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Commit 45f2c9ed authored by Reto Gerber's avatar Reto Gerber Committed by renku 0.15.1
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service: renku init -n "metrics_collect" -s...

service: renku init -n "metrics_collect" -s "https://github.com/SwissDataScienceCenter/renku-proj...
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notebooks
.renku
.git
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# 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
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# 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
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# 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
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
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'@id': https://renkulab.io/projects/reto.gerber/metrics_collect
'@type':
- http://schema.org/Project
- http://www.w3.org/ns/prov#Location
http://schema.org/agent: 0.15.1
http://schema.org/creator:
'@id': mailto:reto.gerber@uzh.ch
'@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: reto.gerber@uzh.ch
http://schema.org/name: Reto Gerber
http://www.w3.org/2000/01/rdf-schema#label: Reto Gerber
http://schema.org/dateCreated: '2021-06-15T13:14:12.824967+00:00'
http://schema.org/name: metrics_collect
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__":
"0.1.21", "__template_id__": "R-minimal", "__namespace__": "reto.gerber", "__automated_update__":
true, "__repository__": "https://renkulab.io/gitlab", "__sanitized_project_name__":
"metrics-collect", "__project_slug__": "reto.gerber/metrics-collect", "description":
"", "name": "metrics_collect"}'
https://swissdatasciencecenter.github.io/renku-ontology#templateReference: 0.1.21
https://swissdatasciencecenter.github.io/renku-ontology#templateSource: https://github.com/SwissDataScienceCenter/renku-project-template
https://swissdatasciencecenter.github.io/renku-ontology#templateVersion: 58ee36de2c9c152d9f51eddc5b685483b6beda73
[renku "interactive"]
default_url = /rstudio
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{".dockerignore": "46625726a43957a07c38550b006dd352ef85af18f7b984a1a87284001d03713a", ".gitignore": "d890ab1ae56fa2761ba26961529e8e010fbf0e607a0fbe5364d34eeba38beab0", ".gitlab-ci.yml": "309bfbc0e2851600908f0fc430e8a41345146dca2b98eb0908f21cc1796db8ce", ".renku/renku.ini": "65a1843e16a112ae8ca9d1329fc3c7f443bc273f814c209fe6aa9c6327fca0e7", ".renkulfsignore": "12c531ec689d4b6aac36f4e1834d6e333d85837142f5f178a155f1431378029c", "Dockerfile": "ff931f333b57d5183a28eb8c516c18bffeece3c14750bb9b437488b3f171d8e4", "README.md": "f01eb36594fa03cd40304f142222384ae3c748981a37e74e6f0432e8c1ef1653", "data/.gitkeep": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", "environment.yml": "f91b4d74abed097afebcfa125fd3de20614384a6555d864e4ac304fee375b27e", "install.R": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", "notebooks/.gitkeep": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", "requirements.txt": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", "{{ __sanitized_project_name__ }}.Rproj": "11345a78148235759cdba4a1352dbb2cfa7bb5940527fcaea797fb0ef2614359"}
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# 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
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# For finding latest versions of the base image see
# https://github.com/SwissDataScienceCenter/renkulab-docker
ARG RENKU_BASE_IMAGE=renku/renkulab-r:4.0.5-0.7.7
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 ${NB_USER}
# install the R dependencies
COPY install.R /tmp/
RUN R -f /tmp/install.R
# install the python dependencies
COPY requirements.txt /tmp/
RUN pip3 install -r /tmp/requirements.txt
# RENKU_VERSION determines the version of the renku CLI
# that will be used in this image. To find the latest version,
# visit https://pypi.org/project/renku/#history.
ARG RENKU_VERSION=0.15.1
########################################################
# Do not edit this section and do not add anything below
RUN if [ -n "$RENKU_VERSION" ] ; then \
pipx uninstall renku && \
pipx install --force renku==${RENKU_VERSION} \
; fi
########################################################
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# metrics_collect
## 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!
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name: "base"
channels:
- defaults
# dependencies:
# - add packages here
# - one per line
prefix: "/opt/conda"
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Version: 1.0
RestoreWorkspace: Default
SaveWorkspace: Default
AlwaysSaveHistory: Default
EnableCodeIndexing: Yes
UseSpacesForTab: Yes
NumSpacesForTab: 2
Encoding: UTF-8
RnwWeave: Sweave
LaTeX: pdfLaTeX
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