From 069f28b512478e5c90740ec05907739d0c659845 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 24 Jan 2024 15:56:40 +0100 Subject: [PATCH 01/10] avoid deprecated pkg_resources --- rocrate/vocabs.py | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/rocrate/vocabs.py b/rocrate/vocabs.py index b459bd9..29b50e0 100644 --- a/rocrate/vocabs.py +++ b/rocrate/vocabs.py @@ -19,15 +19,11 @@ # limitations under the License. import json -import pkg_resources +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" -)) +RO_CRATE = json.loads(importlib.resources.read_text(__name__, "data/ro-crate.jsonld")) +SCHEMA = json.loads(importlib.resources.read_text(__name__, "data/schema.jsonld")) SCHEMA_MAP = dict((e["@id"], e) for e in SCHEMA["@graph"]) From 3c9b9d4168819d192015e375a81928370150af1c Mon Sep 17 00:00:00 2001 From: Simone Leo Date: Tue, 12 Mar 2024 16:59:24 +0100 Subject: [PATCH 02/10] vocabs.py: fix importlib.resources usage Co-authored-by: Eli Chadwick --- rocrate/vocabs.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/rocrate/vocabs.py b/rocrate/vocabs.py index 29b50e0..e440051 100644 --- a/rocrate/vocabs.py +++ b/rocrate/vocabs.py @@ -22,8 +22,12 @@ import importlib.resources # FIXME: Avoid eager loading? -RO_CRATE = json.loads(importlib.resources.read_text(__name__, "data/ro-crate.jsonld")) -SCHEMA = json.loads(importlib.resources.read_text(__name__, "data/schema.jsonld")) +RO_CRATE = json.loads( + importlib.resources.files(__package__).joinpath("data/ro-crate.jsonld").read_text() +) +SCHEMA = json.loads( + importlib.resources.files(__package__).joinpath("data/schema.jsonld").read_text() +) SCHEMA_MAP = dict((e["@id"], e) for e in SCHEMA["@graph"]) From 6fea6d616bb6e7722d6b98a70c3bf41724ced356 Mon Sep 17 00:00:00 2001 From: simleo Date: Tue, 12 Mar 2024 17:47:57 +0100 Subject: [PATCH 03/10] python < 3.9 compat --- rocrate/vocabs.py | 26 +++++++++++++++++++------- 1 file changed, 19 insertions(+), 7 deletions(-) diff --git a/rocrate/vocabs.py b/rocrate/vocabs.py index e440051..25c0370 100644 --- a/rocrate/vocabs.py +++ b/rocrate/vocabs.py @@ -18,16 +18,28 @@ # See the License for the specific language governing permissions and # limitations under the License. +import sys import json -import importlib.resources +if sys.version_info.minor < 9: + import pkg_resources +else: + import importlib.resources # FIXME: Avoid eager loading? -RO_CRATE = json.loads( - importlib.resources.files(__package__).joinpath("data/ro-crate.jsonld").read_text() -) -SCHEMA = json.loads( - importlib.resources.files(__package__).joinpath("data/schema.jsonld").read_text() -) +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() + ) + SCHEMA = json.loads( + importlib.resources.files(__package__).joinpath("data/schema.jsonld").read_text() + ) SCHEMA_MAP = dict((e["@id"], e) for e in SCHEMA["@graph"]) From bf55c2e6af99b43e45e20c00713d1e2dcbb9027a Mon Sep 17 00:00:00 2001 From: simleo Date: Fri, 15 Mar 2024 14:58:34 +0100 Subject: [PATCH 04/10] skip test_ftp_uri on MacOS --- test/test_write.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/test_write.py b/test/test_write.py index b2be9ab..aa66ac3 100644 --- a/test/test_write.py +++ b/test/test_write.py @@ -20,6 +20,7 @@ import pytest import os import uuid +import sys import zipfile from itertools import product from urllib.error import URLError @@ -214,6 +215,7 @@ def test_looks_like_file_uri(tmpdir, monkeypatch): assert (out_path / f_name).is_file() +@pytest.mark.skipif(sys.platform == "darwin", reason="FTP opening broken on macOS CI instances") @pytest.mark.slow @pytest.mark.parametrize("fetch_remote", [False, True]) def test_ftp_uri(tmpdir, fetch_remote): From 325624793dfe167456d5b612c9e516750cd2fb23 Mon Sep 17 00:00:00 2001 From: simleo Date: Fri, 15 Mar 2024 15:15:46 +0100 Subject: [PATCH 05/10] explicitly specify codec --- rocrate/vocabs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/rocrate/vocabs.py b/rocrate/vocabs.py index 25c0370..ab4980a 100644 --- a/rocrate/vocabs.py +++ b/rocrate/vocabs.py @@ -35,10 +35,10 @@ )) else: RO_CRATE = json.loads( - importlib.resources.files(__package__).joinpath("data/ro-crate.jsonld").read_text() + 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() + importlib.resources.files(__package__).joinpath("data/schema.jsonld").read_text("utf8") ) SCHEMA_MAP = dict((e["@id"], e) for e in SCHEMA["@graph"]) From 0ef068b47b3d65d96696c4557188e2b0945c3f41 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Fri, 15 Mar 2024 16:05:20 +0000 Subject: [PATCH 06/10] add authorship and copyright --- .gitpod.yml | 10 ++++++++++ CITATION.cff | 3 +++ rocrate/vocabs.py | 1 + 3 files changed, 14 insertions(+) create mode 100644 .gitpod.yml diff --git a/.gitpod.yml b/.gitpod.yml new file mode 100644 index 0000000..63a3e4f --- /dev/null +++ b/.gitpod.yml @@ -0,0 +1,10 @@ +# This configuration file was automatically generated by Gitpod. +# Please adjust to your needs (see https://www.gitpod.io/docs/introduction/learn-gitpod/gitpod-yaml) +# and commit this file to your remote git repository to share the goodness with others. + +# Learn more from ready-to-use templates: https://www.gitpod.io/docs/introduction/getting-started/quickstart + +tasks: + - init: make + + diff --git a/CITATION.cff b/CITATION.cff index aab9691..cff5fe2 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -13,6 +13,9 @@ 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 diff --git a/rocrate/vocabs.py b/rocrate/vocabs.py index ab4980a..5bdf4df 100644 --- a/rocrate/vocabs.py +++ b/rocrate/vocabs.py @@ -5,6 +5,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. From c999d64e8eded63d4d93c819f323dfd26212bdea Mon Sep 17 00:00:00 2001 From: simleo Date: Mon, 18 Mar 2024 10:17:13 +0100 Subject: [PATCH 07/10] add SciLifeLab copyright notice --- README.md | 1 + examples/read_test_metadata.py | 1 + rocrate/__init__.py | 2 ++ rocrate/cli.py | 1 + rocrate/metadata.py | 1 + rocrate/model/__init__.py | 1 + rocrate/model/computationalworkflow.py | 1 + rocrate/model/computerlanguage.py | 1 + rocrate/model/contextentity.py | 1 + rocrate/model/creativework.py | 1 + rocrate/model/data_entity.py | 1 + rocrate/model/dataset.py | 1 + rocrate/model/entity.py | 1 + rocrate/model/file.py | 1 + rocrate/model/file_or_dir.py | 1 + rocrate/model/metadata.py | 1 + rocrate/model/person.py | 1 + rocrate/model/preview.py | 1 + rocrate/model/root_dataset.py | 1 + rocrate/model/softwareapplication.py | 1 + rocrate/model/testdefinition.py | 1 + rocrate/model/testinstance.py | 1 + rocrate/model/testservice.py | 1 + rocrate/model/testsuite.py | 1 + rocrate/rocrate.py | 1 + rocrate/utils.py | 1 + setup.py | 1 + test/conftest.py | 1 + test/test_cli.py | 1 + test/test_jsonld.py | 1 + test/test_metadata.py | 1 + test/test_model.py | 1 + test/test_read.py | 1 + test/test_readwrite.py | 1 + test/test_test_metadata.py | 1 + test/test_utils.py | 1 + test/test_workflow_ro_crate.py | 1 + test/test_write.py | 1 + tools/add_boilerplate.py | 2 ++ 39 files changed, 41 insertions(+) diff --git a/README.md b/README.md index 76aa7e2..83c1cf6 100644 --- a/README.md +++ b/README.md @@ -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 , diff --git a/examples/read_test_metadata.py b/examples/read_test_metadata.py index 3efa818..91b8a37 100644 --- a/examples/read_test_metadata.py +++ b/examples/read_test_metadata.py @@ -3,6 +3,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/rocrate/__init__.py b/rocrate/__init__.py index 09d5d2f..eaf3b62 100644 --- a/rocrate/__init__.py +++ b/rocrate/__init__.py @@ -5,6 +5,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. @@ -46,6 +47,7 @@ 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 " "") diff --git a/rocrate/cli.py b/rocrate/cli.py index b4ff19e..035d2f9 100644 --- a/rocrate/cli.py +++ b/rocrate/cli.py @@ -3,6 +3,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/rocrate/metadata.py b/rocrate/metadata.py index 0662d02..2cbce35 100644 --- a/rocrate/metadata.py +++ b/rocrate/metadata.py @@ -3,6 +3,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/rocrate/model/__init__.py b/rocrate/model/__init__.py index 996a567..6e3d753 100644 --- a/rocrate/model/__init__.py +++ b/rocrate/model/__init__.py @@ -3,6 +3,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/rocrate/model/computationalworkflow.py b/rocrate/model/computationalworkflow.py index 9fbf270..d150b20 100644 --- a/rocrate/model/computationalworkflow.py +++ b/rocrate/model/computationalworkflow.py @@ -5,6 +5,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/rocrate/model/computerlanguage.py b/rocrate/model/computerlanguage.py index 19ee99d..0dd8409 100644 --- a/rocrate/model/computerlanguage.py +++ b/rocrate/model/computerlanguage.py @@ -3,6 +3,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/rocrate/model/contextentity.py b/rocrate/model/contextentity.py index 8a742dc..6a4040a 100644 --- a/rocrate/model/contextentity.py +++ b/rocrate/model/contextentity.py @@ -5,6 +5,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/rocrate/model/creativework.py b/rocrate/model/creativework.py index a4a894d..8c5c9a7 100644 --- a/rocrate/model/creativework.py +++ b/rocrate/model/creativework.py @@ -5,6 +5,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/rocrate/model/data_entity.py b/rocrate/model/data_entity.py index 1050854..f17c57c 100644 --- a/rocrate/model/data_entity.py +++ b/rocrate/model/data_entity.py @@ -5,6 +5,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/rocrate/model/dataset.py b/rocrate/model/dataset.py index a1d30f0..ce1c12e 100644 --- a/rocrate/model/dataset.py +++ b/rocrate/model/dataset.py @@ -5,6 +5,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/rocrate/model/entity.py b/rocrate/model/entity.py index 5be8c47..c18096e 100644 --- a/rocrate/model/entity.py +++ b/rocrate/model/entity.py @@ -5,6 +5,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/rocrate/model/file.py b/rocrate/model/file.py index 2aae534..23f0e3e 100644 --- a/rocrate/model/file.py +++ b/rocrate/model/file.py @@ -5,6 +5,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/rocrate/model/file_or_dir.py b/rocrate/model/file_or_dir.py index aac31dc..743ac19 100644 --- a/rocrate/model/file_or_dir.py +++ b/rocrate/model/file_or_dir.py @@ -5,6 +5,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/rocrate/model/metadata.py b/rocrate/model/metadata.py index a7c86e4..e69750f 100644 --- a/rocrate/model/metadata.py +++ b/rocrate/model/metadata.py @@ -5,6 +5,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/rocrate/model/person.py b/rocrate/model/person.py index c3c7766..7bce477 100644 --- a/rocrate/model/person.py +++ b/rocrate/model/person.py @@ -5,6 +5,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/rocrate/model/preview.py b/rocrate/model/preview.py index 32d23c0..f39be91 100644 --- a/rocrate/model/preview.py +++ b/rocrate/model/preview.py @@ -5,6 +5,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/rocrate/model/root_dataset.py b/rocrate/model/root_dataset.py index 9a4e19c..b7ef59b 100644 --- a/rocrate/model/root_dataset.py +++ b/rocrate/model/root_dataset.py @@ -5,6 +5,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/rocrate/model/softwareapplication.py b/rocrate/model/softwareapplication.py index 6a2995f..636d185 100644 --- a/rocrate/model/softwareapplication.py +++ b/rocrate/model/softwareapplication.py @@ -3,6 +3,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/rocrate/model/testdefinition.py b/rocrate/model/testdefinition.py index f439c1b..9fb3be0 100644 --- a/rocrate/model/testdefinition.py +++ b/rocrate/model/testdefinition.py @@ -3,6 +3,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/rocrate/model/testinstance.py b/rocrate/model/testinstance.py index 8cf8283..0881180 100644 --- a/rocrate/model/testinstance.py +++ b/rocrate/model/testinstance.py @@ -3,6 +3,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/rocrate/model/testservice.py b/rocrate/model/testservice.py index 9d3ee59..3b88ee5 100644 --- a/rocrate/model/testservice.py +++ b/rocrate/model/testservice.py @@ -3,6 +3,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/rocrate/model/testsuite.py b/rocrate/model/testsuite.py index 87114af..2cae478 100644 --- a/rocrate/model/testsuite.py +++ b/rocrate/model/testsuite.py @@ -3,6 +3,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/rocrate/rocrate.py b/rocrate/rocrate.py index daed143..6b622b8 100644 --- a/rocrate/rocrate.py +++ b/rocrate/rocrate.py @@ -3,6 +3,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/rocrate/utils.py b/rocrate/utils.py index 512d817..88f827b 100644 --- a/rocrate/utils.py +++ b/rocrate/utils.py @@ -5,6 +5,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/setup.py b/setup.py index 2a171b3..850da73 100755 --- a/setup.py +++ b/setup.py @@ -5,6 +5,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/test/conftest.py b/test/conftest.py index 1009d1f..f53db2e 100644 --- a/test/conftest.py +++ b/test/conftest.py @@ -3,6 +3,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/test/test_cli.py b/test/test_cli.py index 28d918e..f8dc96e 100644 --- a/test/test_cli.py +++ b/test/test_cli.py @@ -3,6 +3,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/test/test_jsonld.py b/test/test_jsonld.py index aa3b56c..003a3c8 100644 --- a/test/test_jsonld.py +++ b/test/test_jsonld.py @@ -3,6 +3,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/test/test_metadata.py b/test/test_metadata.py index 354f432..a0fa489 100644 --- a/test/test_metadata.py +++ b/test/test_metadata.py @@ -3,6 +3,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/test/test_model.py b/test/test_model.py index 5c2e086..1935cc8 100644 --- a/test/test_model.py +++ b/test/test_model.py @@ -3,6 +3,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/test/test_read.py b/test/test_read.py index 814f008..48be710 100644 --- a/test/test_read.py +++ b/test/test_read.py @@ -3,6 +3,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/test/test_readwrite.py b/test/test_readwrite.py index 9be736e..8ffd537 100644 --- a/test/test_readwrite.py +++ b/test/test_readwrite.py @@ -3,6 +3,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/test/test_test_metadata.py b/test/test_test_metadata.py index d748255..f5a21a6 100644 --- a/test/test_test_metadata.py +++ b/test/test_test_metadata.py @@ -3,6 +3,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/test/test_utils.py b/test/test_utils.py index f22e65d..753373c 100644 --- a/test/test_utils.py +++ b/test/test_utils.py @@ -3,6 +3,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/test/test_workflow_ro_crate.py b/test/test_workflow_ro_crate.py index 01ac2d0..a6af528 100644 --- a/test/test_workflow_ro_crate.py +++ b/test/test_workflow_ro_crate.py @@ -3,6 +3,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/test/test_write.py b/test/test_write.py index aa66ac3..f748423 100644 --- a/test/test_write.py +++ b/test/test_write.py @@ -3,6 +3,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/tools/add_boilerplate.py b/tools/add_boilerplate.py index 2e6961b..48f3c4b 100644 --- a/tools/add_boilerplate.py +++ b/tools/add_boilerplate.py @@ -3,6 +3,7 @@ # 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 # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. @@ -35,6 +36,7 @@ "Barcelona Supercomputing Center (BSC), ES": "2020", "Center for Advanced Studies, Research and Development in Sardinia (CRS4), IT": "2020", "École Polytechnique Fédérale de Lausanne, CH": "2022", + "Data Centre, SciLifeLab, SE": "2024", } THIS_YEAR = str(datetime.date.today().year) BOILERPLATE_START = "Copyright [yyyy] [name of copyright owner]" From 9a84487028e78948c6628dfddd7d8a9b2cd7c72b Mon Sep 17 00:00:00 2001 From: simleo Date: Mon, 18 Mar 2024 10:36:17 +0100 Subject: [PATCH 08/10] fix author lists --- rocrate/__init__.py | 1 + setup.py | 1 + 2 files changed, 2 insertions(+) diff --git a/rocrate/__init__.py b/rocrate/__init__.py index eaf3b62..ba1e4e4 100644 --- a/rocrate/__init__.py +++ b/rocrate/__init__.py @@ -33,6 +33,7 @@ 'Bert Droesbeke', 'Ignacio Eguinoa', 'Alban Gaignard', + 'Matthias Hörtenhuber', 'Sebastiaan Huber', 'Bruno Kinoshita', 'Simone Leo', diff --git a/setup.py b/setup.py index 850da73..a480f19 100755 --- a/setup.py +++ b/setup.py @@ -61,6 +61,7 @@ 'Bert Droesbeke', 'Ignacio Eguinoa', 'Alban Gaignard', + 'Matthias Hörtenhuber', 'Sebastiaan Huber', 'Bruno Kinoshita', 'Simone Leo', From 823d902f4e11b5fa75b4226dfdae4e2e76dc0017 Mon Sep 17 00:00:00 2001 From: Eli Chadwick Date: Mon, 18 Mar 2024 10:22:54 +0000 Subject: [PATCH 09/10] add Eli to authors --- CITATION.cff | 3 +++ rocrate/__init__.py | 1 + setup.py | 1 + 3 files changed, 5 insertions(+) diff --git a/CITATION.cff b/CITATION.cff index cff5fe2..fd09e4e 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -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 diff --git a/rocrate/__init__.py b/rocrate/__init__.py index ba1e4e4..5efaa44 100644 --- a/rocrate/__init__.py +++ b/rocrate/__init__.py @@ -29,6 +29,7 @@ """ __author__ = ", ".join(( + 'Eli Chadwick', 'Paul De Geest', 'Bert Droesbeke', 'Ignacio Eguinoa', diff --git a/setup.py b/setup.py index a480f19..fdb62d3 100755 --- a/setup.py +++ b/setup.py @@ -57,6 +57,7 @@ long_description_content_type='text/markdown', long_description=long_description, author=", ".join(( + 'Eli Chadwick', 'Paul De Geest', 'Bert Droesbeke', 'Ignacio Eguinoa', From 65fb8edb3d635b33050f7d575b80d8800621501c Mon Sep 17 00:00:00 2001 From: simleo Date: Mon, 18 Mar 2024 11:59:10 +0100 Subject: [PATCH 10/10] remove .gitpod.yml --- .gitpod.yml | 10 ---------- 1 file changed, 10 deletions(-) delete mode 100644 .gitpod.yml diff --git a/.gitpod.yml b/.gitpod.yml deleted file mode 100644 index 63a3e4f..0000000 --- a/.gitpod.yml +++ /dev/null @@ -1,10 +0,0 @@ -# This configuration file was automatically generated by Gitpod. -# Please adjust to your needs (see https://www.gitpod.io/docs/introduction/learn-gitpod/gitpod-yaml) -# and commit this file to your remote git repository to share the goodness with others. - -# Learn more from ready-to-use templates: https://www.gitpod.io/docs/introduction/getting-started/quickstart - -tasks: - - init: make - -