Use Apache 2.0 license everywhere

Confirmation from copyright holders is in #155

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."""

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"

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

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

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"""
 

cwl_utils/expression.py

@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: Apache-2.0
+"""CWL Expression parsing."""
 import asyncio
 import copy
 import inspect

cwl_utils/file_formats.py

@@ -1,3 +1,4 @@
+# SPDX-License-Identifier: Apache-2.0
 """
 CWL file formats utilities.
 

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
 """

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

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

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

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
 

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
 

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
 

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

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

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",

cwl_utils/utils.py

@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: Apache-2.0
+"""Miscellaneous utility functions."""
 import os
 import pathlib
 import subprocess  # nosec

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

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

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

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

tests/test_format.py

@@ -1,3 +1,4 @@
+# SPDX-License-Identifier: Apache-2.0
 """Tests of cwl_utils.file_formats."""
 
 import xml.sax

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

tests/test_meta.py

@@ -1,3 +1,4 @@
+# SPDX-License-Identifier: Apache-2.0
 """Test __meta__ properties."""
 
 from cwl_utils.__meta__ import __version__

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
 

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