Add CLAUDE.md and Claude Code skills for MS webapp development#357
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t0mdavid-m merged 2 commits intomainfrom Mar 27, 2026
Merged
Add CLAUDE.md and Claude Code skills for MS webapp development#357t0mdavid-m merged 2 commits intomainfrom
t0mdavid-m merged 2 commits intomainfrom
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Adds project documentation (CLAUDE.md) and 6 skills to help developers scaffold and extend OpenMS web applications built from this template: - /create-page: add a new Streamlit page with proper registration - /create-workflow: scaffold a full TOPP workflow (class + 4 pages) - /add-python-tool: add a custom Python analysis script with auto-UI - /add-presets: add parameter presets for workflows - /configure-deployment: set up Docker and CI/CD for a new app - /add-visualization: add pyopenms-viz or OpenMS-Insight visualizations https://claude.ai/code/session_01WYotmLfqRtB8WJXj1Eosiz
📝 WalkthroughWalkthroughAdds seven documentation/skill files describing presets, custom Python tools, visualizations, deployment, Streamlit pages, TOPP workflows, and a repository overview for the OpenMS Streamlit WebApp Template. Changes
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🧹 Nitpick comments (1)
CLAUDE.md (1)
15-36: Consider adding language specifier to fenced code block.The ASCII art architecture diagram is missing a language specifier. While this works fine, adding
```textwould satisfy the linter and make the intent clearer.📝 Proposed improvement
-``` +```text app.py # Entry point — registers pages via st.Page() in a dict settings.json # App config: name, version, deployment mode, threading🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@CLAUDE.md` around lines 15 - 36, Update the fenced ASCII-art block in CLAUDE.md to include a language specifier by changing the opening fence from ``` to ```text so the architecture diagram (the block containing app.py, settings.json, src/, Dockerfile, etc.) is marked as plain text and satisfies the linter.
🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.
Nitpick comments:
In `@CLAUDE.md`:
- Around line 15-36: Update the fenced ASCII-art block in CLAUDE.md to include a
language specifier by changing the opening fence from ``` to ```text so the
architecture diagram (the block containing app.py, settings.json, src/,
Dockerfile, etc.) is marked as plain text and satisfies the linter.
ℹ️ Review info
⚙️ Run configuration
Configuration used: Organization UI
Review profile: CHILL
Plan: Pro
Run ID: 30f4e374-82ba-4170-960a-49b274b24993
📒 Files selected for processing (7)
.claude/skills/add-presets.md.claude/skills/add-python-tool.md.claude/skills/add-visualization.md.claude/skills/configure-deployment.md.claude/skills/create-page.md.claude/skills/create-workflow.mdCLAUDE.md
Make it clear to Claude that this is THE framework for building mass spectrometry web applications for proteomics and metabolomics research. Add domain-specific context about MS data types, TOPP tool pipelines, and scientific visualization needs. https://claude.ai/code/session_01WYotmLfqRtB8WJXj1Eosiz
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Actionable comments posted: 1
🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.
Inline comments:
In `@CLAUDE.md`:
- Around line 26-47: The fenced code block in CLAUDE.md listing project files is
missing a language tag; update that opening triple-backtick (the block that
begins with the lines showing app.py, settings.json, etc.) to include a language
identifier such as text (e.g., ```text) so markdownlint MD040 is satisfied—no
other changes to the block contents are needed.
🪄 Autofix (Beta)
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
ℹ️ Review info
⚙️ Run configuration
Configuration used: Organization UI
Review profile: CHILL
Plan: Pro
Run ID: daf2dbe4-54f7-4b5e-9c3a-8c610437c2af
📒 Files selected for processing (4)
.claude/skills/add-python-tool.md.claude/skills/add-visualization.md.claude/skills/create-workflow.mdCLAUDE.md
✅ Files skipped from review due to trivial changes (2)
- .claude/skills/create-workflow.md
- .claude/skills/add-python-tool.md
🚧 Files skipped from review as they are similar to previous changes (1)
- .claude/skills/add-visualization.md
Comment on lines
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| ``` | ||
| app.py # Entry point — registers pages via st.Page() in a dict | ||
| settings.json # App config: name, version, deployment mode, threading | ||
| default-parameters.json # Default workspace parameters (tracked via widget keys) | ||
| presets.json # Parameter presets for TOPP workflows | ||
| content/ # Streamlit pages (one .py per page) | ||
| src/ | ||
| common/common.py # Utilities: page_setup(), save_params(), show_fig(), show_table() | ||
| Workflow.py # Example WorkflowManager subclass (TOPP workflow) | ||
| workflow/ | ||
| WorkflowManager.py # Base class: upload/configure/execution/results pattern | ||
| StreamlitUI.py # Widget library: upload_widget, input_TOPP, input_python, etc. | ||
| ParameterManager.py # JSON parameter persistence + TOPP .ini generation | ||
| CommandExecutor.py # Runs TOPP tools and Python scripts as subprocesses | ||
| FileManager.py # Workspace file organization | ||
| Logger.py # Structured workflow logging | ||
| QueueManager.py # Redis queue for online deployments | ||
| python-tools/ # Custom Python analysis scripts (with DEFAULTS dicts) | ||
| Dockerfile # Full build: OpenMS + TOPP tools + pyOpenMS | ||
| Dockerfile_simple # Lightweight: pyOpenMS only | ||
| docker-compose.yml # Deployment config | ||
| ``` |
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Add a language tag to the fenced code block.
The fence starting at Line 26 is missing a language identifier, which triggers markdownlint MD040.
Proposed fix
-```
+```text
app.py # Entry point — registers pages via st.Page() in a dict
settings.json # App config: name, version, deployment mode, threading
default-parameters.json # Default workspace parameters (tracked via widget keys)
@@
docker-compose.yml # Deployment config</details>
<!-- suggestion_start -->
<details>
<summary>📝 Committable suggestion</summary>
> ‼️ **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.
```suggestion
🧰 Tools
🪛 markdownlint-cli2 (0.22.0)
[warning] 26-26: Fenced code blocks should have a language specified
(MD040, fenced-code-language)
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.
In `@CLAUDE.md` around lines 26 - 47, The fenced code block in CLAUDE.md listing
project files is missing a language tag; update that opening triple-backtick
(the block that begins with the lines showing app.py, settings.json, etc.) to
include a language identifier such as text (e.g., ```text) so markdownlint MD040
is satisfied—no other changes to the block contents are needed.
t0mdavid-m
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Summary
Adds Claude Code project documentation and skills to help developers build and modify mass spectrometry web applications using this template.
CLAUDE.md — MS domain framing
The
CLAUDE.mdestablishes this as the standard framework for building MS web applications for proteomics and metabolomics research. It documents:.plot()extension) and OpenMS-Insight (Vue.js interactive components)6 Claude Code skills (
.claude/skills/)/create-page/create-workflow/add-python-tool/add-presets/configure-deployment/add-visualizationSkills reference derived apps (quantms-web, umetaflow, FLASHApp) as real-world examples so Claude can learn from and modify them.
Recommendations for other repos (not in this PR)
.plot()API, plot types, backends. Consider/add-plot-typeskill./add-componentskill.Test plan
python -m pytest tests/streamlit run app.pystill workshttps://claude.ai/code/session_01WYotmLfqRtB8WJXj1Eosiz