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Merge branch 'main' into renovate/jackson-monorepo
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drernie authored Dec 6, 2024
2 parents 7ebb29b + 03e00f3 commit 77d6631
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6 changes: 3 additions & 3 deletions .github/workflows/mega-linter.yml
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ env: # Comment env block if you do not want to apply fixes
#APPLY_FIXES_MODE: pull_request # If APPLY_FIXES is used, defines if the fixes are directly committed (commit) or posted in a PR (pull_request)
DISABLE_LINTERS: SPELL_CSPELL,COPYPASTE_JSCPD,REPOSITORY_GITLEAKS,GROOVY_NPM_GROOVY_LINT
FILTER_REGEX_EXCLUDE: .*/.*gradle

concurrency:
group: ${{ github.ref }}-${{ github.workflow }}
cancel-in-progress: true
Expand All @@ -31,15 +31,15 @@ jobs:
- name: Checkout Code
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
with:
token: ${{ secrets.GITHUB_TOKEN }} # secrets.PAT ||
token: ${{ secrets.GITHUB_TOKEN }} # secrets.PAT ||
fetch-depth: 0 # If you use VALIDATE_ALL_CODEBASE = true, you can remove this line to improve performances

# MegaLinter
- name: MegaLinter
id: ml
# You can override MegaLinter flavor used to have faster performances
# More info at https://megalinter.github.io/flavors/
uses: oxsecurity/megalinter/flavors/dotnet@v8.1.0
uses: oxsecurity/megalinter/flavors/dotnet@v8.3.0
env:
# All available variables are described in documentation
# https://megalinter.github.io/configuration/
Expand Down
79 changes: 39 additions & 40 deletions .github/workflows/test.yml
Original file line number Diff line number Diff line change
Expand Up @@ -25,49 +25,48 @@ jobs:
runs-on: ${{ matrix.os }}

steps:
# Git Checkout
- name: Checkout Code
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
with:
token: ${{ secrets.GITHUB_TOKEN }}
fetch-depth: 0
# Git Checkout
- name: Checkout Code
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
with:
token: ${{ secrets.GITHUB_TOKEN }}
fetch-depth: 0

- name: Configure AWS Credentials
uses: aws-actions/configure-aws-credentials@v4
with:
role-to-assume: arn:aws:iam::712023778557:role/github/GitHub-Testing-NF-Quilt
aws-region: us-east-1
- name: Configure AWS Credentials
uses: aws-actions/configure-aws-credentials@v4
with:
role-to-assume: arn:aws:iam::712023778557:role/github/GitHub-Testing-NF-Quilt
aws-region: us-east-1

- name: Setup Java ${{matrix.java_version}}
uses: actions/setup-java@v4
with:
java-version: ${{matrix.java_version}}
distribution: 'temurin'
architecture: x64
cache: gradle

- name: Setup Gradle
uses: gradle/actions/setup-gradle@v4
- name: Setup Java ${{matrix.java_version}}
uses: actions/setup-java@v4
with:
java-version: ${{matrix.java_version}}
distribution: "temurin"
architecture: x64
cache: gradle

- name: Run Gradle Tests
run: make test
env:
LOG4J_DEBUG: true
- name: Setup Gradle
uses: gradle/actions/setup-gradle@v4

- name: Archive production artifacts (Windows only)
uses: actions/upload-artifact@v4
if: ${{ always() && matrix.os == 'windows-latest' }}
with:
name: nf-quilt-test-reports-${{ matrix.os }}-${{ matrix.java_version }}
path: |
- name: Run Gradle Tests
run: make test
env:
LOG4J_DEBUG: true

- name: Archive production artifacts (Windows only)
uses: actions/upload-artifact@v4
if: ${{ always() && matrix.os == 'windows-latest' }}
with:
name: nf-quilt-test-reports-${{ matrix.os }}-${{ matrix.java_version }}
path: |
D:\a\nf-quilt\nf-quilt\plugins\nf-quilt\build\reports\
overwrite: true
- name: Archive production artifacts (Linux and MacOS)
uses: actions/upload-artifact@v4
if: ${{ always() && matrix.os != 'windows-latest' }}
with:
name: nf-quilt-test-reports-${{ matrix.os }}-${{ matrix.java_version }}
path: |
overwrite: true
- name: Archive production artifacts (Linux and MacOS)
uses: actions/upload-artifact@v4
if: ${{ always() && matrix.os != 'windows-latest' }}
with:
name: nf-quilt-test-reports-${{ matrix.os }}-${{ matrix.java_version }}
path: |
${{ github.workspace }}/plugins/nf-quilt/build/reports/
overwrite: true

overwrite: true
3 changes: 3 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,8 @@ work
out
results
bin
/bin/
plugins/nf-quilt/bin

# Ignore Gradle GUI config
gradle-app.setting
Expand All @@ -32,3 +34,4 @@ params.yaml
null
# quilt+*
# nextflow
.aider*
180 changes: 90 additions & 90 deletions .groovylintrc.json
Original file line number Diff line number Diff line change
@@ -1,92 +1,92 @@
{
"extends": "recommended",
"rules": {
"CatchException": {
"enabled": false
},
"CatchThrowable": {
"enabled": false
},
"ClassJavadoc": {
"enabled": false
},
"ClosureAsLastMethodParameter": {
"enabled": false
},
"DuplicateNumberLiteral": {
"enabled": false
},
"DuplicateStringLiteral": {
"enabled": false
},
"FieldTypeRequired": {
"enabled": false
},
"ImplicitClosureParameter": {
"enabled": false
},
"JUnitPublicNonTestMethod": {
"enabled": false
},
"JUnitTestMethodWithoutAssert": {
"enabled": false
},
"JavaIoPackageAccess": {
"enabled": false
},
"JavadocEmptyFirstLine": {
"enabled": false
},
"JavadocEmptyReturnTag": {
"enabled": false
},
"JavadocMissingParamDescription": {
"enabled": false
},
"JavadocMissingThrowsDescription": {
"enabled": false
},
"MethodCount": {
"enabled": false
},
"MethodParameterTypeRequired": {
"enabled": false
},
"MethodSize": {
"enabled": false
},
"NoDef": {
"enabled": false
},
"PrintStackTrace": {
"enabled": false
},
"PropertyName": {
"enabled": false
},
"SpaceAroundMapEntryColon": {
"enabled": false
},
"SpaceAroundOperator": {
"enabled": false
},
"SystemExit": {
"enabled": false
},
"UnnecessaryGetter": {
"enabled": false
},
"UnnecessaryObjectReferences": {
"enabled": false
},
"UnnecessarySetter": {
"enabled": false
},
"VariableName": {
"enabled": false
},
"VariableTypeRequired": {
"enabled": false
}
"extends": "recommended",
"rules": {
"CatchException": {
"enabled": false
},
"CatchThrowable": {
"enabled": false
},
"ClassJavadoc": {
"enabled": false
},
"ClosureAsLastMethodParameter": {
"enabled": false
},
"DuplicateNumberLiteral": {
"enabled": false
},
"DuplicateStringLiteral": {
"enabled": false
},
"FieldTypeRequired": {
"enabled": false
},
"ImplicitClosureParameter": {
"enabled": false
},
"JUnitPublicNonTestMethod": {
"enabled": false
},
"JUnitTestMethodWithoutAssert": {
"enabled": false
},
"JavaIoPackageAccess": {
"enabled": false
},
"JavadocEmptyFirstLine": {
"enabled": false
},
"JavadocEmptyReturnTag": {
"enabled": false
},
"JavadocMissingParamDescription": {
"enabled": false
},
"JavadocMissingThrowsDescription": {
"enabled": false
},
"MethodCount": {
"enabled": false
},
"MethodParameterTypeRequired": {
"enabled": false
},
"MethodSize": {
"enabled": false
},
"NoDef": {
"enabled": false
},
"PrintStackTrace": {
"enabled": false
},
"PropertyName": {
"enabled": false
},
"SpaceAroundMapEntryColon": {
"enabled": false
},
"SpaceAroundOperator": {
"enabled": false
},
"SystemExit": {
"enabled": false
},
"UnnecessaryGetter": {
"enabled": false
},
"UnnecessaryObjectReferences": {
"enabled": false
},
"UnnecessarySetter": {
"enabled": false
},
"VariableName": {
"enabled": false
},
"VariableTypeRequired": {
"enabled": false
}
}
}
}
6 changes: 3 additions & 3 deletions .vscode/settings.json
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
{
"java.compile.nullAnalysis.mode": "disabled",
"java.configuration.updateBuildConfiguration": "disabled"
}
"java.compile.nullAnalysis.mode": "disabled",
"java.configuration.updateBuildConfiguration": "disabled"
}
22 changes: 16 additions & 6 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,16 @@
- Improve handling of dynamically-specified URIs
- Rewrite README.md, splitting out developer documentation to README_DEV.md

## [0.8.12] 2024-12-03 UNPUBLISHED

- Extract flags and metadata from `nextflow.config`
- Remove unused methods and keys
- Remove support for propertyName
- Use IntelliJ to fix types and lint

## [0.8.11] 2024-11-5 UNPUBLISHED

- Catch *all* toJson errors
- Catch _all_ toJson errors

## [0.8.10] 2024-11-4 UNPUBLISHED

Expand All @@ -27,8 +34,8 @@

## [0.8.7] 2024-10-23 UNPUBLISHED

- Use package cache instead of `params` to find output URIs
(in order to support dynamic URIs set by, e.g. `main.nf`)
- Use package cache instead of `params` to find output URIs (in order to support
dynamic URIs set by, e.g. `main.nf`)
- Allow setting metadata from inside the workflow

## [0.8.6] 2024-09-11
Expand All @@ -52,7 +59,8 @@

## [0.8.2] 2024-09-07

- Use copyFile rather than writeString for overlay files [requires NextFlow 23 or later]
- Use copyFile rather than writeString for overlay files [requires NextFlow 23
or later]
- Restore README and quilt_summarize to output

## [0.8.1] 2024-09-05
Expand Down Expand Up @@ -198,7 +206,8 @@ Beta release (not yet on nextflow-io/plugins)

- Use `msg` fragment parameter as commit message when writing packages
- Removed Benchling support (will add back in a future release)
- Don't crash when writing to Quilt+ URIs with `&path=` fragments (by ignoring that part)
- Don't crash when writing to Quilt+ URIs with `&path=` fragments (by ignoring
that part)

## [0.3.5] 2023-04-05

Expand All @@ -219,5 +228,6 @@ Beta release (not yet on nextflow-io/plugins)

## [0.3.2] 2023-02-24

- First official release on [nextflow-io/plugins](https://github.com/nextflow-io/plugins/commits/main/plugins.json)
- First official release on
[nextflow-io/plugins](https://github.com/nextflow-io/plugins/commits/main/plugins.json)
- Read and write from Quilt+ URIs
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