Use Apache 2.0 license everywhere

mr-c · mr-c · commit 2f5e0a42273e · 2022-09-02T12:10:51.000+02:00
Confirmation from copyright holders is in #155
diff --git a/cwl_utils/__init__.py b/cwl_utils/__init__.py
@@ -0,0 +1,2 @@
+# SPDX-License-Identifier: Apache-2.0
+"""Python Utilities and Autogenerated Classes for loading and parsing CWL documents."""
diff --git a/cwl_utils/__meta__.py b/cwl_utils/__meta__.py
@@ -1,2 +1,3 @@
+# SPDX-License-Identifier: Apache-2.0
 """Global version number for the cwl_utils package."""
 __version__ = "0.16"
diff --git a/cwl_utils/cite_extract.py b/cwl_utils/cite_extract.py
@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
-# SPDX-License-Identifier: GPL-3.0-only
+# SPDX-License-Identifier: Apache-2.0
 import argparse
 import sys
 from typing import Iterator, List, Union, cast
diff --git a/cwl_utils/docker_extract.py b/cwl_utils/docker_extract.py
@@ -1,5 +1,5 @@
 #!/usr/bin/env python3
-# SPDX-License-Identifier: GPL-3.0-only
+# SPDX-License-Identifier: Apache-2.0
 import argparse
 import os
 import sys
diff --git a/cwl_utils/errors.py b/cwl_utils/errors.py
@@ -1,3 +1,7 @@
+# SPDX-License-Identifier: Apache-2.0
+"""Common Exceptions."""
+
+
 class ArrayMissingItems(BaseException):
     """From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py"""
 
diff --git a/cwl_utils/expression.py b/cwl_utils/expression.py
@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: Apache-2.0
+"""CWL Expression parsing."""
 import asyncio
 import copy
 import inspect
diff --git a/cwl_utils/file_formats.py b/cwl_utils/file_formats.py
@@ -1,3 +1,4 @@
+# SPDX-License-Identifier: Apache-2.0
 """
 CWL file formats utilities.
 
diff --git a/cwl_utils/graph_split.py b/cwl_utils/graph_split.py
@@ -1,5 +1,5 @@
 #!/usr/bin/env python
-# SPDX-License-Identifier: GPL-3.0-only
+# SPDX-License-Identifier: Apache-2.0
 # Copyright 2019-2020 Michael R. Crusoe
 # Copyright 2020 Altair Wei
 """
diff --git a/cwl_utils/image_puller.py b/cwl_utils/image_puller.py
@@ -1,4 +1,4 @@
-# SPDX-License-Identifier: GPL-3.0-only
+# SPDX-License-Identifier: Apache-2.0
 """Classes for docker-extract."""
 import logging
 import os
diff --git a/cwl_utils/loghandler.py b/cwl_utils/loghandler.py
@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: Apache-2.0
+"""Shared logging object."""
 import logging
 
 _logger = logging.getLogger("cwl_utils")  # pylint: disable=invalid-name
diff --git a/cwl_utils/pack.py b/cwl_utils/pack.py
@@ -1,3 +1,7 @@
+# SPDX-License-Identifier: Apache-2.0
+#  Copyright (c) 2021 Michael R. Crusoe
+#  Copyright (c) 2020 Seven Bridges
+#  See https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/LICENSE
 """
 The link resolution is as follows:
 
@@ -9,9 +13,6 @@
 From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py
 """
 
-#  Copyright (c) 2021 Michael R. Crusoe
-#  Copyright (c) 2020 Seven Bridges
-#  See https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/LICENSE
 
 import logging
 import os
diff --git a/cwl_utils/parser/cwl_v1_0_utils.py b/cwl_utils/parser/cwl_v1_0_utils.py
@@ -1,3 +1,4 @@
+# SPDX-License-Identifier: Apache-2.0
 import hashlib
 from typing import Any, List, Optional, Union
 
diff --git a/cwl_utils/parser/cwl_v1_1_utils.py b/cwl_utils/parser/cwl_v1_1_utils.py
@@ -1,3 +1,4 @@
+# SPDX-License-Identifier: Apache-2.0
 import hashlib
 from typing import Any, List, Optional, Union, cast
 
diff --git a/cwl_utils/parser/cwl_v1_2_utils.py b/cwl_utils/parser/cwl_v1_2_utils.py
@@ -1,3 +1,4 @@
+# SPDX-License-Identifier: Apache-2.0
 import hashlib
 from typing import Any, List, Optional, Union, cast
 
diff --git a/cwl_utils/sandboxjs.py b/cwl_utils/sandboxjs.py
@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: Apache-2.0
+"""Safe execution of CWL Expressions in a NodeJS sandbox."""
 import collections
 import errno
 import json
diff --git a/cwl_utils/schemadef.py b/cwl_utils/schemadef.py
@@ -1,3 +1,7 @@
+# SPDX-License-Identifier: Apache-2.0
+#  Copyright (c) 2021 Michael R. Crusoe
+#  Copyright (c) 2020 Seven Bridges
+#  See https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/LICENSE
 """
 Valid forms of user defined types stored in external file
 
@@ -10,9 +14,6 @@
 From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py
 """
 
-#  Copyright (c) 2021 Michael R. Crusoe
-#  Copyright (c) 2020 Seven Bridges
-#  See https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/LICENSE
 
 import sys
 import urllib.parse
diff --git a/cwl_utils/types.py b/cwl_utils/types.py
@@ -1,6 +1,8 @@
+# SPDX-License-Identifier: Apache-2.0
+# From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py
+"""Shared Python type definitions for commons JSON like CWL objects."""
 from typing import Any, MutableMapping, MutableSequence, Optional, Union
 
-# From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py
 built_in_types = [
     "null",
     "boolean",
diff --git a/cwl_utils/utils.py b/cwl_utils/utils.py
@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: Apache-2.0
+"""Miscellaneous utility functions."""
 import os
 import pathlib
 import subprocess  # nosec
diff --git a/tests/test_cite_extract.py b/tests/test_cite_extract.py
@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: Apache-2.0
+"""Tests for cwl-cite-extract."""
 from pathlib import Path
 
 import cwl_utils.parser.cwl_v1_0 as parser
diff --git a/tests/test_docker_extract.py b/tests/test_docker_extract.py
@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: Apache-2.0
+"""Tests for cwl-docker-extract."""
 from pathlib import Path
 from shutil import which
 from tempfile import TemporaryDirectory
diff --git a/tests/test_etools_to_clt.py b/tests/test_etools_to_clt.py
@@ -1,3 +1,4 @@
+# SPDX-License-Identifier: Apache-2.0
 """Test the CWL Expression refactoring tool."""
 import os
 import shutil
diff --git a/tests/test_examples.py b/tests/test_examples.py
@@ -1,3 +1,4 @@
+# SPDX-License-Identifier: Apache-2.0
 """Tests of example Python scripts."""
 import os
 from pathlib import Path
diff --git a/tests/test_format.py b/tests/test_format.py
@@ -1,3 +1,4 @@
+# SPDX-License-Identifier: Apache-2.0
 """Tests of cwl_utils.file_formats."""
 
 import xml.sax
diff --git a/tests/test_graph_split.py b/tests/test_graph_split.py
@@ -1,3 +1,4 @@
+# SPDX-License-Identifier: Apache-2.0
 """Test the CWL $graph document splitter tool."""
 import os
 from io import StringIO
diff --git a/tests/test_meta.py b/tests/test_meta.py
@@ -1,3 +1,4 @@
+# SPDX-License-Identifier: Apache-2.0
 """Test __meta__ properties."""
 
 from cwl_utils.__meta__ import __version__
diff --git a/tests/test_parser.py b/tests/test_parser.py
@@ -1,3 +1,4 @@
+# SPDX-License-Identifier: Apache-2.0
 """Test the load and save functions for CWL."""
 from pathlib import Path
 
diff --git a/tests/test_parser_utils.py b/tests/test_parser_utils.py
@@ -1,3 +1,4 @@
+# SPDX-License-Identifier: Apache-2.0
 """Test the CWL parsers utility functions."""
 from pathlib import Path
 

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+# SPDX-License-Identifier: Apache-2.0`
	`2`	`+"""Python Utilities and Autogenerated Classes for loading and parsing CWL documents."""`
Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,3 @@`
	`1`	`+# SPDX-License-Identifier: Apache-2.0`
`1`	`2`	`"""Global version number for the cwl_utils package."""`
`2`	`3`	`__version__ = "0.16"`
Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,5 @@`
	`1`	`+# SPDX-License-Identifier: Apache-2.0`
	`2`	`+"""CWL Expression parsing."""`
`1`	`3`	`import asyncio`
`2`	`4`	`import copy`
`3`	`5`	`import inspect`
Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,4 @@`
	`1`	`+# SPDX-License-Identifier: Apache-2.0`
`1`	`2`	`"""`
`2`	`3`	`CWL file formats utilities.`
`3`	`4`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-# SPDX-License-Identifier: GPL-3.0-only`
	`1`	`+# SPDX-License-Identifier: Apache-2.0`
`2`	`2`	`"""Classes for docker-extract."""`
`3`	`3`	`import logging`
`4`	`4`	`import os`
Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,5 @@`
	`1`	`+# SPDX-License-Identifier: Apache-2.0`
	`2`	`+"""Shared logging object."""`
`1`	`3`	`import logging`
`2`	`4`
`3`	`5`	`_logger = logging.getLogger("cwl_utils") # pylint: disable=invalid-name`