Develop #789

Grifs · 2024-12-16T13:11:00Z

Describe your changes

Related issue(s)

Closes #xxxx

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

fix a range of issues until it compiles. This won't work though, too much stuff bypassed.

still need to tweak methods a bit but it's progress

…t, enable either decoder/encoder back again I thought either was supported in circe now, need to double check

fix platforms being able to encode fix executablerunner not using the correct encoder other small cleanup

To be solved later by either fixing the recursion that is happening or by the reflection code to call stripMargin on the fields. TBD, but the second solution could potentially cleanup some of the annotation code.

Manually written code, I bet there is a better way

Temporary way of getting the class name Not fetching the valid fields yet

Mark regex issues as unchecked to be solved later

… through the schemas super-classes

Add some minor type annotations in CollectedSchemas, which will refactoring easier because we'll now know what was previously expected

seems likely that the code can be streamlined a bit more, tbd

…rgin on all annotations Committing removal of the 'stripMargin' in the annotations in next commit

… already or not

move some memberData to part2 because gha is failing for java 17. See what this does. \o/

Both circe in general as circe-yaml need to be reverted to maximum these versions Circe made changes in 0.14.8 broke history but was supposed to be fixed in the meanwhile Circe-yaml also influences this through the set dependencies

…ithDeprecationCheck.scala

nextflow help now throws an error if it can't find Java, even for the help.

WIP upgrade to scala 3

Add `internalDependencyTargetScope` field in dependencies to track what's going on

Add Scope & ScopeEnum classes. Add .scope in config

* add `---` parameter to component help messages * Update CHANGELOG.md * fix nextflow help testbench * Add help entries for ---cpus and ---memory * Update src/main/scala/io/viash/wrapper/BashWrapper.scala Co-authored-by: Robrecht Cannoodt <[email protected]> --------- Co-authored-by: Robrecht Cannoodt <[email protected]>

* update actions * fix ci

…inite loop

…hing display help message for illegal command instead of hanging in an inf…

rcannood

LGTM! I didn't check all 146 changed files 🫣

Grifs and others added 30 commits August 8, 2024 16:43

Disable any reflection & circe calls as it was tripping over its toes

d19a0d3

fix a range of issues until it compiles. This won't work though, too much stuff bypassed.

Merge branch 'develop' into feature/scala3

76595ff

Start re-enabling circe calls with replaced encoder and decoders

f9226ab

still need to tweak methods a bit but it's progress

Start to re-enable decoders and encoders

673570b

fudge BuildStatus type to assist type matching, set max-inlines in sb…

b186934

…t, enable either decoder/encoder back again I thought either was supported in circe now, need to double check

re-enable json encoding and decoding calls that were previously disabled

1b8d8ae

Fix another handful of issues, start to fix some tests

e30ee82

Fix another bunch of issues with testbenches

c9d10b8

post release changes

0e0c620

Re-enable code & provide temporary methods as needed. Further cleanup

b008154

minor cleanup

664a782

fix temporary code still being present

dfdf294

fix platforms being able to encode fix executablerunner not using the correct encoder other small cleanup

Tweak how the encoder & decoder placeholders are formatted

ef49859

remove all stripMargins from field case class annotations

25891ca

To be solved later by either fixing the recursion that is happening or by the reflection code to call stripMargin on the fields. TBD, but the second solution could potentially cleanup some of the annotation code.

Add custom encoder & decoder for Status enum

9ed9d94

Manually written code, I bet there is a better way

Add back some validation code to assist with invalid fields

b299ac9

Temporary way of getting the class name Not fetching the valid fields yet

provide safeguard to solve empty packageconfig issues

3e9da39

Start using reflection to get class name and fields

83aaaee

Mark regex issues as unchecked to be solved later

reactivate some code

8d422d0

fix broken indentation

e39672c

treat warnings as errors

c618e01

update changelog

10866d9

function was renamed

daa4929

Start progressing to Circe to use mirroring directly instead of going…

fd79c50

… through the schemas super-classes

Add implementation of fieldsInternalFunctionality

4fde75b

Add some minor type annotations in CollectedSchemas, which will refactoring easier because we'll now know what was previously expected

add deprecation & removal annotation code

f7e2d0b

seems likely that the code can be streamlined a bit more, tbd

Refactor mirror method names

ba38803

Fix empty package configs failing as it gets parsed as false

0d98639

rename niceNameOf to typeOf and improve output of e.g. List[String]

7d84d7d

use packages.viash-hub.com for git clone

5377ef5

Grifs and others added 28 commits November 22, 2024 13:43

Tweak mirroring to output thing in the format we want, always stripMa…

3473615

…rgin on all annotations Committing removal of the 'stripMargin' in the annotations in next commit

remove .stripMargin from annotations. Regardless of being in comments…

583f144

… already or not

cleanup mirroring code

e3cdc9b

prune some stale code

b2dc774

move some memberData to part2 because gha is failing for java 17. See what this does. \o/

try splitting into 3 parts

88c8ef2

Cleanup of changed code, removing some code put in comments etc

7f4d5fe

Revert circe to slightly older packages

e7a05fb

Both circe in general as circe-yaml need to be reverted to maximum these versions Circe made changes in 0.14.8 broke history but was supposed to be fixed in the meanwhile Circe-yaml also influences this through the set dependencies

cleanup status enum circe code & switch Logger to use enums too

25d5e41

Minor code cleanup

9a4b0ba

Update src/main/scala/io/viash/helpers/circe/DeriveConfiguredDecoderW…

d1b0920

…ithDeprecationCheck.scala

Update src/main/scala/io/viash/helpers/circe/DeriveConfiguredDecoderW…

bf1c76b

…ithDeprecationCheck.scala

Install nextflow after java and other supporting languages (#780)

381b0c0

nextflow help now throws an error if it can't find Java, even for the help.

Merge remote-tracking branch 'origin/develop' into feature/scala3

b9b2a90

FEAT: asynchronous publishing for the nextflow runner. (#736)

3e33053

Add changelog entry, fixes for website output

e514e9c

Remove testbench for method that was removed

4c8cb7d

Merge pull request #759 from viash-io/feature/scala3

570b10f

WIP upgrade to scala 3

Add Scope & ScopeEnum classes. Add .scope in config

f365280

Add tests for scope handling

ef474ea

add changelog entry

7cdc262

Add scope into the target folder name

cce1752

Add `internalDependencyTargetScope` field in dependencies to track what's going on

Merge pull request #782 from viash-io/feature/scope_publishmode

e3e674b

Add Scope & ScopeEnum classes. Add .scope in config

update actions (#787)

573fbb2

* update actions * fix ci

display help message for illegal command instead of hanging in an inf…

ee632f0

…inite loop

Merge pull request #788 from viash-io/fix/configure_script_loose_matc…

a00a1d5

…hing display help message for illegal command instead of hanging in an inf…

set sbt version, finalize changelog

95a07d4

Mark conversion enabled explicitly (#790)

6fe9985

rcannood approved these changes Dec 17, 2024

View reviewed changes

Grifs merged commit ca5cef9 into main Dec 17, 2024
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Develop #789

Develop #789

Grifs commented Dec 16, 2024

rcannood left a comment

Develop #789

Develop #789

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Grifs commented Dec 16, 2024

Describe your changes

Related issue(s)

Type of Change

Checklist

Test Environment

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