Python SDK and CLI for the Renku platform.
Project description
A Python library for the Renku collaborative data science platform. It includes a CLI and SDK for end-users as well as a service backend. It provides functionality for the creation and management of projects and datasets, and simple utilities to capture data provenance while performing analysis tasks.
- NOTE:
renku-python is the python library and core service for Renku - it does not start the Renku platform itself - for that, refer to the Renku docs on running the platform.
Renku for Users
Installation
Renku releases and development versions are available from PyPI. You can install it using any tool that knows how to handle PyPI packages. Our recommendation is to use :code:pipx.
pipx
First, install pipx and make sure that the $PATH is correctly configured.
$ python3 -m pip install --user pipx $ pipx ensurepath
Once pipx is installed use following command to install renku.
$ pipx install renku $ which renku ~/.local/bin/renku
pipx installs renku into its own virtual environment, making sure that it does not pollute any other packages or versions that you may have already installed.
To install a development release:
$ pipx install --pip-args pre renku
pip
$ pip install renku
The latest development versions are available on PyPI or from the Git repository:
$ pip install --pre renku # - OR - $ pip install -e git+https://github.com/SwissDataScienceCenter/renku-python.git#egg=renku
Use following installation steps based on your operating system and preferences if you would like to work with the command line interface and you do not need the Python library to be importable.
Docker
The containerized version of the CLI can be launched using Docker command.
$ docker run -it -v "$PWD":"$PWD" -w="$PWD" renku/renku-python renku
It makes sure your current directory is mounted to the same place in the container.
CLI Example
Initialize a renku project:
$ mkdir -p ~/temp/my-renku-project $ cd ~/temp/my-renku-project $ renku init
Create a dataset and add data to it:
$ renku dataset create my-dataset $ renku dataset add my-dataset https://raw.githubusercontent.com/SwissDataScienceCenter/renku-python/master/README.rst
Run an analysis:
$ renku run wc < data/my-dataset/README.rst > wc_readme
Trace the data provenance:
$ renku log wc_readme
These are the basics, but there is much more that Renku allows you to do with your data analysis workflows. The full documentation will soon be available at: https://renku-python.readthedocs.io/
Renku as a Service
This repository includes a renku-core RPC service written as a Flask application that provides (almost) all of the functionality of the Renku CLI. This is used to provide one of the backends for the RenkuLab web UI. The service can be deployed in production as a Helm chart (see helm-chart.
Developing Renku
For testing the functionality from source it is convenient to install renku in editable mode using pipx. Clone the repository and then do:
$ pipx install \
--editable \
<path-to-renku-python>[all] \
renku
This will install all the extras for testing and debugging.
Running tests
To run tests locally with specific version of Python:
$ pyenv install 3.7.5rc1 $ pipenv --python ~/.pyenv/versions/3.7.5rc1/bin/python install $ pipenv run tests
To recreate environment with different version of Python, it’s easy to do so with the following commands:
$ pipenv --rm $ pyenv install 3.6.9 $ pipenv --python ~/.pyenv/versions/3.6.9/bin/python install $ pipenv run tests
Using External Debuggers
To run renku via e.g. the Visual Studio Code debugger you need run it via the python executable in whatever virtual environment was used to install renku. If there is a package needed for the debugger, you need to inject it into the virtual environment first, e.g.:
$ pipx inject renku ptvsd
Finally, run renku via the debugger:
$ ~/.local/pipx/venvs/renku/bin/python -m ptvsd --host localhost --wait -m renku.cli <command>
If using Visual Studio Code, you may also want to set the Remote Attach configuration PathMappings so that it will find your source code, e.g.
{
"name": "Python: Remote Attach",
"type": "python",
"request": "attach",
"port": 5678,
"host": "localhost",
"pathMappings": [
{
"localRoot": "<path-to-renku-python-source-code>",
"remoteRoot": "<path-to-renku-python-source-code>"
}
]
},
Changes
0.11.6 (2020-10-16)
Bug Fixes
0.11.5 (2020-10-13)
Bug Fixes
core: fix importing a dataset referenced from non-existent projects (#1574) (4bb13ef)
core: fixes git encoding of paths with unicode characters (#1538) (9790707)
dataset: fix broken directory hierarchy after renku dataset imports (#1576) (41e3e72)
dataset: abort importing a dataset when cannot pull LFS objects (#1590) (9877a98)
dataset: fix invalid dataset name after migration (#1593) (c7ec249)
dataset: update dataset files metadata when adding and overwriting local files (#1582) (0a23e82)
0.11.4 (2020-10-05)
Bug Fixes
0.11.3 (2020-09-29)
Bug Fixes
core: make Run migration ids unique by relative path instead of absolute (686b9f9)
0.11.2 (2020-09-24)
Bug Fixes
Features
cli: show existing paths when initializing non-empty dir (#1535) (07c559f)
core: follow URL redirections for dataset files (#1516) (5a37b3c)
service: add additional template parameters (#1469) (6372a32)
service: adds additional fields to datasets listings (#1508) (f8a395f)
service: adds project details and renku operation on jobs endpoint (#1492) (6b3fafd)
service: execute read operations via git remote (#1488) (84a0eb3)
0.11.1 (2020-08-18)
Bug Fixes
0.11.0 (2020-08-14)
Bug Fixes
cli: disable version check in githook calls (#1300) (5132db3)
core: Only update project metadata if any migrations were executed (#1308) (1056a03)
service: adds more custom logging and imp. except handling (#1435) (6c3adb5)
service: fixes handlers for internal loggers (#1433) (a312f7c)
service: move project_id to query string on migrations check (#1367) (0f89726)
Features
cli: Show detailed commands for renku log output (#1345) (19fb819)
core: disabling of inputs/outputs auto-detection (#1406) (3245ca0)
core: Move workflow serialisation over to calamus (#1386) (f0fbc49)
service: added endpoints to execute all migrations on a project (#1322) (aca8cc2)
service: adds endpoint for explicit migrations check (#1326) (146b1a7)
service: adds source and destination versions to migrations check (#1372) (ea76b48)
service: adds endpoints for dataset remove (#1383) (289e4b9)
service: adds endpoints for unlinking files from a dataset (#1314) (1b78b16)
service: create new projects from templates (#1287) (552f85c), closes #862
0.10.5 (2020-07-16)
Bug Fixes
0.10.4 (2020-05-18)
Bug Fixes
Features
cli: Adds warning messages for LFS, fix output redirection (#1199) (31969f5)
core: Adds lfs file size limit and lfs ignore file (#1210) (1f3c81c)
core: git hook to avoid committing large files (#1238) (e8f1a8b)
core: renku doctor check for lfs migrate info (#1234) (480da06)
dataset: fail early when external storage not installed (#1239) (e6ea6da)
core: project clone API support for revision checkout (#1208) (74116e9)
dataset: no failure when adding ignored files (#1213) (b1e275f)
0.10.3 (2020-04-22)
Bug Fixes
Features
0.10.1 (2020-03-31)
Bug Fixes
Features
0.10.0 (2020-03-25)
This release brings about several important Dataset features:
importing renku datasets (#838)
working with data external to the repository (#974)
editing dataset metadata (#1111)
Please see the Dataset documentation for details.
Additional features were implemented for the backend service to facilitate a smoother user experience for dataset file manipulation.
IMPORTANT: starting with this version, a new metadata migration mechanism is in place (#1003). Renku commands will insist on migrating a project immediately if the metadata is found to be outdated.
Bug Fixes
Features
0.9.1 (2020-02-24)
Bug Fixes
Features
0.9.0 (2020-02-07)
Bug Fixes
adds git user check before running renku init (#892) (2e52dff)
Deletes temporary branch after renku init –force (#887) (eac0463)
Fixes JSON-LD translation and related issues (#846) (65e5469)
Fixes renku update workflow failure handling and renku status error handling (#888) (3879124)
Fixes sameAs property to follow schema.org spec (#944) (291380e)
Features
0.8.0 (2019-11-21)
Bug Fixes
Features
0.7.0 (2019-10-15)
Bug Fixes
0.6.1 (2019-10-10)
Bug Fixes
Features
0.6.0 (2019-09-18)
Bug Fixes
adds _label and commit data to imported dataset files, single commit for imports (#651) (75ce369)
always add commit to dataset if possible (#648) (7659bc8), closes #646
cleanup needed for integration tests on py35 (#653) (fdd7215)
fixed serialization of datetime to iso format (#629) (693d59d)
hide image, pull, runner, show, workon and deactivate commands (#672) (a3e9998)
Removes unneccesary call to git lfs with no paths (#658) (e32d48b)
use latest_html for version check (#647) (c6b0309), closes #641
zenodo export failing with relative paths (d40967c)
Features
0.5.2 (2019-07-26)
Bug Fixes
Features
0.5.1 (2019-07-12)
Bug Fixes
ensure external storage is handled correctly (#592) (7938ac4)
cli: allow renku run with many inputs (f60783e), closes #552
modify json-ld for datasets (#534) (ab6a719), closes #525 #526
refactored tests and docs to align with updated pydoctstyle (#586) (6f981c8)
cli: add check of missing references (9a373da)
cli: fail when removing non existing dataset (dd728db)
status: fix renku status output when not in root folder (#564) (873270d), closes #551
datasets: strip query string from data filenames (450898b)
cli: remove dataset aliases (6206e62)
cwl: detect script as input parameter (e23b75a), closes #495
deps: updated dependencies (691644d)
Features
added support for working on dirty repo (ae67be7)
0.5.0 (2019-03-28)
Bug Fixes
Features
api: list datasets from a commit (04a9fe9)
cli: add dataset rm command (a70c7ce)
cli: add rm command (cf0f502)
cli: configurable format of dataset output (d37abf3)
dataset: add existing file from current repo (575686b), closes #99
datasets: added ls-files command (ccc4f59)
models: reference context for relative paths (5d1e8e7), closes #452
add JSON-LD output format for datasets (c755d7b), closes #426
generate Makefile with log –format Makefile (1e440ce)
v0.4.0
(released 2019-03-05)
Adds renku mv command which updates dataset metadata, .gitattributes and symlinks.
Pulls LFS objects from submodules correctly.
Adds listing of datasets.
Adds reduced dot format for renku log.
Adds doctor command to check missing files in datasets.
Moves dataset metadata to .renku/datasets and adds migrate datasets command and uses UUID for metadata path.
Gets git attrs for files to prevent duplicates in .gitattributes.
Fixes renku show outputs for directories.
Runs Git LFS checkout in a worktrees and lazily pulls necessary LFS files before running commands.
Asks user before overriding an existing file using renku init or renku runner template.
Fixes renku init --force in an empty dir.
Renames CommitMixin._location to _project.
Addresses issue with commits editing multiple CWL files.
Exports merge commits for full lineage.
Exports path and parent directories.
Adds an automatic check for the latest version.
Simplifies issue submission from traceback to GitHub or Sentry. Requires SENTRY_DSN variable to be set and sentry-sdk package to be installed before sending any data.
Removes outputs before run.
Allows update of directories.
Improves readability of the status message.
Checks ignored path when added to a dataset.
Adds API method for finding ignored paths.
Uses branches for init --force.
Fixes CVE-2017-18342.
Fixes regex for parsing Git remote URLs.
Handles --isolation option using git worktree.
Renames client.git to client.repo.
Supports python -m renku.
Allows ‘.’ and ‘-’ in repo path.
v0.3.3
(released 2018-12-07)
Fixes generated Homebrew formula.
Renames renku pull path to renku storage pull with deprecation warning.
v0.3.2
(released 2018-11-29)
Fixes display of workflows in renku log.
v0.3.1
(released 2018-11-29)
Fixes issues with parsing remote Git URLs.
v0.3.0
(released 2018-11-26)
Adds JSON-LD context to objects extracted from the Git repository (see renku show context --list).
Uses PROV-O and WFPROV as provenance vocabularies and generates “stable” object identifiers (@id) for RDF and JSON-LD output formats.
Refactors the log output to allow linking files and directories.
Adds support for aliasing tools and workflows.
Adds option to install shell completion (renku --install-completion).
Fixes initialization of Git submodules.
Uses relative submodule paths when appropriate.
Simplifies external storage configuration.
v0.2.0
(released 2018-09-25)
Refactored version using Git and Common Workflow Language.
v0.1.0
(released 2017-09-06)
Initial public release as Renga.
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