renku init

renku-transaction: b204f31a23ed480b9323904a193047db

.dockerignore

@@ -1,15 +1,4 @@
-data/
+data
-figures/
+notebooks
-pipelines/params/
+.renku
-envs/
+.git
-logs/
-*.pyc
-__pycache__/
-*.h5
-.Trash-0/
-.ipynb_checkpoints/
-env_setup.sh
-docker-compose.yaml
-run_container.sh
-TODO.md
-.env

.gitattributes

@@ -0,0 +1 @@
+.renku/metadata/**    merge=renkumerge

.gitignore

@@ -5,3 +5,342 @@ logs/
 __pycache__/
 *.h5
 .env
+
+
+# Created by https://www.gitignore.io/api/macos,python,R,linux,vim,emacs,visualstudiocode,intellij
+# Edit at https://www.gitignore.io/?templates=macos,python,R,linux,vim,emacs,visualstudiocode,intellij
+
+### Emacs ###
+# -*- mode: gitignore; -*-
+*~
+\#*\#
+/.emacs.desktop
+/.emacs.desktop.lock
+*.elc
+auto-save-list
+tramp
+.\#*
+
+# Org-mode
+.org-id-locations
+*_archive
+
+# flymake-mode
+*_flymake.*
+
+# eshell files
+/eshell/history
+/eshell/lastdir
+
+# elpa packages
+/elpa/
+
+# reftex files
+*.rel
+
+# AUCTeX auto folder
+/auto/
+
+# cask packages
+.cask/
+dist/
+
+# Flycheck
+flycheck_*.el
+
+# server auth directory
+/server/
+
+# projectiles files
+.projectile
+
+# directory configuration
+.dir-locals.el
+
+# network security
+/network-security.data
+
+
+### Intellij ###
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio and WebStorm
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+
+# User-specific stuff
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/**/usage.statistics.xml
+.idea/**/dictionaries
+.idea/**/shelf
+
+# Generated files
+.idea/**/contentModel.xml
+
+# Sensitive or high-churn files
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+.idea/**/dbnavigator.xml
+
+# Gradle
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# Gradle and Maven with auto-import
+# When using Gradle or Maven with auto-import, you should exclude module files,
+# since they will be recreated, and may cause churn.  Uncomment if using
+# auto-import.
+# .idea/modules.xml
+# .idea/*.iml
+# .idea/modules
+
+# CMake
+cmake-build-*/
+
+# Mongo Explorer plugin
+.idea/**/mongoSettings.xml
+
+# File-based project format
+*.iws
+
+# IntelliJ
+out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+.idea/replstate.xml
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+# Editor-based Rest Client
+.idea/httpRequests
+
+# Android studio 3.1+ serialized cache file
+.idea/caches/build_file_checksums.ser
+
+# JetBrains templates
+**___jb_tmp___
+
+### Intellij Patch ###
+# Comment Reason: https://github.com/joeblau/gitignore.io/issues/186#issuecomment-215987721
+
+# *.iml
+# modules.xml
+# .idea/misc.xml
+# *.ipr
+
+# Sonarlint plugin
+.idea/sonarlint
+
+### Linux ###
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*
+
+### macOS ###
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+### Vim ###
+# Swap
+[._]*.s[a-v][a-z]
+[._]*.sw[a-p]
+[._]s[a-rt-v][a-z]
+[._]ss[a-gi-z]
+[._]sw[a-p]
+
+# Session
+Session.vim
+
+# Temporary
+.netrwhist
+# Auto-generated tag files
+tags
+# Persistent undo
+[._]*.un~
+
+### VisualStudioCode ###
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+
+### VisualStudioCode Patch ###
+# Ignore all local history of files
+.history
+
+# End of https://www.gitignore.io/api/macos,python,R,linux,vim,emacs,visualstudiocode,intellij
+
+# Renku
+.renku.lock
+.renku/tmp
+.renku/cache

.gitlab-ci.yml

@@ -0,0 +1,18 @@
+variables:
+  GIT_STRATEGY: fetch
+  GIT_SSL_NO_VERIFY: "true"
+  GIT_LFS_SKIP_SMUDGE: 1
+  DOCKER_BUILDKIT: 1
+
+stages:
+  - build
+
+image_build:
+  stage: build
+  image: docker:stable
+  before_script:
+    - docker login -u gitlab-ci-token -p $CI_JOB_TOKEN http://$CI_REGISTRY
+  script: |
+    CI_COMMIT_SHA_7=$(echo $CI_COMMIT_SHA | cut -c1-7)
+    docker build --tag $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA_7 .
+    docker push $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA_7

.renku/metadata.yml

@@ -0,0 +1,2 @@
+# Dummy file kept for backwards compatibility, does not contain actual version
+'http://schema.org/schemaVersion': '9'

.renku/metadata/29/65/296522fff8334ccea75df004fe8f6f16e5eb4fcec86d472fb0125e0e64e74b27

@@ -0,0 +1,87 @@
+{
+  "@renku_data_type": "BTrees.OOBTree.OOBucket",
+  "@renku_data_value": {
+    "@renku_data_type": "builtins.tuple",
+    "@renku_data_value": [
+      {
+        "@renku_data_type": "builtins.tuple",
+        "@renku_data_value": [
+          "BTree",
+          {
+            "@renku_data_type": "type",
+            "@renku_data_value": "BTrees.OOBTree.OOBTree"
+          },
+          "Bucket",
+          {
+            "@renku_data_type": "type",
+            "@renku_data_value": "BTrees.OOBTree.OOBucket"
+          },
+          "Set",
+          {
+            "@renku_data_type": "type",
+            "@renku_data_value": "BTrees.OOBTree.OOSet"
+          },
+          "TreeSet",
+          {
+            "@renku_data_type": "type",
+            "@renku_data_value": "BTrees.OOBTree.OOTreeSet"
+          },
+          "attrname",
+          "upstream",
+          "call",
+          false,
+          "difference",
+          {
+            "@renku_data_type": "function",
+            "@renku_data_value": "BTrees._OOBTree.difference"
+          },
+          "dump",
+          {
+            "@renku_data_type": "function",
+            "@renku_data_value": "renku.infrastructure.gateway.database_gateway.dump_activity"
+          },
+          "element",
+          {
+            "@renku_data_type": "zope.interface.interface.Attribute",
+            "@renku_data_value": {
+              "_Element__tagged_values": null,
+              "__doc__": "the upstream activities",
+              "__name__": "upstream",
+              "interface": {
+                "@renku_data_type": "type",
+                "@renku_data_value": "renku.infrastructure.gateway.database_gateway.IActivityDownstreamRelation"
+              }
+            }
+          },
+          "interface",
+          {
+            "@renku_data_type": "type",
+            "@renku_data_value": "renku.infrastructure.gateway.database_gateway.IActivityDownstreamRelation"
+          },
+          "intersection",
+          {
+            "@renku_data_type": "function",
+            "@renku_data_value": "BTrees._OOBTree.intersection"
+          },
+          "load",
+          {
+            "@renku_data_type": "function",
+            "@renku_data_value": "renku.infrastructure.gateway.database_gateway.load_activity"
+          },
+          "multiple",
+          false,
+          "multiunion",
+          null,
+          "name",
+          "upstream",
+          "union",
+          {
+            "@renku_data_type": "function",
+            "@renku_data_value": "BTrees._OOBTree.union"
+          }
+        ]
+      }
+    ]
+  },
+  "@renku_oid": "296522fff8334ccea75df004fe8f6f16e5eb4fcec86d472fb0125e0e64e74b27"
+}

.renku/metadata/43/79/437974a24f284fba8c463258f768218d2ac86a5b99aa4537a85acec9b4905906

@@ -0,0 +1,87 @@
+{
+  "@renku_data_type": "BTrees.OOBTree.OOBucket",
+  "@renku_data_value": {
+    "@renku_data_type": "builtins.tuple",
+    "@renku_data_value": [
+      {
+        "@renku_data_type": "builtins.tuple",
+        "@renku_data_value": [
+          "BTree",
+          {
+            "@renku_data_type": "type",
+            "@renku_data_value": "BTrees.OOBTree.OOBTree"
+          },
+          "Bucket",
+          {
+            "@renku_data_type": "type",
+            "@renku_data_value": "BTrees.OOBTree.OOBucket"
+          },
+          "Set",
+          {
+            "@renku_data_type": "type",
+            "@renku_data_value": "BTrees.OOBTree.OOSet"
+          },
+          "TreeSet",
+          {
+            "@renku_data_type": "type",
+            "@renku_data_value": "BTrees.OOBTree.OOTreeSet"
+          },
+          "attrname",
+          "upstream",
+          "call",
+          false,
+          "difference",
+          {
+            "@renku_data_type": "function",
+            "@renku_data_value": "BTrees._OOBTree.difference"
+          },
+          "dump",
+          {
+            "@renku_data_type": "function",
+            "@renku_data_value": "renku.infrastructure.gateway.database_gateway.dump_activity"
+          },
+          "element",
+          {
+            "@renku_data_type": "zope.interface.interface.Attribute",
+            "@renku_data_value": {
+              "_Element__tagged_values": null,
+              "__doc__": "the upstream activities",
+              "__name__": "upstream",
+              "interface": {
+                "@renku_data_type": "type",
+                "@renku_data_value": "renku.infrastructure.gateway.database_gateway.IActivityDownstreamRelation"
+              }
+            }
+          },
+          "interface",
+          {
+            "@renku_data_type": "type",
+            "@renku_data_value": "renku.infrastructure.gateway.database_gateway.IActivityDownstreamRelation"
+          },
+          "intersection",
+          {
+            "@renku_data_type": "function",
+            "@renku_data_value": "BTrees._OOBTree.intersection"
+          },
+          "load",
+          {
+            "@renku_data_type": "function",
+            "@renku_data_value": "renku.infrastructure.gateway.database_gateway.load_activity"
+          },
+          "multiple",
+          false,
+          "multiunion",
+          null,
+          "name",
+          "upstream",
+          "union",
+          {
+            "@renku_data_type": "function",
+            "@renku_data_value": "BTrees._OOBTree.union"
+          }
+        ]
+      }
+    ]
+  },
+  "@renku_oid": "437974a24f284fba8c463258f768218d2ac86a5b99aa4537a85acec9b4905906"
+}

.renku/metadata/45/7c/457cec4a297b4280824923e332aeb4ffc95f7fcf1dfb4708872fc2f79c7ae294

@@ -0,0 +1,87 @@
+{
+  "@renku_data_type": "BTrees.OOBTree.OOBucket",
+  "@renku_data_value": {
+    "@renku_data_type": "builtins.tuple",
+    "@renku_data_value": [
+      {
+        "@renku_data_type": "builtins.tuple",
+        "@renku_data_value": [
+          "BTree",
+          {
+            "@renku_data_type": "type",
+            "@renku_data_value": "BTrees.OOBTree.OOBTree"
+          },
+          "Bucket",
+          {
+            "@renku_data_type": "type",
+            "@renku_data_value": "BTrees.OOBTree.OOBucket"
+          },
+          "Set",
+          {
+            "@renku_data_type": "type",
+            "@renku_data_value": "BTrees.OOBTree.OOSet"
+          },
+          "TreeSet",
+          {
+            "@renku_data_type": "type",
+            "@renku_data_value": "BTrees.OOBTree.OOTreeSet"
+          },
+          "attrname",
+          "downstream",
+          "call",
+          false,
+          "difference",
+          {
+            "@renku_data_type": "function",
+            "@renku_data_value": "BTrees._OOBTree.difference"
+          },
+          "dump",
+          {
+            "@renku_data_type": "function",
+            "@renku_data_value": "renku.infrastructure.gateway.database_gateway.dump_activity"
+          },
+          "element",
+          {
+            "@renku_data_type": "zope.interface.interface.Attribute",
+            "@renku_data_value": {
+              "_Element__tagged_values": null,
+              "__doc__": "the downstream activities",
+              "__name__": "downstream",
+              "interface": {
+                "@renku_data_type": "type",
+                "@renku_data_value": "renku.infrastructure.gateway.database_gateway.IActivityDownstreamRelation"
+              }
+            }
+          },
+          "interface",
+          {
+            "@renku_data_type": "type",
+            "@renku_data_value": "renku.infrastructure.gateway.database_gateway.IActivityDownstreamRelation"
+          },
+          "intersection",
+          {
+            "@renku_data_type": "function",
+            "@renku_data_value": "BTrees._OOBTree.intersection"
+          },
+          "load",
+          {
+            "@renku_data_type": "function",
+            "@renku_data_value": "renku.infrastructure.gateway.database_gateway.load_activity"
+          },
+          "multiple",
+          false,
+          "multiunion",
+          null,
+          "name",
+          "downstream",
+          "union",
+          {
+            "@renku_data_type": "function",
+            "@renku_data_value": "BTrees._OOBTree.union"
+          }
+        ]
+      }
+    ]
+  },
+  "@renku_oid": "457cec4a297b4280824923e332aeb4ffc95f7fcf1dfb4708872fc2f79c7ae294"
+}

.renku/metadata/92/f6/92f6be8c8aae49c6b2c48dc8a414519f565c56a2c53a4a86beae76ab620dcc03

@@ -0,0 +1,26 @@
+{
+  "@renku_data_type": "BTrees.OOBTree.OOBucket",
+  "@renku_data_value": {
+    "@renku_data_type": "builtins.tuple",
+    "@renku_data_value": [
+      {
+        "@renku_data_type": "builtins.tuple",
+        "@renku_data_value": [
+          "downstream",
+          {
+            "@renku_data_type": "BTrees.OOBTree.OOBucket",
+            "@renku_oid": "457cec4a297b4280824923e332aeb4ffc95f7fcf1dfb4708872fc2f79c7ae294",
+            "@renku_reference": true
+          },
+          "upstream",
+          {
+            "@renku_data_type": "BTrees.OOBTree.OOBucket",
+            "@renku_oid": "437974a24f284fba8c463258f768218d2ac86a5b99aa4537a85acec9b4905906",
+            "@renku_reference": true
+          }
+        ]
+      }
+    ]
+  },
+  "@renku_oid": "92f6be8c8aae49c6b2c48dc8a414519f565c56a2c53a4a86beae76ab620dcc03"
+}

.renku/metadata/9e/10/9e10d562c1ba4355b04ee58e3e296eb2a6e76e10664740a8aa070d93aed1435b

@@ -0,0 +1,87 @@
+{
+  "@renku_data_type": "BTrees.OOBTree.OOBucket",
+  "@renku_data_value": {
+    "@renku_data_type": "builtins.tuple",
+    "@renku_data_value": [
+      {
+        "@renku_data_type": "builtins.tuple",
+        "@renku_data_value": [
+          "BTree",
+          {
+            "@renku_data_type": "type",
+            "@renku_data_value": "BTrees.OOBTree.OOBTree"
+          },
+          "Bucket",
+          {
+            "@renku_data_type": "type",
+            "@renku_data_value": "BTrees.OOBTree.OOBucket"
+          },
+          "Set",
+          {
+            "@renku_data_type": "type",
+            "@renku_data_value": "BTrees.OOBTree.OOSet"
+          },
+          "TreeSet",
+          {
+            "@renku_data_type": "type",
+            "@renku_data_value": "BTrees.OOBTree.OOTreeSet"
+          },
+          "attrname",
+          "downstream",
+          "call",
+          false,
+          "difference",
+          {
+            "@renku_data_type": "function",
+            "@renku_data_value": "BTrees._OOBTree.difference"
+          },
+          "dump",
+          {
+            "@renku_data_type": "function",
+            "@renku_data_value": "renku.infrastructure.gateway.database_gateway.dump_activity"
+          },
+          "element",
+          {
+            "@renku_data_type": "zope.interface.interface.Attribute",
+            "@renku_data_value": {
+              "_Element__tagged_values": null,
+              "__doc__": "the downstream activities",
+              "__name__": "downstream",
+              "interface": {
+                "@renku_data_type": "type",
+                "@renku_data_value": "renku.infrastructure.gateway.database_gateway.IActivityDownstreamRelation"
+              }
+            }
+          },
+          "interface",
+          {
+            "@renku_data_type": "type",
+            "@renku_data_value": "renku.infrastructure.gateway.database_gateway.IActivityDownstreamRelation"
+          },
+          "intersection",
+          {
+            "@renku_data_type": "function",
+            "@renku_data_value": "BTrees._OOBTree.intersection"
+          },
+          "load",
+          {
+            "@renku_data_type": "function",
+            "@renku_data_value": "renku.infrastructure.gateway.database_gateway.load_activity"
+          },
+          "multiple",
+          false,
+          "multiunion",
+          null,
+          "name",
+          "downstream",
+          "union",
+          {
+            "@renku_data_type": "function",
+            "@renku_data_value": "BTrees._OOBTree.union"
+          }
+        ]
+      }
+    ]
+  },
+  "@renku_oid": "9e10d562c1ba4355b04ee58e3e296eb2a6e76e10664740a8aa070d93aed1435b"
+}

.renku/metadata/_downstream_relations

@@ -0,0 +1,5 @@
+{
+  "@renku_data_type": "renku.infrastructure.database.RenkuOOBTree",
+  "@renku_data_value": null,
+  "@renku_oid": "_downstream_relations"
+}

.renku/metadata/activities

@@ -0,0 +1,5 @@
+{
+  "@renku_data_type": "renku.infrastructure.database.RenkuOOBTree",
+  "@renku_data_value": null,
+  "@renku_oid": "activities"
+}

.renku/metadata/activities-by-generation

@@ -0,0 +1,5 @@
+{
+  "@renku_data_type": "renku.infrastructure.database.RenkuOOBTree",
+  "@renku_data_value": null,
+  "@renku_oid": "activities-by-generation"
+}

.renku/metadata/activities-by-usage

@@ -0,0 +1,5 @@
+{
+  "@renku_data_type": "renku.infrastructure.database.RenkuOOBTree",
+  "@renku_data_value": null,
+  "@renku_oid": "activities-by-usage"
+}

.renku/metadata/activity-catalog

@@ -0,0 +1,81 @@
+{
+  "@renku_data_type": "zc.relation.catalog.Catalog",
+  "@renku_oid": "activity-catalog",
+  "_EMPTY_name_TO_relcount_relset": {
+    "@renku_data_type": "BTrees.OOBTree.OOBTree",
+    "@renku_oid": "858d7628fe5a438bbf51e336cb18f7421ef51da8e4774338aaa970e2037bb1ea",
+    "@renku_reference": true
+  },
+  "_attrs": {
+    "@renku_data_type": "BTrees.OOBTree.OOBucket",
+    "@renku_oid": "f05b6e08af204b8897ee70197bd9efd0ad51384135314fc2b9c274724c7afb78",
+    "@renku_reference": true
+  },
+  "_name_TO_mapping": {
+    "@renku_data_type": "BTrees.OOBTree.OOBTree",
+    "@renku_oid": "e2338d3976674343b39f5108416f8b36fa2c27be05774ce4924f19a3502899e0",
+    "@renku_reference": true
+  },
+  "_queryFactories": {
+    "@renku_data_type": "builtins.tuple",
+    "@renku_data_value": [
+      {
+        "@renku_data_type": "zc.relation.queryfactory.TransposingTransitive",
+        "@renku_oid": "bbc23412ab474e23b4fbaef11ab07402f7f8497995114cef9e802be4ed698b19",
+        "@renku_reference": true
+      }
+    ]
+  },
+  "_relLength": {
+    "@renku_data_type": "BTrees.Length.Length",
+    "@renku_data_value": 0
+  },
+  "_relTokens": {
+    "@renku_data_type": "BTrees.OOBTree.OOTreeSet",
+    "@renku_data_value": null
+  },
+  "_relTools": {
+    "BTree": {
+      "@renku_data_type": "type",
+      "@renku_data_value": "BTrees.OOBTree.OOBTree"
+    },
+    "Bucket": {
+      "@renku_data_type": "type",
+      "@renku_data_value": "BTrees.OOBTree.OOBucket"
+    },
+    "Set": {
+      "@renku_data_type": "type",
+      "@renku_data_value": "BTrees.OOBTree.OOSet"
+    },
+    "TreeSet": {
+      "@renku_data_type": "type",
+      "@renku_data_value": "BTrees.OOBTree.OOTreeSet"
+    },
+    "difference": {
+      "@renku_data_type": "function",
+      "@renku_data_value": "BTrees._OOBTree.difference"
+    },
+    "dump": {
+      "@renku_data_type": "function",
+      "@renku_data_value": "renku.infrastructure.gateway.database_gateway.dump_downstream_relations"
+    },
+    "intersection": {
+      "@renku_data_type": "function",
+      "@renku_data_value": "BTrees._OOBTree.intersection"
+    },
+    "load": {
+      "@renku_data_type": "function",
+      "@renku_data_value": "renku.infrastructure.gateway.database_gateway.load_downstream_relations"
+    },
+    "multiunion": null,
+    "union": {
+      "@renku_data_type": "function",
+      "@renku_data_value": "BTrees._OOBTree.union"
+    }
+  },
+  "_reltoken_name_TO_objtokenset": {
+    "@renku_data_type": "BTrees.OOBTree.OOBTree",
+    "@renku_oid": "df86305035964e66a883a2755e164dfe851bfcc8a10c4320968ac3e828213bf0",
+    "@renku_reference": true
+  }
+}

.renku/metadata/activity-collections

@@ -0,0 +1,5 @@
+{
+  "@renku_data_type": "renku.infrastructure.database.RenkuOOBTree",
+  "@renku_data_value": null,
+  "@renku_oid": "activity-collections"
+}

.renku/metadata/datasets

@@ -0,0 +1,5 @@
+{
+  "@renku_data_type": "renku.infrastructure.database.RenkuOOBTree",
+  "@renku_data_value": null,
+  "@renku_oid": "datasets"
+}

.renku/metadata/datasets-provenance-tails

@@ -0,0 +1,5 @@
+{
+  "@renku_data_type": "renku.infrastructure.database.RenkuOOBTree",
+  "@renku_data_value": null,
+  "@renku_oid": "datasets-provenance-tails"
+}

.renku/metadata/datasets-tags

@@ -0,0 +1,5 @@
+{
+  "@renku_data_type": "renku.infrastructure.database.RenkuOOBTree",
+  "@renku_data_value": null,
+  "@renku_oid": "datasets-tags"
+}

.renku/metadata/f0/5b/f05b6e08af204b8897ee70197bd9efd0ad51384135314fc2b9c274724c7afb78

@@ -0,0 +1,26 @@
+{
+  "@renku_data_type": "BTrees.OOBTree.OOBucket",
+  "@renku_data_value": {
+    "@renku_data_type": "builtins.tuple",
+    "@renku_data_value": [
+      {
+        "@renku_data_type": "builtins.tuple",
+        "@renku_data_value": [
+          "downstream",
+          {
+            "@renku_data_type": "BTrees.OOBTree.OOBucket",
+            "@renku_oid": "9e10d562c1ba4355b04ee58e3e296eb2a6e76e10664740a8aa070d93aed1435b",
+            "@renku_reference": true
+          },
+          "upstream",
+          {
+            "@renku_data_type": "BTrees.OOBTree.OOBucket",
+            "@renku_oid": "296522fff8334ccea75df004fe8f6f16e5eb4fcec86d472fb0125e0e64e74b27",
+            "@renku_reference": true
+          }
+        ]
+      }
+    ]
+  },
+  "@renku_oid": "f05b6e08af204b8897ee70197bd9efd0ad51384135314fc2b9c274724c7afb78"
+}

.renku/metadata/plans

@@ -0,0 +1,5 @@
+{
+  "@renku_data_type": "renku.infrastructure.database.RenkuOOBTree",
+  "@renku_data_value": null,
+  "@renku_oid": "plans"
+}

.renku/metadata/plans-by-name

@@ -0,0 +1,5 @@
+{
+  "@renku_data_type": "renku.infrastructure.database.RenkuOOBTree",
+  "@renku_data_value": null,
+  "@renku_oid": "plans-by-name"
+}

.renku/metadata/project

@@ -0,0 +1,39 @@
+{
+  "@renku_data_type": "renku.domain_model.project.Project",
+  "@renku_oid": "project",
+  "agent_version": "2.9.4",
+  "annotations": [],
+  "creator": {
+    "@renku_data_type": "renku.domain_model.provenance.agent.Person",
+    "@renku_data_value": {
+      "affiliation": null,
+      "alternate_name": null,
+      "email": "juan.florez-ospina@psi.ch",
+      "id": "mailto:juan.florez-ospina@psi.ch",
+      "name": "Juan Felipe Florez Ospina"
+    }
+  },
+  "date_created": {
+    "@renku_data_type": "datetime.datetime",
+    "@renku_data_value": "2025-06-04T14:52:46.207682+02:00"
+  },
+  "description": null,
+  "id": "/projects/apog/acsmnode",
+  "image": null,
+  "keywords": [],
+  "minimum_renku_version": "2.8.0",
+  "name": "acsmnode",
+  "template_metadata": {
+    "@renku_data_type": "renku.domain_model.project.ProjectTemplateMetadata",
+    "@renku_data_value": {
+      "immutable_template_files": [],
+      "metadata": "{\"__template_source__\": \"renku\", \"__template_ref__\": \"0.7.1\", \"__template_id__\": \"python-minimal\", \"__namespace__\": \"apog\", \"__sanitized_project_name__\": \"\", \"__repository__\": \"\", \"__project_slug__\": \"\", \"__project_description__\": null, \"__renku_version__\": \"2.9.4\", \"__name__\": \"acsmnode\", \"name\": \"acsmnode\", \"__template_version__\": \"0.7.1\", \"__automated_update__\": true}",
+      "ssh_supported": true,
+      "template_id": "python-minimal",
+      "template_ref": "0.7.1",
+      "template_source": "renku",
+      "template_version": "0.7.1"
+    }
+  },
+  "version": 10
+}

.renku/metadata/root

@@ -0,0 +1,152 @@
+{
+  "@renku_data_type": "renku.infrastructure.database.RenkuOOBTree",
+  "@renku_data_value": {
+    "@renku_data_type": "builtins.tuple",
+    "@renku_data_value": [
+      {
+        "@renku_data_type": "builtins.tuple",
+        "@renku_data_value": [
+          {
+            "@renku_data_type": "builtins.tuple",
+            "@renku_data_value": [
+              {
+                "@renku_data_type": "builtins.tuple",
+                "@renku_data_value": [
+                  "_downstream_relations",
+                  {
+                    "@renku_data_type": "renku.infrastructure.database.RenkuOOBTree",
+                    "@renku_oid": "_downstream_relations",
+                    "@renku_reference": true
+                  },
+                  "activities",
+                  {
+                    "@renku_data_type": "renku.infrastructure.database.Index",
+                    "@renku_oid": "activities-index",
+                    "attribute": "id",
+                    "entries": {
+                      "@renku_data_type": "renku.infrastructure.database.RenkuOOBTree",
+                      "@renku_oid": "activities",
+                      "@renku_reference": true
+                    },
+                    "key_type": null,
+                    "name": "activities",
+                    "object_type": "renku.domain_model.provenance.activity.Activity"
+                  },
+                  "activities-by-generation",
+                  {
+                    "@renku_data_type": "renku.infrastructure.database.RenkuOOBTree",
+                    "@renku_oid": "activities-by-generation",
+                    "@renku_reference": true
+                  },
+                  "activities-by-usage",
+                  {
+                    "@renku_data_type": "renku.infrastructure.database.RenkuOOBTree",
+                    "@renku_oid": "activities-by-usage",
+                    "@renku_reference": true
+                  },
+                  "activity-catalog",
+                  {
+                    "@renku_data_type": "zc.relation.catalog.Catalog",
+                    "@renku_oid": "activity-catalog",
+                    "@renku_reference": true
+                  },
+                  "activity-collections",
+                  {
+                    "@renku_data_type": "renku.infrastructure.database.Index",
+                    "@renku_oid": "activity-collections-index",
+                    "attribute": "id",
+                    "entries": {
+                      "@renku_data_type": "renku.infrastructure.database.RenkuOOBTree",
+                      "@renku_oid": "activity-collections",
+                      "@renku_reference": true
+                    },
+                    "key_type": null,
+                    "name": "activity-collections",
+                    "object_type": "renku.domain_model.provenance.activity.ActivityCollection"
+                  },
+                  "datasets",
+                  {
+                    "@renku_data_type": "renku.infrastructure.database.Index",
+                    "@renku_oid": "datasets-index",
+                    "attribute": "name",
+                    "entries": {
+                      "@renku_data_type": "renku.infrastructure.database.RenkuOOBTree",
+                      "@renku_oid": "datasets",
+                      "@renku_reference": true
+                    },
+                    "key_type": null,
+                    "name": "datasets",
+                    "object_type": "renku.domain_model.dataset.Dataset"
+                  },
+                  "datasets-provenance-tails",
+                  {
+                    "@renku_data_type": "renku.infrastructure.database.Index",
+                    "@renku_oid": "datasets-provenance-tails-index",
+                    "attribute": "id",
+                    "entries": {
+                      "@renku_data_type": "renku.infrastructure.database.RenkuOOBTree",
+                      "@renku_oid": "datasets-provenance-tails",
+                      "@renku_reference": true
+                    },
+                    "key_type": null,
+                    "name": "datasets-provenance-tails",
+                    "object_type": "renku.domain_model.dataset.Dataset"
+                  },
+                  "datasets-tags",
+                  {
+                    "@renku_data_type": "renku.infrastructure.database.Index",
+                    "@renku_oid": "datasets-tags-index",
+                    "attribute": null,
+                    "entries": {
+                      "@renku_data_type": "renku.infrastructure.database.RenkuOOBTree",
+                      "@renku_oid": "datasets-tags",
+                      "@renku_reference": true
+                    },
+                    "key_type": null,
+                    "name": "datasets-tags",
+                    "object_type": "persistent.list.PersistentList"
+                  },
+                  "plans",
+                  {
+                    "@renku_data_type": "renku.infrastructure.database.Index",
+                    "@renku_oid": "plans-index",
+                    "attribute": "id",
+                    "entries": {
+                      "@renku_data_type": "renku.infrastructure.database.RenkuOOBTree",
+                      "@renku_oid": "plans",
+                      "@renku_reference": true
+                    },
+                    "key_type": null,
+                    "name": "plans",
+                    "object_type": "renku.domain_model.workflow.plan.AbstractPlan"
+                  },
+                  "plans-by-name",
+                  {
+                    "@renku_data_type": "renku.infrastructure.database.Index",
+                    "@renku_oid": "plans-by-name-index",
+                    "attribute": "name",
+                    "entries": {
+                      "@renku_data_type": "renku.infrastructure.database.RenkuOOBTree",
+                      "@renku_oid": "plans-by-name",
+                      "@renku_reference": true
+                    },
+                    "key_type": null,
+                    "name": "plans-by-name",
+                    "object_type": "renku.domain_model.workflow.plan.AbstractPlan"
+                  },
+                  "project",
+                  {
+                    "@renku_data_type": "renku.domain_model.project.Project",
+                    "@renku_oid": "project",
+                    "@renku_reference": true
+                  }
+                ]
+              }
+            ]
+          }
+        ]
+      }
+    ]
+  },
+  "@renku_oid": "root"
+}

.renku/renku.ini

@@ -0,0 +1,2 @@
+[interactive]
+default_url = /lab

.renku/template_checksums.json

@@ -0,0 +1 @@
+{".gitlab-ci.yml": "c55bc2b275655014ea91b5cc651384965b166b546843bda85215233a6e091090", "environment.yml": "e81e9a061f19645b9a0e8e353982289338ec158a72534456917ddae832794911", ".renkulfsignore": "b418745d4f9f40d3b05b88c305041316b8c3e9fc6af877a21a37ccc6b43d6d66", "Dockerfile": "b48ea1420ad1931a8f0ecc25aece8f70d7519a5b0fb151adcd67998ef6de61ad", ".gitignore": "7a908bfd4db867f62fa279c53311f117ca4a567feef463203f85b62d8d0b140c", ".dockerignore": "abc0b37932c96cf447b2930bcb2455fac0be146ee9cf1d447f8aef537a531c41", "requirements.txt": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", "README.md": "8a06667b08b3f69a240508c7c038160b9890f384f0d0accf5414d7d8d3416264", "data/.gitkeep": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", "notebooks/.gitkeep": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", ".renku/renku.ini": "5490dcea1aa22839b454ac51d66a1195fd30af11a08e2399cf082d3496bb21e4", "workflows/my-workflow.yaml": "2ef60829869b81bc8f7dcd64ee2140e461af6330591516c2526e801c99554f20"}

.renkulfsignore

@@ -0,0 +1,22 @@
+# WARNING: editing this file will impact the behavior of renku commands
+# by telling renku to *not track* listed files with git LFS.
+#
+# By default, renku commands track all files above the renku configured lfs_threshold
+# with git LFS to prevent accidentally checking in large files (default=100kb).
+# You can update this threshold by calling 'renku config lfs_threshold <size>kb'.
+#
+# Use this file to specify particular paths to *not track* with LFS regardless of
+# their size. The syntax is the same as .gitignore (https://git-scm.com/docs/gitignore).
+# Remember: files listed here, when generated during renku commands, will add to
+# the size of your repo, and could slow things down.
+#
+# See https://github.com/SwissDataScienceCenter/renku-project-template for proper
+# usage.
+
+# Warning: removing these lines will check source files (e.g. generated ipynb files from papermill) into LFS and they
+# will no longer be displayed in the renku UI
+*.ipynb
+*.py
+*.r
+*.md
+*.rst

Dockerfile

@@ -0,0 +1,52 @@
+########################################################
+#        Renku install section - do not edit           #
+
+FROM renku/renkulab-py:3.10-0.18.1 as builder
+
+# RENKU_VERSION determines the version of the renku CLI
+# that will be used in this image. To find the latest version,
+# visit https://pypi.org/project/renku/#history.
+ARG RENKU_VERSION=2.9.4
+
+# Install renku from pypi or from github if a dev version
+RUN if [ -n "$RENKU_VERSION" ] ; then \
+        source .renku/venv/bin/activate ; \
+        currentversion=$(renku --version) ; \
+        if [ "$RENKU_VERSION" != "$currentversion" ] ; then \
+            pip uninstall renku -y ; \
+            gitversion=$(echo "$RENKU_VERSION" | sed -n "s/^[[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+\(rc[[:digit:]]\+\)*\(\.dev[[:digit:]]\+\)*\(+g\([a-f0-9]\+\)\)*\(+dirty\)*$/\4/p") ; \
+            if [ -n "$gitversion" ] ; then \
+                pip install --no-cache-dir --force "git+https://github.com/SwissDataScienceCenter/renku-python.git@$gitversion" ;\
+            else \
+                pip install --no-cache-dir --force renku==${RENKU_VERSION} ;\
+            fi \
+        fi \
+    fi
+#             End Renku install section                #
+########################################################
+
+FROM renku/renkulab-py:3.10-0.18.1
+
+# Uncomment and adapt if code is to be included in the image
+# COPY src /code/src
+
+# Uncomment and adapt if your R or python packages require extra linux (ubuntu) software
+# e.g. the following installs apt-utils and vim; each pkg on its own line, all lines
+# except for the last end with backslash '\' to continue the RUN line
+#
+# USER root
+# RUN apt-get update && \
+#    apt-get install -y --no-install-recommends \
+#    apt-utils \
+#    vim
+# USER ${NB_USER}
+
+# install the python dependencies
+COPY requirements.txt environment.yml /tmp/
+RUN mamba env update -q -f /tmp/environment.yml && \
+    /opt/conda/bin/pip install -r /tmp/requirements.txt --no-cache-dir && \
+    mamba clean -y --all && \
+    mamba env export -n "root" && \
+    rm -rf ${HOME}/.renku/venv
+
+COPY --from=builder ${HOME}/.renku/venv ${HOME}/.renku/venv

environment.yml

@@ -0,0 +1,14 @@
+name: "base"
+# WARNING : As Renku makes use of mamba for more efficient package builds, please use the popular "conda-forge" channel
+# For more details : https://mamba.readthedocs.io/en/latest/user_guide/troubleshooting.html#mixing-the-defaults-and-conda-forge-channels
+# Using the defaults channel from Anaconda can easily result in getting your
+# laptop, CI pipeline, etc. blacklisted by Anaconda which makes building packages
+# impossible. To get permission to use Anaconda again you need to either pay or prove that
+# you meet the requirements for a free license. Using the conda-forge channel avoids 
+# these restrictions completely.
+channels:
+  - conda-forge
+# dependencies:
+# - add packages here
+# - one per line
+prefix: "/opt/conda"

requirements.txt

@@ -1,10 +0,0 @@
-dash==2.17.1
-dash-bootstrap-components==1.6.0
-flask==3.0.3
-h5py==3.10.0
-matplotlib==3.8.4
-numpy==1.26.4
-openai==1.25.1
-pandas==2.2.2
-plotly==5.18.0
-requests==2.31.0

workflows/my-workflow.yaml

@@ -0,0 +1,37 @@
+# === Welcome to the template Renku Workflow file! ===
+# You can use this file to encode in what order your data processing steps should be run,
+# making it easier for you to run your workflow, and for others to understand it!
+
+# === How to use this template ===
+# Replace the script and data paths in the template below to match your analysis commands. 
+# Then, run `renku run my-workflow.yaml` in a terminal to execute the workflow!
+# If you are working in a notebook, run `! renku run my-workflow.yaml` in a notebook cell. 
+
+# === Docs ===
+# To learn much more about what you can do with the Renku Workflow File, see our docs:
+# https://renku.readthedocs.io/en/stable/topic-guides/workflows/workflow-file.html
+
+name: my-workflow
+steps:
+  step-one:
+    command: python $n $my-script $input-data $output-data
+    inputs:
+      - my-script:
+          path: src/script.py
+      - input-data:
+          path: data/input/sample_data.csv
+    outputs:
+      - output-data:
+          path: data/output/results.csv
+    parameters:
+      - n:
+          prefix: -n
+          value: 10
+
+  # === Adding more steps ===
+  # You can add as many steps as you want to your workflow by copy and pasting the step template above
+  # TIP: To run just one step from a workflow, simply add the step name to the command, like this:
+  #   `renku run my-workflow.yaml make-plot`
+  # make-plot:
+    # command: python $another-script $output-data $my-plot
+    # ...