service: renku init -n "svbox-renku" -s...

service: renku init -n "svbox-renku" -s "https://github.com/SwissDataScienceCenter/renku-project-...

.dockerignore

+data
+notebooks
+.renku
+.git
\ No newline at end of file

.gitignore

+
+# 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/
+
+### R ###
+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+/*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+### R.Bookdown Stack ###
+# R package: bookdown caching files
+/*_files/
+
+### 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
\ No newline at end of file

.gitlab-ci.yml

+variables:
+  GIT_STRATEGY: fetch
+  GIT_SSL_NO_VERIFY: "true"
+  GIT_LFS_SKIP_SMUDGE: 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
\ No newline at end of file

.renku/metadata.yml

+'@id': https://renkulab.io/projects/phgrosjean/svbox-renku
+'@type':
+- http://schema.org/Project
+- http://www.w3.org/ns/prov#Location
+http://schema.org/agent: 0.16.0
+http://schema.org/creator:
+  '@id': mailto:phgrosjean@sciviews.org
+  '@type':
+  - http://schema.org/Person
+  - http://www.w3.org/ns/prov#Person
+  http://schema.org/affiliation: null
+  http://schema.org/alternateName: null
+  http://schema.org/email: phgrosjean@sciviews.org
+  http://schema.org/name: Philippe Grosjean
+  http://www.w3.org/2000/01/rdf-schema#label: Philippe Grosjean
+http://schema.org/dateCreated: '2021-08-23T08:04:10.807976+00:00'
+http://schema.org/name: svbox-renku
+http://schema.org/schemaVersion: '8'
+https://swissdatasciencecenter.github.io/renku-ontology#automatedTemplateUpdate: false
+https://swissdatasciencecenter.github.io/renku-ontology#immutableTemplateFiles: []
+https://swissdatasciencecenter.github.io/renku-ontology#templateId: R-minimal
+https://swissdatasciencecenter.github.io/renku-ontology#templateMetadata: '{"__template_source__":
+  "https://github.com/SwissDataScienceCenter/renku-project-template", "__template_ref__":
+  "0.1.22", "__template_id__": "R-minimal", "__namespace__": "sciviews", "__automated_update__":
+  true, "__repository__": "https://renkulab.io/gitlab", "__sanitized_project_name__":
+  "svbox-renku", "__project_slug__": "sciviews/svbox-renku", "__renku_version__":
+  "0.16.0", "description": "The Reku/Renkulab version of the SciViews Box. Use the
+  branch corresponding to the year, please.", "name": "svbox-renku"}'
+https://swissdatasciencecenter.github.io/renku-ontology#templateReference: 0.1.22
+https://swissdatasciencecenter.github.io/renku-ontology#templateSource: https://github.com/SwissDataScienceCenter/renku-project-template
+https://swissdatasciencecenter.github.io/renku-ontology#templateVersion: dff01d39f5f081f07a452c4d6fd4d0e4a0e63213

.renku/renku.ini

+[renku "interactive"]
+default_url = /rstudio
\ No newline at end of file

.renku/template_checksums.json

+{".dockerignore": "46625726a43957a07c38550b006dd352ef85af18f7b984a1a87284001d03713a", ".gitignore": "d890ab1ae56fa2761ba26961529e8e010fbf0e607a0fbe5364d34eeba38beab0", ".gitlab-ci.yml": "309bfbc0e2851600908f0fc430e8a41345146dca2b98eb0908f21cc1796db8ce", ".renku/renku.ini": "65a1843e16a112ae8ca9d1329fc3c7f443bc273f814c209fe6aa9c6327fca0e7", ".renkulfsignore": "12c531ec689d4b6aac36f4e1834d6e333d85837142f5f178a155f1431378029c", "Dockerfile": "2120d2d854de878b46df715a2a47dfdf184e8b80f1960fc152939d31fb2e76c8", "README.md": "513f02e2edd415515a890ca048df64e84b36e30a1c84964fa0c8a4aa6d184865", "data/.gitkeep": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", "environment.yml": "f91b4d74abed097afebcfa125fd3de20614384a6555d864e4ac304fee375b27e", "install.R": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", "notebooks/.gitkeep": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", "requirements.txt": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", "{{ __sanitized_project_name__ }}.Rproj": "11345a78148235759cdba4a1352dbb2cfa7bb5940527fcaea797fb0ef2614359"}
\ No newline at end of file

.renkulfsignore

+# 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.
+
+*.ipynb # Warning: removing this line will check generated ipynb files (e.g. from papermill) into LFS: they will no longer be displayed in the renku UI
+*.py
+*.r
+*.md
+*.rst
\ No newline at end of file

Dockerfile

+# For finding latest versions of the base image see
+# https://github.com/SwissDataScienceCenter/renkulab-docker
+ARG RENKU_BASE_IMAGE=renku/renkulab-r:4.0.5-0.8.0
+FROM ${RENKU_BASE_IMAGE}
+
+# 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 ${NB_USER}
+
+# install the R dependencies
+COPY install.R /tmp/
+RUN R -f /tmp/install.R
+
+# install the python dependencies
+COPY requirements.txt /tmp/
+RUN pip3 install -r /tmp/requirements.txt
+
+# RENKU_VERSION determines the version of the renku CLI
+# that will be used in this image. To find the latest version,
+# visit https://pypi.org/project/renku/#history.
+ARG RENKU_VERSION=0.16.0
+
+########################################################
+# Do not edit this section and do not add anything below
+
+# Install renku from pypi or from github if it's a dev version
+RUN if [ -n "$RENKU_VERSION" ] ; then \
+        currentversion=$(pipx list | sed -n "s/^\s*package\srenku\s\([^,]\+\),.*$/\1/p") ; \
+        if [ "$RENKU_VERSION" != "$currentversion" ] ; then \
+            pipx uninstall renku ; \
+            gitversion=$(echo "$RENKU_VERSION" | sed -n "s/^[[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+\(\.dev[[:digit:]]\+\)*\(+g\([a-f0-9]\+\)\)*\(+dirty\)*$/\3/p"); \
+            if [ -n "$gitversion" ] ; then \
+                pipx install --force "git+https://github.com/SwissDataScienceCenter/renku-python.git@$gitversion" ;\
+            else \
+                pipx install --force renku==${RENKU_VERSION} ;\
+            fi \
+        fi \
+    fi
+
+########################################################
\ No newline at end of file

README.md

+# svbox-renku
+
+The Reku/Renkulab version of the SciViews Box. Use the branch corresponding to the year, please.
+
+## Introduction
+
+This is a Renku project - basically a git repository with some
+bells and whistles. You'll find we have already created some
+useful things like `data` and `notebooks` directories and
+a `Dockerfile`.
+
+## Working with the project
+
+The simplest way to start your project is right from the Renku
+platform - just click on the `Environments` tab and start a new session.
+This will start an interactive environment right in your browser.
+
+To work with the project anywhere outside the Renku platform,
+click the `Settings` tab where you will find the
+git repo URLs - use `git` to clone the project on whichever machine you want.
+
+### Changing interactive environment dependencies
+
+Initially we install a very minimal set of packages to keep the images small.
+However, you can add python and conda packages in `requirements.txt` and
+`environment.yml`, and R packages to `install.R` (listed as, for example,
+`install.packages("ggplot2")`), to your heart's content. If you need more fine-grained
+control over your environment, please see [the documentation](https://renku.readthedocs.io/en/latest/user/advanced_interfaces.html#dockerfile-modifications).
+
+## Project configuration
+
+Project options can be found in `.renku/renku.ini`. In this
+project there is currently only one option, which specifies
+the default type of environment to open, in this case `/rstudio`.
+
+## Moving forward
+
+Once you feel at home with your project, we recommend that you replace
+this README file with your own project documentation! Happy data wrangling!
\ No newline at end of file

environment.yml

+name: "base"
+channels:
+  - defaults
+# dependencies:
+# - add packages here
+# - one per line
+prefix: "/opt/conda"
\ No newline at end of file

svbox-renku.Rproj

+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
\ No newline at end of file