docs: add deployment guide, update env docs and changelog#202
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- Add docs/DEPLOYMENT.md with comprehensive env var reference - Update docs/README.md with deployment section link - Update .env.example with full inline documentation for all variables - Document resolution order, override vs mode defaults, optional vs required
- Add [3.0.1] - 2026-05-12 section with user-facing UI/UX changes - Move [Unreleased] section to top per Keep a Changelog convention - Include only user-visible changes (search, filters, tooltips, comments, polish) - Strip backend/config changes from changelog entries
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Pull request overview
Documentation-focused PR to improve how contributors/operators configure ModelSEED-UI deployments, by centralizing and expanding environment-variable guidance and recording a new 3.0.1 release entry in the changelog.
Changes:
- Added a new deployment guide documenting env var resolution, modes, and common setups.
- Expanded
.env.examplewith detailed inline documentation for each variable. - Updated the docs index and reorganized the changelog to follow Keep a Changelog conventions.
Reviewed changes
Copilot reviewed 4 out of 4 changed files in this pull request and generated 7 comments.
| File | Description |
|---|---|
| docs/README.md | Adds the new deployment guide to the documentation registry. |
| docs/DEPLOYMENT.md | Introduces a comprehensive deployment/environment configuration reference. |
| .env.example | Adds extensive inline docs for env vars and resolution behavior. |
| CHANGELOG.md | Adds a 3.0.1 section and moves [Unreleased] to the top. |
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| # | ||
| # Override: Required in manual mode, otherwise optional (mode default used) | ||
| # Mode default: staging=https://staging.modelseed.org | production=https://modelseed.org | ||
| # Hardcoded: (none -- mode defaults always available) |
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| - **Override:** Required in manual mode, optional otherwise | ||
| - **Mode defaults:** `staging=https://staging.modelseed.org` / `production=https://modelseed.org` | ||
| - **Hardcoded fallback:** (none -- mode defaults always available) |
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| - **When `USE_NEW_PROXY=true` and this is empty:** Resolves to `{SITE_BASE_URL}/api/model` | ||
| - **When `USE_NEW_PROXY=false`:** This is ignored; the legacy URL is used instead. |
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| - **When empty:** RDKit.js loads from the unpkg CDN (`https://unpkg.com/@rdkit/rdkit@{VERSION}/dist`). | ||
| - **When set:** Must point to a directory containing `RDKit_minimal.js` and `RDKit_minimal.wasm`. | ||
| Example for self-hosting via the `/public` directory: `/public/rdkit` |
| # When unset, the app loads RDKit.js from the unpkg CDN: | ||
| # https://unpkg.com/@rdkit/rdkit@{VERSION}/dist | ||
| # | ||
| # Set this only if you are self-hosting RDKit.js (e.g. /public/rdkit). |
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| **Default:** `staging` (when the variable is unset or empty) | ||
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| **Required:** Yes. The app will not start with an invalid or unrecognized value. |
| # | ||
| # Values: staging | production | manual | ||
| # Default: staging (when unset or empty) | ||
| # Required: Yes |
- .env.example: fix deployment mode required wording, SITE_BASE_URL hardcoded fallback, RDKit.js self-host path - docs/DEPLOYMENT.md: fix deployment mode required wording, SITE_BASE_URL hardcoded fallback, ProbModelSEED proxy var name, RDKit.js /public path, improve clarity
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Summary
Documentation updates for the env system and release tracking:
Changes
.env.example— Full inline documentation for every environment variable, including resolution order (override → mode default → hardcoded fallback), optional vs required status, and deployment mode descriptions.docs/DEPLOYMENT.md— New comprehensive deployment guide covering all env vars, the three-tier resolution system, deployment modes (staging/production/manual), common scenarios (local dev, production, custom), and runtime code locations.docs/README.md— Added DEPLOYMENT.md to the documentation index.CHANGELOG.md— Added[3.0.1] - 2026-05-12release notes with user-facing UI/UX changes only (find-in-page search, AND/OR filters, pathway tooltips, reaction comments, PlantSEED copy, compound synonyms, gene reaction chips, page polish). Moved[Unreleased]to top per Keep a Changelog convention.