Renku

-----

New feature
~~~~~~~~~~~~

⭐️ Project details now include a listing of the commit history

Notable improvements
~~~~~~~~~~~~~~~~~~~~

🚄 Environments: auto-saved branches are filtered per username

🚄 Improve markdown rendering and code highlighting

🚄 Editing markdown files is easier as ``ckeditor`` is partially integrated inside Renku

Bug fixes
~~~~~~~~~

* Dataset contains all folders from unzipped file
* Failing to retrieve metadata for one dataset does not cause the others to fail
* Improved UX for when datasets take too long
* Datasets: no failure when adding ignored files

Miscellaneous
^^^^^^^^^^^^^

- The default R template now uses the latest R (4.0.0). To update it in an existing R project, replace the first line in the Dockerfile with ``FROM renku/renkulab-r:4.0.0-renku0.10.4-0.6.3``
- A Bioconductor image with `bioc 3_11 <https://www.bioconductor.org/news/bioc_3_11_release>`__ is now available. To use it replace the first line in the Dockerfile with ``FROM renku/renkulab-bioc:RELEASE_3_11-renku0.10.4-0.6.3``
- Docker images in project templates use ``renku`` `0.10.4 <https://github.com/SwissDataScienceCenter/renku-python/releases/tag/v0.10.4>`__

Breaking changes
~~~~~~~~~~~~~~~~

GitLab version: the Renku chart now installs GitLab >= 12.9.0 by default.
GitLab versions < 12.7.0 are supported too, but a ``.gateway.oldGitLabLogout: true`` has to be set explicitly. Note that GitLab versions where `12.7.0 <= version < 12.9.0` are not supported.

Individual components
~~~~~~~~~~~~~~~~~~~~~

For changes to individual components, check:

-------------------------------------------------------------------------------------------------------

Bug Fixes
~~~~~~~~~

- add ``.renku/tmp`` to default .gitignore (`728`_) (`6212148`_)
- dataset import causes renku exception due to duplicate LocalClient
(`724`_) (`89411b0`_)
- delete new dataset ref if file add fails (`729`_) (`2dea711`_)
- fixes bug with deleted files not getting committed (`741`_)
(`5de4b6f`_)
- force current project for entities (`707`_) (`538ef07`_)
- integration tests for `681`_ (`747`_) (`b08435d`_)
- use commit author for project creator (`715`_) (`1a40ebe`_), closes
`713`_
- Zenodo dataset import error (`f1d623a`_)

Features
~~~~~~~~

- adds basic QA checklist (`698`_) (`c97e9bd`_)
- dataset tagging (`693`_) (`797161f`_)
- include creator in project metadata (`687`_) ([9c7753e](https://git

.. _0.7.0: https://github.com/SwissDataScienceCenter/renku-python/compare/v0.6.1...v
.. _701: https://github.com/SwissDataScienceCenter/renku-python/issues/701
.. _dfcc9e6: https://github.com/SwissDataScienceCenter/renku-python/commit/dfcc9e6aa1899cf89d90223f2adc2b0dd8676ef4
.. _0.6.1: https://github.com/SwissDataScienceCenter/renku-python/compare/v0.6.0...v
.. _728: https://github.com/SwissDataScienceCenter/renku-python/issues/728
.. _6212148: https://github.com/SwissDataScienceCenter/renku-python/commit/62121485119ed02a28a5b2e2990395bee284e348
.. _724: https://github.com/SwissDataScienceCenter/renku-python/issues/724
.. _89411b0: https://github.com/SwissDataScienceCenter/renku-python/commit/89411b010a2671790aafccaa42216e5ccdf5a660
.. _729: https://github.com/SwissDataScienceCenter/renku-python/issues/729
.. _2dea711: https://github.com/SwissDataScienceCenter/renku-python/commit/2dea711939a11c8c8c358bfd76499ae8865958ee
.. _741: https://github.com/SwissDataScienceCenter/renku-python/issues/741
.. _5de4b6f: https://github.com/SwissDataScienceCenter/renku-python/commit/5de4b6feaa17d4db3fbec8e65523c28cfd80ca3e
.. _707: https://github.com/SwissDataScienceCenter/renku-python/issues/707
.. _538ef07: https://github.com/SwissDataScienceCenter/renku-python/commit/538ef078b95c78d43907294147ca4fd359779b9e
.. _681: https://github.com/SwissDataScienceCenter/renku-python/issues/681
.. _747: https://github.com/SwissDataScienceCenter/renku-python/issues/747
.. _b08435d: https://github.com/SwissDataScienceCenter/renku-python/commit/b08435d26a19e69bff9a9b376526aee9ab3ecd70
.. _715: https://github.com/SwissDataScienceCenter/renku-python/issues/715
.. _1a40ebe: https://github.com/SwissDataScienceCenter/renku-python/commit/1a40ebe75ea7c49cf52a9fce5c757d7352f159b0
.. _713: https://github.com/SwissDataScienceCenter/renku-python/issues/713
.. _f1d623a: https://github.com/SwissDataScienceCenter/renku-python/commit/f1d623abf16287d62a3a0fecaf40e16d4ed5fc8b
.. _698: https://github.com/SwissDataScienceCenter/renku-python/issues/698
.. _c97e9bd: https://github.com/SwissDataScienceCenter/renku-python/commit/c97e9bdc0c65fb6b06c7467624a988bf533f0b80
.. _693: https://github.com/SwissDataScienceCenter/renku-python/issues/693
.. _797161f: https://github.com/SwissDataScienceCenter/renku-python/commit/797161fe48746137ae4c2761dfcbc7819124f154
.. _687: https://github.com/SwissDataScienceCenter/renku-python/issues/687

-------------------------------------------------------------------------------------------------------

Bug Fixes
~~~~~~~~~

- adds \_label and commit data to imported dataset files, single commit
for imports
(`651 <https://github.com/SwissDataScienceCenter/renku-python/issues/651>`__)
(`75ce369 <https://github.com/SwissDataScienceCenter/renku-python/commit/75ce369>`__)
- always add commit to dataset if possible
(`648 <https://github.com/SwissDataScienceCenter/renku-python/issues/648>`__)
(`7659bc8 <https://github.com/SwissDataScienceCenter/renku-python/commit/7659bc8>`__),
closes
`646 <https://github.com/SwissDataScienceCenter/renku-python/issues/646>`__
- cleanup needed for integration tests on py35
(`653 <https://github.com/SwissDataScienceCenter/renku-python/issues/653>`__)
(`fdd7215 <https://github.com/SwissDataScienceCenter/renku-python/commit/fdd7215>`__)
- fixed serialization of datetime to ISO format
(`629 <https://github.com/SwissDataScienceCenter/renku-python/issues/629>`__)
(`693d59d <https://github.com/SwissDataScienceCenter/renku-python/commit/693d59d>`__)
- fixes broken integration test
(`649 <https://github.com/SwissDataScienceCenter/renku-python/issues/649>`__)
(`04eba66 <https://github.com/SwissDataScienceCenter/renku-python/commit/04eba66>`__)
- hide ``image``, ``pull``, ``runner``, ``show``, ``workon`` and ``deactivate`` commands
(`672 <https://github.com/SwissDataScienceCenter/renku-python/issues/672>`__)
(`a3e9998 <https://github.com/SwissDataScienceCenter/renku-python/commit/a3e9998>`__)
- integration tests fixed
(`685 <https://github.com/SwissDataScienceCenter/renku-python/issues/685>`__)
(`f0ea8f0 <https://github.com/SwissDataScienceCenter/renku-python/commit/f0ea8f0>`__)
- migration of old datasets
(`639 <https://github.com/SwissDataScienceCenter/renku-python/issues/639>`__)
(`4d4d7d2 <https://github.com/SwissDataScienceCenter/renku-python/commit/4d4d7d2>`__)
- migration time zones
(`683 <https://github.com/SwissDataScienceCenter/renku-python/issues/683>`__)
(`58c2de4 <https://github.com/SwissDataScienceCenter/renku-python/commit/58c2de4>`__)
- Removes unnecessary call to git lfs with no paths
(`658 <https://github.com/SwissDataScienceCenter/renku-python/issues/658>`__)
(`e32d48b <https://github.com/SwissDataScienceCenter/renku-python/commit/e32d48b>`__)
- renku home directory overwrite in tests
(`657 <https://github.com/SwissDataScienceCenter/renku-python/issues/657>`__)
(`90e1c48 <https://github.com/SwissDataScienceCenter/renku-python/commit/90e1c48>`__)
- upload metadata before actual files
(`652 <https://github.com/SwissDataScienceCenter/renku-python/issues/652>`__)
(`95ed468 <https://github.com/SwissDataScienceCenter/renku-python/commit/95ed468>`__)
- use ``latest_html`` for version check
(`647 <https://github.com/SwissDataScienceCenter/renku-python/issues/647>`__)
(`c6b0309 <https://github.com/SwissDataScienceCenter/renku-python/commit/c6b0309>`__),
closes
`641 <https://github.com/SwissDataScienceCenter/renku-python/issues/641>`__
- user-related metadata
(`655 <https://github.com/SwissDataScienceCenter/renku-python/issues/655>`__)
(`44183e6 <https://github.com/SwissDataScienceCenter/renku-python/commit/44183e6>`__)
- Zenodo export failing with relative paths
(`d40967c <https://github.com/SwissDataScienceCenter/renku-python/commit/d40967c>`__)

Features
~~~~~~~~

- dataverse import
(`626 <https://github.com/SwissDataScienceCenter/renku-python/issues/626>`__)
(`9f0f9a1 <https://github.com/SwissDataScienceCenter/renku-python/commit/9f0f9a1>`__)
- enable all datasets command to operate on dirty repository
(`607 <https://github.com/SwissDataScienceCenter/renku-python/issues/607>`__)
(`74e328b <https://github.com/SwissDataScienceCenter/renku-python/commit/74e328b>`__)
- explicit input output specification
(`598 <https://github.com/SwissDataScienceCenter/renku-python/issues/598>`__)
(`ce8ba67 <https://github.com/SwissDataScienceCenter/renku-python/commit/ce8ba67>`__)
- export filename as schema:name
(`643 <https://github.com/SwissDataScienceCenter/renku-python/issues/643>`__)
(`aed54bf <https://github.com/SwissDataScienceCenter/renku-python/commit/aed54bf>`__),
closes
`640 <https://github.com/SwissDataScienceCenter/renku-python/issues/640>`__
- support for indirect inputs and outputs
(`650 <https://github.com/SwissDataScienceCenter/renku-python/issues/650>`__)
(`e960a98 <https://github.com/SwissDataScienceCenter/renku-python/commit/e960a98>`__)

-------------------------------------------------------------------------------------------------------

Bug Fixes
~~~~~~~~~

- safe_path check always operates on str
(`603 <https://github.com/SwissDataScienceCenter/renku-python/issues/603>`__)
(`7c1c34e <https://github.com/SwissDataScienceCenter/renku-python/commit/7c1c34e>`__)

Features
~~~~~~~~

- add SoftwareAgent to Activity
(`590 <https://github.com/SwissDataScienceCenter/renku-python/issues/590>`__)
(`a60c20c <https://github.com/SwissDataScienceCenter/renku-python/commit/a60c20c>`__),
closes
`508 <https://github.com/SwissDataScienceCenter/renku-python/issues/508>`__

-------------------------------------------------------------------------------------------------------

Bug Fixes
~~~~~~~~~

- ensure external storage is handled correctly
(`592 <https://github.com/SwissDataScienceCenter/renku-python/issues/592>`__)
(`7938ac4 <https://github.com/SwissDataScienceCenter/renku-python/commit/7938ac4>`__)
- only check local repo for lfs filter
(`575 <https://github.com/SwissDataScienceCenter/renku-python/issues/575>`__)
(`a64dc79 <https://github.com/SwissDataScienceCenter/renku-python/commit/a64dc79>`__)
- **cli:** allow renku run with many inputs
(`f60783e <https://github.com/SwissDataScienceCenter/renku-python/commit/f60783e>`__),
closes
`552 <https://github.com/SwissDataScienceCenter/renku-python/issues/552>`__
- added check for overwriting datasets
(`541 <https://github.com/SwissDataScienceCenter/renku-python/issues/541>`__)
(`8c697fb <https://github.com/SwissDataScienceCenter/renku-python/commit/8c697fb>`__)
- escape whitespace in notebook name
(`584 <https://github.com/SwissDataScienceCenter/renku-python/issues/584>`__)
(`0542fcc <https://github.com/SwissDataScienceCenter/renku-python/commit/0542fcc>`__)
- modify json-ld for datasets
(`534 <https://github.com/SwissDataScienceCenter/renku-python/issues/534>`__)
(`ab6a719 <https://github.com/SwissDataScienceCenter/renku-python/commit/ab6a719>`__),
closes
`525 <https://github.com/SwissDataScienceCenter/renku-python/issues/525>`__
`526 <https://github.com/SwissDataScienceCenter/renku-python/issues/526>`__
- refactored tests and docs to align with updated ``pydocstyle``
(`586 <https://github.com/SwissDataScienceCenter/renku-python/issues/586>`__)
(`6f981c8 <https://github.com/SwissDataScienceCenter/renku-python/commit/6f981c8>`__)
- **cli:** add check of missing references
(`9a373da <https://github.com/SwissDataScienceCenter/renku-python/commit/9a373da>`__)
- **cli:** fail when removing non existing dataset
(`dd728db <https://github.com/SwissDataScienceCenter/renku-python/commit/dd728db>`__)
- **status:** fix renku status output when not in root folder
(`564 <https://github.com/SwissDataScienceCenter/renku-python/issues/564>`__)
(`873270d <https://github.com/SwissDataScienceCenter/renku-python/commit/873270d>`__),
closes
`551 <https://github.com/SwissDataScienceCenter/renku-python/issues/551>`__
- added dependencies for SSL support
(`565 <https://github.com/SwissDataScienceCenter/renku-python/issues/565>`__)
(`4fa0fed <https://github.com/SwissDataScienceCenter/renku-python/commit/4fa0fed>`__)
- **datasets:** strip query string from data filenames
(`450898b <https://github.com/SwissDataScienceCenter/renku-python/commit/450898b>`__)
- fixed serialization of creators
(`550 <https://github.com/SwissDataScienceCenter/renku-python/issues/550>`__)
(`6a9173c <https://github.com/SwissDataScienceCenter/renku-python/commit/6a9173c>`__)
- updated docs
(`539 <https://github.com/SwissDataScienceCenter/renku-python/issues/539>`__)
(`ff9a67c <https://github.com/SwissDataScienceCenter/renku-python/commit/ff9a67c>`__)
- **cli:** remove dataset aliases
(`6206e62 <https://github.com/SwissDataScienceCenter/renku-python/commit/6206e62>`__)
- **cwl:** detect script as input parameter
(`e23b75a <https://github.com/SwissDataScienceCenter/renku-python/commit/e23b75a>`__),
closes
`495 <https://github.com/SwissDataScienceCenter/renku-python/issues/495>`__
- **deps:** updated dependencies
(`691644d <https://github.com/SwissDataScienceCenter/renku-python/commit/691644d>`__)


Features
~~~~~~~~

- add dataset metadata to the KG
(`558 <https://github.com/SwissDataScienceCenter/renku-python/issues/558>`__)
(`fb443d7 <https://github.com/SwissDataScienceCenter/renku-python/commit/fb443d7>`__)
- **datasets:** export dataset to Zenodo
(`529 <https://github.com/SwissDataScienceCenter/renku-python/issues/529>`__)
(`fc6fd4f <https://github.com/SwissDataScienceCenter/renku-python/commit/fc6fd4f>`__)
- added support for working on dirty repo
(`ae67be7 <https://github.com/SwissDataScienceCenter/renku-python/commit/ae67be7>`__)
- **datasets:** edit dataset metadata
(`549 <https://github.com/SwissDataScienceCenter/renku-python/issues/549>`__)
(`db39083 <https://github.com/SwissDataScienceCenter/renku-python/commit/db39083>`__)
- integrate metadata from Zenodo
(`545 <https://github.com/SwissDataScienceCenter/renku-python/issues/545>`__)
(`4273d2a <https://github.com/SwissDataScienceCenter/renku-python/commit/4273d2a>`__)
- **config:** added global config manager
(`533 <https://github.com/SwissDataScienceCenter/renku-python/issues/533>`__)
(`938f820 <https://github.com/SwissDataScienceCenter/renku-python/commit/938f820>`__)
- **datasets:** import data from Zenodo
(`509 <https://github.com/SwissDataScienceCenter/renku-python/issues/509>`__)
(`52b2769 <https://github.com/SwissDataScienceCenter/renku-python/commit/52b2769>`__)