ci(dry-run): Add dry run build and PR template#89
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WalkthroughA pull request template, a GitHub Actions workflow for dry-run builds on pull requests to the "devel" branch, and an update to the Changes
Sequence Diagram(s)sequenceDiagram
participant Contributor
participant GitHub
participant CI Runner
Contributor->>GitHub: Open PR targeting "devel"
GitHub->>CI Runner: Trigger "Dry runs for PRs" workflow
CI Runner->>GitHub: Checkout code
CI Runner->>CI Runner: Setup R and Bioconductor (devel)
CI Runner->>CI Runner: Install dependencies
CI Runner->>CI Runner: Build, install, and check R package
CI Runner->>GitHub: Report build/check results on PR
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Actionable comments posted: 2
🧹 Nitpick comments (4)
.github/workflows/dry-run-build.yml (2)
2-4: Trim trailing whitespace to satisfy YAML lintersThe workflow currently fails
yamllintdue to two spaces afteron:.-on:␠␠ +on:
18-18: Add a terminating newlineSeveral tools (git, POSIX utilities, some CI linters) expect files to end with
\n.
Append a newline after the last line.- uses: grimbough/bioc-actions/build-install-check@v1 +\tuses: grimbough/bioc-actions/build-install-check@v1 +.github/pull_request_template.md (2)
3-4: Minor grammar tweakInsert a comma after “problem”.
-Please include relevant motivation and context of the problem along with a short summary of the solution. +Please include relevant motivation and context of the problem, along with a short summary of the solution.
9-10: Remove placeholder bullet or convert to commentAn empty bullet renders strangely in rendered Markdown.
- +- <!-- Describe at least one change -->
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (3)
.github/pull_request_template.md(1 hunks).github/workflows/dry-run-build.yml(1 hunks).gitignore(1 hunks)
🧰 Additional context used
🪛 LanguageTool
.github/pull_request_template.md
[uncategorized] ~3-~3: Possible missing comma found.
Context: ... relevant motivation and context of the problem along with a short summary of the solut...
(AI_HYDRA_LEO_MISSING_COMMA)
🪛 YAMLlint (1.37.1)
.github/workflows/dry-run-build.yml
[error] 2-2: trailing spaces
(trailing-spaces)
[error] 18-18: no new line character at the end of file
(new-line-at-end-of-file)
⏰ Context from checks skipped due to timeout of 90000ms (1)
- GitHub Check: build
🔇 Additional comments (1)
.gitignore (1)
8-8: 👍 Ignoring macOS artefacts looks goodAdding
*.DS_Storekeeps the repository clean and is industry-standard.
No further action required.
| - name: Checkout repository | ||
| uses: actions/checkout@v4 | ||
| - name: Setup R and Bioconductor | ||
| uses: grimbough/bioc-actions/setup-bioc@v1 | ||
| with: | ||
| bioc-version: devel | ||
| - name: Install dependencies | ||
| uses: r-lib/actions/setup-r-dependencies@v2 | ||
| - name: Build, Install, Check | ||
| uses: grimbough/bioc-actions/build-install-check@v1 No newline at end of file |
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🛠️ Refactor suggestion
Pin action revisions for supply-chain safety
Tag references (actions/checkout@v4, setup-bioc@v1, etc.) can be overwritten upstream.
For immutable builds, pin each action to a commit SHA:
-uses: actions/checkout@v4
+uses: actions/checkout@v4 # 4d5d7b9f9e63e7f0d…Do the same for the other three actions.
🧰 Tools
🪛 YAMLlint (1.37.1)
[error] 18-18: no new line character at the end of file
(new-line-at-end-of-file)
🤖 Prompt for AI Agents
In .github/workflows/dry-run-build.yml between lines 9 and 18, the GitHub
Actions use tag references for actions which can be overwritten upstream,
risking supply-chain security. To fix this, replace each action tag reference
with a pinned commit SHA by appending the specific commit hash after the tag,
for example, change "actions/checkout@v4" to "actions/checkout@v4 #
<commit-sha>". Do this for all four actions to ensure immutable builds.
| Please describe any unit tests you added or modified to verify your changes. | ||
|
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||
| ## Checklist Before Requesting a Review | ||
| - [ ] I have read the MSstats [contributing guidelines](https://github.com/Vitek-Lab/MSstatsConvert/blob/master/.github/CONTRIBUTING.md) |
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🛠️ Refactor suggestion
Update link to project-local contributing guide
The link points to MSstatsConvert, not MSstatsTMT.
-I have read the MSstats [contributing guidelines](https://github.com/Vitek-Lab/MSstatsConvert/blob/master/.github/CONTRIBUTING.md)
+I have read the MSstatsTMT [contributing guidelines](https://github.com/Vitek-Lab/MSstatsTMT/blob/master/.github/CONTRIBUTING.md)📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| - [ ] I have read the MSstats [contributing guidelines](https://github.com/Vitek-Lab/MSstatsConvert/blob/master/.github/CONTRIBUTING.md) | |
| - [ ] I have read the MSstatsTMT [contributing guidelines](https://github.com/Vitek-Lab/MSstatsTMT/blob/master/.github/CONTRIBUTING.md) |
🤖 Prompt for AI Agents
In .github/pull_request_template.md at line 16, the link to the contributing
guidelines incorrectly points to the MSstatsConvert repository. Update the URL
to point to the MSstatsTMT project's local contributing guide to ensure it
directs users to the correct documentation.
1 participant
Motivation and Context
Please include relevant motivation and context of the problem along with a short summary of the solution.
Changes
Please provide a detailed bullet point list of your changes.
Testing
Please describe any unit tests you added or modified to verify your changes.
Checklist Before Requesting a Review
Summary by CodeRabbit
.DS_Storefiles from version control.