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avoid deprecated pkg_resources #173

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merged 10 commits into from
Mar 18, 2024
Merged

avoid deprecated pkg_resources #173

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069f28b
avoid deprecated pkg_resources
mashehu Jan 24, 2024
3c9b9d4
vocabs.py: fix importlib.resources usage
simleo Mar 12, 2024
6fea6d6
python < 3.9 compat
simleo Mar 12, 2024
bf55c2e
skip test_ftp_uri on MacOS
simleo Mar 15, 2024
3256247
explicitly specify codec
simleo Mar 15, 2024
0ef068b
add authorship and copyright
mashehu Mar 15, 2024
c999d64
add SciLifeLab copyright notice
simleo Mar 18, 2024
9a84487
fix author lists
simleo Mar 18, 2024
823d902
add Eli to authors
elichad Mar 18, 2024
65fb8ed
remove .gitpod.yml
simleo Mar 18, 2024
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6 changes: 6 additions & 0 deletions CITATION.cff
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@@ -1,6 +1,9 @@
cff-version: 1.1.0
message: "Cite as"
authors:
- family-names: Chadwick
given-names: Eli
orcid: https://orcid.org/0000-0002-0035-6475
- family-names: De Geest
given-names: Paul
orcid: https://orcid.org/0000-0002-8940-4946
Expand All @@ -13,6 +16,9 @@ authors:
- family-names: Gaignard
given-names: Alban
orcid: https://orcid.org/0000-0002-3597-8557
- family-names: Hörtenhuber
given-names: Matthias
orcid: https://orcid.org/0000-0002-5599-5565
- family-names: Huber
given-names: Sebastiaan
orcid: https://orcid.org/0000-0001-5845-8880
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -404,6 +404,7 @@ Options:
* Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
* Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
* Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
* Copyright 2024 Data Centre, SciLifeLab, SE

Licensed under the
Apache License, version 2.0 <https://www.apache.org/licenses/LICENSE-2.0>,
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1 change: 1 addition & 0 deletions examples/read_test_metadata.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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4 changes: 4 additions & 0 deletions rocrate/__init__.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
Expand All @@ -28,10 +29,12 @@
"""

__author__ = ", ".join((
'Eli Chadwick',
'Paul De Geest',
'Bert Droesbeke',
'Ignacio Eguinoa',
'Alban Gaignard',
'Matthias Hörtenhuber',
'Sebastiaan Huber',
'Bruno Kinoshita',
'Simone Leo',
Expand All @@ -46,6 +49,7 @@
Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
Copyright 2024 Data Centre, SciLifeLab, SE
"""
__license__ = ("Apache License, version 2.0 "
"<https://www.apache.org/licenses/LICENSE-2.0>")
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1 change: 1 addition & 0 deletions rocrate/cli.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions rocrate/metadata.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions rocrate/model/__init__.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions rocrate/model/computationalworkflow.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions rocrate/model/computerlanguage.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions rocrate/model/contextentity.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions rocrate/model/creativework.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions rocrate/model/data_entity.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions rocrate/model/dataset.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions rocrate/model/entity.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions rocrate/model/file.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions rocrate/model/file_or_dir.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions rocrate/model/metadata.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions rocrate/model/person.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions rocrate/model/preview.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions rocrate/model/root_dataset.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions rocrate/model/softwareapplication.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions rocrate/model/testdefinition.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions rocrate/model/testinstance.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions rocrate/model/testservice.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions rocrate/model/testsuite.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions rocrate/rocrate.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions rocrate/utils.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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27 changes: 20 additions & 7 deletions rocrate/vocabs.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
Expand All @@ -18,16 +19,28 @@
# See the License for the specific language governing permissions and
# limitations under the License.

import sys
import json
import pkg_resources
if sys.version_info.minor < 9:
import pkg_resources
else:
import importlib.resources

# FIXME: Avoid eager loading?
RO_CRATE = json.loads(pkg_resources.resource_string(
__name__, "data/ro-crate.jsonld"
))
SCHEMA = json.loads(pkg_resources.resource_string(
__name__, "data/schema.jsonld"
))
if sys.version_info.minor < 9:
RO_CRATE = json.loads(pkg_resources.resource_string(
__name__, "data/ro-crate.jsonld"
))
SCHEMA = json.loads(pkg_resources.resource_string(
__name__, "data/schema.jsonld"
))
else:
RO_CRATE = json.loads(
importlib.resources.files(__package__).joinpath("data/ro-crate.jsonld").read_text("utf8")
)
SCHEMA = json.loads(
importlib.resources.files(__package__).joinpath("data/schema.jsonld").read_text("utf8")
)
SCHEMA_MAP = dict((e["@id"], e) for e in SCHEMA["@graph"])


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3 changes: 3 additions & 0 deletions setup.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
Expand Down Expand Up @@ -56,10 +57,12 @@
long_description_content_type='text/markdown',
long_description=long_description,
author=", ".join((
'Eli Chadwick',
'Paul De Geest',
'Bert Droesbeke',
'Ignacio Eguinoa',
'Alban Gaignard',
'Matthias Hörtenhuber',
'Sebastiaan Huber',
'Bruno Kinoshita',
'Simone Leo',
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1 change: 1 addition & 0 deletions test/conftest.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions test/test_cli.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions test/test_jsonld.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions test/test_metadata.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions test/test_model.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions test/test_read.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions test/test_readwrite.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions test/test_test_metadata.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions test/test_utils.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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1 change: 1 addition & 0 deletions test/test_workflow_ro_crate.py
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# Copyright 2020-2024 Barcelona Supercomputing Center (BSC), ES
# Copyright 2020-2024 Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT
# Copyright 2022-2024 École Polytechnique Fédérale de Lausanne, CH
# Copyright 2024 Data Centre, SciLifeLab, SE
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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