Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of https://github.com/clinical-genomics/housekeeper

https://github.com/clinical-genomics/housekeeper - Release 4.13.12

Updste virtulenv (#216)

Changed

  • Updated virtul env

- Python
Published by clingen-sthlm about 1 year ago

https://github.com/clinical-genomics/housekeeper - Release 4.13.11

129 add file already in bundle directory (#215)(patch)

Changed

  • Change logic in housekeeper add file to check if the file exists in the bundle directory and skip hard linking if the given file is the one already in the bundle directory.
  • If there already is a file with the same name in the bundle directory, the command aborts and to file should be hard linked to the directory or added to housekeeper in order to not override the original file.
  • Removed function link_to_housekeeper_path as it is unused given the new logic.

- Python
Published by clingen-sthlm about 1 year ago

https://github.com/clinical-genomics/housekeeper - Release 4.13.10

feat(linters): (#213)

Changed

  • Update linbters

- Python
Published by clingen-sthlm about 1 year ago

https://github.com/clinical-genomics/housekeeper - Release 4.13.9

feat(get_files): Refactor (#212)

Changed

  • Refactor get_files

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/housekeeper - Release 4.13.8

fix(python): Syntax warning (#210)

Changed

  • Fix Python Syntax warning

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/housekeeper - Release 4.13.7

feat(python): Update (#208)

Changed

  • Updated Python to 3.12

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/housekeeper - Release 4.13.6

Update actions (#207)

Changed

  • Update Github actions

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/housekeeper - Release 4.13.5

fix(pypi): Action (#206)

Changed

  • Fix bPyPi build action

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/housekeeper - Release 4.13.4

feat(docker): Use Poetry (#205)

Changed

  • Avoid using PIP and lock container to using only Housekeeper

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/housekeeper - Release 4.13.3

fix(bump-version) (#204)

Changed

  • Fix bump version action

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/housekeeper - Release 4.13.2

feat(update): Linters (#202)

Changed

  • Update linters

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/housekeeper - Release 4.13.1

Add cryptography to dependencies (#200)(patch)

Added

  • cryptography package to requirements

- Python
Published by clingen-sthlm over 1 year ago

https://github.com/clinical-genomics/housekeeper - Release 4.13.0

Separate remote and local files (#196)(minor)

Closes https://github.com/Clinical-Genomics/housekeeper/issues/195.

Production wants a clear separation available locally on the cluster and those that only exist in an archive location on a remote server.

- Python
Published by clingen-sthlm almost 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.12.0

feat(CLI get) Improve get bundle command (#199)(minor)

Description

The CLI command housekeeper get bundle is always used with the -v flag and the output is hard to read. (see linked issue)

Changed

  • The verbose option is now always passed in housekeeper get bundle
  • Deep blue text colour changed to cyan

- Python
Published by clingen-sthlm almost 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.11.5

Update test deployment instructions (#198)(patch)

- Python
Published by clingen-sthlm almost 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.11.4

feat(sql): Rename filter attributes (#193)

Changed

  • Rename filter attributes to not include FILTER_

- Python
Published by clingen-sthlm almost 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.11.3

Refactor sql handlers (#191)

Changed

  • Refactor sql handlers

- Python
Published by clingen-sthlm about 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.11.2

feat(update): Black (#190)

Changed

  • Update black

- Python
Published by clingen-sthlm about 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.11.1

(Archiving) Filter on tags in getretrievedfiles (#189) (patch)

Added

  • Tag filtering in getretrievedfiles

- Python
Published by clingen-sthlm about 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.11.0

(Archiving) Add retrieved_at filter (#188) (minor)

Added

  • method getfilesretrieved_before

- Python
Published by clingen-sthlm about 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.10.17

(Archiving) Abort delete file command when file is archived (#186) (patch)

Changed

  • Archived files can no longer be removed via the Housekeeper CLI.

- Python
Published by clingen-sthlm about 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.10.16

(Archiving) Add cascade property to Archive (#184) (patch)

Fixed

  • Deleting a file now cascades to the archive table.

- Python
Published by clingen-sthlm about 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.10.15

feat(update): Ruff and Black (#183)

Changed

  • Update Ruff and Black

- Python
Published by clingen-sthlm about 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.10.14

feat(refactor): PEP0604 (#182)

Changed

  • Refactor to pep 0604

- Python
Published by clingen-sthlm about 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.10.13

(Archiving) Add support for limited fetching (#181) (patch)

Changed

  • Renamed getarchivedfiles and getnonarchivedfiles to getarchivedfilesforbundle and getnonarchivedfilesforbundle respectively.
  • Renamed getallnonarchivedfiles to getnonarchived_files and added the option to limit the number of files returned.

- Python
Published by clingen-sthlm about 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.10.12

Add missing dependency (#177)(patch)

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.10.11

Update templates (#176)(patch)

Update instructions for using the housekeeper containers

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.10.10

Upgrade action versions (#175)(patch)

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.10.9

Fix docker credentials in workflow (#174)(patch)

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.10.8

Add missing latest tag (#173)(patch)

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.10.7

Fix action workflows (#172)(patch)

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.10.6

Containerize and push images (#170)(patch)

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.10.5

Upgrade SQLAlchemy to 2.0 (#168)(patch)

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.10.4

Toggle future flag on engine (#166)(patch)

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.10.3

Extract database initialisation (#151)(patch)

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.10.2

Return full archive model (#165) (patch)

Fixed

  • Return full Archive models in getongoingarchivals and getongoingretrievals

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.10.1

Fix session merge warnings (#161)(patch)

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.10.0

(Archive) Get archive entries by archival/retrieval id (#164) (minor)

Added

  • Method get_archives.

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.8.21

Refactor to pep 0585 (#160)

Changed

  • Refactor to pep 0585

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.8.20

Update PULLREQUESTTEMPLATE (#162)

Changed

  • PR template to use Scg instead of Smain

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.8.19

Fix deprecated joins (#154)(patch)

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.8.18

Add Ruff to pyproject.toml (#159)

Added

  • Add Ruff to pyproject.toml

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.8.17

feat(black): Action (#158)

Added

  • Black GitHub action

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.8.16

feat(black): Update (#157)

Changed

  • Update black

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.8.15

Remove models as properties (#152)(patch)

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.8.14

Replace deprecated import (#150)(patch)

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.8.13

Upgrade Python 3.11 (#148)(patch)

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.8.12

feat(ruff): Add (#149)

Added

  • Add Ruff to pre-commit

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.8.11

Upgrade to Python 3.10 (#147)(patch)

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.8.10

Upgrade to Python 3.9 (#146)(patch)

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.8.8

Upgrade to Python 3.11

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.8.7

Update deployment instructions (#145)(patch)

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.8.6

Upgrade to Python 3.8 (#144)(patch)

Upgrade from Python 3.7 to 3.8

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.8.5

Upgrade to click 8 (#143)(patch)

Remove Click 6 lock, the actual version used will still be 6 in practice due to the lock in cg. Unlocking it here will allow for upgrading it in cg which will then mean Click 8 will be used in housekeeper as well.

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.8.4

Allow for latest sqlalchemy 1.4 version (#142)(patch)

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.8.3

refactor(moving log info to debug) (#141) (patch)

Description

Moving the LOG level from the Housekeeper store handlers to DEBUG. These messages clutter the output when functions are called repeatedly in other scripts.

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.8.2

Upgrade sqlalchemy to 1.4 (#140)(patch)

  • Update sqlalchemy requirement to <=1.4
  • Fix deprecation warnings in 1.4

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.8.1

feat(isort): Add (#139)

Added

  • Adding isort to pre-commit

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.8.0

Include bundle by default (#138) (minor)

Added

  • Flag to exclude bundle when running housekeeper add bundle.

Changed

  • By default housekeeper add bundle includes the bundle.

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.7.2

Remove pytest fixture prefix snd name arg in decorator (#137)

Changed

  • Remove pytest fixture prefix snd name arg in decorator

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.7.1

Update CODEOWNERS (#134)

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.7.0

Functionality for updating archiving/retrieval task ids (#132) (minor)

Added

  • Method updateretrievaltask_id.
  • Method updatearchivingtask_id.
  • Tests for both methods.

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.6.0

feat(archiving) Add function to fetch all unarchived files (#130) (minor)

Added

  • getbundlenamefromfile_path returns the name of the bundle associated with given file
  • getallnonarchivedfiles fetches all non-archive files with given tags

- Python
Published by clingen-sthlm over 2 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.5.0

115 - include file in housekeeper-bundles by default (#125) (minor)

Changed

  • Added files are now included by default.

- Python
Published by clingen-sthlm almost 3 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.4.0

feat(archiving) Adds functions for task interactions (#124)(minor)

Added

  • An UpdateHandler class
  • Functions to fetch unfinished tasks
  • Functions to update archiving/retrieval time stamps
  • Functions to filter archives by task ids

- Python
Published by clingen-sthlm almost 3 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.3.0

feat(Archiving) Adds functions interacting with the new Archive table (#122)(minor)

Added

  • Function to add Archive
  • Function to get archived files
  • Function to get un-archive files
  • Supporting Queries and filtes for functions above

Changed

  • Refactored filter file from just having tag functions, to also include archive

- Python
Published by clingen-sthlm almost 3 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.2.1

Remove log with database connection string (#123)(patch)

  • Remove log with database connection string

- Python
Published by clingen-sthlm almost 3 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.2.0

feat(Archiving) Add new database table (#120)(minor)

Added

  • New table archive

- Python
Published by clingen-sthlm almost 3 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.1.2

Add missing module (#121)

Fixed

  • Add init file for handlers

- Python
Published by clingen-sthlm almost 3 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.1.1

Move and rename handlers (#117)(patch)

Changed

  • Rename FindHandler to ReadHandler and find.py to handlers/read.py
  • Rename AddHandler to CreateHandler and add.py to handlers/create.py

- Python
Published by clingen-sthlm almost 3 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.1.0

Remove alchy (#112)(minor)

Changed

  • Replaced commit with session.commit
  • Replaced add_commit with session.add followed by session.commit
  • Replaced delete with session.delete
  • Replaced all alchy imports with sqlalchemy
  • The Store is now instantiated with a session, which is sent up to all the handlers.
  • Remove alchy in requirements.txt

- Python
Published by clingen-sthlm almost 3 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.0.1

Move get_query into base handler (#109)(patch)

Fixed

  • Move get_query into base handler to decrease code duplication

- Python
Published by clingen-sthlm almost 3 years ago

https://github.com/clinical-genomics/housekeeper - Release 4.0.0

Refactor file sql filters (#96)(major)

Added

The following functions were added: python - get_bundle_by_id(bundle_id: int) -> Bundle - get_bundle_by_name(bundle_name: str) -> Bundle - get_version_by_id(version_id: int) -> Version - get_version_by_date_and_bundle_name(version_date: datetime, bundle_name: str) -> Version - get_file_by_id(file_id: int) -> File - get_files(bundle_name: str = None, tag_names: List[str] = None, version_id: int = None, file_path: str = None) -> Query - get_files_not_on_disk(files: List[File]) -> List[File] - get_files_before(bundle_name: str = None, tag_names: List[str] = None, before_date: dt.datetime = None) -> List[File]

Changed

The following functions were removed: ```python - version(bundle: str = None, date: dt.datetime = None, versionid: int = None) -> Version - bundle(name: str = None, bundleid: int = None) -> Bundle - file(fileid: int) -> File - files(, bundle: str = None, tags: List[str] = None, version: int = None, path: str = None) -> Iterable[File] - files_before(, bundle: str = None, tags: List[str] = None, before: str = None) -> File - filesondisk(fileobjs: File) -> Set[File]

```

- Python
Published by clingen-sthlm almost 3 years ago

https://github.com/clinical-genomics/housekeeper - Release 3.2.7

Fix build and publish action (#104)(patch)

The deployment instructions in github actions so that the release is done to pypi when there is a new version

- Python
Published by clingen-sthlm almost 3 years ago

https://github.com/clinical-genomics/housekeeper - Release 3.2.6

Refactor tag filtering (#99)(patch)

Added

  • Filter functions for tags
  • Tests for new filter functions

Fixed

  • Punctuation in some fixtures docstrings

- Python
Published by clingen-sthlm almost 3 years ago

https://github.com/clinical-genomics/housekeeper - Release 3.2.5

Update PULLREQUESTTEMPLATE (#100)

Change housekeeper specific script in favour of the general deployment script and made more similar to cg

Co-authored-by: Henrik Stranneheim henrik.stranneheim@scilifelab.se

- Python
Published by clingen-sthlm almost 3 years ago

https://github.com/clinical-genomics/housekeeper - Release 3.2.4

Fix invalid query (#97)

- Python
Published by clingen-sthlm almost 3 years ago

https://github.com/clinical-genomics/housekeeper - Release 3.2.3

Refactor version filters (#93)

Changed

  • Refactored version filters

- Python
Published by clingen-sthlm almost 3 years ago

https://github.com/clinical-genomics/housekeeper - Release 3.2.2

Automate version bump (#95)(patch)

Add

  • Bump workflow

Change

  • Update deployment instructions

- Python
Published by clingen-sthlm almost 3 years ago