Changes

0.11.1 (2020-08-18)

Bug Fixes

• fixes shacl for DatasetFile when used inside a qualifiedGeneration (#1477) (99dd4a4)

0.11.0 (2020-08-14)

Bug Fixes

• cli: disable version check in githook calls (#1300) (5132db3)

• core: fix paths in migration of workflows (#1371) (8c3d34b)

• core: Fixes SoftwareAgent person context (#1323) (a207a7f)

• 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)

• tests: integration tests (#1351) (3974a39)

Features

• cli: Adds renku save command (#1273) (4ddc1c2)

• cli: prompt for missing variables (1e1d408), closes #1126

• cli: Show detailed commands for renku log output (#1345) (19fb819)

• core: Calamus integration (#1281) (bda538f)

• core: configurable data dir (#1347) (e388773)

• core: disabling of inputs/outputs auto-detection (#1406) (3245ca0)

• core: migration check in core (#1320) (4bc52f4)

• core: Move workflow serialisation over to calamus (#1386) (f0fbc49)

• core: save and load workflow as jsonld (#1185) (d403289)

• core: separate models for migrations (#1431) (127d606)

• dataset: source and url for DatasetFile (#1451) (b4fa5db)

• 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)

• decode base64 headers (#1407) (9901cc3)

• service: adds endpoints for dataset remove (#1383) (289e4b9)

• service: adds endpoints for unlinking files from a dataset (#1314) (1b78b16)

• service: async migrations execution (#1344) (ff66953)

• service: create new projects from templates (#1287) (552f85c), closes #862

0.10.5 (2020-07-16)

Bug Fixes

• core: Pin dependencies to prevent downstream dependency updates from breaking renku. Fix pyshacl dependency. (#785) (30beedd)

• core: Fixes SoftwareAgent person context. (#1323) (fa62f58)

0.10.4 (2020-05-18)

Bug Fixes

• dataset: update default behaviour and messaging on dataset unlink (#1275) (98d6728)

• dataset: correct url in different domain (#1211) (49e8b8b)

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: Adds renku storage clean command (#1235) (7029400)

• 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)

• service: protected branches support (#1222) (8405ce5)

• dataset: doi variations for import (#1216) (0f329dd)

• dataset: keywords in metadata (#1209) (f98a800)

• dataset: no failure when adding ignored files (#1213) (b1e275f)

• service: read template manifest (#1254) (7eac85b)

0.10.3 (2020-04-22)

Bug Fixes

• dataset: avoid recursive addition of data directory (#1163) (79e3b03)

• dataset: commit after unlinking files (#1120) (97e8754)

• dataset: Dataverse export (#1028) (737cecf)

Features

• core: CLI warning when in non-root directory (#1162) (115e462)

• dataset: migrate submodule-based datasets (#1092) (dba20c4)

• dataset: no failure when adding existing files (#1177) (a68dcb7)

• dataset: remove –link flag (#1164) (969d4f8)

• dataset: show file size in ls-files (#1123) (0951930)

• datasets: specify title on dataset creation (#1204) (fb70ac5)

• init: read and display template variables (#1134) (0f86dc5), closes #1126

• service: add remote files to dataset (#1139) (f6bebfe)

0.10.1 (2020-03-31)

Bug Fixes

• core: directory input regression (#1155) (b17c843)

• dataset: correct url when importing with DOI (#1156) (025b735)

Features

• renku init options refactor (#1127) (78b208b)

• datasets: add files from dropbox (#1135) (bf5f2db)

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

• cli: consistenly show correct contexts (#1096) (b333f0f)

• dataset: –no-external-storage flag not working (#1130) (c183e97)

• dataset: commit only updated dataset files (#1116) (d9739df)

• datasets: fixed importing large amount of small files (#1119) (8d61473)

• datasets: raises correct error message on import of protected dataset (#1112) (e579904)

Features

• core: new migration mechanism (#1003) (1cc33d4)

• dataset: adding external data without copying (#974) (6a17512)

• dataset: bypass import confirmation (#1124) (947210a)

• dataset: import renku datasets (#838) (6aa3651)

• dataset: metadata edit (#1111) (66cfbbc)

• dataset: wildcard support when adding data from git (#1128) (baa1c9f)

0.9.1 (2020-02-24)

Bug Fixes

• added test utility functions and cleanup (#1014) (f41100d)

• cache instance cleanup (#1051) (12f5446)

• enable dataset cmd in sub directories (#1012) (e3191e1)

• fields with default need to come last (#1046) (649b159)

• fixes renku show sibling handling with no paths (#1026) (8df678f)

• flush old keys for user projects and files (#1002) (7438c73)

• generate https IDs for entities instead of file:// (#1009) (87f7750)

• handle errors correctly (#1040) (950eeac)

• improved list datasets and files (#1034) (fd96d68)

• pin idna to 2.8 (#1020) (19ea7af)

• resync repo after import action (#1052) (b38341b)

• standardize test assertions (#1016) (16e8e63)

• temporarily disable integration tests (#1036) (8c8fd7a)

• updated readme to include local testing (#1000) (351a650)

• run tests via pipenv run commands (#999) (d8095e3)

Features

• svc: adds job details endpoint (#1050) (9c58a08)

• svc: added list user jobs endpoint (#1001) (f3c200c)

• svc: dataset import via service (#1023) (d6c670a)

0.9.0 (2020-02-07)

Bug Fixes

• adds git user check before running renku init (#892) (2e52dff)

• adds sorting to file listing (#960) (bcf6bcd)

• avoid empty commits when adding files (#842) (8533a7a)

• Fixes dataset naming (#898) (418deb3)

• Deletes temporary branch after renku init –force (#887) (eac0463)

• enforces label on SoftwareAgent (#869) (71badda)

• Fixes JSON-LD translation and related issues (#846) (65e5469)

• Fixes renku run error message handling (#961) (81d31ff)

• Fixes renku update workflow failure handling and renku status error handling (#888) (3879124)

• Fixes sameAs property to follow schema.org spec (#944) (291380e)

• handle missing renku directory (#989) (f938be9)

• resolves symlinks when pulling LFS (#981) (68bd8f5)

• serializes all zenodo metadata (#941) (787978a)

• Fixes various bugs in dataset import (#882) (be28bf5)

Features

• add project initialization from template (#809) (4405744)

• added renku service with cache and datasets (#788) (7a7068d), closes #767 #846

• Adds protection for renku relevant paths in dataset add (#939) (a3c02e8)

• Adds prov:Invalidated output to renku log (008ab20)

• better UX when adding to a dataset (#911) (c6ac967)

• check for required git hooks (#854) (54ba91d)

• Dataverse export (#909) (7e9e647)

• improve dataset command output (#927) (c7639d3)

• metadata on dataset creation (#850) (b357ee7)

• Plugin support for renku-run (#883) (7dbda83)

• python 3.8 compatibility (#861) (4aaac8d)

• SHACL Validation (#767) (255a01d)

• update bug_report template to be more renku-relevant (#988) (e00ded7)

0.8.0 (2019-11-21)

Bug Fixes

• addressed CI problems with git submodules (#783) (0d3eeb7)

• adds simple check on empty filename (#786) (8cd061b)

• ensure all Person instances have valid ids (4f80efc), closes #812

• Fixes jsonld issue when importing from dataverse (#759) (ffe36c6)

• fixes nested type scoped handling if a class only has a single class (#804) (16d03b6)

• ignore deleted paths in generated entities (86fedaf), closes #806

• integration tests (#831) (a4ad7f9)

• make Creator a subclass of Person (ac9bac3), closes #793

• Redesign scoped context in jsonld (#750) (2b1948d)

Features

• avoid creation of nested datasets (#796) (6084c87)

• do not create dataset implicitly (#779) (84e59d0)

• local git repo not treated as remote (8cc2834)

• renku clone command (#828) (4b3b615)

0.7.0 (2019-10-15)

Bug Fixes

• use UI-resolved project path as project ID (#701) (dfcc9e6)

0.6.1 (2019-10-10)

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

0.6.0 (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)

• fixes broken integration test (#649) (04eba66)

• hide image, pull, runner, show, workon and deactivate commands (#672) (a3e9998)

• integration tests fixed (#685) (f0ea8f0)

• migration of old datasets (#639) (4d4d7d2)

• migration timezones (#683) (58c2de4)

• Removes unneccesary call to git lfs with no paths (#658) (e32d48b)

• renku home directory overwrite in tests (#657) (90e1c48)

• upload metadata before actual files (#652) (95ed468)

• use latest_html for version check (#647) (c6b0309), closes #641

• user-related metadata (#655) (44183e6)

• zenodo export failing with relative paths (d40967c)

Features

• dataverse import (#626) (9f0f9a1)

• enable all datasets command to operate on dirty repository (#607) (74e328b)

• explicit input output specification (#598) (ce8ba67)

• export filename as schema:name (#643) (aed54bf), closes #640

• support for indirect inputs and outputs (#650) (e960a98)

0.5.2 (2019-07-26)

Bug Fixes

• safe_path check always operates on str (#603) (7c1c34e)

Features

• add SoftwareAgent to Activity (#590) (a60c20c), closes #508

0.5.1 (2019-07-12)

Bug Fixes

• ensure external storage is handled correctly (#592) (7938ac4)

• only check local repo for lfs filter (#575) (a64dc79)

• cli: allow renku run with many inputs (f60783e), closes #552

• added check for overwriting datasets (#541) (8c697fb)

• escape whitespaces in notebook name (#584) (0542fcc)

• 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

• added dependencies for SSL support (#565) (4fa0fed)

• datasets: strip query string from data filenames (450898b)

• fixed serialization of creators (#550) (6a9173c)

• updated docs (#539) (ff9a67c)

• cli: remove dataset aliases (6206e62)

• cwl: detect script as input parameter (e23b75a), closes #495

• deps: updated dependencies (691644d)

Features

• add dataset metadata to the KG (#558) (fb443d7)

• datasets: export dataset to zenodo (#529) (fc6fd4f)

• added support for working on dirty repo (ae67be7)

• datasets: edit dataset metadata (#549) (db39083)

• integrate metadata from zenodo (#545) (4273d2a)

• config: added global config manager (#533) (938f820)

• datasets: import data from zenodo (#509) (52b2769)

0.5.0 (2019-03-28)

Bug Fixes

• api: make methods lock free (1f63964), closes #486

• use safe_load for parsing yaml (5383d1e), closes #464

• datasets: link flag on dataset add (eae30f4)

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.