1.0.0rc0

This is the first release candidate release, and the first one having an official docker image, available at https://github.com/inab/WfExS-backend/pkgs/container/wfexs-backend .

What's Changed

• Docker and Singularity container recipes are considered mature enough.
• Added GitHub CI workflow to automatically generate a docker image on each new tag.
• Added instructions about how to used WfExS-backend in different containerized scenarios (see https://github.com/inab/WfExS-backend/blob/1.0.0rc0/WFEXS-in-CONTAINERS.md).
• Added "disclosable", "cacheable" and "clonable" flags to parameters from the stage definition. These definitions should tell the orchestrator whether the datasets associated to those input parameters contents can be transferred to generated RO-Crates or exported, whether a copy can be kept in the common cache, or whether a copy can be placed in the working directory.
• Now it is allowed to label a dataset cache entry as "clonable" or non "clonable", so it restricts the copies of its contents.
• More publications/posters for the README by @stain in #112
• Several documentation and small fixes.

Full Changelog: 1.0.0b0...1.0.0rc0

1.0.0b0

What's Changed

• Added metadata file locking mechanism at the working directory level, so it is possible to check and update metadata associated to the different stages in an ordered way.
• Added capability to execute workflows in background, reporting the different rough states of the execution: queued, running, finished or died.
• Added capability to detect workflow executions which have died.
• Added a mechanism to override the maximum step processing time declared in a Nextflow workflow. Some real life workflows (like the ones from nf-core) have in place these limits, which can kill workflow executions because it was taking too long.
• Added several core tests to check both basic bootstrapping and workflow instantiation are working.
• Added core test to check parallel workflow executions do not corrupt metadata.
• Many minor fixes.

Full Changelog: 1.0.0a2...1.0.0b0

1.0.0a2

What's Changed

• Major internal changes in order to switch from bare path handling using os.path to pathlib.Path. Fetcher interfaces now support either bare path handling or os.PathLike instances.
• Major internal changes in order to simplify the parameters being passed to workflow engines and container factories.
• Both representation of nextflow profiles and "content with metadata" inputs have been properly integrated into generation and consumption of Workflow Run RO-Crates.
• Fixed several metadata corruption corner case, which were leading to lose the stage state and overwriting previous execution states.
• Working directories should now be relocatable now, in the sense that embedded paths in their status metadata are now represented as relative routes.
• Avoided issue in cwltool which arises when WfExS CWL engine tries generating the graphical representation of the workflow, just forcing pydot 2.0 in newly created cwltool virtual environments.
• Added more robust support for cwltool versions, searching for the nearest compatible one to the requested one (newer versions of cwltool do not support python 3.7).
• Added the capability to use custom python interpreters for cwltool, so WfExS CWL engine can use a different one for cwltool from the used for WfExS core.
• Added initial docker and singularity recipes to build a container of WfExS-backend, along with all its dependencies (and embedded copies of docker, apptainer, gocryptfs and encfs clients).
• Many other improvements and fixes.

Full Changelog: 1.0.0a0...1.0.0a2

1.0.0a0

What's Changed

Full Changelog: 0.99.0...1.0.0a0

v0.99.0

What's Changed

• Reimplemented the export APIs and flow, and added deposition capabilities to sites like Zenodo, B2SHARE, Dataverse, etc...
• Added test battery for all the implemented export plugins.
• Both fetch and export plugins are now discovered, which opens the door to install them separately from WfExS as a side dependency.
• Lots of fixes.
• Version bump to v0.99.0.

Full Changelog: 0.10.1...0.99.0

0.10.1

The main milestones achieved are the generation of compliant Workflow Run RO-Crates, and the rework of how containers are materialized and cached on stage and presented on execution.

There have been also lots of fixes for different corner cases.

Full Changelog: 0.9.3...0.10.1

Almost there...

This release has support for complex workflows as well as the generation of RO-Crate metadata containing provenance (either prospective or retrospective)

Changed indirect set of dependencies pulled by jsonschema

Removed indirect GPLv3+ dependency which was fetched as an optional jsonschema dependency.

Also, updated the version tag and copyright year in headers.

Reimplemented dependency on nextcloud export feature

Due project license collisions on nextcloud-api-wrapper library used by nextcloud export pusher (WfExS-backend is Apache 2.0, nextcloud-api-wrapper is GPLv3+), that export pusher has been reimplemented around pyncclient-ext (MIT license), written by @jmfernandez to provide a subclass of pyncclient (MIT license) with the needed features.

Properly updated CITATION.cff version

Previous release did not have properly synchronized CITATION.cff with the repo itself. So, at the code level there is no change.