Merge pull request #613 from viash-io/develop_0_8

Release 0.8.2
viash-io · Dec 14, 2023 · 066cc43 · 066cc43
2 parents cc18870 + bad1139
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.yaml b/.github/ISSUE_TEMPLATE/bug_report.yaml
@@ -0,0 +1,106 @@
+name: Bug Report
+description: Create a report to help us improve
+title: "[BUG] "
+labels: [bug]
+
+body:
+  - type: markdown
+    attributes:
+      value: |
+        ## Thank you for taking the time to report a bug
+        Please fill out this form as completely as possible.
+
+  - type: input
+    id: what-happened
+    attributes:
+      label: What happened?
+      description: A clear and concise description of what the bug is.
+      placeholder: e.g., I get the following error when building a component with Viash.
+    validations:
+      required: true
+
+  - type: input
+    id: reproduce
+    attributes:
+      label: Steps to reproduce
+      description: Steps to reproduce the behavior.
+      placeholder: |
+        Contents of `config.vsh.yaml`:
+
+        ```yaml
+        ...
+        ```
+        
+        Contents of `script.py`:
+          
+        ```python
+        ...
+        ```
+
+        Steps to reproduce:
+
+        ```bash
+        ...
+        ``
+    validations:
+      required: true
+
+  - type: input
+    id: expected-behavior
+    attributes:
+      label: Expected behavior
+      description: A clear and concise description of what you expected to happen.
+      placeholder: e.g., The application should save my data and remain stable.
+    validations:
+      required: true
+
+  - type: textarea
+    id: logs
+    attributes:
+      label: Relevant log output
+      description: Please add any relevant logs or error messages.
+      placeholder: |
+        ```
+        Your log output here.
+        ```
+
+  - type: input
+    id: version
+    attributes:
+      label: Version
+      description: The version of the software where the bug was encountered.
+      placeholder: |
+        - OS: [e.g., Ubuntu 20.04]
+        - Java Version: [e.g., 11]
+        - Viash Version: [e.g. 0.8.1]
+        - Python Version: [if applicable, e.g. 3.10]
+        - R Version: [if applicable, e.g. 4.0]
+        - Docker Version: [if applicable]
+        - Nextflow Version: [if applicable]
+    validations:
+      required: true
+
+  - type: input
+    id: possible-solution
+    attributes:
+      label: Possible solution
+      description: Feel free to suggest a possible solution for the bug.
+
+
+  - type: checkboxes
+    id: confirm
+    attributes:
+      label: Confirmation
+      description: |
+        Please make sure you have checked the following.
+      options:
+        - label: I have searched the existing issues to make sure this is not a duplicate.
+          required: true
+        - label: I have provided clear and concise information about the bug.
+          required: true
+
+  - type: input
+    id: additional-context
+    attributes:
+      label: Additional context
+      description: Add any other context about the problem here.
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yaml b/.github/ISSUE_TEMPLATE/feature_request.yaml
@@ -0,0 +1,70 @@
+name: Feature Request
+description: Suggest an idea for this project
+title: "[FEATURE] "
+labels: [enhancement]
+
+body:
+  - type: markdown
+    attributes:
+      value: |
+        ## Thank you for your feature request
+        Please fill out this form to help us understand your idea.
+
+  - type: input
+    id: feature-summary
+    attributes:
+      label: Feature summary
+      description: A brief summary of the feature.
+      placeholder: e.g., Add a dark mode option.
+    validations:
+      required: true
+
+  - type: textarea
+    id: feature-description
+    attributes:
+      label: Feature description
+      description: A detailed description of the feature.
+      placeholder: Describe the feature you'd like to see, how it works, and what it would accomplish.
+    validations:
+      required: true
+
+  - type: textarea
+    id: motivation
+    attributes:
+      label: Why is this feature beneficial?
+      description: Explain why this feature would be useful to the project and its users.
+      placeholder: e.g., A dark mode would reduce eye strain for users working in low-light conditions.
+    validations:
+      required: true
+
+  - type: textarea
+    id: alternatives-considered
+    attributes:
+      label: Alternatives considered
+      description: Describe any alternative solutions or features you've considered.
+      placeholder: e.g., Instead of a full dark mode, a feature to adjust screen brightness could be implemented.
+
+
+  - type: input
+    id: possible-solution
+    attributes:
+      label: Possible solution
+      description: Feel free to suggest a possible implementation for the feature.
+
+  - type: checkboxes
+    id: confirm
+    attributes:
+      label: Confirmation
+      description: |
+        Please confirm the following before submitting.
+      options:
+        - label: I have searched the existing issues to make sure this is not a duplicate request.
+          required: true
+        - label: I have provided clear and concise information about the feature.
+          required: true
+
+  - type: markdown
+    attributes:
+      value: |
+        ### Thank you for contributing to our project!
+        Your feature request will be reviewed, and we'll get back to you as soon as possible.
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -1,18 +1,45 @@
 ## Describe your changes
 
-## Issue ticket number and link
-Closes #xxxx (Replace xxxx with the GitHub issue number)
+<!-- 
+Please include a summary of the change and which issue is fixed.
+-->
 
-## Checklist before requesting a review
-- [ ] I have performed a self-review of my code
+## Related issue(s)
 
-- Does this PR contain:
-  - [ ] Breaking changes
-  - [ ] New functionality
-  - [ ] Major changes
-  - [ ] Minor changes
-  - [ ] Bug fixes
+<!-- Replace xxxx with the GitHub issue number. -->
 
-- [ ] Proposed changes are described in the CHANGELOG.md
+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](CONTRIBUTING.md) 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
+
+<!--
+Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test environment.
+-->
 
-- [ ] Relevant unit tests have been added
diff --git a/.github/workflows/ns_test.yml b/.github/workflows/ns_test.yml
@@ -10,7 +10,7 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Set up sbt
-      uses: actions/setup-java@v3
+      uses: actions/setup-java@v4
       with:
         distribution: temurin
         java-version: '11'

diff --git a/.github/workflows/sbt_test.yml b/.github/workflows/sbt_test.yml
@@ -14,9 +14,9 @@ jobs:
           - { name: 'ubuntu_latest', os: ubuntu-latest }
           - { name: 'macos_latest', os: macos-latest }
         java:
-          - { ver: '11', run_nextflow: true, run_coverage: false }
-          - { ver: '17', run_nextflow: true, run_coverage: true }
-          - { ver: '20', run_nextflow: false, run_coverage: false }
+          - { ver: '11', run_nextflow: true, run_coverage: false, nxf_ver: "22.04.5" }
+          - { ver: '17', run_nextflow: true, run_coverage: true, nxf_ver: latest }
+          - { ver: '20', run_nextflow: true, run_coverage: false, nxf_ver: latest-edge }
 
     steps:
     - uses: actions/checkout@v4
@@ -26,12 +26,9 @@ jobs:
 
     - name: Set up Nextflow
       if: ${{ runner.os == 'Linux' && matrix.java.run_nextflow }}
-      run: |
-        mkdir -p "$HOME/.local/bin"
-        echo "$HOME/.local/bin" >> $GITHUB_PATH
-        curl -s https://get.nextflow.io 2> /dev/null | bash > /dev/null
-        mv nextflow "$HOME/.local/bin"
-        nextflow -version
+      uses: nf-core/setup-nextflow@v1
+      with:
+        version: ${{ matrix.java.nxf_ver }}
 
     - name: Set up R
       uses: r-lib/actions/setup-r@v2
@@ -46,7 +43,7 @@ jobs:
           testthat
 
     - name: Set up sbt
-      uses: actions/setup-java@v3
+      uses: actions/setup-java@v4
       with:
         distribution: temurin
         java-version: ${{ matrix.java.ver }}

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,35 @@
+# Viash 0.8.2 (2023-12-14): Minor changes and bug fixes
+
+This release fixes a few bugs regarding dependencies and how the Nextflow platform handles Paths.
+
+## MINOR CHANGES
+
+* `NextflowTestHelper`: Do not hardcode a version of Nextflow in the testbench, 
+  but use the version of Nextflow that is installed on the system (PR #593).
+
+* GitHub Actions: Test different versions of Nextflow (22.04.5, latest, and latest-edge) (PR #593).
+  Testing the latest Edge version of Nextflow will allow us to catch notice changes in Nextflow earlier.
+
+* Updates to the documentation and templates in the Git repo (#598, PR #600):
+
+  - Add contributing guidelines.
+
+  - Add issue templates.
+
+  - Reworked the pull request template.
+
+## BUG FIXES
+
+* `config`: Fix the main level of a component config not enforcing strict mode and instead allowing any field to be specified (PR #585).
+
+* `dependencies`: Allow the user to define a local dependency with specifying `repository: local` as sugar syntax (PR #609). A local repository is the default value so it's not required to be filled in, but allowing it with a sensible sugar syntax makes sense.
+
+* `Repositories`: Fix a structural issue where a repository defined directly in a `dependency` would require the `name` field to be set (PR #607). Repository variants are created with and without the `name` field. Repositories under `.functionality.dependencies[]` use repositories without the `name` field, while repositories under `.functionality.repositories[]` use repositories with the `name` field.
+
+* `NextflowPlatform`: Do not resolve remote paths relative to the --param_list file (PR #592).
+
+* `NextflowPlatform`: Allow finding `.build.yaml` file when worktree contains a directory that is a symlink (PR #611). 
+
 # Viash 0.8.1 (2023-11-20): Minor bug fix to Nextflow workflows
 
 This release fixes a bug in the Nextflow platform where calling a workflow with the `.run()` function without specifying the `fromState` argument would result in an error when the input channel contained tuples with more than two elements.