opensyndrome 0.1.0__tar.gz

opensyndrome-0.1.0/.env.example

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+OLLAMA_BASE_URL=http://localhost:11434

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

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+name: Test
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v3
+      - name: Pre-commit to rule them all
+        run: uv run pre-commit run --all-files
+
+  test:
+    name: Run tests
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v3
+      - run: uv run pytest

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

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+name: Release
+
+on:
+  workflow_dispatch:
+  push:
+    tags:
+      # Publish on any tag starting with a `v`, e.g. v1.2.3
+      - v*
+
+jobs:
+  pypi:
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+    # Environment and permissions trusted publishing.
+    environment:
+      # Create this environment in the GitHub repository under Settings -> Environments
+      name: release
+      url: https://pypi.org/p/osi
+    permissions:
+      contents: read
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v3
+      - run: uv build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

opensyndrome-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# PyPI configuration file
+.pypirc
+
+# temporary
+schema.json
+ollama_schema.json
+osi/to_be_updated__schema.py
+
+# data
+*.csv

opensyndrome-0.1.0/.idea/.gitignore

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+# Default ignored files
+/shelf/
+/workspace.xml

opensyndrome-0.1.0/.idea/inspectionProfiles/Project_Default.xml

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+<component name="InspectionProjectProfileManager">
+  <profile version="1.0">
+    <option name="myName" value="Project Default" />
+    <inspection_tool class="PyInterpreterInspection" enabled="false" level="WARNING" enabled_by_default="false" />
+    <inspection_tool class="PyPackageRequirementsInspection" enabled="true" level="WARNING" enabled_by_default="true">
+      <option name="ignoredPackages">
+        <value>
+          <list size="1">
+            <item index="0" class="java.lang.String" itemvalue="numpy" />
+          </list>
+        </value>
+      </option>
+    </inspection_tool>
+  </profile>
+</component>

opensyndrome-0.1.0/.idea/inspectionProfiles/profiles_settings.xml

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+<component name="InspectionProjectProfileManager">
+  <settings>
+    <option name="USE_PROJECT_PROFILE" value="false" />
+    <version value="1.0" />
+  </settings>
+</component>

opensyndrome-0.1.0/.idea/misc.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="Black">
+    <option name="sdkName" value="Python 3.11 (open-syndrome-python)" />
+  </component>
+  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.11 (open-syndrome-python)" project-jdk-type="Python SDK" />
+</project>

opensyndrome-0.1.0/.idea/modules.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/open-syndrome-python.iml" filepath="$PROJECT_DIR$/.idea/open-syndrome-python.iml" />
+    </modules>
+  </component>
+</project>

opensyndrome-0.1.0/.idea/open-syndrome-python.iml

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+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$">
+      <excludeFolder url="file://$MODULE_DIR$/.venv" />
+      <excludeFolder url="file://$MODULE_DIR$/dist" />
+    </content>
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+</module>

opensyndrome-0.1.0/.idea/vcs.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="" vcs="Git" />
+  </component>
+</project>

opensyndrome-0.1.0/.idea/workspace.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="AutoImportSettings">
+    <option name="autoReloadType" value="SELECTIVE" />
+  </component>
+  <component name="ChangeListManager">
+    <list default="true" id="30af56eb-4595-48f7-b4f7-768062c1e361" name="Changes" comment="">
+      <change beforePath="$PROJECT_DIR$/osi/__init__.py" beforeDir="false" afterPath="$PROJECT_DIR$/opensyndrome/__init__.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/osi/cli.py" beforeDir="false" afterPath="$PROJECT_DIR$/opensyndrome/cli.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/osi/converters.py" beforeDir="false" afterPath="$PROJECT_DIR$/opensyndrome/converters.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/osi/filtering.py" beforeDir="false" afterPath="$PROJECT_DIR$/opensyndrome/filtering.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/osi/schema.py" beforeDir="false" afterPath="$PROJECT_DIR$/opensyndrome/schema.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/osi/validators.py" beforeDir="false" afterPath="$PROJECT_DIR$/opensyndrome/validators.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/pyproject.toml" beforeDir="false" afterPath="$PROJECT_DIR$/pyproject.toml" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/uv.lock" beforeDir="false" afterPath="$PROJECT_DIR$/uv.lock" afterDir="false" />
+    </list>
+    <option name="SHOW_DIALOG" value="false" />
+    <option name="HIGHLIGHT_CONFLICTS" value="true" />
+    <option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />
+    <option name="LAST_RESOLUTION" value="IGNORE" />
+  </component>
+  <component name="FileTemplateManagerImpl">
+    <option name="RECENT_TEMPLATES">
+      <list>
+        <option value="Python Script" />
+      </list>
+    </option>
+  </component>
+  <component name="Git.Settings">
+    <option name="RECENT_GIT_ROOT_PATH" value="$PROJECT_DIR$" />
+  </component>
+  <component name="ProjectColorInfo">{
+  &quot;associatedIndex&quot;: 6
+}</component>
+  <component name="ProjectId" id="2sX9mWP0rVfSY8fQDo7aatsQlvD" />
+  <component name="ProjectLevelVcsManager">
+    <ConfirmationsSetting value="1" id="Add" />
+  </component>
+  <component name="ProjectViewState">
+    <option name="hideEmptyMiddlePackages" value="true" />
+    <option name="showLibraryContents" value="true" />
+  </component>
+  <component name="PropertiesComponent"><![CDATA[{
+  "keyToString": {
+    "RunOnceActivity.ShowReadmeOnStart": "true",
+    "git-widget-placeholder": "main",
+    "last_opened_file_path": "/Users/Gomes-FerreiraA-Dev/workspace/osi-python/examples"
+  }
+}]]></component>
+  <component name="RecentsManager">
+    <key name="CopyFile.RECENT_KEYS">
+      <recent name="$PROJECT_DIR$/examples" />
+      <recent name="$PROJECT_DIR$/tests/definitions/v1/a" />
+      <recent name="$PROJECT_DIR$/tests/definitions/v1/e" />
+      <recent name="$PROJECT_DIR$/tests/definitions/v1/c" />
+      <recent name="$PROJECT_DIR$/tests/definitions/v1/u" />
+    </key>
+    <key name="MoveFile.RECENT_KEYS">
+      <recent name="$PROJECT_DIR$/examples" />
+      <recent name="$PROJECT_DIR$/tests/definitions/v1" />
+    </key>
+  </component>
+  <component name="SharedIndexes">
+    <attachedChunks>
+      <set>
+        <option value="bundled-python-sdk-975db3bf15a3-31b6be0877a2-com.jetbrains.pycharm.community.sharedIndexes.bundled-PC-241.18034.82" />
+      </set>
+    </attachedChunks>
+  </component>
+  <component name="SpellCheckerSettings" RuntimeDictionaries="0" Folders="0" CustomDictionaries="0" DefaultDictionary="application-level" UseSingleDictionary="true" transferred="true" />
+  <component name="TaskManager">
+    <task active="true" id="Default" summary="Default task">
+      <changelist id="30af56eb-4595-48f7-b4f7-768062c1e361" name="Changes" comment="" />
+      <created>1738591211638</created>
+      <option name="number" value="Default" />
+      <option name="presentableId" value="Default" />
+      <updated>1738591211638</updated>
+    </task>
+    <servers />
+  </component>
+</project>

opensyndrome-0.1.0/.pre-commit-config.yaml

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+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+- repo: https://github.com/ambv/black
+  rev: 25.1.0
+  hooks:
+  - id: black
+    args: [
+      "--force-exclude=.*tests\/fixtures\/.*"
+    ]
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.9.4
+  hooks:
+    - id: ruff
+      args: [
+        "--fix"
+      ]

opensyndrome-0.1.0/Dockerfile

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+FROM python:3.11-slim
+
+WORKDIR /app
+
+RUN pip install --no-cache-dir poetry==2.1.1
+
+COPY . /app
+
+RUN poetry config virtualenvs.create false && poetry install
+
+ENTRYPOINT ["poetry", "run", "osi"]

opensyndrome-0.1.0/Makefile

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+# load .env file
+ifneq (,$(wildcard .env))
+    include .env
+    export
+endif
+
+SCHEMA_FILE := $(HOME)/.open_syndrome/v1/schema.json
+
+ask_ollama_schema:
+	@echo "Generate JSON schema compatible with Ollama..."
+	@ollama run mistral "Convert this JSON schema to the simplified version supported by Ollama. Do not include description or examples. Do not create new fields. Only work with the JSON: $$(cat $(SCHEMA_FILE))" --format json > ollama_schema.json
+	@echo "Done!"
+
+ollama_schema:
+	@datamodel-codegen --input-file-type jsonschema \
+					   --output-model-type pydantic_v2.BaseModel \
+					   --use-unique-items-as-set \
+					   --use-default \
+					   --input $(SCHEMA_FILE) \
+					   --output osi/to_be_updated__schema.py

opensyndrome-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: opensyndrome
+Version: 0.1.0
+Author-email: Ana Paula Gomes <apgomes88@gmail.com>
+Requires-Python: ~=3.11
+Requires-Dist: click<9,>=8.1.8
+Requires-Dist: datamodel-code-generator<0.29,>=0.28.1
+Requires-Dist: jsonschema<5,>=4.23.0
+Requires-Dist: numpy<3,>=2.3.1
+Requires-Dist: ollama<0.6,>=0.5.1
+Requires-Dist: plotly[express]<7,>=6.1.2
+Requires-Dist: pyarrow<21,>=20.0.0
+Requires-Dist: pydantic<3,>=2.10.6
+Requires-Dist: pygments<3,>=2.19.1
+Requires-Dist: python-dotenv<2,>=1.0.1
+Requires-Dist: requests>=2.32.5
+Description-Content-Type: text/markdown
+
+# open-syndrome-python
+
+[![Test](https://github.com/OpenSyndrome/open-syndrome-python/actions/workflows/ci.yml/badge.svg)](https://github.com/OpenSyndrome/open-syndrome-python/actions/workflows/ci.yml)
+
+## Installation
+
+You can install it from PyPI or from Docker.
+
+From PyPi, install the package with `pip install opensyndrome`. Then run it with `osi`.
+
+From Docker, you can run the following command to build the image, tagged `osi`:
+
+```bash
+docker build -t osi .
+```
+
+Run the container interactively, removing it when it exits
+
+```bash
+docker run --rm osi
+```
+
+To read a `.env` file, mount it:
+
+```bash
+docker run --rm -it \
+  -v "$(pwd)/.env:/app/.env:ro" \
+  osi
+```
+
+To name the container and keep it around:
+
+```bash
+docker run --name osi-cli -it osi
+```
+
+## Usage
+
+First, download the schema and definitions in order to work with the CLI locally.
+
+```bash
+osi download schema
+osi download definitions
+```
+
+The files will be placed in the folder `.open_syndrome` in `$HOME`.
+
+### Convert a human-readable syndrome definition to a machine-readable JSON
+
+You need to have [Ollama](https://github.com/ollama/ollama) installed locally
+to use this feature. Pull the models you want to use with `osi` before running the command.
+We have tested llama3.2, mistral, and deepseek-r1 so far.
+
+Don't go well with structured output: qwen2.5-coder
+
+```bash
+osi convert
+osi convert --model mistral
+
+# to have the JSON translated to a specific language and edit it just after conversion
+osi convert --language "Português do Brasil" --model mistral --edit
+
+# include a validation step after conversion
+osi convert --validate
+```
+
+### Convert a machine-readable JSON syndrome definition to a human-readable format
+
+```bash
+osi humanize <path-to-json-file>
+osi humanize <path-to-json-file> --model mistral
+osi humanize <path-to-json-file> --model mistral --language "Português do Brasil"
+```
+
+### Validate a machine-readable JSON syndrome definition
+
+```bash
+osi validate
+```
+
+## Development
+
+To get started with development, you need to have [Poetry](https://python-poetry.org/) installed.
+
+### Install dependencies
+
+```bash
+uv sync
+```
+
+### Generate Ollama-compatible JSON
+
+> You only need to do this if you are a maintainer adding a new OSI schema or updating an existing one.
+
+Since Ollama requires a specific, more simple, JSON format, we need to generate an Ollama-compatible schema.
+To do this, we use `datamodel-code-generator` to generate a Pydantic schema. Run the following command to update it:
+
+```bash
+make ollama_schema
+```
+
+It will create a `schema.py` file in the root of the project. Be careful when editing this file manually.
+
+## Citing & Authors
+
+If you find this repository helpful, feel free to cite our publication: The Open Syndrome Definition
+
+```
+@misc{ferreira2025opensyndromedefinition,
+      title={The Open Syndrome Definition},
+      author={Ana Paula Gomes Ferreira and Aleksandar Anžel and Izabel Oliva Marcilio de Souza and Helen Hughes and Alex J Elliot and Jude Dzevela Kong and Madlen Schranz and Alexander Ullrich and Georges Hattab},
+      year={2025},
+      eprint={2509.25434},
+      archivePrefix={arXiv},
+      primaryClass={cs.AI},
+      url={https://arxiv.org/abs/2509.25434},
+}
+```