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Prepare public noncommercial release
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‎.dockerignore‎

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.git
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.gitignore
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.env
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.venv
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.venv-pdf
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__pycache__
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pathologybook
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data/processed
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data/training
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data/evals
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tmp

‎.env.example‎

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APP_ENV=development
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APP_HOST=0.0.0.0
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APP_PORT=8000
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OPENAI_API_KEY=
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OPENAI_MODEL=gpt-5.4
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OPENAI_EMBEDDING_MODEL=text-embedding-3-large
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PATHOLOGY_PDF_ROOT=pathologybook
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PATHOLOGY_DATA_DIR=data
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PATHOLOGY_LIBRARY_CONFIG=config/library.local.yaml
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PATHOLOGY_CHUNK_TOKENS=900
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PATHOLOGY_CHUNK_OVERLAP=120
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PATHOLOGY_TOP_K=6
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PATHOLOGY_EMBEDDING_DIMENSIONS=3072
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PATHOLOGY_EMBEDDING_BATCH_SIZE=16
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POSTGRES_URL=postgresql+psycopg://pathology:pathology@localhost:5432/pathology_ai
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OPENCLAW_PATHOLOGY_API=http://127.0.0.1:8000

‎.gitignore‎

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.DS_Store
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.env
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.venv
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.venv-pdf
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__pycache__/
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.pytest_cache/
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.mypy_cache/
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.ruff_cache/
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*.pyc
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*.pyo
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*.pyd
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*.sqlite3
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*.log
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*.egg-info/
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config/library.local.yaml
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data/raw/*
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!data/raw/.gitkeep
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data/processed/*
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!data/processed/.gitkeep
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data/training/*
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!data/training/.gitkeep
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data/evals/*
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!data/evals/.gitkeep
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tmp/*
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!tmp/.gitkeep
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pathologybook/*
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!pathologybook/.gitkeep
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!pathologybook/README.md
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pathologybook/.cache/

‎CONTRIBUTING.md‎

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# Contributing
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Thanks for contributing to Pathology RAG Workbench.
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## Before You Open a PR
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- Make sure your contribution is compatible with the PolyForm Noncommercial 1.0.0 license.
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- Do not add copyrighted textbooks, extracted page text, screenshots, or embeddings to the repository.
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- Do not add patient-identifiable information or clinical data.
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- Keep changes focused and documented.
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## Development Workflow
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1. Create a feature branch.
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2. Run the test suite before submitting:
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```bash
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pytest
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```
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3. If you change ingestion, retrieval, or API behavior, update the relevant docs.
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4. Prefer small PRs with a clear user-facing motivation.
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## Coding Guidelines
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- Target Python 3.12.
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- Keep defaults safe for an empty local library.
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- Preserve the evidence guardrails for ungrounded medical answers.
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- Avoid checking in generated artifacts from `data/`, `tmp/`, or `pathologybook/`.
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## Corpus and Licensing
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This repository ships without source PDFs. If you test with your own corpus, you are responsible for ensuring you have the right to use it.

‎LICENSE‎

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# PolyForm Noncommercial License 1.0.0
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<https://polyformproject.org/licenses/noncommercial/1.0.0>
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## Acceptance
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In order to get any license under these terms, you must agree
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to them as both strict obligations and conditions to all
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your licenses.
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## Copyright License
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The licensor grants you a copyright license for the
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software to do everything you might do with the software
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that would otherwise infringe the licensor's copyright
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in it for any permitted purpose. However, you may
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only distribute the software according to [Distribution
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License](#distribution-license) and make changes or new works
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based on the software according to [Changes and New Works
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License](#changes-and-new-works-license).
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## Distribution License
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The licensor grants you an additional copyright license
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to distribute copies of the software. Your license
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to distribute covers distributing the software with
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changes and new works permitted by [Changes and New Works
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License](#changes-and-new-works-license).
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## Notices
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You must ensure that anyone who gets a copy of any part of
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the software from you also gets a copy of these terms or the
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URL for them above, as well as copies of any plain-text lines
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beginning with `Required Notice:` that the licensor provided
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with the software. For example:
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> Required Notice: Copyright Yoyodyne, Inc. (http://example.com)
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## Changes and New Works License
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The licensor grants you an additional copyright license to
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make changes and new works based on the software for any
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permitted purpose.
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## Patent License
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The licensor grants you a patent license for the software that
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covers patent claims the licensor can license, or becomes able
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to license, that you would infringe by using the software.
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## Noncommercial Purposes
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Any noncommercial purpose is a permitted purpose.
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## Personal Uses
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Personal use for research, experiment, and testing for
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the benefit of public knowledge, personal study, private
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entertainment, hobby projects, amateur pursuits, or religious
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observance, without any anticipated commercial application,
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is use for a permitted purpose.
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## Noncommercial Organizations
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Use by any charitable organization, educational institution,
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public research organization, public safety or health
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organization, environmental protection organization,
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or government institution is use for a permitted purpose
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regardless of the source of funding or obligations resulting
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from the funding.
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## Fair Use
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You may have "fair use" rights for the software under the
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law. These terms do not limit them.
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## No Other Rights
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These terms do not allow you to sublicense or transfer any of
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your licenses to anyone else, or prevent the licensor from
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granting licenses to anyone else. These terms do not imply
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any other licenses.
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## Patent Defense
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If you make any written claim that the software infringes or
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contributes to infringement of any patent, your patent license
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for the software granted under these terms ends immediately. If
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your company makes such a claim, your patent license ends
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immediately for work on behalf of your company.
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## Violations
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The first time you are notified in writing that you have
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violated any of these terms, or done anything with the software
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not covered by your licenses, your licenses can nonetheless
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continue if you come into full compliance with these terms,
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and take practical steps to correct past violations, within
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32 days of receiving notice. Otherwise, all your licenses
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end immediately.
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## No Liability
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***As far as the law allows, the software comes as is, without
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any warranty or condition, and the licensor will not be liable
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to you for any damages arising out of these terms or the use
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or nature of the software, under any kind of legal claim.***
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## Definitions
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The **licensor** is the individual or entity offering these
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terms, and the **software** is the software the licensor makes
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available under these terms.
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**You** refers to the individual or entity agreeing to these
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terms.
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**Your company** is any legal entity, sole proprietorship,
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or other kind of organization that you work for, plus all
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organizations that have control over, are under the control of,
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or are under common control with that organization. **Control**
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means ownership of substantially all the assets of an entity,
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or the power to direct its management and policies by vote,
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contract, or otherwise. Control can be direct or indirect.
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**Your licenses** are all the licenses granted to you for the
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software under these terms.
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**Use** means anything you do with the software requiring one
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of your licenses.

‎Makefile‎

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PYTHON := .venv/bin/python
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PIP := .venv/bin/pip
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.PHONY: bootstrap doctor ingest api test docker-up docker-down portable-up portable-bundle ui
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bootstrap:
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bash scripts/bootstrap.sh
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doctor:
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bash scripts/doctor.sh
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ingest:
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$(PYTHON) -m apps.ingest_worker.cli build-library
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api:
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$(PYTHON) -m apps.pathology_api.main
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ui:
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$(PYTHON) -m apps.pathology_client.cli ui
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test:
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$(PYTHON) -m pytest
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docker-up:
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docker compose up --build
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docker-down:
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docker compose down
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portable-up:
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bash scripts/deploy_portable.sh
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portable-bundle:
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bash scripts/package_portable.sh

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