simjecture 0.6.0__tar.gz → 0.6.2__tar.gz

simjecture-0.6.2/.gitattributes

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+*.sh text eol=lf
+
+# Preserve autonomous run artifacts byte-for-byte, including model-authored
+# formatting. Generated figures likewise need not satisfy source whitespace
+# checks.
+demos/gray_scott_counterexample/record/** -text -whitespace
+demos/collisionless_gem_reconnection/record/** -text -whitespace
+demos/kepler_energy/record/** -text -whitespace
+demos/resistive_mhd_island_coalescence/minimal_record/** -text -whitespace
+demos/resistive_mhd_island_coalescence/sol_medium_record/** -text -whitespace
+demos/flash_warpx_kinetic_patch/record/** -text -whitespace
+docs/_static/demos/*.svg -whitespace
+
+*.npz binary
+*.png binary
+
+demos/resistive_mhd_island_coalescence/continuation_record/** -text -whitespace
+demos/flash_warpx_kinetic_patch/continuation_record/** -text -whitespace

simjecture-0.6.2/.github/ISSUE_TEMPLATE/bug.yml

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+name: Bug report
+description: Something failed, behaved unexpectedly, or was difficult to use.
+body:
+  - type: markdown
+    attributes:
+      value: |
+        A small reproduction is very helpful. Remove API keys, credentials and private data from logs. For sensitive security reports, follow SECURITY.md instead.
+  - type: textarea
+    id: problem
+    attributes:
+      label: What happened?
+      description: What did you expect, and what did you observe?
+    validations:
+      required: true
+  - type: textarea
+    id: reproduce
+    attributes:
+      label: How can we reproduce it?
+      description: Commands, inputs or interface steps. Include a short log or screenshot if useful.
+    validations:
+      required: true
+  - type: textarea
+    id: environment
+    attributes:
+      label: Version and environment
+      description: Package version or Git commit, OS, local/hosted workspace, agent and execution backend. Mention relevant solver or hardware details.
+    validations:
+      required: true

simjecture-0.6.2/.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: true
+contact_links:
+  - name: Contribution guide
+    url: https://github.com/tomzhu0225/simjecture/blob/main/CONTRIBUTING.md
+    about: Setup, checks, scientific records and attribution.

simjecture-0.6.2/.github/ISSUE_TEMPLATE/contribution.yml

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+name: Tool, study or improvement
+description: Propose a scientific tool, diagnostic, study or project improvement.
+body:
+  - type: textarea
+    id: idea
+    attributes:
+      label: What would you like to contribute or improve?
+      description: Describe the question or user problem and the result you would like to see.
+    validations:
+      required: true
+  - type: textarea
+    id: starting_point
+    attributes:
+      label: Starting point
+      description: Existing code, a paper, a working example, a proposed hypothesis, or a specific documentation/UI change. For upstream software or data, include its license if known.
+  - type: textarea
+    id: validation
+    attributes:
+      label: How could we check it?
+      description: A numerical control, small reproducible case, or behavior to test. Mention hardware or access requirements and any help you need.

simjecture-0.6.2/.github/pull_request_template.md

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+## What changed and why
+
+<!-- Describe the concrete problem and resulting behavior. Link a related issue if there is one. -->
+
+## Validation
+
+<!-- Commands/checks and their results. Separate passes from unavailable, skipped or still-running checks. For UI/docs styling, include a rendered screenshot. -->
+
+## Scientific scope or compatibility
+
+<!-- If applicable: changed assumptions, diagnostics, evidence eligibility, runtime requirements, upstream license/credit, or migration notes. Delete this section when it is not relevant. -->

simjecture-0.6.2/.github/workflows/ci.yml

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+name: ci
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  windows-application-boundary:
+    runs-on: windows-latest
+    timeout-minutes: 5
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.12"]
+    steps:
+      - uses: actions/checkout@v7
+      - uses: actions/setup-python@v7
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Test shared Windows process ownership without vendor applications
+        run: python scripts/check_cst_windows.py
+      - name: Test legacy CST entrypoint compatibility
+        run: python scripts/check_cst_windows.py --runner src/conjecture_solver/cst_windows.py
+
+  documentation:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@v7
+      - uses: actions/setup-python@v7
+        with:
+          python-version: "3.12"
+      - name: Install uv
+        run: python -m pip install uv
+      - name: Install documentation environment
+        run: uv sync --frozen --group docs
+      - name: Build documentation without warnings
+        run: uv run --group docs sphinx-build -W --keep-going -b html docs docs/_build/html
+      - name: Check generated documentation links
+        run: uv run python scripts/check_docs_links.py docs/_build/html
+
+  deterministic-core:
+    runs-on: ubuntu-latest
+    # Pytest takes about 13 minutes; leave time for setup and integration checks.
+    timeout-minutes: 30
+    steps:
+      - uses: actions/checkout@v7
+      - uses: actions/setup-python@v7
+        with:
+          python-version: "3.12"
+      - name: Install sandbox runtime
+        run: |
+          sudo apt-get update
+          sudo apt-get install --yes bubblewrap
+          if sysctl kernel.unprivileged_userns_clone > /dev/null 2>&1; then
+            sudo sysctl -w kernel.unprivileged_userns_clone=1
+          fi
+          if sysctl kernel.apparmor_restrict_unprivileged_userns > /dev/null 2>&1; then
+            sudo sysctl -w kernel.apparmor_restrict_unprivileged_userns=0
+          fi
+          bwrap --unshare-all --die-with-parent \
+            --ro-bind /usr /usr \
+            --ro-bind /lib /lib \
+            --ro-bind /lib64 /lib64 \
+            /usr/bin/true
+      - name: Install uv
+        run: python -m pip install uv
+      - name: Install locked environment
+        run: uv sync --frozen --extra tui --extra dsh --extra workspace --extra public --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"
+          cache: npm
+          cache-dependency-path: integrations/dsh/package-lock.json
+      - name: Install pinned DSH test runtime
+        run: npm ci --prefix integrations/dsh
+      - name: Test DSH adapter and real MCP profile
+        run: SIMJECTURE_MCP_EXECUTABLE="$PWD/.venv/bin/simjecture-mcp" npm test --prefix integrations/dsh
+      - name: Lint
+        run: uv run ruff check .
+      - name: Test
+        run: uv run pytest --cov=conjecture_solver --cov-report=term-missing --durations=20
+      - name: Build source distribution and wheel from it
+        run: uv build --out-dir /tmp/simjecture-python-distributions
+      - 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
+        run: uv run simjecture benchmark electrostatic-pic --assert-falsified
+      - name: Run recoverable planted campaign
+        run: uv run simjecture campaign planted --ledger /tmp/acs-ci.sqlite3 --output /tmp/acs-artifact
+      - name: Verify discovery package
+        run: uv run simjecture package verify /tmp/acs-artifact/discovery_package.json
+      - name: Run PIC discovery campaign
+        run: uv run simjecture campaign pic --ledger /tmp/acs-pic-ci.sqlite3 --output /tmp/acs-pic-artifact
+      - name: Verify PIC discovery package
+        run: uv run simjecture package verify /tmp/acs-pic-artifact/discovery_package.json
+      - name: Run blinded search and independent confirmation
+        run: >-
+          uv run simjecture search blinded --offline-ai-fixture
+          --ledger /tmp/acs-blinded-ci.sqlite3
+          --output /tmp/acs-blinded-artifact
+      - name: Run budgeted multi-action campaign
+        run: >-
+          uv run simjecture orchestrate blinded --offline-ai-fixture
+          --ledger /tmp/acs-multi-action-ci.sqlite3
+          --output /tmp/acs-multi-action-artifact
+      - name: Verify committed schemas
+        run: uv run simjecture schemas --output schemas --check
+      - name: Verify recorded autonomous demos
+        run: |
+          uv run python demos/kepler_energy/verify_record.py
+          uv run python demos/resistive_mhd_island_coalescence/verify_minimal_record.py
+          uv run python scripts/verify_research_audit.py demos/resistive_mhd_island_coalescence/sol_medium_record
+          uv run python scripts/verify_research_audit.py demos/flash_warpx_kinetic_patch/record
+          uv run python scripts/verify_research_audit.py demos/flash_warpx_kinetic_patch/continuation_record
+          uv run python scripts/verify_research_audit.py demos/resistive_mhd_island_coalescence/continuation_record
+          uv run python demos/resistive_mhd_island_coalescence/postrun_coordinate_check.py
+          uv run python demos/gray_scott_counterexample/verify_record.py
+          uv run python demos/collisionless_gem_reconnection/verify_record.py
+          uv run python demos/agent_roles_validation/verify_record.py
+
+  warpx-instrument:
+    runs-on: ubuntu-latest
+    timeout-minutes: 25
+    defaults:
+      run:
+        shell: bash -leo pipefail {0}
+    steps:
+      - uses: actions/checkout@v7
+      - uses: mamba-org/setup-micromamba@v3
+        with:
+          environment-file: environments/warpx-cpu.yml
+          environment-name: acs-warpx-cpu-26-07
+          cache-environment: true
+          init-shell: bash
+      - name: Install project tooling
+        run: |
+          python -m pip install uv
+          uv sync --frozen
+      - name: Verify the deployable WarpX CPU capability
+        run: |
+          sudo apt-get update
+          sudo apt-get install --yes bubblewrap
+          if sysctl kernel.unprivileged_userns_clone > /dev/null 2>&1; then
+            sudo sysctl -w kernel.unprivileged_userns_clone=1
+          fi
+          if sysctl kernel.apparmor_restrict_unprivileged_userns > /dev/null 2>&1; then
+            sudo sysctl -w kernel.apparmor_restrict_unprivileged_userns=0
+          fi
+          mkdir -p .runtime
+          ln -s "$CONDA_PREFIX" .runtime/warpx-cpu
+          uv run simjecture doctor --profile warpx-cpu
+      - name: Compile restricted reference and candidate PICMI inputs
+        run: >-
+          uv run python scripts/qualify_warpx.py
+          --python "$CONDA_PREFIX/bin/python"
+          --work-directory /tmp/acs-warpx-qualification
+          --output /tmp/acs-warpx-qualification.json
+      - name: Qualify openPMD diagnostics and physics on the fixed matrix
+        run: >-
+          uv run python scripts/qualify_warpx_physics.py
+          --warpx-python "$CONDA_PREFIX/bin/python"
+          --work-root /tmp/acs-warpx-physics-qualification
+          --output /tmp/acs-warpx-physics-qualification.json
+      - name: Run the durable analytic-to-qualified-WarpX campaign
+        run: >-
+          uv run python scripts/run_qualified_warpx_campaign.py
+          /tmp/acs-warpx-physics-qualification.json
+          --offline-ai-fixture
+          --warpx-python "$CONDA_PREFIX/bin/python"
+          --work-root /tmp/acs-warpx-confirmation
+          --ledger /tmp/acs-qualified-warpx-campaign.sqlite3
+          --output /tmp/acs-qualified-warpx-campaign
+      - name: Verify qualified WarpX campaign package
+        run: >-
+          uv run simjecture package verify
+          /tmp/acs-qualified-warpx-campaign/qualified_warpx_campaign_package.json
+      - uses: actions/upload-artifact@v7
+        with:
+          name: warpx-instrument-records
+          path: |
+            /tmp/acs-warpx-qualification.json
+            /tmp/acs-warpx-physics-qualification.json
+            /tmp/acs-warpx-physics-qualification_results.json
+            /tmp/acs-qualified-warpx-campaign.sqlite3
+            /tmp/acs-qualified-warpx-campaign/

simjecture-0.6.2/.github/workflows/docs.yml

@@ -0,0 +1,62 @@
+name: Publish documentation
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - docs/**
+      - demos/**
+      - src/conjecture_solver/web/static/brand/**
+      - scripts/check_docs_links.py
+      - pyproject.toml
+      - uv.lock
+      - .github/workflows/docs.yml
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: documentation-pages
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    permissions:
+      contents: read
+      pages: read
+    steps:
+      - uses: actions/checkout@v7
+      - uses: actions/setup-python@v7
+        with:
+          python-version: "3.12"
+      - uses: actions/configure-pages@v6
+      - name: Install locked documentation environment
+        run: |
+          python -m pip install uv
+          uv sync --frozen --group docs
+      - name: Build and validate
+        run: |
+          uv run --group docs sphinx-build -W --keep-going -b html docs docs/_build/html
+          uv run python scripts/check_docs_links.py docs/_build/html
+      - uses: actions/upload-pages-artifact@v5
+        with:
+          path: docs/_build/html
+
+  deploy:
+    if: github.ref == 'refs/heads/main'
+    needs: build
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    permissions:
+      pages: write
+      id-token: write
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Publish validated documentation
+        id: deployment
+        uses: actions/deploy-pages@v5