Merge branch 'main' into renovate/oxsecurity-megalinter-8.x

quiltdata · Dec 6, 2024 · dff8cde · dff8cde
2 parents b54aa91 + 30c7736
commit dff8cde
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diff --git a/.github/workflows/mega-linter.yml b/.github/workflows/mega-linter.yml
@@ -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
@@ -31,7 +31,7 @@ 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

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -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
diff --git a/.gitignore b/.gitignore
@@ -13,6 +13,8 @@ work
 out
 results
 bin
+/bin/
+plugins/nf-quilt/bin
 
 # Ignore Gradle GUI config
 gradle-app.setting
@@ -32,3 +34,4 @@ params.yaml
 null
 # quilt+*
 # nextflow
+.aider*
diff --git a/.groovylintrc.json b/.groovylintrc.json
@@ -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
     }
-}
+  }
+}
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -1,4 +1,4 @@
 {
-    "java.compile.nullAnalysis.mode": "disabled",
-    "java.configuration.updateBuildConfiguration": "disabled"
-}
+  "java.compile.nullAnalysis.mode": "disabled",
+  "java.configuration.updateBuildConfiguration": "disabled"
+}
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -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
 
@@ -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
@@ -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
@@ -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
 
@@ -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