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Develop#769

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Grifs merged 165 commits intomainviash-io/viash:mainfrom developviash-io/viash:developCopy head branch name to clipboardSep 3, 2024

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Commits on Oct 11, 2023

• Bump version to 0.9.0dev and add changelog placeholder

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• Split platforms to runners & engines (#510)

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Commits on Oct 12, 2023

• fix race condition issue in runEach (#562)

  

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Commits on Oct 13, 2023

• Feature/strict json schema (#564)

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• Feature/local dependency test2 (#565)

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• Change minor references to platforms and one grammatical mistake (#568)

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• Handle exception when __merge__ uses an invalid yaml (#570)

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• Feature/replayable multi output stream (#571)

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• Fix github uri -> repo, add local repository and local dependency exa… (#569)

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Commits on Oct 20, 2023

• Add another minimal test for export json_schema --strict and --minimal

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• Fixes to VDSL3 code (#566)

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• Extend VDSL3 test benches (#572)

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Commits on Oct 23, 2023

• Add test for nested VDSL3 workflows (#576)

  

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• Merge branch 'develop_0_8' into develop

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• Fix typo spotted by Kai

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• Merge pull request #575 from viash-io/feature/test_json_strict_minimal

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• Merge pull request #578 from viash-io/fix/docs_minor_typo

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• Merge branch 'develop_0_8' into develop

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Commits on Oct 30, 2023

• Fix config decoding not being enforcing strict mode

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• add PR#

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Commits on Nov 20, 2023

• Fix using .run() without fromState defined an an input channel of tuples with more than two elements. (#587)

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• update changelog

  

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Commits on Dec 11, 2023

• Merge branch 'develop' into fix/non_strict_config

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• Merge pull request #585 from viash-io/fix/non_strict_config

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Commits on Dec 12, 2023

• Merge arguments into argument_groups in preparse step (#574)

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• Feature/bump scala java versions (#602)

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• Merge remote-tracking branch 'origin/develop_0_8' into develop

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Commits on Dec 13, 2023

• Merge remote-tracking branch 'origin/develop_0_8' into develop

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• Define some extra fields in Viash Project Config and add it to a component info field

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Commits on Dec 14, 2023

• Move project_config directly in the config instead of the info field

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Commits on Jan 8, 2024

• Merge branch 'develop_0_8' into develop

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Commits on Jan 15, 2024

• Merge remote-tracking branch 'origin/develop_0_8' into develop

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• Merge branch 'develop_0_8' into develop

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• Add extra fields, no supporting logic yet

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Commits on Jan 17, 2024

• Add fields in the component config and set some values from the project config

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• Anonymize configs before outputting them, either to console or file

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• Add changelog entry

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• Add helper method to anonymize paths and add tests

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• If the path can't be relativized, go for the drastic solution to fully anonymize the path except for the last path section

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Commits on Jan 18, 2024

• Fix anyOf that should be oneOf

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• Merge pull request #626 from viash-io/fix/oneOf_in_json_schema

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Commits on Jan 22, 2024

• Only set component license and organization if it was unset

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• Reduce & simplify lens code

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• Fix config mods AND project config repositories together throwing exceptions

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Commits on Jan 23, 2024

• Add the reference case class as described/requested in the PR

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• improve the documentation for references and links

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• Add a changelog entry

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• Rename ViashProject to ProjectConfig

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Commits on Jan 24, 2024

• Add testbench to verify copying project config values to component config

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• Add test to check project config repositories are copied to .functionality.repositories

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• Move keywords, license and organization under functionality

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• Merge pull request #612 from viash-io/feature/expand_project_config

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• Merge remote-tracking branch 'origin/develop' into anonymize_config_output

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• fix testbenches and further improve the path anonymization logic

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Commits on Jan 25, 2024

• Tweak the ProjectConfig examples and add them to the schema output

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Commits on Jan 26, 2024

• Fix testbench refactor that removed the intended functionality

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• Merge pull request #625 from viash-io/anonymize_config_output

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• Don't override ProjectConfig as Project in schema exports

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• Add changelog entry

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• Merge pull request #631 from viash-io/fix/schema_project_config_name

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• prepare for RC

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• Merge remote-tracking branch 'origin/main' into develop

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Commits on Jan 30, 2024

• Merge remote-tracking branch 'origin/main' into develop

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• Add dash in 0.9.0-RC1

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• post release-candidate changes

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Commits on Feb 7, 2024

• Merge remote-tracking branch 'origin/develop_0_8' into develop

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Commits on Feb 9, 2024

• Fix/schema issues (#636)

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Commits on Feb 12, 2024

• fix argument group warning

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• Merge pull request #646 from viash-io/fix/warning

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• Require the PlainFile resource type to specify it's a 'file' in the strict variant

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• Use native engine when the test will run in docker (#641)

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• Change multiple_sep from : to ; (#645)

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• Rework removing functionality

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• Start fixing testbenches

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• move arguments -> argument_groups code, fix more testbenches

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Commits on Feb 13, 2024

• add json translation for functionality -> config, fix more tests

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• Fix json schema and add changelog entry

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• Reduce namespace test header duplicated definitions of columns and format

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• update documentation of config mods

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Commits on Feb 14, 2024

• Merge pull request #647 from viash-io/fix/make_strict_schema_slightly_stricter

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• Add name field for ns exec and meta_name in BashWrapper

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• Add testbench to test a config with a deprecated Functionality

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Commits on Feb 21, 2024

• Apply suggestions from code review

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• Additional changes wrt code review

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• Merge branch 'develop_0_8' into develop

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• Merge branch 'develop' into feature/remove_functionality_level

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• Merge pull request #649 from viash-io/feature/remove_functionality_level

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Commits on Feb 22, 2024

• Improve changelog for displaying on the website

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Commits on Feb 23, 2024

• pre RC release changes

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• fix make tools command

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• post release changes

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Commits on Mar 21, 2024

• Merge develop_0_8 into develop

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• When an error is found try to improve the error returned to the user (#662)

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Commits on Mar 29, 2024

• Json schema issues (#666)

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Commits on Apr 2, 2024

• Fix changelog where RC-2 and new entries are getting mixed up

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• Improve the circe warning for deprecated & removed fields (#671)

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• Fix/resolved paths in config view (#668)

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Commits on Apr 3, 2024

• Fix/improve config mod exceptions (#672)

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Commits on Apr 5, 2024

• Merge branch 'develop_0_8' into develop

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• Add a message to the assertion for single quotes in requirements.script

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• Merge branch 'develop_0_8' into develop

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Commits on Apr 9, 2024

• Update CHANGELOG.md

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Commits on Apr 17, 2024

• Merge pull request #675 from viash-io/fix/improve_single_quote_assertion

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• Fix docker_id variation when using custom docker registry (#679)

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Commits on Apr 18, 2024

• Merge branch 'develop_0_8' into develop

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Commits on Apr 22, 2024

• Merge branch 'develop_0_8' into develop

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Commits on Apr 23, 2024

• Merge branch 'develop_0_8' into develop

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Commits on Apr 24, 2024

• Feature/si memory units (#686)

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• Capture stderr to catch the ns_power deprecation warning (#688)

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• Merge branch 'develop_0_8' into develop

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Commits on Apr 26, 2024

• Fix querying on empty runners & engines (#691)

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• Prepare build.sbt and changelog.md for release candidate release

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• post release changes

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• post release changes

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Commits on May 2, 2024

• Fix error handling of non-generic errors in the build process or while pushing docker containers

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• fill in PR#

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Commits on May 7, 2024

• Merge pull request #696 from viash-io/fix/generalize_build_errors

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• fix the dependency.name example (#697)

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Commits on May 8, 2024

• Feature/dependency repo caching (#699)

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Commits on May 14, 2024

• fix dependencies of dependencies resolving failing (#701)

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Commits on May 28, 2024

• Allow symlinks when finding files (#704)

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Commits on May 29, 2024

• Fix/dependency repositories with name (#703)

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• Fix changelog entry

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• Add resources_test field in the package config that can be picked u… (#709)

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• Prepare for RC release

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• post release changes

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Commits on Jun 4, 2024

• Remove resources_test again (#711)

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Commits on Jun 13, 2024

• Add a testbench for dependencies of dependencies (#721)

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• make vsh the default organization for vsh repositories (#718)

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• Fix/nextflow executable build info (#720)

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• Merge branch 'develop_0_8' into develop

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• Add package name in the docker image name (#712)

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• Release Viash 0.9.0-RC5

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• post release changes

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Commits on Jun 15, 2024

• Fix docker_engine (#722)

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Commits on Jun 17, 2024

• Release Viash 0.9.0-RC6

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Commits on Jun 18, 2024

• post release changes

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Commits on Jun 19, 2024

• provide backwards compatibility for --platform and --apply_platform (#725)

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Commits on Jun 20, 2024

• add the previous workflower to gitignore as well

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Commits on Jun 26, 2024

• Nextflow runner: fix file ownership of output files. (#727)

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• Refactor ns exec tests and add extra tests (#724)

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Commits on Jul 1, 2024

• Revert "Nextflow runner: fix file ownership of output files." (#732)

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Commits on Jul 10, 2024

• Fix/ns exec relative paths (#737)

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• Update/improve documentation (#730)

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• Add label & summary fields for Config, PackageConfig, argument groups… (#743)

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• fix findstates (#733)

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Commits on Jul 11, 2024

• Allow ns query with a config trailing argument to filter which compon… (#744)

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• Add ---docker_image_id flag to view the Docker image id (#741)

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Commits on Jul 16, 2024

• Make docker runargs configurable (#740)

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Commits on Jul 17, 2024

• update viash dockerfile (#748)

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Commits on Aug 8, 2024

• Add .config.arguments in the non-strict json schema (#755)

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Commits on Aug 9, 2024

• Make viash automount prefix configurable (#739)

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• remove debug statements (#760)

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• Always use local variables when storing the options to prevent overri… (#754)

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• apply changes needed for Scala 3 (#757)

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Commits on Aug 13, 2024

• Add runIf to runEach (#660)

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• Fix/multiple failing components (#761)

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• Release Viash 0.9.0-RC7

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• post release changes

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Commits on Aug 14, 2024

• update scala to 2.13.14 (#764)

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Commits on Aug 16, 2024

• escaping parameters in nextflow wrapper (#756)

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Commits on Aug 26, 2024

• Copy package_config in the testing config (#767)

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• Fix json schema repositories with name adding the withname in the type (#768)

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Commits on Sep 3, 2024

• Prepare for release

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• Strip changelog entries for unreleased 0.8.7 from the changelog

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