Skip to content

Port Nextflow fix, Bump Viash version, Remove deprecated functionality#832

Merged
rcannood merged 28 commits into
developfrom
port_integers_as_doubles
Jun 12, 2025
Merged

Port Nextflow fix, Bump Viash version, Remove deprecated functionality#832
rcannood merged 28 commits into
developfrom
port_integers_as_doubles

Conversation

@rcannood
Copy link
Copy Markdown
Contributor

@rcannood rcannood commented Jun 11, 2025 •
edited
Loading

Describe your changes

Make sure to squash this PR 😬

Changes:

  • Port Nextflow fix
  • Bump Viash version to 0.10.x
  • Remove deprecated functionality: .functionality, .platforms, .runner[.type == "docker"].image, .registry, .tag
  • Remove deprecated Nextflow helper functions: channelFromParams

Related issue(s)

Closes #828

Type of Change

  • Breaking change (fix or feature that would cause existing functionality to not work as expected)
  • New functionality (non-breaking change which adds functionality)
  • Major change (non-breaking change which modifies existing functionality)
  • Minor change (non-breaking change which does not modify existing functionality)
  • Bug fix (non-breaking change which fixes an issue)
  • This change requires a documentation update

Checklist

Requirements:

  • I have read the CONTRIBUTING doc.
  • I have performed a self-review of my code by checking the "Changed Files" tab.
  • My code follows the code style of this project.

Tests:

  • I have added tests that prove my fix is effective or that my feature works.
  • New and existing unit tests pass locally with my changes.

Documentation:

  • Proposed changes are described in the CHANGELOG.md.
  • I have updated the documentation accordingly.

Test Environment

hcannoodt and others added 24 commits February 21, 2024 13:52
@hcannoodt
Merge pull request #653 from viash-io/develop_0_8
703d1c8 
Release 0.8.5
@rcannood @danielskatz
Fix author names in paper (#644)
dbb0876 
* add paper

* update paper

* add more orcids

* move figures

* rename pipeline to workflow

* add section on benefits

* rewrite state of the field

* solve issue with figure 3

* update bibtex

* update bibtex again

* broaden domain

* update figure 2 based on @wilkinson's feedback

* minor changes in paper (#628)

* minor change

* fix refactoring error

* Add JOSS release info

* update readme

* Fix author names

---------

Co-authored-by: Daniel S. Katz <d.katz@ieee.org>
@hcannoodt
Merge pull request #692 from viash-io/develop_0_8
4d7479f 
Develop 0 8
@hcannoodt
Merge pull request #769 from viash-io/develop
259ab85 
Develop
@hcannoodt
Merge pull request #789 from viash-io/develop
ca5cef9 
Develop
@hcannoodt
Merge pull request #804 from viash-io/develop_0_9
3866fc9 
Develop 0 9
@rcannood
use reflection to get viash to fix issue in nextflow edge (#812)
cdcc658 
* use reflection to get viash to fix issue in nextflow edge

* add entry to changelog
@rcannood
Backport: Make sure scripts in Nextflow have the right extension (#815)
73ea72f 
* Backport: Make sure scripts in Nextflow have the right extension

* fix changelog

* Edit -- I'm going to port it in the different direction
@rcannood
Pass session as an argument (#818)
d93f984 
* pass session as an argument

* fix import
@hcannoodt
Prepare for release
05f8a47
@hcannoodt
Merge pull request #820 from viash-io/develop_0_9
74bc58e 
Develop 0 9
@hcannoodt
post release changes, update release guide
0f80126
@hcannoodt
Add entry for 0.8.7
d135e6a
@rcannood
port of #823
f9d4c94
@rcannood
add pr number
2e76d68
@hcannoodt
copied 0.8.8 changelog entry
527f903
@rcannood
update version and changelog
fa0a0ae
@hcannoodt
Update CHANGELOG.md
a6404d3
@hcannoodt
Update CHANGELOG.md
8d9391f
@hcannoodt
Merge pull request #824 from viash-io/port_automatically_convert_inte…
ca751a6 
…gers

`NextflowRunner`: Automatically convert integers to doubles when argument type is `double`
@hcannoodt
Merge branch 'main' into develop_0_9
5271a3b
@hcannoodt
post release changes
90ea37b
@rcannood
cherry pick 5271a3b
baa804e
@rcannood
Merge remote-tracking branch 'origin/develop_0_9' into port_integers_…
f5f0406 
…as_doubles
@rcannood rcannood requested a review from hcannoodt June 11, 2025 15:20
rcannood and others added 2 commits June 11, 2025 20:22
@rcannood
fix test
eb607d9
Remove deprecated things (#833)
60400a6 
* wip deprecate things

* fix components

* fix test

* update tests and yamls

* fix test (recent versions of git require a message)

* remove test code for removed functionality
@rcannood rcannood changed the title Merge 0.9 develop Port Nextflow fix, Bump Viash version, Remove deprecated functionality Jun 11, 2025
hcannoodt
hcannoodt approved these changes Jun 11, 2025
View reviewed changes
Copy link
Copy Markdown
Collaborator

@hcannoodt hcannoodt left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM

rcannood
rcannood commented Jun 11, 2025
View reviewed changes
Comment thread CHANGELOG.md Outdated
@rcannood rcannood merged commit fe0e266 into develop Jun 12, 2025
7 checks passed
@rcannood rcannood deleted the port_integers_as_doubles branch June 12, 2025 13:19
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@hcannoodt hcannoodt hcannoodt approved these changes

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

2 participants

@rcannood @hcannoodt