scitex-agentic-journal 0.1.0a0__tar.gz

scitex_agentic_journal-0.1.0a0/.claude/scheduled_tasks.lock

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+{"sessionId":"8b9f6dd8-9ead-4985-837a-88a4fd926d38","pid":31,"procStart":"11843348","acquiredAt":1781336370538}

scitex_agentic_journal-0.1.0a0/.env.example

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+# scitex-agentic-journal — example environment.
+#
+# Copy to `.env` (or export inline) and edit the values you actually
+# need. Lines beginning with `#` are documentation only; this file is
+# checked into git, the real `.env` is not.
+#
+# The package itself reads no env vars at runtime today; the SCITEX_*
+# vars below are scaffold knobs read by the CLI and the (not-yet-shipped)
+# Gate-1 orchestrator. They are documented here so the PS-129 audit
+# rule can confirm every `SCITEX_AGENTIC_JOURNAL_*` token referenced in
+# `src/` has a discoverable description.
+
+# Path to an alternate YAML config for the CLI / orchestrator. When
+# unset, the CLI falls back to `./config.yaml`, then to
+# `~/.scitex/agentic-journal/config.yaml`.
+# SCITEX_AGENTIC_JOURNAL_CONFIG=/abs/path/to/config.yaml

scitex_agentic_journal-0.1.0a0/.github/workflows/cla.yml

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+name: CLA Assistant
+
+on:
+  issue_comment:
+    types: [created]
+  pull_request_target:
+    types: [opened, closed, synchronize]
+
+permissions:
+  actions: write
+  contents: write
+  pull-requests: write
+  statuses: write
+
+jobs:
+  CLAssistant:
+    runs-on: ubuntu-latest
+    steps:
+      - name: CLA Assistant
+        uses: contributor-assistant/github-action@v2.6.1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          PERSONAL_ACCESS_TOKEN: ${{ secrets.GH_PERSONAL_ACCESS_TOKEN }}
+        with:
+          path-to-signatures: "signatures/cla.json"
+          path-to-document: "https://github.com/ywatanabe1989/scitex-agentic-journal/blob/main/CLA.md"
+          branch: "cla-signatures"
+          allowlist: bot*,ywatanabe1989
+          custom-allsigned-prcomment: |
+            Thank you for signing the SciTeX CLA. Your contribution can now be reviewed.
+          custom-notsigned-prcomment: |
+            Please sign the [SciTeX CLA](https://github.com/ywatanabe1989/scitex-agentic-journal/blob/main/CLA.md) before your contribution can be merged.
+            Comment `I have read and agree to the SciTeX CLA.` to sign.

scitex_agentic_journal-0.1.0a0/.github/workflows/pr-ci.yml

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+name: pr-ci
+
+# Consolidated PR-only CI gate. Runs the per-PR validation suite as a
+# single workflow so the cancel-in-progress concurrency group, path
+# filters, and uv cache apply uniformly. Post-merge validation lives
+# in release-ci.yml.
+#
+# L1 concurrency — cancel superseded PR runs.
+# L3 path filters — skip docs/skills/examples/markdown-only PRs.
+# L4 conditional matrix — full ["3.11", "3.12", "3.13"] on PR (this trigger).
+# L5a uv-managed Python (`uv python install` + `uv venv --python`) so the
+#     matrix leg is not bound to the runner's system Python.
+# L5b .venv/bin on PATH (and explicit `.venv/bin/python` for clarity) so
+#     console scripts resolve without needing `uv run`.
+
+on:
+  pull_request:
+    branches: [main, develop]
+    paths-ignore:
+      - 'docs/**'
+      - '_skills/**'
+      - 'examples/**'
+      - '**.md'
+      - 'CHANGELOG.*'
+      - '.github/CODEOWNERS'
+      - '.github/ISSUE_TEMPLATE/**'
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.event_name == 'pull_request' }}
+
+jobs:
+  import-smoke:
+    name: import-smoke-on-ubuntu-py3-12
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+          cache-dependency-glob: pyproject.toml
+      - name: Set up Python 3.12 (uv-managed)
+        run: uv python install 3.12
+      - name: Install (no extras) in uv venv
+        run: |
+          uv venv --python 3.12 .venv
+          uv pip install --python .venv/bin/python -e .
+      - name: Import smoke
+        run: .venv/bin/python -c "import scitex_agentic_journal; print(getattr(scitex_agentic_journal, '__version__', 'unversioned'))"
+      - name: smoke scitex-agentic-journal --help
+        run: .venv/bin/scitex-agentic-journal --help
+  dep-hygiene-smoke:
+    name: dep-hygiene-smoke
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+          cache-dependency-glob: pyproject.toml
+      - name: Set up Python 3.11 (uv-managed)
+        run: uv python install 3.11
+      - name: Bare install (no extras) in uv venv
+        run: |
+          uv venv --python 3.11 .venv
+          uv pip install --python .venv/bin/python .
+      - name: Import package
+        run: .venv/bin/python -c "import scitex_agentic_journal; print(scitex_agentic_journal.__name__)"
+
+  tests:
+    name: pytest-matrix-on-ubuntu-py${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ${{ github.event_name == 'pull_request' && fromJson('["3.11", "3.12", "3.13"]') || fromJson('["3.12"]') }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+          cache-dependency-glob: pyproject.toml
+      - name: Set up Python ${{ matrix.python-version }} (uv-managed)
+        run: uv python install ${{ matrix.python-version }}
+      - name: Create uv venv on this matrix Python
+        run: uv venv --python ${{ matrix.python-version }} .venv
+      - name: Install dependencies
+        # Fallback chain: prefer [all,dev] so optional-dep code paths
+        # get exercised. Falls back to [dev] then plain editable so a
+        # packaging hiccup doesn't strand CI.
+        run: |
+          uv pip install --python .venv/bin/python -e ".[all,dev]" \
+            || uv pip install --python .venv/bin/python -e ".[dev]" \
+            || uv pip install --python .venv/bin/python -e .
+      - name: Run tests
+        # PATH prepend so any test that subprocess-calls a console script
+        # finds it in .venv/bin/.
+        run: |
+          export PATH="$PWD/.venv/bin:$PATH"
+          .venv/bin/pytest tests/ --cov=src/scitex_agentic_journal --cov-report=xml --cov-report=term
+      - name: Upload coverage to Codecov
+        if: always() && matrix.python-version == '3.12'
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          fail_ci_if_error: false
+
+  audit:
+    name: audit
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+          cache-dependency-glob: pyproject.toml
+      - name: Set up Python 3.12 (uv-managed)
+        run: uv python install 3.12
+      - name: Install package + audit tooling
+        run: |
+          uv venv --python 3.12 .venv
+          uv pip install --python .venv/bin/python -e ".[dev]"
+          uv pip install --python .venv/bin/python "scitex-dev[cli-audit]"
+      - name: Run scitex-dev ecosystem audit-all
+        run: |
+          export PATH="$PWD/.venv/bin:$PATH"
+          scitex-dev ecosystem audit-all scitex-agentic-journal --no-version-check

scitex_agentic_journal-0.1.0a0/.github/workflows/release-ci.yml

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+name: release-ci
+
+# Post-merge validation gate. Runs on push to protected branches
+# (main, develop) and as the canonical scheduled run. Always uses the
+# FULL pytest matrix — no conditional skipping — so the protected-branch
+# history is exercised on every supported Python.
+#
+# L1 concurrency — coalesce overlapping pushes on the same branch.
+# L5a uv-managed Python (`uv python install` + `uv venv --python`) so each
+#     matrix leg pins its interpreter independently of the runner.
+# L5b .venv/bin on PATH so console scripts resolve without `uv run`.
+
+on:
+  push:
+    branches: [main, develop]
+  schedule:
+    - cron: "0 7 * * *"  # nightly 07:00 UTC
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: false
+
+jobs:
+  tests:
+    name: pytest-matrix-on-ubuntu-py${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+          cache-dependency-glob: pyproject.toml
+      - name: Set up Python ${{ matrix.python-version }} (uv-managed)
+        run: uv python install ${{ matrix.python-version }}
+      - name: Create uv venv on this matrix Python
+        run: uv venv --python ${{ matrix.python-version }} .venv
+      - name: Install dependencies
+        run: |
+          uv pip install --python .venv/bin/python -e ".[all,dev]" \
+            || uv pip install --python .venv/bin/python -e ".[dev]" \
+            || uv pip install --python .venv/bin/python -e .
+      - name: Run tests
+        run: |
+          export PATH="$PWD/.venv/bin:$PATH"
+          .venv/bin/pytest tests/ --cov=src/scitex_agentic_journal --cov-report=xml --cov-report=term
+      - name: Upload coverage to Codecov
+        if: always() && matrix.python-version == '3.12'
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          fail_ci_if_error: false
+
+  import-smoke:
+    name: import-smoke-on-ubuntu-py3-12
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+          cache-dependency-glob: pyproject.toml
+      - name: Set up Python 3.12 (uv-managed)
+        run: uv python install 3.12
+      - name: Install (no extras) in uv venv
+        run: |
+          uv venv --python 3.12 .venv
+          uv pip install --python .venv/bin/python -e .
+      - name: Import smoke
+        run: .venv/bin/python -c "import scitex_agentic_journal; print(getattr(scitex_agentic_journal, '__version__', 'unversioned'))"
+
+  audit:
+    name: audit
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+          cache-dependency-glob: pyproject.toml
+      - name: Set up Python 3.12 (uv-managed)
+        run: uv python install 3.12
+      - name: Install package + audit tooling
+        run: |
+          uv venv --python 3.12 .venv
+          uv pip install --python .venv/bin/python -e ".[dev]"
+          uv pip install --python .venv/bin/python "scitex-dev[cli-audit]"
+      - name: Run scitex-dev ecosystem audit-all
+        run: |
+          export PATH="$PWD/.venv/bin:$PATH"
+          scitex-dev ecosystem audit-all scitex-agentic-journal --no-version-check

scitex_agentic_journal-0.1.0a0/.gitignore

@@ -0,0 +1,19 @@
+__pycache__/
+*.py[cod]
+*$py.class
+*.egg-info/
+.eggs/
+build/
+dist/
+.venv/
+venv/
+.coverage
+.coverage.*
+htmlcov/
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+.tox/
+GITIGNORED/
+.DS_Store
+.worktrees/

scitex_agentic_journal-0.1.0a0/.scitex/dev/cli-audit-dict.yaml

@@ -0,0 +1,18 @@
+# Project-local overrides for scitex-dev's CLI audit dictionary.
+#
+# Tokens listed here override the default noun/verb classification
+# the auditor derives from CATALOG / moby. See
+# `scitex_dev._cli.audit._summary._audit:_load_custom_dict`.
+
+# Verbs that don't need a sibling — the CLI verb at the top level is
+# a complete (intransitive) action.
+intransitive_verbs:
+  # `scitex-agentic-journal hub-manifest` is the agentic-journal
+  # mirror of scitex-live-paper's `hub-manifest` Click verb (PR #45).
+  # The verb is intransitive: the action is "emit the wrapper manifest
+  # JSON to stdout"; the verb name reads as a noun ("hub manifest") in
+  # the bare token-classifier sense, but the action it performs is a
+  # complete unit (no object needed; redirect to `> manifest.json` is
+  # the canonical use). Mirrors what live-paper already ships
+  # cross-package.
+  - hub-manifest

scitex_agentic_journal-0.1.0a0/CHANGELOG.md

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+# Changelog
+
+All notable changes to `scitex-agentic-journal` are documented in this file.
+
+## [Unreleased]
+
+### Added
+- Leaf `_django` demo surface (aj-leaf-django): `_django/_leaf.py`
+  (Django-free helpers: real-FS archive list, deterministic mock
+  validator panel, browse/share payloads, HTML payload via the
+  live-paper ports contract — no core fork) + `dashboard/` route
+  (`decision_dashboard()` verdict→badge-status rows + counts for
+  the Monday demo). Placeholder/503 contracts kept. Tests:
+  `tests/scitex_agentic_journal/_django/test__leaf.py` (10 tests).
+- M5 publish hand-off (#9 → PR #27): `_publish.publish_submission`,
+  `_publish.LocalFilesystemLivePaperPort` (default in-process port that
+  writes the Live Paper bundle envelope to
+  `<home>/published/<submission_id>/bundle.json`),
+  `_publish.RemoteLivePaperPortStub` (NotImplementedError stub for the
+  future HTTP/MCP port), `_publish.load_submission_records` +
+  `PublishLoadError` (refuses to publish unless gate1/review/decision/
+  persistent_id are all on disk and the decision verdict is `accept`).
+  CLI: `scitex-agentic-journal publish <submission-id>` with the
+  audit-§6 mutating-verb flags `--dry-run` / `--yes`. Prints
+  `PUBLISHED submission_id=... viewer_url=... persistent_id=...` on
+  success.
+- M4 persistent-ID minting (#8 → PR #26): `_publish.mint_for_submission`
+  + `MintLoadError` (orchestrates a mint over a persisted Gate-1
+  record), `_publish.persist_persistent_id` + `PersistedPersistentId`
+  (drops `persistent_id.json` next to `gate1.json` / `review.json` /
+  `decision.json`). `_publish._zenodo.ZenodoSandboxStub` now mints
+  against the real `sandbox.zenodo.org` REST API over real HTTP — token
+  from `SCITEX_AJ_ZENODO_SANDBOX_TOKEN`. `ZenodoStub` (production)
+  shares the same HTTP code path against `zenodo.org` when
+  `SCITEX_AJ_ZENODO_TOKEN` is set; both raise loud `RuntimeError` on
+  missing token or non-2xx response (no silent fallback). The opt-in
+  network test exercises the sandbox round-trip when
+  `SCITEX_RUN_NETWORK_TESTS=1` + `SCITEX_AJ_ZENODO_SANDBOX_TOKEN` are
+  both present.
+- M3 editorial decision engine (#7 → PR #28): `_decide.DecisionEngine`
+  produces `accept | revise | reject` over the immutable
+  `ReviewRecord` from M2. Rules-set is versioned + auditable
+  (`_decide/rules/v1.yaml`, bundled via
+  `[tool.setuptools.package-data]`) — no silent thresholds in code.
+  Every rule emits a `RuleHit` (both pass and fail) so the persisted
+  `decision.json` proves which rules passed alongside which failed.
+  Verdict precedence: first failing reject rule wins reject; otherwise
+  first failing revise rule wins revise; otherwise accept.
+  `_decide.persist_decision` + `PersistedDecision` drop
+  `decision.json` next to `gate1.json` / `review.json`. CLI:
+  `scitex-agentic-journal decide <submission-id>` prints
+  `DECISION submission_id=... verdict=... rules_version=... content_hash=...`.
+- M2 reviewer-agent harness (#6 → PR #25): `_review.ReviewRunner` runs
+  all four ARA sub-reports (reproducibility, claim verify, novelty,
+  methodology) against one submission in rubric order via a pluggable
+  `ReviewerAdapter` protocol. Ships `LocalDeterministicAdapter` (the
+  in-memory dev/test adapter) and `QwenAdapterStub` (NotImplementedError
+  placeholder until the live endpoint is wired). `_review.persist_review`
+  + `PersistedReview` write `review.json` (sha256 content_hash +
+  `written_at_utc`) next to `gate1.json`. CLI:
+  `scitex-agentic-journal review <submission-id> [--adapter local]
+  [--prompts-version v1]` prints `REVIEW DONE submission_id=...
+  adapter=... content_hash=...`.
+- M1 CLI orchestrator (#5 → PR #24): `_submit.run_gate1` runs the three
+  Gate-1 checks (ORCID → code-repo → Clew DAG) in declared order and
+  short-circuits on the first failure with a structured `Gate1Failure`
+  wrapping the underlying `GateFailure`. `_submit.persist_verdict` +
+  `PersistedSubmission` mint a sortable, opaque submission id
+  (`sub_YYYY_MM_DD_<6-hex>`) and drop `gate1.json` under
+  `$SCITEX_AGENTIC_JOURNAL_HOME/submissions/<id>/`. CLI:
+  `scitex-agentic-journal submit <bundle-dir>` prints
+  `GATE-1 PASS submission_id=...` on success and one structured
+  `GATE-1 FAIL [<check>]: <reason> -- <detail>` line on failure.
+- M1.3 Clew-DAG verification (#4 → PR #21): `_gate1.verify_clew_dag`
+  shells out to the real `clew claim verify` binary against the
+  bundled DAG and returns a `ClewVerification` recording the green /
+  red claim ids and total claim count. Loud `GateFailure` when no
+  green claim is present, when `clew` is missing from PATH, or when
+  the DAG directory is malformed. Opt-in real test gated on
+  `SCITEX_RUN_CLEW_TESTS=1` + `clew` on PATH.
+
+- `_gate1.clone_code_repo(repo_url, destination, *, depth=1, ref=None,
+  timeout_s=60.0)` — second slice of the M1 submission gate. Shells out
+  to the real system `git` binary to shallow-clone the author's code
+  repository. Loud structured `GateFailure` on empty URL, missing `git`
+  binary, pre-existing destination, clone failure (exit code + stderr
+  excerpt), or timeout. On any failure the partially-populated
+  destination is removed.
+- `_gate1.cloned_code_repo(repo_url, ...)` — context-manager helper that
+  clones into a tempdir and cleans up on exit, so the CLI orchestrator
+  (issue #5) does not have to manage tempdirs itself.
+- `_gate1.ClonedRepo` dataclass exposing `repo_url`, `path`,
+  `head_commit`, `head_subject` so downstream gates can identify what
+  was reviewed without re-cloning.
+- `tests/test_gate1_code_repo.py` — hermetic test suite that builds a
+  real local bare git repo with one real commit and clones via a
+  `file://` URL. Real `git` binary, real subprocess, real disk; no
+  `subprocess` patching, no respx/responses replay (STX-NM001-003 /
+  PA-306 compliant). One opt-in `@pytest.mark.network` test clones
+  `github.com/octocat/Hello-World` when `SCITEX_RUN_NETWORK_TESTS=1`.
+- `scitex_agentic_journal._gate1` package — first slice of the M1 submission
+  gate. Public surface: `GateFailure` (structured failure exception),
+  `verify_orcid(orcid_id, *, session=None, base_url=...)`, `OrcidRecord`,
+  and `ORCID_PUB_API_BASE` constant.
+- `verify_orcid` resolves an ORCID iD against the public ORCID v3.0 API
+  via real HTTP (`requests`). Accepts bare iDs and any `orcid.org` /
+  `sandbox.orcid.org` URL form. Verifies the ISO 7064 MOD 11-2 check
+  digit before any network call. Loud, structured `GateFailure` on
+  malformed iD / bad checksum / 404 / non-2xx / non-JSON body /
+  unfamiliar record shape / network unreachable. No silent fallbacks,
+  no mocks.
+- `tests/test_gate1_orcid.py` — hermetic test suite that spins up a real
+  local stdlib `http.server` on an ephemeral port and exercises
+  `verify_orcid` over real TCP via the `base_url` config seam (no
+  monkey-patching, no respx/responses replay library — STX-NM001-003 /
+  PA-306 compliant). One opt-in `@pytest.mark.network` test hits the
+  real `pub.orcid.org` when `SCITEX_RUN_NETWORK_TESTS=1`.
+- `pyproject.toml`: register the `network` pytest marker.
+- README "What it is" section spelling out the AI-agent-driven peer-review /
+  copy-edit / publication-readiness role, and an explicit "MVP loop"
+  (submit → agent review → decision → publish) section that maps to the
+  initial GitHub issues.
+- README "Full pipeline (design target)" section with a 4-gate flow
+  (structural gate → AI review → editorial decision → persistent ID) so the
+  MVP loop and the long-term target are no longer collapsed.
+- Roadmap expanded from 5 to 7 milestones (M1–M7) with an explicit editorial
+  decision engine (M3), persistent ID stage (M4), Live Paper hand-off (M5),
+  reviewer dashboard (M6) and MCP server (M7).
+- `scitex-scholar` added to the dependency direction diagram as the source of
+  novelty / literature triangulation.
+- GitHub Actions CI workflow (`.github/workflows/ci.yml`) running `pytest` on
+  Python 3.10 / 3.11 / 3.12 for `push` and `pull_request` against `main` and
+  `develop`.
+- `pyproject.toml`: `license-files`, extra keywords (`agentic-review`,
+  `peer-review`, `reproducibility`), extra classifiers
+  (`Framework :: Django`, information analysis, LaTeX), and a `Changelog`
+  project URL.
+
+## [0.1.0-alpha] — 2026-06-12
+
+### Added
+- Initial scaffold with purpose + 5-milestone roadmap.
+- README pipeline diagram (submit -> ORCID+code+DAG gate -> AI review -> persistent ID -> Live Paper).
+- Dependency direction documented: consumer of `scitex-clew` (claim model owner), emits to `scitex-live-paper`.
+- `pyproject.toml` with `scitex-dev`, `scitex-ui`, `django`, `click`, `requests`, `pyyaml` runtime deps.
+- Package skeleton at `src/scitex_agentic_journal/` with version export.
+- Smoke test.

scitex_agentic_journal-0.1.0a0/CLA.md

@@ -0,0 +1,71 @@
+# SciTeX Contributor License Agreement (CLA)
+
+Thank you for your interest in contributing to `scitex-agentic-journal`,
+part of the [SciTeX](https://scitex.ai) ecosystem owned by Yusuke
+Watanabe / 株式会社 SciTeX (in formation).
+
+By making a contribution to this project (a commit, a pull request, a
+patch, a code review fix-up, an issue with proposed wording, a
+documentation change, etc.) you agree to the following terms for that
+contribution.
+
+## 1. Definitions
+
+- **You** (or **Your**) means the individual or legal entity submitting
+  a Contribution.
+- **Contribution** means any work of authorship — including any
+  modification or addition to existing work — that is intentionally
+  submitted by You to the project for inclusion in the project.
+- **Project** means `scitex-agentic-journal` and the surrounding SciTeX
+  ecosystem maintained by Yusuke Watanabe / 株式会社 SciTeX.
+
+## 2. Grant of Copyright License
+
+You grant to the Project and to recipients of software distributed by
+the Project a perpetual, worldwide, non-exclusive, no-charge,
+royalty-free, irrevocable copyright license to reproduce, prepare
+derivative works of, publicly display, publicly perform, sublicense and
+distribute Your Contribution and such derivative works under the
+license used by the Project at the time of inclusion
+([AGPL-3.0-only](LICENSE)) as well as under any subsequent license the
+Project's maintainer adopts for the Project.
+
+## 3. Grant of Patent License
+
+You grant to the Project and to recipients of software distributed by
+the Project a perpetual, worldwide, non-exclusive, no-charge,
+royalty-free, irrevocable patent license under the patent claims
+licensable by You that are necessarily infringed by Your Contribution
+alone or by combination of Your Contribution with the Project.
+
+## 4. You Are the Author
+
+You represent that:
+
+- Each Contribution is Your original creation, or You have sufficient
+  rights to grant the licenses in §2 and §3.
+- If Your employer has rights to intellectual property You create that
+  includes Your Contributions, You have received permission to make
+  Contributions on behalf of that employer, or Your employer has
+  waived such rights.
+- You are aware that the Project may treat unsigned Contributions as
+  not received under this CLA and may decline to merge them.
+
+## 5. Signing
+
+By commenting on the relevant pull request
+
+> `I have read and agree to the SciTeX CLA.`
+
+You signify acceptance of this CLA for that Contribution and all future
+Contributions to this Project. The CLA bot
+(`contributor-assistant/github-action`) records your acceptance.
+
+## 6. No Warranty
+
+You provide Your Contributions on an "AS IS" basis, without warranties
+or conditions of any kind, express or implied.
+
+---
+
+Questions: open an issue or email `contact@scitex.ai`.

scitex_agentic_journal-0.1.0a0/CONTRIBUTING.md

@@ -0,0 +1,53 @@
+# Contributing to `scitex-agentic-journal`
+
+Thank you for your interest. This document is the short form. The
+long form lives in the [SciTeX ecosystem guidelines](https://scitex.ai).
+
+## Quick rules
+
+1. **One task = one PR off `develop`.** Open the PR against `develop`,
+   not `main`. CI must be green before merge.
+2. **No mocks.** Production paths use real collaborators (real HTTP,
+   real `git`, real subprocess). Hermetic CI is achieved with real
+   local fixtures (stdlib `http.server`, real on-disk repos), never
+   with `respx` / `responses` / `unittest.mock` replay libraries.
+   See `STX-NM001-003` / `PA-306` in the SciTeX no-mocks discipline.
+3. **No silent fallbacks.** Every failure path raises a structured
+   `GateFailure` (or similar) with `reason` + `detail`.
+4. **Sign the [CLA](CLA.md).** A bot will check on PR open.
+5. **No `Co-Authored-By` trailer** from automated agents.
+6. **No `--no-verify`, no force-push** to protected branches.
+
+## Local development
+
+```bash
+git clone https://github.com/ywatanabe1989/scitex-agentic-journal.git
+cd scitex-agentic-journal
+pip install -e ".[dev]"
+pytest tests/
+```
+
+To exercise the opt-in real-network tests:
+
+```bash
+SCITEX_RUN_NETWORK_TESTS=1 pytest tests/ -m network
+```
+
+## Submitting a change
+
+1. Branch off `develop`: `git checkout -b feat/your-thing develop`.
+2. Implement + add tests.
+3. Update `CHANGELOG.md` under `## [Unreleased]`.
+4. Push, open a PR against `develop`, wait for CI.
+5. Self-merge (squash) once CI is green and the CLA bot is happy.
+
+## What gets reviewed
+
+- Architecture fit (consumes Clew, emits Live Paper; we do not invent
+  new claim models here).
+- No mocks in production paths.
+- Real errors with guidance, not silent fallbacks.
+- Tests describe behaviour, not implementation.
+
+Questions: open an issue, or reach the maintainers via
+`contact@scitex.ai`.