semvec/pypi-packages huggingface dataset:
coreason-protocol 0.3.0
Design and Governance Engine for high-stakes research.
Requires Python: <3.15,>=3.11

# coreason-protocol

The **Design and Governance Engine** for high-stakes research.

[![Organization](https://img.shields.io/badge/org-CoReason--AI-blue)](https://github.com/CoReason-AI)
[![License](https://img.shields.io/badge/license-Prosperity%203.0-blue)](https://github.com/CoReason-AI/coreason-protocol/blob/main/LICENSE)
[![Build Status](https://github.com/CoReason-AI/coreason-protocol/actions/workflows/build.yml/badge.svg)](https://github.com/CoReason-AI/coreason-protocol/actions)
[![Code Style: Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
[![Documentation](https://img.shields.io/badge/docs-product_requirements.md-blue)](docs/product_requirements.md)

## Description

`coreason-protocol` transforms natural language intent into a **Rigorous, Audited, and Executable Search Protocol**. It acts as the "Study Director" or Design Plane, ensuring that research protocols are designed with rigor, validated with logic (PRESS guidelines), and approved with authority before execution.

Unlike simple RAG retrieval, this package enforces a scientific workflow:
1.  **AI Draft:** Generates PICO blocks and expands terms using ontologies (via `coreason-codex`).
2.  **Human Governance:** Allows experts to override or inject terms.
3.  **Strict Validation:** Checks structural integrity and PRESS guidelines.
4.  **Immutable Registration:** Locks and registers approved protocols (via `coreason-veritas`).

## Service Architecture (Service P)

`coreason-protocol` can be deployed as a microservice ("Service P") exposing a FastAPI-based REST API. This service handles the lifecycle of the protocol, from drafting to compilation, while integrating with the Veritas audit system.

For details on API endpoints and usage, see [Usage Guide](docs/usage.md).

## Installation

```bash
pip install coreason-protocol
```

Or using poetry:

```bash
poetry add coreason-protocol
```

## Dependencies

For a full list of dependencies, see [Requirements](docs/requirements.md).

## Features

*   **PICO Architecture:** Structuring of research intent into Population, Intervention, Comparator, and Outcome.
*   **Ontology Expansion:** Integration with `coreason-codex` for term hydration (Concept IDs).
*   **Strategy Compilation:** Translation of PICO models into executable queries for:
    *   PubMed/Ovid (Boolean strings with MeSH/TiAb mapping).
    *   LanceDB (Vector embeddings + metadata filters).
    *   Graph (Cypher queries).
*   **HITL Governance:** Support for human review with `override_term` and `inject_term` capabilities.
*   **Audit Fidelity:** Soft-deletion of terms to maintain a complete history of design decisions.
*   **Multi-Format Rendering:** Export to HTML (visual diff), PRISMA-S text, and JSON-LD.

## Documentation

For detailed product requirements and architectural philosophy, see [docs/product_requirements.md](docs/product_requirements.md).
pgdsn2env 1.1.0
Parse PostgreSQL DSNs into PG* environment variables with export helpers.
Requires Python: >=3.10

# pgdsn2env

[![CD](https://github.com/kafai-lam/pgdsn2env/actions/workflows/cd.yml/badge.svg)](https://github.com/kafai-lam/pgdsn2env/actions/workflows/cd.yml)
[![PyPI Version](https://img.shields.io/pypi/v/pgdsn2env)](https://pypi.org/project/pgdsn2env/)
[![Python Versions](https://img.shields.io/badge/python-3.10%20%7C%203.11%20%7C%203.12%20%7C%203.13%20%7C%203.14-blue)](https://www.python.org/)

Parse PostgreSQL DSN strings into `PG*` environment variables and emit shell-friendly outputs.

## Install

```bash
uv add pgdsn2env
# or
pip install pgdsn2env
```

## CLI usage

```bash
# Basic
❯ pgdsn2env "postgresql://user@location:5432/test"
export PGDATABASE=test
export PGHOST=location
export PGPORT=5432
export PGUSER=user

# With Keyword/Value Connection Strings, in JSON format
❯  pgdsn2env "host=localhost port=5432 dbname=mydb user=postgres password=secret" --format json
{"PGDATABASE": "mydb", "PGHOST": "localhost", "PGPASSWORD": "secret", "PGPORT": "5432", "PGUSER": "postgres"}

# Invoked as Python module, with advanced params
❯ python -m pgdsn2env --format dotenv "postgresql://postgres:secret@localhost:5432/mydb?sslmode=require&application_name=myapp"
PGAPPNAME=myapp
PGDATABASE=mydb
PGHOST=localhost
PGPASSWORD=secret
PGPORT=5432
PGSSLMODE=require
PGUSER=postgres
```

## Python usage

```python
from pgdsn2env import pg_dsn_to_env

pg_env = pg_dsn_to_env("postgresql://user@location:5432/test")
print(pg_env) # {'PGHOST': 'location', 'PGPORT': '5432', 'PGDATABASE': 'test', 'PGUSER': 'user'}
```

## Recipes

Set `PG*` environment variables in your current shell:

```bash
source <(pgdsn2env "$DATABASE_URL")
```

Then verify the variables are set:

```bash
echo $PGHOST $PGPORT $PGDATABASE $PGUSER
```

## Notes

- Accept both keyword-value pair and URI style PostgreSQL connection strings
- Only parameters present in the DSN are emitted.
- Values are shell-quoted in CLI output.
PycWB 0.31.0
A Python package for coherent gravitational wave burst analysis
Requires Python: >=3.8
Keywords: ligo, physics, gravity, signal processing, gravitational waves, cwb, coherent wave burst

# PycWB

[![Documentations](https://readthedocs.org/projects/pycwb/badge/?version=latest)](https://pycwb.readthedocs.io)
[![Build Status](https://git.ligo.org/yumeng.xu/pycwb/badges/main/pipeline.svg)](https://git.ligo.org/yumeng.xu/pycwb/-/pipelines)
[![Releases](https://git.ligo.org/yumeng.xu/pycwb/-/badges/release.svg)](https://git.ligo.org/yumeng.xu/pycwb/-/releases)
[![PyPI version](https://badge.fury.io/py/pycWB.svg)](https://badge.fury.io/py/pycWB)
[![License](https://img.shields.io/badge/license-GPLv3-blue)](https://git.ligo.org/yumeng.xu/pycwb/-/blob/main/LICENSE)

PycWB is a modularized Python package for gravitational wave burst search based on the core function of cWB.
The documentation can be found at [pycwb.readthedocs.io](https://pycwb.readthedocs.io).

## Installation

### Install PycWB with pip

PycWB is available on [PyPI](https://pypi.org/project/pycWB/). You can install it with pip.
Some dependencies are required to be installed before installing pycWB with pip. 
The easiest way is to install them with conda.

```bash
conda create -n pycwb "python>=3.9,<3.11"
conda activate pycwb
conda install -c conda-forge root=6.26.10 healpix_cxx=3.81 nds2-client python-nds2-client lalsuite setuptools_scm cmake pkg-config
python3 -m pip install pycwb
```

Currently, pycWB is only available for x64 architecture.
For Apple Silicon users, you can install the dependencies with the following commands:

```bash
# make sure rosetta is installed
softwareupdate --install-rosetta --agree-to-license
# Optional: export CONDA_BUILD=1
conda create -n pycwb
conda activate pycwb
conda config --env --set subdir osx-64
conda install -c conda-forge "python>=3.9,<3.11" root=6.26.10 healpix_cxx=3.81 nds2-client python-nds2-client lalsuite setuptools_scm cmake pkg-config ruamel.yaml htcondor
```

### Install pycWB from source

```bash
conda create -n pycwb python
conda activate pycwb
conda install -c conda-forge root=6.26.10 healpix_cxx=3.81 nds2-client python-nds2-client lalsuite setuptools_scm cmake pkg-config
git clone git@git.ligo.org:yumeng.xu/pycwb.git
cd pycwb
make install
```

## Usage

Example project can be found in [examples](https://git.ligo.org/yumeng.xu/pycwb/-/tree/main/examples)

```python
from pycwb.workflow.run import search

search('./user_parameters.yaml')
```

or run with command line

```bash
pycwb run ./user_parameters.yaml
```

## Interactive tutorial

 - Google Colab tutorial: [pycWB_GW150914.ipynb](https://colab.research.google.com/github/PycWB/pycwb/blob/main/examples/colab/pycWB_GW150914.ipynb)