GraphPaper 0.3: Science research mode, APA manuscripts and model-aware reasoning

.github/workflows/quality.yml

@@ -37,6 +37,8 @@ jobs:
       - run: python -m pip install -r requirements-dev.txt
       - run: python -m playwright install --with-deps chromium
       - run: python scripts/ui_smoke.py
+      - run: python scripts/ui_studio_smoke.py
+      - run: python scripts/ui_science_smoke.py
       - uses: actions/upload-artifact@v4
         if: always()
         with:

.github/workflows/windows.yml

@@ -18,6 +18,7 @@ jobs:
       - run: python -m playwright install --with-deps chromium
       - run: python scripts/ui_smoke.py
       - run: python scripts/ui_studio_smoke.py
+      - run: python scripts/ui_science_smoke.py
   windows:
     needs: quality
     runs-on: windows-latest
@@ -35,7 +36,7 @@ jobs:
           GITHUB_TOKEN: ${{ github.token }}
         run: ./scripts/build_release.ps1
       - name: Exercise the actual Windows window, native dialogs and save-on-close
-        run: python scripts/native_smoke.py --executable dist/GraphPaper/GraphPaper.exe --out test-results/native-package
+        run: python scripts/native_smoke.py --science --executable dist/GraphPaper/GraphPaper.exe --out test-results/native-package
       - uses: actions/upload-artifact@v4
         with:
           name: GraphPaper-Windows-x64
@@ -51,8 +52,15 @@ jobs:
           $version = python -c "from graphpaper import __version__; print(__version__)"
           if ($env:GITHUB_REF_NAME -ne "v$version") { throw 'Tag does not match application version.' }
           gh release view $env:GITHUB_REF_NAME *> $null
-          if ($LASTEXITCODE -ne 0) { gh release create $env:GITHUB_REF_NAME --verify-tag --title "GraphPaper $env:GITHUB_REF_NAME" --notes-file docs/RELEASE-0.2.1.md }
-          gh release upload $env:GITHUB_REF_NAME "dist/GraphPaper-v$version-Windows-x64.zip" dist/SHA256SUMS.txt --clobber
+          if ($LASTEXITCODE -ne 0) { gh release create $env:GITHUB_REF_NAME --verify-tag --title "GraphPaper $env:GITHUB_REF_NAME" --notes-file docs/RELEASE-0.3.0.md }
+          $packageName = "GraphPaper-v$version-Windows-x64.zip"
+          $release = gh release view $env:GITHUB_REF_NAME --json assets | ConvertFrom-Json
+          if ($release.assets.name -contains $packageName) {
+            Write-Host 'A verified release package already exists; keeping it unchanged. This rebuild remains available as an Actions artifact.'
+          } else {
+            gh release upload $env:GITHUB_REF_NAME "dist/$packageName" dist/SHA256SUMS.txt
+            if ($LASTEXITCODE -ne 0) { throw 'Release upload did not complete.' }
+          }
       - uses: actions/upload-artifact@v4
         if: always()
         with:

CHANGELOG.md

@@ -1,5 +1,14 @@
 # Changelog
 
+## 0.3.0
+
+- Provider-native, model-aware reasoning effort for writer/editor/extraction roles, with Codex catalog support and explicit thinking budgets.
+- Third Science workspace with real scholarly database searches, documented screening, open full text, evidence appraisal and scientific drafting.
+- APA 7 professional manuscripts, metadata-based references, research-package export and manuscript-specific author confirmation.
+- Retained the 0.2.1 private native bridge and nonblocking save-on-close fix; added native Science regression coverage.
+- Rendered export inspection fixed empty-page overflow and inherited heading-theme fonts.
+
+
 ## 0.2.1 ? 2026-10-06
 
 - Fix recursive native-window exposure in the JavaScript bridge.

README.md

@@ -3,17 +3,28 @@
 ![GraphPaper — Graph-first AI writing studio](docs/images/graphpaper-header.svg)
 ### A studio for connected thought.
 
-**Windows fix: [v0.2.1](https://github.com/AronAxe/GraphPaper/releases/tag/v0.2.1)** fixes the native interface freeze and the save-on-close deadlock. Existing projects remain intact. See the [patch notes](docs/RELEASE-0.2.1.md).
+**Current release: [GraphPaper 0.3.0](https://github.com/AronAxe/GraphPaper/releases/latest)** adds model-specific reasoning controls and a dedicated Science workspace. The native Windows freeze and save-on-close fixes are retained. Existing projects remain intact.
 
 
 **Source material → knowledge graph → a distinctive angle → an editable outline → writing worth reading.**
 
-GraphPaper is a local-first, Windows-oriented writing studio for **nonfiction and fiction**. It is a graphical application, not a command-line writing tool. Bring your sources, see how their ideas connect, guide the interpretation, and keep authorship of the result.
+GraphPaper is a local-first, Windows-oriented writing studio for **nonfiction, fiction and scientific manuscripts**. It is a graphical application, not a command-line writing tool. Bring your sources, see how their ideas connect, guide the interpretation, and keep authorship of the result.
 
 ![GraphPaper's interactive graph studio](docs/images/graph.webp)
 *Actual app screenshot using the explicitly illustrative project included with the application.*
 
-## GraphPaper 0.2.0
+## New in 0.3.0
+
+[**Download GraphPaper for Windows**](https://github.com/AronAxe/GraphPaper/releases/latest) ? [Science and reasoning guide](docs/UPDATE-0.3.md)
+
+**Reasoning depth:** choose independently for the writer, editor and extractor. Codex supplies its supported levels through model discovery; other providers receive their native reasoning parameters. Defaults are preserved and unsupported levels are not silently substituted.
+
+**Science:** search PubMed, Semantic Scholar, arXiv, Crossref and Europe PMC; screen studies, retrieve available full text, inspect the evidence matrix, and draft a source-linked scientific manuscript. APA 7 Word export generates author-year citations and hanging references from retrieved metadata. A research package adds BibTeX, RIS, the protocol and the actual search log. Search limits and abstract-only evidence stay visible; author checks do not pretend to confer journal or ethics approval.
+
+![The Science research desk](docs/images/research-v0.3.webp)
+*Actual interface using clearly labelled synthetic workflow-test material.*
+
+## Author voice, folders and prose tools (retained from 0.2)
 
 [**Download the Windows release**](https://github.com/AronAxe/GraphPaper/releases/latest) · [What is new](docs/UPDATE-0.2.md)
 
@@ -28,12 +39,13 @@ Your own writing voice from uploads or article URLs; a project Inbox with automa
 
 There is no need to type commands. The native window uses Microsoft Edge WebView2. See [Windows setup and troubleshooting](docs/WINDOWS.md).
 
-**Executable packaging:** a Windows build script and GitHub Actions workflow are included. They generate a portable `GraphPaper.exe` folder/ZIP; this source package is not a prebuilt or signed Windows executable. Version 0.2 has native Windows automated tests and real-HTTP browser validation; see [validation scope](docs/QUALITY.md). Interactive native dialogs remain a separate check.
+**Executable packaging:** a Windows build script and GitHub Actions workflow are included. They generate a portable `GraphPaper.exe` folder/ZIP; this source package is not a prebuilt or signed Windows executable. The release workflow includes automated, real-HTTP browser and actual native Windows interaction checks; see [validation scope](docs/QUALITY.md). The compiled executable is checked separately from the source edition.
 
 ## A connected writing workflow
 
 | Stage | What you control |
 |---|---|
+| **Research (Science)** | Define the protocol, search scholarly databases, screen records and inspect evidence, full-text availability and the search log. |
 | **Sources** | Drag in PDF, DOCX, text, Markdown, CSV or HTML. Paste notes, import a public article URL, or import a saved project. Label material as evidence, fiction canon, inspiration or a voice sample. |
 | **Graph** | Build an evidence-linked graph, or import Graphify/NetworkX JSON. Pan, zoom, drag nodes, inspect quote anchors, highlight a path, and pin or exclude concepts. |
 | **Angles** | Discover distinct interpretations from contradictions, branches, convergences and cross-community connections. Edit the title/thesis, inspect the evidence gaps, or write your own angle. Nothing is selected for you. |
@@ -60,7 +72,7 @@ JEV/TypeSafe is used for **candidate screening, angle evaluation, evidence-gap s
 
 The preferred connection is **OpenRouter**, with a **direct TypeSafe route** available. Auto uses an available OpenRouter key first, then direct TypeSafe. You can select a route explicitly or switch JEV off; the app labels unscored results honestly. Scores are model judgments, not empirically calibrated probabilities of truth or writing quality.
 
-Writing providers: OpenRouter, OpenAI-compatible APIs including local endpoints, and direct Anthropic. Writer, extraction and editorial-review models can be set separately. No model name is hard-coded as a universal best choice.
+Writing providers: Codex / ChatGPT OAuth, OpenRouter, OpenAI-compatible APIs including local endpoints, and direct Anthropic. Writer, extraction and editorial-review models can be set separately. No model name is hard-coded as a universal best choice.
 
 ### Graphify without making setup painful
 

docs/QUALITY.md

@@ -1,5 +1,18 @@
 # Quality, tests and known limits
 
+## Version 0.3.0 validation
+
+Validated on 7 October 2026 in an isolated native Windows build environment:
+
+- **172 automated tests passed; one symlink-permission test skipped.**
+- **39 real-HTTP browser workflow checks passed**, with no JavaScript page errors: 17 base, 9 author-voice/folder/prose-tool, and 13 Science/reasoning checks.
+- **10 native Windows source checks and 10 checks against the compiled executable passed.** These include a genuine Windows mouse interaction, Science protocol editing, bridge initialization, Connections, a native Save As dialog, and pending manuscript persistence before normal process exit.
+- Actual metadata queries succeeded for PubMed, arXiv, Crossref and Europe PMC. Anonymous Semantic Scholar returned HTTP 429; that limitation is recorded, and its optional API-key route remains available.
+- The APA exporter was rendered and visually inspected across four synthetic manuscript pages. Blank-page and inherited font-theme issues were fixed. This was a LibreOffice-rendered check of the same exporter source, not a Microsoft Word automation claim.
+- The release uses streaming ZIP packaging and archive CRC/checksum verification, avoiding the large in-memory buffer used by PowerShell compression. Three packaging regression tests are included.
+
+No real user OAuth ceremony or paid writing/JEV call was used in these tests. Model/database fixtures in UI tests are explicitly synthetic; live metadata connectivity is tested separately. Full reports are in [validation/v0.3.0](validation/v0.3.0/). Earlier version results below are historical.
+
 ## 0.2.1 native Windows correction ? 6 October 2026
 
 The reported interface freeze exposed a gap in the earlier validation: the

docs/RELEASE-0.3.0.md

@@ -0,0 +1,31 @@
+# GraphPaper 0.3.0 - Science mode and reasoning depth
+
+## New
+
+- **Three modes:** Nonfiction, Fiction and Science, with a separate research desk for scientific work.
+- **Per-role reasoning:** independently select writer, editor and extraction/research effort. Codex options come from the runtime's model catalog, including extended levels only when advertised. OpenRouter, OpenAI-compatible and Anthropic routes use their native fields. Explicit thinking budgets and configurable request timeouts are supported where appropriate.
+- **Live scholarly search:** PubMed, Semantic Scholar, arXiv, Crossref and Europe PMC, with query logs, timestamps, caps, duplicate merging and explicit partial failures. Optional NCBI/Semantic Scholar keys are stored securely.
+- **Evidence workflow:** include/exclude decisions, exclusion reasons, open full text or uploaded-paper attachment, study appraisal, exact source quotations, design/limitations and an evidence matrix.
+- **Scientific manuscripts:** editable question/protocol, IMRaD-style outlines, evidence-led drafting, abstract, keywords, author declarations and source-support review. Empirical mode requires the author's actual completed results; it does not invent experiments or analyses.
+- **APA 7 Word export:** professional title/author-note page, abstract, consistent typography, running head and page numbers, author-year citations and hanging references generated from metadata. A research package adds BibTeX, RIS, the evidence CSV, protocol and search log.
+- **Submission checks:** unresolved blockers and author confirmations are visible. Changes invalidate prior approval. The checklist is not a claim of journal acceptance or ethics approval.
+
+The author-voice, project-folder, humanizer/deslop and Codex OAuth features remain available. The Windows bridge freeze and save-on-close fixes are retained.
+
+## Install
+
+Download **GraphPaper-v0.3.0-Windows-x64.zip**, extract the whole folder into a new location, and run **GraphPaper.exe**. Keep `_internal` with the executable. No Python installation or terminal workflow is required. Existing projects and credentials use the same local data directory. The binary is unsigned.
+
+Use **Connections -> Load available models -> Reasoning depth** to choose effort levels. Create a **Science** project and open its **Research protocol** to begin scholarly work.
+
+## Scope
+
+Database search is real network retrieval, not simulated research. Searches are bounded and never presented as exhaustive when capped. Abstracts/preprints are labelled. Systematic/scoping review completeness checks are stricter. The author must verify original sources, specialized references and the target journal's reporting requirements. Live metadata checks are separate from controlled model tests; no real user OAuth sign-in or paid writing-model call is claimed as part of release validation.
+
+Detailed instructions: [UPDATE-0.3.md](https://github.com/AronAxe/GraphPaper/blob/main/docs/UPDATE-0.3.md). Validation reports are under `docs/validation/v0.3.0`. SHA256SUMS.txt identifies the exact downloadable archive.
+
+## Verified release build
+
+172 automated Windows tests passed (one symlink-permission skip), all 39 browser workflow checks passed, and all 10 native checks passed against the actual compiled executable. The APA export received a four-page visual check. Live metadata retrieval succeeded on PubMed, arXiv, Crossref and Europe PMC; Semantic Scholar anonymous access was rate-limited with HTTP 429, reported explicitly. These are native local-build results, not a claim that a hosted Actions run completed.
+
+Windows ZIP: **157,726,720 bytes**. SHA-256: `b32cb385726f185ee50c1347a31eb4631d924e7fc4247b46afc2003c14de0a1b`. The official Codex runtime remains bundled and its signed-out protocol check passed.