Merge branch 'develop' into update-license

SwissDataScienceCenter · Nov 8, 2023 · 2bc9973 · 2bc9973
2 parents afca8dc + d3eedb5
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diff --git a/.dockerignore b/.dockerignore
@@ -8,4 +8,5 @@
 !.git
 !.gitignore
 !Makefile
+!gunicorn.conf.py
 .git/config
diff --git a/.github/workflows/acceptance-tests.yml b/.github/workflows/acceptance-tests.yml
@@ -26,6 +26,7 @@ jobs:
       renku-graph: ${{ steps.deploy-comment.outputs.renku-graph}}
       renku-notebooks: ${{ steps.deploy-comment.outputs.renku-notebooks}}
       renku-ui: ${{ steps.deploy-comment.outputs.renku-ui}}
+      renku-data-services: ${{ steps.deploy-comment.outputs.renku-data-services}}
       test-enabled: ${{ steps.deploy-comment.outputs.test-enabled}}
       extra-values: ${{ steps.deploy-comment.outputs.extra-values}}
       persist: ${{ steps.deploy-comment.outputs.persist}}
@@ -66,6 +67,7 @@ jobs:
           renku_graph: "${{ needs.check-deploy.outputs.renku-graph }}"
           renku_notebooks: "${{ needs.check-deploy.outputs.renku-notebooks }}"
           renku_ui: "${{ needs.check-deploy.outputs.renku-ui }}"
+          renku_data_services: "${{ needs.check-deploy.outputs.renku-data-services }}"
           extra_values: "${{ needs.check-deploy.outputs.extra-values }}"
       - name: Check existing renkubot comment
         uses: peter-evans/find-comment@v2

diff --git a/.github/workflows/test_deploy.yml b/.github/workflows/test_deploy.yml
@@ -496,9 +496,7 @@ jobs:
           CLOUD_STORAGE_AZURE_KEY: ${{ secrets.CLOUD_STORAGE_AZURE_KEY }}
           CLOUD_STORAGE_S3_ACCESS_KEY_ID: ${{ secrets.CLOUD_STORAGE_S3_ACCESS_KEY_ID }}
           CLOUD_STORAGE_S3_SECRET_ACCESS_KEY: ${{ secrets.CLOUD_STORAGE_S3_SECRET_ACCESS_KEY }}
-        run: pytest -m "integration and not serial and not service" -v
-      - name: Start Redis
-        uses: supercharge/[email protected]
+        run: pytest -m "integration and not serial and not service and not redis" -v
       - name: Test with pytest (serial)
         env:
           POETRY_VIRTUALENVS_CREATE: false

diff --git a/.gitignore b/.gitignore
@@ -35,6 +35,7 @@ var/
 *.egg-info/
 .installed.cfg
 *.egg
+.python-version
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

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/Dockerfile b/Dockerfile
@@ -15,7 +15,7 @@ RUN apt-get install --no-install-recommends -y build-essential && \
 # time the code changes
 # set the BUILD_CORE_SERVICE to non null to install additional service dependencies
 ARG BUILD_CORE_SERVICE
-COPY pyproject.toml poetry.lock README.rst CHANGES.rst Makefile /code/renku/
+COPY pyproject.toml poetry.lock README.rst CHANGES.rst Makefile gunicorn.conf.py /code/renku/
 COPY .git /code/renku/.git
 COPY renku /code/renku/renku
 WORKDIR /code/renku
@@ -46,6 +46,7 @@ RUN addgroup -gid 1000 shuhitsu && \
     if [ -n "${BUILD_CORE_SERVICE}" ]; then mkdir /svc && chown shuhitsu:shuhitsu /svc ; fi
 
 COPY --from=builder /code/renku /code/renku
+WORKDIR /code/renku
 ENV PATH="${PATH}:/code/renku/.venv/bin"
 
 # shuhitsu (執筆): The "secretary" of the renga, as it were, who is responsible for
@@ -55,5 +56,6 @@ USER shuhitsu
 ENV RENKU_SVC_NUM_WORKERS 4
 ENV RENKU_SVC_NUM_THREADS 8
 ENV RENKU_DISABLE_VERSION_CHECK=1
+ENV PROMETHEUS_MULTIPROC_DIR /tmp
 
 ENTRYPOINT ["tini", "-g", "--", "renku"]
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/_static/cheatsheet/cheatsheet.json b/docs/_static/cheatsheet/cheatsheet.json
@@ -325,6 +325,20 @@
             "rp"
           ]
         },
+        {
+          "command": "$ renku session pause <name>",
+          "description": "Pause the specified session.",
+          "target": [
+            "rp"
+          ]
+        },
+        {
+          "command": "$ renku session resume <name>",
+          "description": "Resume the specified paused session.",
+          "target": [
+            "rp"
+          ]
+        },
         {
           "command": "$ renku session stop <name>",
           "description": "Stop the specified session.",

diff --git a/docs/_static/cheatsheet/cheatsheet.pdf b/docs/_static/cheatsheet/cheatsheet.pdf
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/cheatsheet_hash b/docs/cheatsheet_hash
@@ -1,2 +1,2 @@
-ad86ac1d0614ccb692c96e893db4d20d  cheatsheet.tex
+5316163d742bdb6792ed8bcb35031f6c  cheatsheet.tex
 c70c179e07f04186ec05497564165f11  sdsc_cheatsheet.cls
diff --git a/docs/cheatsheet_json_hash b/docs/cheatsheet_json_hash
@@ -1 +1 @@
-1ac51267cefdf4976c29c9d7657063b8  cheatsheet.json
+1856fb451165d013777c7c4cdd56e575  cheatsheet.json
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).
 
@@ -33,6 +33,25 @@ data science pipeline.
 `Documentation <https://github.com/ratschlab/renku-mls/blob/master/docs/gettingstarted.rst>`_
 `Example Project <https://renkulab.io/projects/learn-renku/plugins/renku-mls-plugin>`_
 
+renku-graph-vis
+---------------
+
+`renku-graph-vis <https://github.com/oda-hub/renku-graph-vis/>`_ is a plugin that
+provides a graphical representation of the renku repository's knowledge graph. 
+In particular, the plugin enables an interactive graph visualization feature 
+for real-time monitoring during a renku session introducing the ability to have 
+a live overview of the ongoing development. It also provides two CLI commands:
+
+* ``display`` to generate a representation of the graph over a png output image
+* ``show-graph`` to start an interactive visualization of the graph over the browser
+
+renku-aqs-annotation
+--------------------
+
+`renku-aqs-annotation <https://github.com/oda-hub/renku-aqs-annotation/>`_ is a plugin that
+intercepts several key astroquery methods and stores a number of dedicated annotations 
+containing information about the calls to these methods (like the arguments used in the call) 
+to the project's Knowledge Graph. 
 
 Developing a plugin?
 --------------------

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).
 
@@ -65,6 +65,10 @@ Schema classes used to serialize domain models to JSON-LD.
    :members:
    :show-inheritance:
 
+.. automodule:: renku.command.schema.image
+   :members:
+   :show-inheritance:
+
 .. automodule:: renku.command.schema.parameter
    :members:
    :show-inheritance:
@@ -105,10 +109,6 @@ Datasets
    :members:
    :show-inheritance:
 
-.. automodule:: renku.core.dataset.request_model
-   :members:
-   :show-inheritance:
-
 .. automodule:: renku.core.dataset.tag
    :members:
    :show-inheritance:
@@ -237,6 +237,17 @@ Errors that can be raised by ``renku.core``.
    :members:
    :show-inheritance:
 
+Project/Dataset Images
+----------------------
+
+.. automodule:: renku.core.image
+   :members:
+   :show-inheritance:
+
+.. automodule:: renku.domain_model.image
+   :members:
+
+
 Utilities
 ---------
 

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).
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		@@ -1 +1 @@
		1ac51267cefdf4976c29c9d7657063b8 cheatsheet.json
		1856fb451165d013777c7c4cdd56e575 cheatsheet.json