simjecture 0.5.1__tar.gz → 0.5.2__tar.gz

{simjecture-0.5.1 → simjecture-0.5.2}/.github/workflows/ci.yml

@@ -50,7 +50,9 @@ jobs:
       - name: Install uv
         run: python -m pip install uv
       - name: Install locked environment
-        run: uv sync --frozen --extra tui --extra dsh
+        run: uv sync --frozen --extra tui --extra dsh --extra workspace --group browser
+      - name: Install browser test runtime
+        run: uv run playwright install --with-deps chromium
       - uses: actions/setup-node@v4
         with:
           node-version: "22.23.1"
@@ -64,6 +66,10 @@ jobs:
         run: uv run ruff check .
       - name: Test
         run: uv run pytest --cov=conjecture_solver --cov-report=term-missing
+      - name: Validate packaged workspace install
+        run: |
+          uv run python scripts/package_workspace.py --output dist
+          uv run python scripts/verify_workspace_install.py --release-dir dist --work-dir /tmp/simjecture-installer-validation
       - name: Reproduce planted benchmark
         run: uv run simjecture benchmark kinetic-sufficiency --assert-falsified
       - name: Reproduce independent PIC benchmark

{simjecture-0.5.1 → simjecture-0.5.2}/.github/workflows/release.yml

@@ -15,7 +15,7 @@ jobs:
       name: pypi
       url: https://pypi.org/p/simjecture
     permissions:
-      contents: read
+      contents: write
       id-token: write
     steps:
       - uses: actions/checkout@v7
@@ -40,7 +40,9 @@ jobs:
             --ro-bind /lib64 /lib64 \
             /usr/bin/true
       - name: Install locked test environment
-        run: uv sync --frozen --extra tui --extra dsh
+        run: uv sync --frozen --extra tui --extra dsh --extra workspace --group browser
+      - name: Install browser test runtime
+        run: uv run playwright install --with-deps chromium
       - uses: actions/setup-node@v4
         with:
           node-version: "22.23.1"
@@ -69,5 +71,20 @@ jobs:
           PY
       - name: Build source and wheel distributions
         run: uv build
+      - name: Package and verify the one-command workspace installer
+        run: |
+          uv run python scripts/package_workspace.py --output dist
+          uv run python scripts/verify_workspace_install.py --release-dir dist --work-dir /tmp/simjecture-installer-validation
+      - name: Attach installable release assets
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: gh release upload "$GITHUB_REF_NAME" dist/install.sh dist/SHA256SUMS dist/*-workspace.tar.gz --clobber
+      - name: Collect Python distributions
+        run: |
+          mkdir pypi-dist
+          cp dist/*.whl pypi-dist/
+          find dist -maxdepth 1 -name '*.tar.gz' ! -name '*-workspace.tar.gz' -exec cp {} pypi-dist/ \;
       - name: Publish with PyPI Trusted Publishing
         uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: pypi-dist/

{simjecture-0.5.1 → simjecture-0.5.2}/CHANGELOG.md

@@ -2,6 +2,104 @@
 
 This project follows semantic versioning. Dates use ISO 8601.
 
+## 0.5.2 — 2026-09-29
+
+Stable release of the conversation-first research workspace tested in rc1/rc2,
+plus continuation, steering, review recovery and the ITER diagnostics pack.
+Minimal mode remains the default; structured/frontier modes remain selectable.
+The versioned installer preserves existing research data and older program folders.
+
+- Add an optional ITER diagnostics/data pack with pinned CHERAB/Raysect,
+  CHERAB-ITER/IMAS extensions and IMAS tools. Install/check from the CLI or GUI;
+  run a visible, monitored numerical demo with plots. Add source-based agent
+  guidance and separate setup entries for JOREK, SOLPS-ITER and DINA-PS.
+
+- Offer Prepare directly or Prepare with agent from the continuation dialog.
+  Chat preparation carries parent context across turns and lets the agent draft
+  the brief and select inherited files without losing lineage or instruments.
+- Add Continue investigation and Send guidance to study cards and the experiment
+  monitor. Review a linked phase's brief, selected inherited files, model and new
+  budget before launch; retain the original study and evidence status.
+- Snapshot continuation context with verified hashes and immutable parent lineage.
+  Add CLI continuation and advisory steering; show queued/checkpoint delivery in
+  the web interface and include guidance in independent review packets.
+- Detect empty/truncated built-in review replies, record finish reasons and usage,
+  and use bounded recovery with a larger output allocation and a DeepSeek
+  non-thinking retry. Back off repeated invalid oversight without granting approval.
+- Reconcile expired deadlines/dead supervisors in live status and write final
+  reports when a supervisor exits through an external error.
+
+## 0.5.2rc2 (preview) — 2026-09-27
+
+- Provision scientific compilers, MPI, HDF5 and other prerequisites in managed
+  environments for the included tools. Preserve diagnostic logs and validate the
+  installed runtime using the selected execution backend before reporting success.
+- Verify all five one-click tools from empty runtime directories, real agent-assisted
+  FLASH and WarpX CUDA builds, GPU execution, and browser uploads of licensed source.
+- Handle restricted root installations with a dedicated non-root account, safe
+  launchers, failed-install retry and upgrade rollback.
+- Make the autonomous research screen follow preparation, proposal, execution and
+  results. Return finished reports to the interactive agent without interrupting
+  active work; preserve queued delivery across restarts and link explanations to evidence.
+- Support follow-up studies in the same conversation with separate briefs and reports.
+  Remove duplicate navigation labels and collapse routine workspace metadata.
+- Accept source archive uploads up to 64 MiB. Keep installation commands separate
+  from simulations, support checks for registered custom tools, and reject runtimes
+  whose host paths or interpreter symlinks cannot work in the execution backend.
+
+- Keep installation skills readable while runtimes are incomplete; retry the
+  pinned Singularity-EOS source fetch after transient transport failures and
+  populate its required ports-of-call dependency. Package a relocatable Python
+  runtime when using uv-managed Python, avoiding broken sandbox symlinks. Incomplete runtimes with missing
+  declared identity files are not listed as installed.
+- Require an explicit completion handoff after DeepSeek text-only progress replies,
+  continuing tools instead of marking promises as completed answers. Bound repeated
+  protocol failures and retain usage accounting for completion-check requests.
+- Move routine workspace controls and execution status into the left sidebar,
+  remove the redundant top bar, and make execution warnings dismissible with
+  expandable diagnostics. Keep conversation-blocking notices prominent.
+- Use draggable sidebar edges and compact chevron tabs instead of text hide/show
+  buttons. Drag to the outer edge to collapse, pull or click the tab to reopen,
+  and retain panel widths and collapsed state across reloads.
+- Replace source-path dialogs for FLASH and WarpX CUDA with **Install with agent**,
+  opening prepared setup conversations that reference the bundled deployment skills.
+- Prefer Bubblewrap, with a checked PRoot cooperative fallback for namespace-restricted
+  hosts running under a dedicated non-root account. Show a dismissible sidebar warning
+  about the lack of filesystem/network security isolation; retain explicit backend
+  choices and immutable study execution modes. Use the selected backend for tool checks.
+- Show failed tool installations directly on catalogue cards, including tools
+  that are not yet installed. Bootstrap checksummed Micromamba for WarpX CPU
+  and separate solver provisioning from experiment-sandbox readiness.
+- Support DeepSeek thinking-mode tool choice and plain-text final answers. Keep
+  required provider reasoning metadata in private session storage and preserve
+  it when resuming a conversation, without displaying it in chat or activity.
+- Clarify SSH forwarding when a local port is already occupied.
+- Show only simulations in the left sidebar. Separate Simulations and Commands
+  into right-side tabs with independent selections, counts and links; incoming
+  commands no longer open the simulation monitor.
+
+## 0.5.2rc1 (preview) — 2026-09-27
+
+- Add a Linux/WSL one-command installer with checksummed release bundles, automatic
+  Python/uv setup, a persistent launcher, SSH forwarding guidance and separate version/data folders.
+- Add the conversation-first research workspace with optional compatible API setup,
+  auto-detected native CLIs, per-conversation agent/model controls and agent-prepared studies.
+- Keep named simulation folders and live logs beside conversations; link interactive
+  runs, figures, files and autonomous studies with a resizable side monitor.
+- Render equations, highlighted code and saved figures; add larger typography, persistent
+  light/dark themes and confirmed conversation/folder deletion with active-run guards.
+- Preserve scroll position and expanded details during live refreshes.
+- Discover existing FLASH applications and WarpX CPU/GPU builds, including native-input
+  versus Python-binding availability; expose shipped research skills to browser workers.
+- Resume native chat sessions and retain structured API history per conversation/model/
+  connection. Never reuse worker sessions for independent review.
+- Remove the default interactive-turn time ceiling, show public progress and recent tools,
+  and retain user-selected autonomous/simulation deadlines. Clarify interruptions and
+  preserve job statuses; discourage untracked temporary simulation
+  runs, and include an HDF5 reader in the workspace environment.
+- Accept an independently reviewed negative answer as completion when the study's
+  selected policy is `answer`; retain the existing `repair` policy.
+
 ## 0.5.1 — 2026-09-26
 
 - Update bundled FLASH and Python experiment skills with guided-study/HDF5 lessons,

{simjecture-0.5.1 → simjecture-0.5.2}/CITATION.cff

@@ -2,8 +2,8 @@ cff-version: 1.2.0
 message: "If you use this software, please cite the exact software version and Git commit."
 title: "Simjecture"
 type: software
-version: 0.5.1
-date-released: 2026-09-26
+version: 0.5.2
+date-released: 2026-09-29
 abstract: >-
   An evidence-governed runtime for autonomous computational experimentation and
   falsification over hypothesis trees.

{simjecture-0.5.1 → simjecture-0.5.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: simjecture
-Version: 0.5.1
+Version: 0.5.2
 Summary: Evidence-governed autonomous experimentation and falsification for computational science
 Project-URL: Homepage, https://github.com/tomzhu0225/simjecture
 Project-URL: Documentation, https://github.com/tomzhu0225/simjecture/tree/main/docs
@@ -35,6 +35,10 @@ Provides-Extra: process
 Requires-Dist: psutil<8,>=6; extra == 'process'
 Provides-Extra: tui
 Requires-Dist: textual<9,>=2.0; extra == 'tui'
+Provides-Extra: workspace
+Requires-Dist: h5py<4,>=3.10; extra == 'workspace'
+Requires-Dist: psutil<8,>=6; extra == 'workspace'
+Requires-Dist: smolagents[openai]<2,>=1.24; extra == 'workspace'
 Description-Content-Type: text/markdown
 
 # Simjecture
@@ -48,19 +52,48 @@ experiments, searches for counterexamples, and proposes small, testable repairs
 failed hypotheses. The harness records what actually ran and requires independent
 review before a scientific claim can close.
 
-**v0.5.1 is a research preview.** Minimal mode is the default: agents keep their
+**v0.5.2 is the current stable release.** Minimal mode is the default: agents keep their
 native tools and choose their research strategy, while Simjecture manages recorded
 evidence, review and deadlines. Structured and frontier modes remain available.
 The system does not establish physical truth from a successful simulation or promise
 that a long agent run will produce a useful result.
 
-## Start a study
+The workspace includes visible **Continue investigation** and **Send
+guidance** actions in the study view and experiment monitor. Continue with a new
+budget and selected prior files, or send advisory guidance at the next checkpoint.
+See [continuation and steering](docs/how-to/continuation-steering.md).
+
+## Install and open the workspace
+
+On Linux or inside WSL, run:
+
+```bash
+curl -fsSL https://github.com/tomzhu0225/simjecture/releases/download/v0.5.2/install.sh | bash
+```
+
+The installer downloads the versioned release, verifies its checksum, installs uv,
+Python 3.12 and the workspace dependencies, and starts the local GUI. Git and a CLI
+agent are not required. Enter a compatible API endpoint and key in **Connections**, or
+select an existing local CLI from the message composer. Choose **Interactive research**
+for a task, or prepare an **Autonomous research** study together with the agent.
+
+Software lives under `~/simjecture/app/<version>`; conversations, inputs, simulations
+and studies stay in `~/simjecture/artifacts/projects`. Reopen the GUI with
+`~/simjecture/start-workspace`. On SSH hosts the installer prints forwarding instructions
+for your local browser. Keep the server terminal open, or run the launcher in your usual
+session manager. Ubuntu/Debian may request sudo to install Bubblewrap; restricted
+containers can open the GUI but may need a separately configured execution backend.
+
+See [installation options](docs/getting-started/installation.md) and the
+[workspace walkthrough](docs/getting-started/research-workspace.md).
+
+## Start a study from an external CLI
 
 Use Linux with Python 3.11+, [uv](https://docs.astral.sh/uv/), and an installed,
 authenticated native agent CLI. Bubblewrap is the default numerical execution backend.
 
 ```bash
-uv tool install 'simjecture[tui]==0.5.1'
+uv tool install 'simjecture[tui]==0.5.2'
 simjecture install core
 simjecture doctor --execution-backend bubblewrap
 
@@ -180,11 +213,18 @@ simjecture install warpx-cpu
 simjecture doctor --profile warpx-cpu
 ```
 
+The release also includes an [ITER ecosystem pack](docs/how-to/iter-pack.md):
+CHERAB/Raysect synthetic diagnostics, CHERAB-ITER/IMAS adapters and IMAS data tools.
+Use **Research tools → ITER pack → Install**, then **Run demo** for a monitored
+example with plots, or run `simjecture install iter-pack`. JOREK, SOLPS-ITER and
+DINA-PS have separate **Install with agent** entries and source-based guidance;
+they are not silently included in the diagnostics installation.
+
 FLASH source is not redistributed. Solver source inspection can be configured separately
 from a writable problem/build area. See [runtime deployment](docs/how-to/deploy-runtimes.md)
 and the [scientific skills](skills/).
 
-## What v0.5.1 changes
+## Research core introduced in v0.5.1
 
 This release builds on v0.5.0's minimal default and shared interfaces:
 

{simjecture-0.5.1 → simjecture-0.5.2}/README.md

@@ -9,19 +9,48 @@ experiments, searches for counterexamples, and proposes small, testable repairs
 failed hypotheses. The harness records what actually ran and requires independent
 review before a scientific claim can close.
 
-**v0.5.1 is a research preview.** Minimal mode is the default: agents keep their
+**v0.5.2 is the current stable release.** Minimal mode is the default: agents keep their
 native tools and choose their research strategy, while Simjecture manages recorded
 evidence, review and deadlines. Structured and frontier modes remain available.
 The system does not establish physical truth from a successful simulation or promise
 that a long agent run will produce a useful result.
 
-## Start a study
+The workspace includes visible **Continue investigation** and **Send
+guidance** actions in the study view and experiment monitor. Continue with a new
+budget and selected prior files, or send advisory guidance at the next checkpoint.
+See [continuation and steering](docs/how-to/continuation-steering.md).
+
+## Install and open the workspace
+
+On Linux or inside WSL, run:
+
+```bash
+curl -fsSL https://github.com/tomzhu0225/simjecture/releases/download/v0.5.2/install.sh | bash
+```
+
+The installer downloads the versioned release, verifies its checksum, installs uv,
+Python 3.12 and the workspace dependencies, and starts the local GUI. Git and a CLI
+agent are not required. Enter a compatible API endpoint and key in **Connections**, or
+select an existing local CLI from the message composer. Choose **Interactive research**
+for a task, or prepare an **Autonomous research** study together with the agent.
+
+Software lives under `~/simjecture/app/<version>`; conversations, inputs, simulations
+and studies stay in `~/simjecture/artifacts/projects`. Reopen the GUI with
+`~/simjecture/start-workspace`. On SSH hosts the installer prints forwarding instructions
+for your local browser. Keep the server terminal open, or run the launcher in your usual
+session manager. Ubuntu/Debian may request sudo to install Bubblewrap; restricted
+containers can open the GUI but may need a separately configured execution backend.
+
+See [installation options](docs/getting-started/installation.md) and the
+[workspace walkthrough](docs/getting-started/research-workspace.md).
+
+## Start a study from an external CLI
 
 Use Linux with Python 3.11+, [uv](https://docs.astral.sh/uv/), and an installed,
 authenticated native agent CLI. Bubblewrap is the default numerical execution backend.
 
 ```bash
-uv tool install 'simjecture[tui]==0.5.1'
+uv tool install 'simjecture[tui]==0.5.2'
 simjecture install core
 simjecture doctor --execution-backend bubblewrap
 
@@ -141,11 +170,18 @@ simjecture install warpx-cpu
 simjecture doctor --profile warpx-cpu
 ```
 
+The release also includes an [ITER ecosystem pack](docs/how-to/iter-pack.md):
+CHERAB/Raysect synthetic diagnostics, CHERAB-ITER/IMAS adapters and IMAS data tools.
+Use **Research tools → ITER pack → Install**, then **Run demo** for a monitored
+example with plots, or run `simjecture install iter-pack`. JOREK, SOLPS-ITER and
+DINA-PS have separate **Install with agent** entries and source-based guidance;
+they are not silently included in the diagnostics installation.
+
 FLASH source is not redistributed. Solver source inspection can be configured separately
 from a writable problem/build area. See [runtime deployment](docs/how-to/deploy-runtimes.md)
 and the [scientific skills](skills/).
 
-## What v0.5.1 changes
+## Research core introduced in v0.5.1
 
 This release builds on v0.5.0's minimal default and shared interfaces:
 

{simjecture-0.5.1 → simjecture-0.5.2}/THIRD_PARTY_NOTICES.md

@@ -29,3 +29,11 @@ Model providers, literature services, and externally supplied guided
 commissioning packages are services or inputs rather than sublicensed parts of
 this source distribution. Run artifacts must retain the provenance and license
 information supplied by their generators.
+
+The optional ITER ecosystem pack downloads CHERAB, Raysect, CHERAB-IMAS,
+CHERAB-ITER, IMAS-Python, IMAS-Validator and their dependencies under their
+respective upstream licenses. Solver guides refer to separately distributed
+JOREK, SOLPS-ITER/EIRENE and DINA-PS. Their component code, data, citation and
+redistribution terms remain upstream terms; Simjecture does not relicense them
+or imply ITER endorsement. The diagnostic demo is independently authored using
+public APIs; its CHERAB bremsstrahlung API reference is credited in the script.

simjecture-0.5.2/capabilities/iter-pack-1.0.json

@@ -0,0 +1,32 @@
+{
+  "environment": {
+    "MPLBACKEND": "Agg",
+    "OMP_NUM_THREADS": "1",
+    "OPENBLAS_NUM_THREADS": "1",
+    "PYTHONDONTWRITEBYTECODE": "1"
+  },
+  "executable": "bin/python",
+  "identity_files": [
+    "share/build-record.json",
+    "share/installed-requirements.txt"
+  ],
+  "manifest": {
+    "description": "CHERAB/Raysect synthetic diagnostics and IMAS data tools; does not include JOREK, SOLPS or DINA binaries",
+    "executable_kind": "python-iter-pack",
+    "name": "iter-pack-1.0",
+    "preflight_checks": [
+      "checks.completed",
+      "checks.chord_integral",
+      "checks.density_scaling",
+      "checks.imas_roundtrip",
+      "checks.imas_bolometers",
+      "checks.iter_geometry"
+    ],
+    "preflight_resource": "examples/diagnostics_demo.py",
+    "preflight_result": "iter_pack_demo.json",
+    "schema_version": "0.1.0",
+    "skill": "iter-pack",
+    "version": "1.0"
+  },
+  "runtime_root": "../.runtime/iter-pack-1.0"
+}

{simjecture-0.5.1 → simjecture-0.5.2}/capabilities/optab-1.3.1.json

@@ -13,7 +13,9 @@
   "identity_files": [
     "bin/optab",
     "bin/mpi-launcher",
-    "share/build-record.json"
+    "share/build-record.json",
+    "share/preflight/h5/NIST.h5",
+    "share/preflight/1016620_Supplementary_Data/gauntff.dat"
   ],
   "manifest": {
     "description": "Operator-supplied Optab 1.3 MPI/HDF5 opacity-table generator",
@@ -29,7 +31,8 @@
       "checks.process_completed",
       "checks.return_code_zero",
       "checks.hdf5_output_created",
-      "checks.hdf5_output_readable"
+      "checks.hdf5_output_readable",
+      "checks.nist_data_complete"
     ],
     "preflight_resource": "examples/optab_runtime_smoke.py",
     "preflight_result": "optab_capability_smoke.json",

{simjecture-0.5.1 → simjecture-0.5.2}/capabilities/warpx-cuda-openpmd-26.07.json

@@ -36,5 +36,9 @@
     "/opt/acs-dependencies/io": "../.runtime/warpx-cuda-openpmd-deps",
     "/opt/acs-dependencies/wsl-lib": "/usr/lib/wsl/lib"
   },
-  "runtime_root": "../.runtime/warpx-cuda-openpmd"
+  "runtime_root": "../.runtime/warpx-cuda-openpmd",
+  "identity_files": [
+    "share/build-record.json",
+    "lib/python3.12/site-packages/pywarpx/__init__.py"
+  ]
 }

{simjecture-0.5.1 → simjecture-0.5.2}/docs/conf.py

@@ -3,7 +3,7 @@ from __future__ import annotations
 project = "Simjecture"
 author = "Bowen Zhu"
 copyright = "2026, Bowen Zhu and contributors"
-release = "0.5.1"
+release = "0.5.2"
 
 extensions = [
     "myst_parser",

simjecture-0.5.2/docs/development/releasing.md

@@ -0,0 +1,53 @@
+# Release process
+
+Simjecture publishes from a GitHub Release. The release workflow builds the
+source distribution and wheel, verifies that the tag matches the version in
+`pyproject.toml`, and uploads to PyPI with an OpenID Connect credential. No
+long-lived PyPI token is stored in GitHub.
+
+## One-time account connections
+
+Configure a PyPI pending trusted publisher with these exact values:
+
+- PyPI project name: `simjecture`
+- GitHub owner: `tomzhu0225`
+- GitHub repository: `simjecture`
+- Workflow filename: `release.yml`
+- Environment name: `pypi`
+
+In Zenodo's GitHub settings, enable the `tomzhu0225/simjecture` repository.
+Zenodo then archives each new GitHub Release and assigns a version DOI.
+`CITATION.cff` supplies its software metadata.
+
+## Publish a version
+
+1. Update the version in `pyproject.toml`, `CITATION.cff`, `docs/conf.py`,
+   `src/conjecture_solver/__init__.py`, `scripts/install-workspace.sh`, and the changelog.
+   Run `uv lock` and build both Python distributions (`uv build`) and the checksummed
+   workspace bundle (`python scripts/package_workspace.py --output dist`).
+   Verify the installer with `python scripts/verify_workspace_install.py --release-dir dist
+   --work-dir /tmp/simjecture-release-install-check`. This uses a fresh HOME, no API key
+   or CLI agent, and does not change host system packages.
+2. Run the complete local checks and merge them into `main`.
+3. Create an annotated `v<version>` tag on the tested commit.
+4. Publish a GitHub Release from that tag using the matching changelog section.
+5. Verify the GitHub workflow, installer assets/checksums, PyPI files, and Zenodo deposit before announcing
+   the release.
+
+Publishing the GitHub Release is intentionally last: it triggers both external
+publication paths and cannot be treated as a rehearsal.
+
+## Preview policy
+
+Ship user-facing changes first as explicit release candidates (`0.5.2rc1`, `0.5.2rc2`, …).
+Use matching GitHub tags (`v0.5.2rc1`) and mark the GitHub release **prerelease**, without
+moving the stable/latest release. PyPI receives the PEP 440 prerelease version; ordinary
+stable installs do not automatically select it. The optional npm bundle uses the matching
+SemVer spelling (`0.5.2-rc.1`). Document a versioned, one-command installer URL so testing
+is repeatable. Never replace an already published preview's artifacts with different code.
+
+Record setup, interface, simulation and session-continuity feedback against the exact
+preview version. Publish a new candidate for fixes. The installer keeps versioned program
+folders and stable research-data folders; retain old versions during the preview period.
+After user testing and release checks pass, publish `0.5.2` as stable and update the default
+installer link. A preview is not a claim of scientific qualification for solver applications.

{simjecture-0.5.1 → simjecture-0.5.2}/docs/getting-started/first-run.md

@@ -13,18 +13,21 @@ uv run simjecture web demos/gray_scott_counterexample/record --read-only
 See [Recorded Gray–Scott demo](../demos/gray-scott.md) for the scientific result
 and the boundaries of that record.
 
-To start a new study, install and log in to a supported native agent CLI
-(Codex GLM, Codex, Grok or AGY), then open the browser:
+For a fresh setup, use the [one-command installer](installation.md), then open the
+workspace. Enter a compatible API endpoint/key in **Connections**, or use a native CLI
+that you have already installed and authenticated. Choose the agent/model in the composer.
 
-```bash
-uv run simjecture web
-```
+Ask the agent to prepare a bounded study, for example:
+
+> Test whether explicit Euler for y' = -y preserves nonnegativity for every positive
+> time step. Search for a counterexample, record the Python calculation, and request
+> independent review. A reviewed negative answer completes the study. Budget five minutes.
 
-In **New hypothesis**, choose mode, backend and model separately. **Minimal** is
-the default. It keeps the agent's native tools and planning freedom while recording
-experiments, counterexample searches, hypothesis repairs and independent reviews.
-Structured and frontier modes remain selectable. DSH and direct API routes are
-explicit legacy choices and require their separate provider configuration.
+Review the prepared brief, open **Autonomous research**, and start it. The workspace
+uses the existing minimal research core, with recorded experiments and independent
+review. A timeout without review is incomplete work, not an accepted negative answer.
+The advanced **New hypothesis** form remains at `/monitor` for explicit mode and
+execution configuration. See the [workspace walkthrough](research-workspace.md).
 
 For a terminal run, write a bounded statement in `hypothesis.txt` and its test
 scope, resource constraints and acceptance criteria in `instructions.md`:
@@ -42,7 +45,7 @@ deadline are retained on resume.
 
 Minimal records include `research.json`, immutable experiment snapshots,
 prospective repair commitments, independent review receipts and a final
-`research_report.json`. A clean agent exit is only a checkpoint. A supported root
+`research_report.json`. A clean agent exit is only a checkpoint. Under the default CLI `repair` completion policy, a supported root
 or an accepted falsification followed by a supported repair completes the study;
 uncertainty stays unresolved. Numerical convergence and physical validity remain
 scientific obligations. See [minimal research](../how-to/research-service.md).