tekmeria 0.1.0__tar.gz

tekmeria-0.1.0/.github/workflows/ci.yml

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+name: ci
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+permissions:
+  contents: read
+
+jobs:
+  python:
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    steps:
+      - uses: actions/checkout@fbc6f3992d24b796d5a048ff273f7fcc4a7b6c09 # v5.1.0
+      - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
+        with:
+          enable-cache: true
+      - run: uv python install 3.12
+      - run: uv sync --locked
+      - run: uv run ruff check
+      - run: uv run ruff format --check
+      - run: uv run pyright
+      - run: uv run pytest
+      - name: Offline demo must catch every planted case
+        run: uv run tekmeria demo
+      - name: The audit must give every planted case its verdict
+        run: uv run tekmeria evaluate
+      - name: The evaluation must catch every injected fault it can
+        run: uv run python -m tekmeria.evaluation.faults --per-category 10
+      - name: The wheel ships the audit view
+        run: |
+          uv build --wheel --out-dir dist
+          uv run python -c "import glob, sys, zipfile; names = zipfile.ZipFile(glob.glob('dist/*.whl')[0]).namelist(); sys.exit(0 if 'tekmeria/ui/audit-view.html' in names else 'the wheel has no tekmeria/ui/audit-view.html')"
+
+  web:
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    defaults:
+      run:
+        working-directory: web
+    steps:
+      - uses: actions/checkout@fbc6f3992d24b796d5a048ff273f7fcc4a7b6c09 # v5.1.0
+      - uses: actions/setup-node@949feb2413d6458794dcd2491c4babbbce0c15c1 # v7.1.0
+        with:
+          node-version: 24
+          cache: npm
+          cache-dependency-path: web/package-lock.json
+      - run: npm ci
+      - run: npm run typecheck
+      - run: npm test
+      - run: npm run build
+      - name: The committed audit view must match the build
+        run: git diff --exit-code -- ../src/tekmeria/ui/audit-view.html

tekmeria-0.1.0/.github/workflows/live.yml

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+name: live-smoke
+
+# Calls real upstream APIs to catch drift. Never part of the default test run.
+on:
+  schedule:
+    - cron: "0 6 * * 1"  # Mondays 06:00 UTC
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  live:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@fbc6f3992d24b796d5a048ff273f7fcc4a7b6c09 # v5.1.0
+      - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
+      - run: uv python install 3.12
+      - run: uv sync --locked
+      - run: uv run pytest -m live
+        env:
+          NCBI_EMAIL: ${{ secrets.NCBI_EMAIL }}
+          NCBI_API_KEY: ${{ secrets.NCBI_API_KEY }}

tekmeria-0.1.0/.github/workflows/mutants.yml

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+name: mutants
+
+# How much of the audit the evaluation exercises: one mutant at a time, run on request.
+on:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  mutants:
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    steps:
+      - uses: actions/checkout@fbc6f3992d24b796d5a048ff273f7fcc4a7b6c09 # v5.1.0
+      - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
+      - run: uv python install 3.12
+      - run: uv sync --locked
+      - name: Mutation score of the evaluation
+        run: uv run python -m tekmeria.evaluation.mutants >> "$GITHUB_STEP_SUMMARY"

tekmeria-0.1.0/.github/workflows/pages.yml

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+name: pages
+
+# Publishes the audit view with the offline demo's report (spec 10).
+# Runs after CI passes on a push to main and deploys the commit CI tested; it can also be
+# started by hand. Pages must be set to "GitHub Actions" in the repository settings, which
+# needs a public repository (or a paid plan).
+on:
+  workflow_run:
+    workflows: [ci]
+    types: [completed]
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: pages
+  cancel-in-progress: false  # a newer run waits; a deployment is never cut short
+
+jobs:
+  build:
+    if: >-
+      github.event_name == 'workflow_dispatch' ||
+      (github.event.workflow_run.conclusion == 'success' &&
+       github.event.workflow_run.event == 'push')
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@fbc6f3992d24b796d5a048ff273f7fcc4a7b6c09 # v5.1.0
+        with:
+          ref: ${{ github.event.workflow_run.head_sha || github.sha }}
+      - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
+        with:
+          enable-cache: true
+      - run: uv python install 3.12
+      - run: uv sync --locked
+      - run: uv run tekmeria demo --json-out site/demo-report.json --html-out site/index.html
+      - uses: actions/configure-pages@45bfe0192ca1faeb007ade9deae92b16b8254a0d # v6.0.0
+      - uses: actions/upload-pages-artifact@fc324d3547104276b827a68afc52ff2a11cc49c9 # v5.0.0
+        with:
+          path: site
+
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - id: deployment
+        uses: actions/deploy-pages@368f82528645a54fb793d4d04e342629a3f51346 # v5.0.1

tekmeria-0.1.0/.github/workflows/release.yml

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+name: release
+
+# A published GitHub release goes to PyPI by trusted publishing: PyPI trusts this workflow's
+# identity token, so no PyPI password or API token is stored anywhere. The upload waits in
+# the pypi environment for the maintainer's approval.
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    steps:
+      - uses: actions/checkout@fbc6f3992d24b796d5a048ff273f7fcc4a7b6c09 # v5.1.0
+      - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
+      - run: uv python install 3.12
+      - run: uv sync --locked
+      - name: The release tag must name the package version
+        run: test "$GITHUB_REF_NAME" = "v$(uv version --short)"
+      - name: The demo page the README links to must be live
+        run: curl --fail --silent --show-error --location --output /dev/null https://pedromarkovicz.github.io/tekmeria/
+      - run: uv run pytest
+      - run: uv build --out-dir dist
+      - uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    environment:
+      name: pypi
+      url: https://pypi.org/project/tekmeria/
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2
+        with:
+          name: dist
+          path: dist/
+      - uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2

tekmeria-0.1.0/.gitignore

@@ -0,0 +1,30 @@
+# Old project, kept locally for reference only
+healthcare_mcp_codespaces/
+
+# Python
+__pycache__/
+*.py[cod]
+.venv/
+.pytest_cache/
+.hypothesis/
+.ruff_cache/
+.mypy_cache/
+.coverage
+htmlcov/
+dist/
+build/
+*.egg-info/
+
+# Node
+node_modules/
+web/dist/
+
+# GitHub Pages build (pages workflow)
+site/
+
+# Local config and secrets
+.env
+*.key
+
+# Working notes, kept locally
+docs/plans/

tekmeria-0.1.0/.python-version

@@ -0,0 +1 @@
+3.12

tekmeria-0.1.0/CHANGELOG.md

@@ -0,0 +1,15 @@
+# Changelog
+
+## 0.1.0
+
+The first release.
+
+- **Tools.** Seven MCP tools: `search_literature` (PubMed and Europe PMC), `search_trials` (ClinicalTrials.gov), `search_drug_labels` (openFDA), `fetch_passages`, `resolve_handles`, `audit_answer` and `describe_contract`.
+- **Handles.** Every passage carries a handle, `scheme:id[@version]/path~check`, whose check code is the first 25 bits of HMAC-SHA256 over the locator, under a key created once per installation.
+- **Audit.** Each citation gets one verdict (`malformed`, `forged`, `unavailable`, `withdrawn`, `quote_mismatch` or `ok`) and flags (`retracted`, `preprint`, `version_changed`); each sentence a status; the answer metrics and an overall verdict. An answer passes only when every sentence is cited and every citation is valid.
+- **Audit view.** Hosts that support MCP Apps render the report in an interactive view.
+- **Offline demo.** `tekmeria demo` and `tekmeria --demo` run on recorded responses, with a public demo key.
+- **Evaluation.** `tekmeria evaluate` plants citations in 34 categories: 1,600 audits and 257 whole answers, all correct. A fault harness and a mutation harness measure what the evaluation would miss.
+- **Contract.** The citation contract, version 0.1.0, is in [docs/CONTRACT.md](docs/CONTRACT.md).
+
+Known limits are listed in the README.

tekmeria-0.1.0/CITATION.cff

@@ -0,0 +1,26 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it using the metadata below."
+type: software
+title: tekmeria
+abstract: >-
+  An MCP server for biomedical evidence from PubMed, Europe PMC, ClinicalTrials.gov and
+  openFDA. Every passage it returns carries a handle whose check code is a truncated keyed
+  MAC over the passage's locator, so the installation that issued it can tell a genuine
+  citation from a fabricated one, and a deterministic audit checks each citation of an
+  answer: malformed, forged, unavailable, withdrawn, misquoted or valid, with flags for
+  retracted, preprint and outdated sources.
+authors:
+  - family-names: Markovicz
+    given-names: Pedro
+    orcid: "https://orcid.org/0009-0006-6878-793X"
+version: 0.1.0
+license: Apache-2.0
+repository-code: "https://github.com/PedroMarkovicz/tekmeria"
+url: "https://pedromarkovicz.github.io/tekmeria/"
+keywords:
+  - mcp
+  - citations
+  - biomedical
+  - pubmed
+  - llm
+  - provenance

tekmeria-0.1.0/LICENSE

@@ -0,0 +1,202 @@
+
+                                 Apache License
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+      meet the following conditions:
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+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
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+          of the NOTICE file are for informational purposes only and
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+
+   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
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tekmeria-0.1.0/NOTICE

@@ -0,0 +1,36 @@
+tekmeria
+Copyright 2026 Pedro Markovicz
+
+Licensed under the Apache License, Version 2.0 (see LICENSE).
+
+Third-party data
+----------------
+
+The recorded API responses in src/tekmeria/demo/fixtures/ are kept so that the demo
+and the tests run offline. They are not covered by the Apache License; each keeps the
+terms of its source:
+
+- ClinicalTrials.gov (National Library of Medicine) and openFDA drug labels (Food
+  and Drug Administration): United States government data.
+- Crossref metadata: bibliographic facts, which Crossref makes available without
+  restriction.
+- PubMed and PubTator (National Library of Medicine): bibliographic records, and
+  abstracts only of the records the demo, the tests and the evaluation fetch and of
+  search results that Europe PMC lists as CC BY or CC0; the recorder removes every
+  other PubMed abstract. Abstracts remain under the copyright of their publishers or
+  authors.
+- Europe PMC search results: an abstract is kept only when Europe PMC lists the
+  article under CC BY or CC0, or when the result is the lookup of a record the demo
+  or the evaluation fetches. The recorder removes every other abstract.
+- Full text: Jiao B, Sato R, Mak J, et al. Financial risk protection from vaccines
+  in 52 Gavi-eligible low- and middle-income countries: a modeling study. PLoS
+  Medicine. 2025. doi:10.1371/journal.pmed.1004764. Licensed under CC BY 4.0
+  (https://creativecommons.org/licenses/by/4.0/), recorded unmodified from Europe
+  PMC (PMC12585062).
+- Preprint: Garba A, Usman S, Hussaini A. Mapping immune targets in peste des petits
+  ruminants virus hemagglutinin: an integrated computational framework for vaccine
+  candidate prioritization. Research Square. 2026. doi:10.21203/rs.3.rs-10665898/v1.
+  Licensed under CC BY 4.0.
+
+A rights holder who wants a recorded item removed can open an issue in the
+repository.