Merge branch 'develop' into 3621-session-hibernation-in-cli

SwissDataScienceCenter · Oct 10, 2023 · f4a1d0e · f4a1d0e
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diff --git a/AUTHORS.rst b/AUTHORS.rst
@@ -1,5 +1,5 @@
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,5 +1,5 @@
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/Makefile b/Makefile
@@ -1,7 +1,5 @@
-# -*- coding: utf-8 -*-
-#
-# Copyright 2017-2023 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/QA_PROTOCOL.rst b/QA_PROTOCOL.rst
@@ -1,5 +1,5 @@
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/README.rst b/README.rst
@@ -1,5 +1,5 @@
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/docs/_ext/cheatsheet.py b/docs/_ext/cheatsheet.py
@@ -1,7 +1,5 @@
-# -*- coding: utf-8 -*-
-#
-# Copyright 2018-2023- Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/docs/changes.rst b/docs/changes.rst
@@ -1,5 +1,5 @@
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/docs/cheatsheet/conf.py b/docs/cheatsheet/conf.py
@@ -1,7 +1,5 @@
-# -*- coding: utf-8 -*-
-#
-# Copyright 2017-2023 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/docs/conf.py b/docs/conf.py
@@ -1,7 +1,5 @@
-# -*- coding: utf-8 -*-
-#
-# Copyright 2017-2023 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/docs/gettingstarted.rst b/docs/gettingstarted.rst
@@ -1,5 +1,5 @@
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -1,7 +1,7 @@
 :orphan:
 
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -1,5 +1,5 @@
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/docs/introduction.rst b/docs/introduction.rst
@@ -1,5 +1,5 @@
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/docs/license.rst b/docs/license.rst
@@ -3,7 +3,7 @@ License
 
 .. code-block:: text
 
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/docs/plugins.rst b/docs/plugins.rst
@@ -1,5 +1,5 @@
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/docs/reference/api.rst b/docs/reference/api.rst
@@ -1,5 +1,5 @@
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/docs/reference/commands/index.rst b/docs/reference/commands/index.rst
@@ -1,5 +1,5 @@
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/docs/reference/core.rst b/docs/reference/core.rst
@@ -1,5 +1,5 @@
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/docs/reference/database.rst b/docs/reference/database.rst
@@ -1,5 +1,5 @@
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/docs/reference/gateways.rst b/docs/reference/gateways.rst
@@ -1,5 +1,5 @@
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/docs/reference/index.rst b/docs/reference/index.rst
@@ -1,5 +1,5 @@
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/docs/reference/models/dataset_provider.rst b/docs/reference/models/dataset_provider.rst
@@ -1,5 +1,5 @@
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/docs/reference/models/datasets.rst b/docs/reference/models/datasets.rst
@@ -1,5 +1,5 @@
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/docs/reference/models/projects.rst b/docs/reference/models/projects.rst
@@ -1,5 +1,5 @@
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/docs/reference/models/provenance.rst b/docs/reference/models/provenance.rst
@@ -1,5 +1,5 @@
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/docs/reference/models/workflow.rst b/docs/reference/models/workflow.rst
@@ -1,5 +1,5 @@
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/docs/reference/plugins.rst b/docs/reference/plugins.rst
@@ -1,5 +1,5 @@
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/docs/reference/service.rst b/docs/reference/service.rst
@@ -1,5 +1,5 @@
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/docs/reference/service_errors.rst b/docs/reference/service_errors.rst
@@ -1,5 +1,5 @@
 ..
-    Copyright 2017-2023 - Swiss Data Science Center (SDSC)
+    Copyright Swiss Data Science Center (SDSC).
     A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
     Eidgenössische Technische Hochschule Zürich (ETHZ).
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,7 +1,5 @@
-# -*- coding: utf-8 -*-
-#
-# Copyright 2017-2023 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/renku/command/__init__.py b/renku/command/__init__.py
@@ -1,6 +1,5 @@
-#
-# Copyright 2017-2023 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/renku/command/checks/datasets.py b/renku/command/checks/datasets.py
@@ -77,17 +77,17 @@ def check_missing_files(dataset_gateway: IDatasetGateway, **_):
             path = project_context.path / file_.entity.path
             file_exists = path.exists() or (file_.is_external and os.path.lexists(path))
             if not file_exists:
-                missing[dataset.name].append(file_.entity.path)
+                missing[dataset.slug].append(file_.entity.path)
 
     if not missing:
         return True, False, None
 
     problems = WARNING + "There are missing files in datasets."
 
-    for dataset_name, files in missing.items():
+    for dataset_slug, files in missing.items():
         problems += (
             "\n\t"
-            + click.style(dataset_name, fg="yellow")
+            + click.style(dataset_slug, fg="yellow")
             + ":\n\t  "
             + "\n\t  ".join(click.style(path, fg="red") for path in files)
         )
@@ -114,9 +114,9 @@ def fix_or_report(dataset):
             dataset.unfreeze()
             dataset.derived_from = None
             dataset.freeze()
-            communication.info(f"Fixing dataset '{dataset.name}'")
+            communication.info(f"Fixing dataset '{dataset.slug}'")
         else:
-            invalid_datasets.append(dataset.name)
+            invalid_datasets.append(dataset.slug)
 
     for dataset in dataset_gateway.get_provenance_tails():
         while dataset.derived_from is not None and dataset.derived_from.url_id is not None:
@@ -137,7 +137,7 @@ def fix_or_report(dataset):
         WARNING
         + "There are invalid dataset metadata in the project (use 'renku doctor --fix' to fix them):"
         + "\n\n\t"
-        + "\n\t".join(click.style(name, fg="yellow") for name in invalid_datasets)
+        + "\n\t".join(click.style(slug, fg="yellow") for slug in invalid_datasets)
         + "\n"
     )
 
@@ -177,12 +177,12 @@ def check_dataset_files_outside_datadir(fix, dataset_gateway: IDatasetGateway, *
             continue
 
         if fix:
-            communication.info(f"Fixing dataset '{dataset.name}' files.")
+            communication.info(f"Fixing dataset '{dataset.slug}' files.")
             dataset.unfreeze()
             for file in detected_files:
                 dataset.unlink_file(file.entity.path)
             dataset.freeze()
-            add_to_dataset(dataset.name, urls=[file.entity.path for file in detected_files], link=True)
+            add_to_dataset(dataset.slug, urls=[file.entity.path for file in detected_files], link=True)
         else:
             invalid_files.extend(detected_files)
 
@@ -220,7 +220,7 @@ def check_external_files(fix, dataset_gateway: IDatasetGateway, **_):
         for file in dataset.files:
             if file.is_external:
                 external_files.append(file.entity.path)
-                datasets[dataset.name].append(file)
+                datasets[dataset.slug].append(file)
 
     if not external_files:
         return True, False, None
@@ -240,7 +240,7 @@ def check_external_files(fix, dataset_gateway: IDatasetGateway, **_):
         f"dataset with an external storage backend:\n\t{external_files_str}"
     )
 
-    for name, files in datasets.items():
-        file_unlink(name=name, yes=True, dataset_files=files)
+    for slug, files in datasets.items():
+        file_unlink(slug=slug, yes=True, dataset_files=files)
 
     return True, False, None
diff --git a/renku/command/checks/validate_shacl.py b/renku/command/checks/validate_shacl.py
@@ -104,15 +104,15 @@ def check_datasets_structure(dataset_gateway: IDatasetGateway, **_):
         try:
             conform, graph, t = _check_shacl_structure(data)
         except (Exception, BaseException) as e:
-            problems.append(f"Couldn't validate dataset '{dataset.name}': {e}\n\n")
+            problems.append(f"Couldn't validate dataset '{dataset.slug}': {e}\n\n")
             continue
 
         if conform:
             continue
 
         ok = False
 
-        problems.append(f"{dataset.name}\n\t{_shacl_graph_to_string(graph)}\n")
+        problems.append(f"{dataset.slug}\n\t{_shacl_graph_to_string(graph)}\n")
 
     if ok:
         return True, False, None

diff --git a/renku/command/clone.py b/renku/command/clone.py
@@ -1,6 +1,5 @@
-#
-# Copyright 2018-2023- Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/renku/command/config.py b/renku/command/config.py
@@ -1,6 +1,5 @@
-#
-# Copyright 2017-2023 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/renku/command/dataset.py b/renku/command/dataset.py
@@ -1,6 +1,5 @@
-#
-# Copyright 2017-2023 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -39,7 +38,7 @@
 
 
 def search_datasets_command():
-    """Command to get all the datasets whose name starts with the given string."""
+    """Command to get all the datasets whose slug starts with the given string."""
     return Command().command(search_datasets).require_migration().with_database()
 
 

diff --git a/renku/command/doctor.py b/renku/command/doctor.py
@@ -1,6 +1,5 @@
-#
-# Copyright 2020 - Swiss Data Science Center (SDSC)
-# A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
+# Copyright Swiss Data Science Center (SDSC). A partnership between
+# École Polytechnique Fédérale de Lausanne (EPFL) and
 # Eidgenössische Technische Hochschule Zürich (ETHZ).
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/renku/command/format/dataset_files.py b/renku/command/format/dataset_files.py
@@ -73,7 +73,10 @@ def get_lfs_tracking():
                 record.is_lfs = False
 
     def naturalize(value) -> str:
-        return naturalsize(value).upper().replace("BYTES", " B")
+        try:
+            return naturalsize(value).upper().replace("BYTES", " B")
+        except ValueError:
+            return str(value)
 
     def get_file_sizes():
         if not any(r for r in records if r.size is None):  # All records already have a size
@@ -181,8 +184,8 @@ def json(records, **_):
     "dataset": ("title", "dataset"),
     "full_path": ("full_path", None),
     "path": ("path", None),
-    "short_name": ("dataset_name", "dataset name"),
-    "dataset_name": ("dataset_name", "dataset name"),
+    "short_name": ("dataset_slug", "dataset slug"),
+    "dataset_slug": ("dataset_slug", "dataset slug"),
     "size": ("size", None),
     "lfs": ("is_lfs", "lfs"),
     "source": ("source", None),