@@ -43,7 +43,7 @@ While `pip` can be used to install WfCommons, we suggest the following
 approach for reliable installation when many Python environments are available:
 
 ```
-$ python3 -m pip install workflowhub
+$ python3 -m pip install wfcommons
 ```
 
 ### Retrieving the latest unstable version
@@ -87,8 +87,8 @@ that paper, as it provides a recent and general overview on the framework.
 
 [build-badge]:         https://github.com/wfcommons/wfcommons/workflows/Build/badge.svg
 [build-link]:          https://github.com/wfcommons/wfcommons/actions
-[pypi-badge]:          https://badge.fury.io/py/workflowhub.svg
-[pypi-link]:           https://badge.fury.io/py/workflowhub
+[pypi-badge]:          https://badge.fury.io/py/wfcommons.svg
+[pypi-link]:           https://badge.fury.io/py/wfcommons
 [license-badge]:       https://img.shields.io/badge/License-LGPL%20v3-blue.svg
 [codefactor-badge]:    https://www.codefactor.io/repository/github/wfcommons/wfcommons/badge
 [codefactor-link]:     https://www.codefactor.io/repository/github/wfcommons/wfcommons
diff --git a/docs/source/quickstart_installation.rst b/docs/source/quickstart_installation.rst
@@ -1,7 +1,7 @@
 Installation
 ============
 
-WfCommons is available on `PyPI <https://pypi.org/project/workflowhub>`_.
+WfCommons is available on `PyPI <https://pypi.org/project/wfcommons>`_.
 WfCommons requires Python3.6+ and has been tested on Linux and macOS.
 
 Requirements
@@ -40,7 +40,7 @@ approach for reliable installation when many Python environments are available:
 
 .. code-block:: bash
 
-    $ python3 -m pip install workflowhub
+    $ python3 -m pip install wfcommons
 
 Retrieving the latest unstable version
 --------------------------------------
diff --git a/wfcommons/common/file.py b/wfcommons/common/file.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020-2021 The WorkflowHub Team.
+# Copyright (c) 2020-2021 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
diff --git a/wfcommons/common/machine.py b/wfcommons/common/machine.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020-2021 The WorkflowHub Team.
+# Copyright (c) 2020-2021 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
diff --git a/wfcommons/common/task.py b/wfcommons/common/task.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020-2021 The WorkflowHub Team.
+# Copyright (c) 2020-2021 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
diff --git a/wfcommons/common/workflow.py b/wfcommons/common/workflow.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020-2021 The WorkflowHub Team.
+# Copyright (c) 2020-2021 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
@@ -49,12 +49,12 @@ def __init__(self,
                  makespan: Optional[int] = 0.0
                  ) -> None:
         """Create an object of a workflow representation."""
-        self.description = description if description else 'Trace generated with WorkflowHub - https://workflowhub.org'
+        self.description = description if description else 'Trace generated with WfCommons - https://wfcommons.org'
         self.created_at = str(datetime.utcnow().isoformat())
         self.schema_version = '1.0'
-        self.wms_name = 'WorkflowHub' if not wms_name else wms_name
+        self.wms_name = 'WfCommons' if not wms_name else wms_name
         self.wms_version = str(__version__) if not wms_version else wms_version
-        self.wms_url = 'https://workflowhub.readthedocs.io/en/v{}/'.format(__version__) if not wms_url else wms_url
+        self.wms_url = 'https://wfcommons.readthedocs.io/en/v{}/'.format(__version__) if not wms_url else wms_url
         self.executed_at = datetime.now().astimezone().strftime("%Y%m%dT%H%M%S%z") if not executed_at else executed_at
         self.makespan = makespan
         super().__init__(name=name, makespan=self.makespan, executedat=self.executed_at)
diff --git a/wfcommons/generator/__init__.py b/wfcommons/generator/__init__.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020-2021 The WorkflowHub Team.
+# Copyright (c) 2020-2021 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
diff --git a/wfcommons/generator/generator.py b/wfcommons/generator/generator.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020-2021 The WorkflowHub Team.
+# Copyright (c) 2020-2021 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
diff --git a/wfcommons/generator/workflow/__init__.py b/wfcommons/generator/workflow/__init__.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020-2021 The WorkflowHub Team.
+# Copyright (c) 2020-2021 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
diff --git a/wfcommons/generator/workflow/abstract_recipe.py b/wfcommons/generator/workflow/abstract_recipe.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020-2021 The WorkflowHub Team.
+# Copyright (c) 2020-2021 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
diff --git a/wfcommons/generator/workflow/blast_recipe.py b/wfcommons/generator/workflow/blast_recipe.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2021 The WorkflowHub Team.
+# 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
diff --git a/wfcommons/generator/workflow/bwa_recipe.py b/wfcommons/generator/workflow/bwa_recipe.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2021 The WorkflowHub Team.
+# 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
diff --git a/wfcommons/generator/workflow/cycles_recipe.py b/wfcommons/generator/workflow/cycles_recipe.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020-2021 The WorkflowHub Team.
+# Copyright (c) 2020-2021 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
diff --git a/wfcommons/generator/workflow/epigenomics_recipe.py b/wfcommons/generator/workflow/epigenomics_recipe.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020-2021 The WorkflowHub Team.
+# Copyright (c) 2020-2021 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
diff --git a/wfcommons/generator/workflow/genome_recipe.py b/wfcommons/generator/workflow/genome_recipe.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020-2021 The WorkflowHub Team.
+# Copyright (c) 2020-2021 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
diff --git a/wfcommons/generator/workflow/montage_recipe.py b/wfcommons/generator/workflow/montage_recipe.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020-2021 The WorkflowHub Team.
+# Copyright (c) 2020-2021 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
diff --git a/wfcommons/generator/workflow/seismology_recipe.py b/wfcommons/generator/workflow/seismology_recipe.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020-2021 The WorkflowHub Team.
+# Copyright (c) 2020-2021 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
diff --git a/wfcommons/generator/workflow/soykb_recipe.py b/wfcommons/generator/workflow/soykb_recipe.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020-2021 The WorkflowHub Team.
+# Copyright (c) 2020-2021 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
diff --git a/wfcommons/generator/workflow/srasearch_recipe.py b/wfcommons/generator/workflow/srasearch_recipe.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2021 The WorkflowHub Team.
+# 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
diff --git a/wfcommons/trace/__init__.py b/wfcommons/trace/__init__.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020-2021 The WorkflowHub Team.
+# Copyright (c) 2020-2021 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
diff --git a/wfcommons/trace/logs/__init__.py b/wfcommons/trace/logs/__init__.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020-2021 The WorkflowHub Team.
+# Copyright (c) 2020-2021 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
diff --git a/wfcommons/trace/logs/abstract_logs_parser.py b/wfcommons/trace/logs/abstract_logs_parser.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020-2021 The WorkflowHub Team.
+# Copyright (c) 2020-2021 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
diff --git a/wfcommons/trace/logs/makeflow.py b/wfcommons/trace/logs/makeflow.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2021 The WorkflowHub Team.
+# 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
diff --git a/wfcommons/trace/logs/pegasus.py b/wfcommons/trace/logs/pegasus.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020-2021 The WorkflowHub Team.
+# Copyright (c) 2020-2021 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
diff --git a/wfcommons/trace/schema.py b/wfcommons/trace/schema.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020 The WorkflowHub Team.
+# Copyright (c) 2020 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
@@ -20,10 +20,10 @@
 
 class SchemaValidator:
     """
-    Validate JSON files against WorkflowHub schema. If schema file path is not
-    provided, it will look for a local copy of the WorkflowHub schema, and if
+    Validate JSON files against WfCommons schema. If schema file path is not
+    provided, it will look for a local copy of the WfCommons schema, and if
     not available it will fetch the latest schema from the
-    `WorkflowHub schema GitHub <https://github.com/workflowhub/workflow-schema>`_
+    `WfCommons schema GitHub <https://github.com/wfcommons/workflow-schema>`_
     repository.
 
     :param schema_file: JSON schema file path.
@@ -49,7 +49,7 @@ def validate_trace(self, data: Dict[str, Any]):
     def _load_schema(self, schema_file: Optional[str] = None):
         """
         Load the schema file. If schema file path is not provided, it will look for
-        a local copy of the WorkflowHub schema, and if not available it will fetch
+        a local copy of the WfCommons schema, and if not available it will fetch
         the latest schema from the GitHub repository.
 
         :param schema_file: JSON schema file path.
@@ -70,7 +70,7 @@ def _load_schema(self, schema_file: Optional[str] = None):
             return json.loads(open(schema_path).read())
 
         # fetching latest schema file from GitHub repository
-        url = 'https://raw.githubusercontent.com/workflowhub/workflow-schema/master/workflowhub-schema.json'
+        url = 'https://raw.githubusercontent.com/wfcommons/workflow-schema/master/wfcommons-schema.json'
         response = requests.get(url)
         schema = json.loads(response.content)
         with open(schema_path, 'w') as outfile:
diff --git a/wfcommons/trace/trace.py b/wfcommons/trace/trace.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020-2021 The WorkflowHub Team.
+# Copyright (c) 2020-2021 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
@@ -38,9 +38,9 @@ class Trace:
     :type input_trace: str
     :param schema_file: The path to the JSON schema that defines the trace.
                         If no schema file is provided, it will look for a local
-                        copy of the WorkflowHub schema, and if not available
+                        copy of the WfCommons schema, and if not available
                         it will fetch the latest schema from the
-                        `WorkflowHub schema GitHub <https://github.com/workflowhub/workflow-schema>`_
+                        `WfCommons schema GitHub <https://github.com/wfcommons/workflow-schema>`_
                         repository.
     :type schema_file: str
     :param logger: The logger where to log information/warning or errors.
diff --git a/wfcommons/trace/trace_analyzer.py b/wfcommons/trace/trace_analyzer.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (c) 2020-2021 The WorkflowHub Team.
+# Copyright (c) 2020-2021 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

Original file line number	Diff line number	Diff line change
`@@ -1,7 +1,7 @@`
`1`	`1`	`#!/usr/bin/env python`
`2`	`2`	`# -- coding: utf-8 --`
`3`	`3`	`#`
`4`		`-# Copyright (c) 2020-2021 The WorkflowHub Team.`
	`4`	`+# Copyright (c) 2020-2021 The WfCommons Team.`
`5`	`5`	`#`
`6`	`6`	`# This program is free software: you can redistribute it and/or modify`
`7`	`7`	`# it under the terms of the GNU General Public License as published by`