target-mcp 0.1.0__tar.gz

target_mcp-0.1.0/LICENSE

@@ -0,0 +1,202 @@
+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You 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 the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright [yyyy] [name of copyright owner]
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

target_mcp-0.1.0/NOTICE

@@ -0,0 +1,29 @@
+TARGET Checklist MCP Server
+Copyright 2026 Black Swan Causal Labs
+
+Licensed under the Apache License, Version 2.0 (the "License"); see the LICENSE
+file. You may not use this software except in compliance with the License.
+
+--------------------------------------------------------------------------------
+Third-party / upstream attribution
+--------------------------------------------------------------------------------
+
+This software operationalizes the TARGET reporting guideline:
+
+    Cashin AG, Hansford HJ, Hernán MA, Swanson SA, Lee H, Jones MD, et al.
+    Transparent Reporting of Observational Studies Emulating a Target Trial:
+    The TARGET Statement. JAMA 2025. doi:10.1001/jama.2025.13350
+    (co-published BMJ 2025;390:e087179).
+
+The encoded specification (target_mcp/specs/*.yaml) re-expresses the *intent* of
+each checklist item in original wording and does not reproduce the published
+checklist text. Where the published item wording IS reproduced verbatim — the
+OFFICIAL_TEXT mapping in target_mcp/render.py, used to project a completed
+checklist onto the published form — it is © 2025 Cashin et al. and reproduced
+under the Creative Commons Attribution-NoDerivatives 4.0 International license
+(CC BY-ND 4.0), with attribution. That wording is not covered by the Apache-2.0
+grant above and must not be modified when redistributed.
+
+The bundled TARGET logo (target_mcp/assets/target-logo.png) is a trademark of the
+TARGET group, included only for the author self-report ("official") view. It is
+not licensed for endorsement use and is off by default.

target_mcp-0.1.0/PKG-INFO

@@ -0,0 +1,426 @@
+Metadata-Version: 2.4
+Name: target-mcp
+Version: 0.1.0
+Summary: MCP server operationalizing the TARGET reporting guideline (Cashin et al., JAMA/BMJ 2025) as a deterministic, provenanced scoring engine for target trial emulation studies
+Author: Black Swan Causal Labs
+License: 
+                                         Apache License
+                                   Version 2.0, January 2004
+                                http://www.apache.org/licenses/
+        
+           TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+        
+           1. Definitions.
+        
+              "License" shall mean the terms and conditions for use, reproduction,
+              and distribution as defined by Sections 1 through 9 of this document.
+        
+              "Licensor" shall mean the copyright owner or entity authorized by
+              the copyright owner that is granting the License.
+        
+              "Legal Entity" shall mean the union of the acting entity and all
+              other entities that control, are controlled by, or are under common
+              control with that entity. For the purposes of this definition,
+              "control" means (i) the power, direct or indirect, to cause the
+              direction or management of such entity, whether by contract or
+              otherwise, or (ii) ownership of fifty percent (50%) or more of the
+              outstanding shares, or (iii) beneficial ownership of such entity.
+        
+              "You" (or "Your") shall mean an individual or Legal Entity
+              exercising permissions granted by this License.
+        
+              "Source" form shall mean the preferred form for making modifications,
+              including but not limited to software source code, documentation
+              source, and configuration files.
+        
+              "Object" form shall mean any form resulting from mechanical
+              transformation or translation of a Source form, including but
+              not limited to compiled object code, generated documentation,
+              and conversions to other media types.
+        
+              "Work" shall mean the work of authorship, whether in Source or
+              Object form, made available under the License, as indicated by a
+              copyright notice that is included in or attached to the work
+              (an example is provided in the Appendix below).
+        
+              "Derivative Works" shall mean any work, whether in Source or Object
+              form, that is based on (or derived from) the Work and for which the
+              editorial revisions, annotations, elaborations, or other modifications
+              represent, as a whole, an original work of authorship. For the purposes
+              of this License, Derivative Works shall not include works that remain
+              separable from, or merely link (or bind by name) to the interfaces of,
+              the Work and Derivative Works thereof.
+        
+              "Contribution" shall mean any work of authorship, including
+              the original version of the Work and any modifications or additions
+              to that Work or Derivative Works thereof, that is intentionally
+              submitted to Licensor for inclusion in the Work by the copyright owner
+              or by an individual or Legal Entity authorized to submit on behalf of
+              the copyright owner. For the purposes of this definition, "submitted"
+              means any form of electronic, verbal, or written communication sent
+              to the Licensor or its representatives, including but not limited to
+              communication on electronic mailing lists, source code control systems,
+              and issue tracking systems that are managed by, or on behalf of, the
+              Licensor for the purpose of discussing and improving the Work, but
+              excluding communication that is conspicuously marked or otherwise
+              designated in writing by the copyright owner as "Not a Contribution."
+        
+              "Contributor" shall mean Licensor and any individual or Legal Entity
+              on behalf of whom a Contribution has been received by Licensor and
+              subsequently incorporated within the Work.
+        
+           2. Grant of Copyright License. Subject to the terms and conditions of
+              this License, each Contributor hereby grants to You 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 the
+              Work and such Derivative Works in Source or Object form.
+        
+           3. Grant of Patent License. Subject to the terms and conditions of
+              this License, each Contributor hereby grants to You a perpetual,
+              worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+              (except as stated in this section) patent license to make, have made,
+              use, offer to sell, sell, import, and otherwise transfer the Work,
+              where such license applies only to those patent claims licensable
+              by such Contributor that are necessarily infringed by their
+              Contribution(s) alone or by combination of their Contribution(s)
+              with the Work to which such Contribution(s) was submitted. If You
+              institute patent litigation against any entity (including a
+              cross-claim or counterclaim in a lawsuit) alleging that the Work
+              or a Contribution incorporated within the Work constitutes direct
+              or contributory patent infringement, then any patent licenses
+              granted to You under this License for that Work shall terminate
+              as of the date such litigation is filed.
+        
+           4. Redistribution. You may reproduce and distribute copies of the
+              Work or Derivative Works thereof in any medium, with or without
+              modifications, and in Source or Object form, provided that You
+              meet the following conditions:
+        
+              (a) You must give any other recipients of the Work or
+                  Derivative Works a copy of this License; and
+        
+              (b) You must cause any modified files to carry prominent notices
+                  stating that You changed the files; and
+        
+              (c) You must retain, in the Source form of any Derivative Works
+                  that You distribute, all copyright, patent, trademark, and
+                  attribution notices from the Source form of the Work,
+                  excluding those notices that do not pertain to any part of
+                  the Derivative Works; and
+        
+              (d) If the Work includes a "NOTICE" text file as part of its
+                  distribution, then any Derivative Works that You distribute must
+                  include a readable copy of the attribution notices contained
+                  within such NOTICE file, excluding those notices that do not
+                  pertain to any part of the Derivative Works, in at least one
+                  of the following places: within a NOTICE text file distributed
+                  as part of the Derivative Works; within the Source form or
+                  documentation, if provided along with the Derivative Works; or,
+                  within a display generated by the Derivative Works, if and
+                  wherever such third-party notices normally appear. The contents
+                  of the NOTICE file are for informational purposes only and
+                  do not modify the License. You may add Your own attribution
+                  notices within Derivative Works that You distribute, alongside
+                  or as an addendum to the NOTICE text from the Work, provided
+                  that such additional attribution notices cannot be construed
+                  as modifying the License.
+        
+              You may add Your own copyright statement to Your modifications and
+              may provide additional or different license terms and conditions
+              for use, reproduction, or distribution of Your modifications, or
+              for any such Derivative Works as a whole, provided Your use,
+              reproduction, and distribution of the Work otherwise complies with
+              the conditions stated in this License.
+        
+           5. Submission of Contributions. Unless You explicitly state otherwise,
+              any Contribution intentionally submitted for inclusion in the Work
+              by You to the Licensor shall be under the terms and conditions of
+              this License, without any additional terms or conditions.
+              Notwithstanding the above, nothing herein shall supersede or modify
+              the terms of any separate license agreement you may have executed
+              with Licensor regarding such Contributions.
+        
+           6. Trademarks. This License does not grant permission to use the trade
+              names, trademarks, service marks, or product names of the Licensor,
+              except as required for reasonable and customary use in describing the
+              origin of the Work and reproducing the content of the NOTICE file.
+        
+           7. Disclaimer of Warranty. Unless required by applicable law or
+              agreed to in writing, Licensor provides the Work (and each
+              Contributor provides its Contributions) on an "AS IS" BASIS,
+              WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+              implied, including, without limitation, any warranties or conditions
+              of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+              PARTICULAR PURPOSE. You are solely responsible for determining the
+              appropriateness of using or redistributing the Work and assume any
+              risks associated with Your exercise of permissions under this License.
+        
+           8. Limitation of Liability. In no event and under no legal theory,
+              whether in tort (including negligence), contract, or otherwise,
+              unless required by applicable law (such as deliberate and grossly
+              negligent acts) or agreed to in writing, shall any Contributor be
+              liable to You for damages, including any direct, indirect, special,
+              incidental, or consequential damages of any character arising as a
+              result of this License or out of the use or inability to use the
+              Work (including but not limited to damages for loss of goodwill,
+              work stoppage, computer failure or malfunction, or any and all
+              other commercial damages or losses), even if such Contributor
+              has been advised of the possibility of such damages.
+        
+           9. Accepting Warranty or Additional Liability. While redistributing
+              the Work or Derivative Works thereof, You may choose to offer,
+              and charge a fee for, acceptance of support, warranty, indemnity,
+              or other liability obligations and/or rights consistent with this
+              License. However, in accepting such obligations, You may act only
+              on Your own behalf and on Your sole responsibility, not on behalf
+              of any other Contributor, and only if You agree to indemnify,
+              defend, and hold each Contributor harmless for any liability
+              incurred by, or claims asserted against, such Contributor by reason
+              of your accepting any such warranty or additional liability.
+        
+           END OF TERMS AND CONDITIONS
+        
+           APPENDIX: How to apply the Apache License to your work.
+        
+              To apply the Apache License to your work, attach the following
+              boilerplate notice, with the fields enclosed by brackets "[]"
+              replaced with your own identifying information. (Don't include
+              the brackets!)  The text should be enclosed in the appropriate
+              comment syntax for the file format. We also recommend that a
+              file or class name and description of purpose be included on the
+              same "printed page" as the copyright notice for easier
+              identification within third-party archives.
+        
+           Copyright [yyyy] [name of copyright owner]
+        
+           Licensed under the Apache License, Version 2.0 (the "License");
+           you may not use this file except in compliance with the License.
+           You may obtain a copy of the License at
+        
+               http://www.apache.org/licenses/LICENSE-2.0
+        
+           Unless required by applicable law or agreed to in writing, software
+           distributed under the License is distributed on an "AS IS" BASIS,
+           WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+           See the License for the specific language governing permissions and
+           limitations under the License.
+        
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE
+Requires-Dist: mcp[cli]>=1.0
+Requires-Dist: pypdf>=5.0
+Requires-Dist: pdfplumber>=0.11
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: anthropic>=0.40
+Requires-Dist: httpx>=0.27
+Requires-Dist: python-docx>=1.1
+Dynamic: license-file
+
+# TARGET Checklist MCP Server
+
+An MCP server that operationalizes the **TARGET** reporting guideline
+(TrAnsparent ReportinG of observational studies Emulating a Target trial;
+Cashin et al., JAMA/BMJ, September 2025) as a deterministic, provenanced
+scoring engine for target trial emulation (TTE) studies.
+
+This is the *executable* TARGET: not a manuscript auditor that renders an
+opinion, but a measurement instrument that produces a structured,
+item-by-item, evidence-linked matrix with fixed model provenance, so a
+corpus-scale result is reproducible.
+
+See `../target-mcp-server-design.md` for the full design rationale.
+
+## Status — vertical slice
+
+Built and proven end-to-end:
+
+- **Spec layer** — the 21 published items decomposed into **39 scoreable leaf
+  subitems**, encoded as versioned YAML (`target_mcp/specs/target-0.1.0.yaml`)
+  with own-words intent, verdict boundaries, signal terms, the 6x↔7x
+  specification/emulation pairing, and applicability rules. Structurally
+  validated on load (`spec.py`).
+- **Ingestion layer** — PDF/text/docx → `SectionMap` with character-offset,
+  **source-tagged** section spans (main vs `supplement:<file>`), protocol-table
+  and flow-diagram detection, extractor version + text hash stamps, and
+  whitespace-insensitive quote→span resolution. Supports **multi-document
+  bundles** (main text + supplements) via `build_bundle` (`ingest.py`).
+- **Retrieval layer** — the corpus/batch and convenience path: fetch
+  open-access articles by PMCID from Europe PMC (JATS main text plus PMC-hosted
+  supplementary files, merged into one bundle). Use this when there is no file
+  in hand or to auto-fetch an OA paper's supplement; for a manuscript you were
+  given, ingest the file directly (`retrieve.py`).
+- **Assessment layer** — batched, single-pass scoring of all applicable leaves.
+  **Scaffold mode (default)** is the path for reviewing a publication: the agent
+  already in the loop is the scorer, so the server returns the exact prompt +
+  schema for it to run, then validates the verdicts it submits. **Judge mode**
+  is for the headless/batch case (no LLM in the loop) — the server makes its own
+  pinned model call so a corpus run is reproducible and caller-independent. Both
+  share one validation path that enforces leaf coverage, verdict vocabulary, and
+  mandatory verbatim evidence resolved to spans with a `source_document` tag
+  (`assess.py`).
+- **Rendering layer** — `render_checklist` projects a finalized assessment onto
+  the published TARGET checklist form (all 39 rows, verbatim item wording under
+  CC BY-ND, a Location-reported column from the resolved evidence spans; the
+  enriched view adds verdict + evidence). `render_checklist_docx` writes the
+  same as a submission-ready Word file (`render.py`, `render_docx.py`).
+- **Corpus & validation layers** — `aggregate_corpus` rolls many assessments
+  into per-item completeness rates with coverage denominators (`corpus.py`);
+  `validate.py` provides blind human coding-sheet generation and per-leaf
+  agreement (raw, Cohen's κ, Gwet's AC1, sensitivity/specificity) against a
+  gold standard.
+- **Composition layer** — FastMCP server (`server.py`) exposing eleven tools.
+  The primary manuscript flow is **`parse_manuscript`** (parse the file you
+  were given, with `supplements=` when available) → **`assess_manuscript`** →
+  **`submit_scaffold_verdicts`** → **`render_checklist`** (or
+  `render_checklist_docx`). Supporting tools: `parse_pmcid` (corpus/batch or
+  OA-supplement fetch), `get_checklist` (introspect the spec),
+  `aggregate_corpus`, `build_coding_sheet`, and `validate_against_gold`.
+
+Not yet built (see design doc): `assess_item`, `check_emulation_coherence`,
+`export_identifiability_spec`, publisher-site supplement retrieval (beyond the
+PMC-OA tier), better table extraction, and the separate materiality/design-risk
+layer.
+
+### Provenance stamped on every assessment
+
+`spec_version`, resolved `model` id, `temperature`, `prompt_hash`,
+`prompt_template_version`, `extractor_version`, `text_sha256`, `assessed_at`,
+`full_text_available`, `supplement_status`, and a per-source `documents` list;
+each evidence item carries its resolved span, section, and `source_document`.
+A span is only meaningful alongside the extractor version and text hash, so
+they travel together.
+
+## Reporting completeness, not a pass/fail verdict
+
+The instrument scores how *completely* a manuscript reports what the checklist
+requires — not study quality, and it issues **no pass/fail judgment**. TARGET
+presents all 21 items as essential minimum items with **no tiering**, and this
+tool follows suit: the output is the 39 per-leaf verdicts with evidence and a
+completeness tally. (An earlier "critical floor" — a BSCL pass/fail overlay over
+six leaves — was removed in 2026-07-19 as off-message and confusing; see
+`docs/DECISIONS.md`.) Do not present a verdict matrix as TARGET compliance.
+
+## Install
+
+The server and the optional orchestration skill ship together in this repo, but
+they **activate through two separate mechanisms** — installing one does not
+enable the other. Getting the files (clone/download) gives you both; then do the
+two activation steps below.
+
+### 1. Install the server
+
+```bash
+git clone https://github.com/Black-Swan-Causal-Labs/target-mcp.git
+cd target-mcp
+python3 -m venv .venv
+.venv/bin/pip install -e .
+```
+
+(Once published to PyPI: `pip install target-mcp`.)
+
+Run it standalone (stdio transport) to smoke-test:
+
+```bash
+.venv/bin/target-mcp
+```
+
+### 2. Register the server with your MCP client
+
+Add it to the client's MCP config with an **absolute** path. For Claude Desktop
+that file is `~/Library/Application Support/Claude/claude_desktop_config.json`
+(macOS); for a Claude Code project use `.mcp.json`:
+
+```json
+{
+  "mcpServers": {
+    "target-checklist": {
+      "command": "/ABSOLUTE/PATH/TO/target-mcp/.venv/bin/python",
+      "args": ["-m", "target_mcp.server"]
+    }
+  }
+}
+```
+
+Restart / reconnect the client. Confirm it exposes **11 tools** (a stale process
+may show fewer — respawn it). The server is now fully usable on its own: any MCP
+client can run parse → assess → submit → render in a single scaffold pass.
+
+### 3. (Optional, Claude Code only) Activate the fan-out skill
+
+`.claude/skills/target-checklist-fanout/` encodes the parallel-subagent
+orchestration that scores the 39 leaves concurrently (~2 min vs ~20 min). It is
+**an accelerator, not a dependency** — it only works in clients that can spawn
+subagents (the Claude Code CLI, or the Claude Desktop **Code/Cowork** tabs; the
+plain **Chat** tab cannot, and non-Claude clients like Codex ignore it). Without
+it, everything still works via the single-pass fallback.
+
+A Claude Code session discovers the skill when its working directory is this
+repo. To make it available in **every** session regardless of directory, copy it
+to the user scope:
+
+```bash
+mkdir -p ~/.claude/skills
+cp -R .claude/skills/target-checklist-fanout ~/.claude/skills/
+```
+
+For the skill to actually run, all three must be present: the **server**
+(step 2), the **skill** (this step), and a **subagent-capable client**.
+
+### Judge mode (headless/batch, optional)
+
+Judge mode needs `ANTHROPIC_API_KEY` in the environment. The pinned model is
+`claude-sonnet-5` by default; override with `TARGET_JUDGE_MODEL`.
+
+## Batch / corpus runs
+
+Scoring hundreds of papers is a **headless** job, not an interactive MCP call (a
+multi-hour tool call would blow the client's request timeout). Use the
+`target-mcp-corpus` CLI: it fetches + judges a list of PMCIDs **concurrently**,
+isolates per-paper failures, retries transient errors, and rolls up the
+aggregate.
+
+```bash
+# ids.txt: one PMCID per line (#-comments and blanks ignored)
+ANTHROPIC_API_KEY=sk-... target-mcp-corpus ids.txt -o out/ -j 12
+```
+
+- `-j/--workers` bounds concurrency (default 8; raise toward your API rate
+  limit). Judge is ~a few minutes/paper, so wall-clock ≈ `papers / workers ×
+  per-paper` — e.g. 300 papers at 12 concurrent ≈ 1–1.5h, versus ~10–20h serial.
+- `-o/--out-dir` writes one JSON per assessment plus `aggregate.json` and
+  `summary.json` (with per-paper stamps, verdict tallies, and any failures).
+  Without `-o`, the aggregate prints to stdout.
+- `--model` overrides the pinned judge model; `--no-supplements` skips
+  supplement retrieval.
+
+Judge mode records the **resolved** model id per paper, so a corpus aggregate is
+truthfully provenanced and caller-independent. Re-roll-up saved assessments any
+time with the `aggregate_corpus` MCP tool.
+
+## Tests
+
+```bash
+.venv/bin/python -m pytest tests/ -q
+```
+
+Covers spec validation, section mapping and quote resolution, the finalize +
+evidence-resolution path, evidence-required and coverage-mismatch guards,
+applicability rules, abstract-only full-text gating, corpus aggregation,
+the validation harness, checklist rendering (Markdown + .docx), and prompt-hash
+stability.
+
+## Licensing / commons hygiene
+
+The encoded checklist is a re-encoding of item *intent* in own words plus
+assessor notes; it does not reproduce the TARGET checklist wording verbatim.
+The original checklist is © the TARGET group under CC BY-ND 4.0. When the
+Explanation & Elaboration document is released, leaves flagged
+`e_e_pending: true` should be re-checked and the spec bumped to a clean minor
+release. Do not copy E&E text verbatim.