lorax-arg 0.1__tar.gz

lorax_arg-0.1/PKG-INFO

@@ -0,0 +1,131 @@
+Metadata-Version: 2.4
+Name: lorax-arg
+Version: 0.1
+Summary: Lorax single-port app (bundled UI + backend)
+Author: Lorax Team
+License: MIT
+Keywords: lorax,arg,visualization,evolution,genomics,biology
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: fastapi>=0.100.0
+Requires-Dist: uvicorn>=0.20.0
+Requires-Dist: python-socketio>=5.0.0
+Requires-Dist: python-dotenv>=1.0.0
+Requires-Dist: click>=8.0.0
+Requires-Dist: aiofiles>=24.0.0
+Requires-Dist: aiohttp>=3.0.0
+Requires-Dist: numpy>=2.0.0
+Requires-Dist: pandas>=2.0.0
+Requires-Dist: pyarrow>=18.0.0
+Requires-Dist: tskit>=1.0.0
+Requires-Dist: tszip>=0.2.0
+Requires-Dist: redis>=5.0.0
+Requires-Dist: google-cloud-storage>=3.0.0
+Requires-Dist: starlette>=0.40.0
+Requires-Dist: psutil>=5.0.0
+Requires-Dist: ete3>=3.1.0
+Requires-Dist: numba>0.57.1
+Requires-Dist: python-multipart>=0.0.10
+Provides-Extra: prod
+Requires-Dist: gunicorn>=23.0.0; extra == "prod"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: pytest-asyncio>=0.21.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
+Requires-Dist: httpx>=0.24.0; extra == "dev"
+Requires-Dist: locust>=2.15.0; extra == "dev"
+Requires-Dist: python-socketio[client]>=5.0.0; extra == "dev"
+Requires-Dist: msprime>=1.2.0; extra == "dev"
+
+# lorax-arg
+
+`lorax-arg` is a pip-installable distribution that runs Lorax as a **single-port app**.
+It ships the backend package in the same wheel so the install does not depend on a separate `lorax` PyPI release.
+CLI entrypoint: `lorax` (with `lorax-arg` as an alias).
+
+- React UI served at `/`
+- Backend API served at `/api/*`
+- Socket.IO served at `/api/socket.io/`
+
+## Development (monorepo)
+
+This package can run against the backend Python package from `packages/backend/` during development.
+
+### Build + sync UI assets (for wheel builds)
+
+Build the website with `VITE_API_BASE=/api`, then copy the `dist/` output into the Python package:
+
+```bash
+npm ci
+VITE_API_BASE=/api npm --workspace packages/website run build
+python packages/app/scripts/sync_ui_assets.py
+```
+
+### Run from source without copying assets
+
+```bash
+export LORAX_APP_STATIC_DIR=packages/website/dist
+python -m pip install -e .
+lorax
+```
+
+## Clean (remove build artifacts)
+
+```bash
+rm -rf build dist *.egg-info
+find packages/app -type d -name __pycache__ -prune -exec rm -rf {} +
+```
+
+## Production build (bundled UI)
+
+Build the UI and bundle it into the Python package, then build the wheel/sdist:
+
+```bash
+npm ci
+VITE_API_BASE=/api npm --workspace packages/website run build
+python packages/app/scripts/sync_ui_assets.py
+
+python -m pip install -U build
+python -m build .
+```
+
+You can also run:
+
+```bash
+lorax build
+```
+
+## Production install
+
+Install the built wheel locally (recommended for production verification):
+
+```bash
+python -m pip install --force-reinstall dist/lorax_arg-*.whl
+lorax
+```
+
+## Publish online (PyPI)
+
+1) Update `version` in the repo-root `pyproject.toml`.
+2) Build fresh artifacts:
+
+```bash
+rm -rf build dist *.egg-info
+npm ci
+VITE_API_BASE=/api npm --workspace packages/website run build
+python packages/app/scripts/sync_ui_assets.py
+python -m pip install -U build twine
+python -m build .
+```
+
+3) Upload to TestPyPI (recommended), then PyPI:
+
+```bash
+python -m twine upload --repository testpypi dist/*
+# verify: python -m pip install -i https://test.pypi.org/simple lorax-arg
+python -m twine upload dist/*
+```
+
+Notes:
+- You need PyPI credentials (or a token) configured in `~/.pypirc` or via `TWINE_USERNAME`/`TWINE_PASSWORD`.
+- Keep `README.md` and metadata in sync with what you want on PyPI.

lorax_arg-0.1/README.md

@@ -0,0 +1,176 @@
+# Lorax
+
+**Lorax** is an essential tool for the **interactive exploration and visualization of Ancestral Recombination Graphs (ARGs)**.
+
+> Visit the official Lorax Website: [https://lorax.in/](https://lorax.in/)
+
+## Local Installation and Usage
+
+### Option 1: Using the Pre-built Docker Image (Recommended)
+
+The simplest way to get started is by pulling the image directly from Docker Hub.
+
+```bash
+docker pull pratikkatte7/lorax
+```
+### Option 2: Building the Docker Image from Source
+
+If you prefer to build the image locally, follow these steps:
+
+1. Clone the Repository
+```bash
+git clone https://github.com/pratikkatte/lorax.git
+cd lorax
+```
+2. Built the docker image. 
+
+```bash
+docker build -t lorax .
+```
+
+### Running Lorax and Accessing the Interface
+
+Once the Docker image is available (either pulled or built), you can run the container and access the web interface.
+
+#### Running the Container
+
+Use the following command to run Lorax. It maps the container's internal port 80 to your machine's port 80 (or any other port you specify).
+
+```bash
+# Maps container port 80 to host port 80
+docker run -it -p 80:80 lorax
+```
+
+> ⚠️ Note: If port 80 is in use on your system, you can choose a different host port, such as 5173:
+> ```bash
+> docker run -it -p 5173:80 lorax
+> ```
+-- The tool can be accessed via http://localhost:80. You can provide any other port. For instance 5173, http://localhost:5173
+
+### Accessing the Tool
+
+After running the container, open your web browser and navigate to the appropriate address:
+
+- If you used port 80: http://localhost:80/
+> If you used other port: http://localhost:[port]/
+
+## Using Your Own ARG Data Files
+Lorax supports files in `.trees`, `.tsz` (tskit format) or `.csv` format.
+
+1. Simple File Upload via Web Interface
+
+For smaller files, you can easily use the dedicated upload panel located within the Lorax web page once the tool is running.
+
+2. Mounting a Local Directory (Recommended for Large Datasets)
+
+This method is the easiest and fastest when working with large ARG files, as it avoids slow web uploads by directly sharing your file system with the container.
+
+To make a local directory of your data available inside the container, use the -v (volume mount) flag:
+
+- Example: If your ARG files are located in a folder named ts_files in your current directory (`$(pwd)`), use this command:
+> ```
+> docker run -it -p 80:80 -v $(pwd)/ts_files:/app/UPLOADS/ts_files lorax
+> ```
+
+After the volume is mounted, your files will be accessible by Lorax when you use the interface.
+
+---
+
+## Monorepo Docker (single Dockerfile, two targets)
+
+This repo can be built from the **repo-root `Dockerfile`** with two targets:
+- **`full` (default)**: website + backend in one container (nginx on **:3000**)
+- **`backend`**: backend-only image (API on **:8080**, for GCP)
+
+### Full image (website + backend, port 3000)
+
+This image includes:
+- `packages/backend` (FastAPI + Socket.IO) running internally on `127.0.0.1:8080`
+- `packages/website` served by **nginx on port 3000**
+- same-origin proxying so the browser only needs **port 3000**
+
+### Build
+
+```bash
+docker build -t lorax-monorepo .
+```
+
+### Run
+
+```bash
+docker run --rm -p 3000:3000 lorax-monorepo
+```
+
+Then open: `http://localhost:3000`
+
+### Mount local data (recommended)
+
+```bash
+docker run --rm -p 3000:3000 \
+  -v "$(pwd)/ts_files:/app/UPLOADS/ts_files" \
+  lorax-monorepo
+```
+
+---
+
+### Backend-only image (GCP, port 8080)
+
+Build the backend-only target from the repo root:
+
+```bash
+docker build --target backend -t lorax-backend .
+```
+
+Run locally:
+
+```bash
+docker run --rm -p 8080:8080 lorax-backend
+```
+
+Then open: `http://localhost:8080`
+
+---
+
+## Pip (single-port app, port 3000)
+
+This repo also contains a pip-installable single-port app distribution at `packages/app/` (named `lorax-arg`).
+
+- **UI**: served at `/`
+- **Backend API**: served at `/api/*`
+- **Socket.IO**: served at `/api/socket.io/`
+
+### Run from source (developer workflow)
+
+```bash
+# Build website once (requires Node 20.19+ or 22.12+; Node 22 recommended)
+npm ci
+VITE_API_BASE=/api npm --workspace packages/website run build
+
+# Install python packages
+python -m pip install -e packages/backend
+python -m pip install -e packages/app
+
+# Run (uses packaged static assets by default)
+lorax --port 3000
+```
+
+### Build a self-contained wheel
+
+```bash
+# Build UI and sync into the Python package
+npm ci
+VITE_API_BASE=/api npm --workspace packages/website run build
+python packages/app/scripts/sync_ui_assets.py
+
+# Build wheel
+python -m pip install build
+python -m build .
+```
+
+---
+
+## Maintainer
+
+**Pratik Katte** \
+Department of Biomolecular Engineering & Bioinformatics \
+University of California, Santa Cruz

lorax_arg-0.1/lorax_arg.egg-info/PKG-INFO

@@ -0,0 +1,131 @@
+Metadata-Version: 2.4
+Name: lorax-arg
+Version: 0.1
+Summary: Lorax single-port app (bundled UI + backend)
+Author: Lorax Team
+License: MIT
+Keywords: lorax,arg,visualization,evolution,genomics,biology
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: fastapi>=0.100.0
+Requires-Dist: uvicorn>=0.20.0
+Requires-Dist: python-socketio>=5.0.0
+Requires-Dist: python-dotenv>=1.0.0
+Requires-Dist: click>=8.0.0
+Requires-Dist: aiofiles>=24.0.0
+Requires-Dist: aiohttp>=3.0.0
+Requires-Dist: numpy>=2.0.0
+Requires-Dist: pandas>=2.0.0
+Requires-Dist: pyarrow>=18.0.0
+Requires-Dist: tskit>=1.0.0
+Requires-Dist: tszip>=0.2.0
+Requires-Dist: redis>=5.0.0
+Requires-Dist: google-cloud-storage>=3.0.0
+Requires-Dist: starlette>=0.40.0
+Requires-Dist: psutil>=5.0.0
+Requires-Dist: ete3>=3.1.0
+Requires-Dist: numba>0.57.1
+Requires-Dist: python-multipart>=0.0.10
+Provides-Extra: prod
+Requires-Dist: gunicorn>=23.0.0; extra == "prod"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: pytest-asyncio>=0.21.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
+Requires-Dist: httpx>=0.24.0; extra == "dev"
+Requires-Dist: locust>=2.15.0; extra == "dev"
+Requires-Dist: python-socketio[client]>=5.0.0; extra == "dev"
+Requires-Dist: msprime>=1.2.0; extra == "dev"
+
+# lorax-arg
+
+`lorax-arg` is a pip-installable distribution that runs Lorax as a **single-port app**.
+It ships the backend package in the same wheel so the install does not depend on a separate `lorax` PyPI release.
+CLI entrypoint: `lorax` (with `lorax-arg` as an alias).
+
+- React UI served at `/`
+- Backend API served at `/api/*`
+- Socket.IO served at `/api/socket.io/`
+
+## Development (monorepo)
+
+This package can run against the backend Python package from `packages/backend/` during development.
+
+### Build + sync UI assets (for wheel builds)
+
+Build the website with `VITE_API_BASE=/api`, then copy the `dist/` output into the Python package:
+
+```bash
+npm ci
+VITE_API_BASE=/api npm --workspace packages/website run build
+python packages/app/scripts/sync_ui_assets.py
+```
+
+### Run from source without copying assets
+
+```bash
+export LORAX_APP_STATIC_DIR=packages/website/dist
+python -m pip install -e .
+lorax
+```
+
+## Clean (remove build artifacts)
+
+```bash
+rm -rf build dist *.egg-info
+find packages/app -type d -name __pycache__ -prune -exec rm -rf {} +
+```
+
+## Production build (bundled UI)
+
+Build the UI and bundle it into the Python package, then build the wheel/sdist:
+
+```bash
+npm ci
+VITE_API_BASE=/api npm --workspace packages/website run build
+python packages/app/scripts/sync_ui_assets.py
+
+python -m pip install -U build
+python -m build .
+```
+
+You can also run:
+
+```bash
+lorax build
+```
+
+## Production install
+
+Install the built wheel locally (recommended for production verification):
+
+```bash
+python -m pip install --force-reinstall dist/lorax_arg-*.whl
+lorax
+```
+
+## Publish online (PyPI)
+
+1) Update `version` in the repo-root `pyproject.toml`.
+2) Build fresh artifacts:
+
+```bash
+rm -rf build dist *.egg-info
+npm ci
+VITE_API_BASE=/api npm --workspace packages/website run build
+python packages/app/scripts/sync_ui_assets.py
+python -m pip install -U build twine
+python -m build .
+```
+
+3) Upload to TestPyPI (recommended), then PyPI:
+
+```bash
+python -m twine upload --repository testpypi dist/*
+# verify: python -m pip install -i https://test.pypi.org/simple lorax-arg
+python -m twine upload dist/*
+```
+
+Notes:
+- You need PyPI credentials (or a token) configured in `~/.pypirc` or via `TWINE_USERNAME`/`TWINE_PASSWORD`.
+- Keep `README.md` and metadata in sync with what you want on PyPI.

lorax_arg-0.1/lorax_arg.egg-info/SOURCES.txt

@@ -0,0 +1,70 @@
+README.md
+pyproject.toml
+lorax_arg.egg-info/PKG-INFO
+lorax_arg.egg-info/SOURCES.txt
+lorax_arg.egg-info/dependency_links.txt
+lorax_arg.egg-info/entry_points.txt
+lorax_arg.egg-info/requires.txt
+lorax_arg.egg-info/top_level.txt
+packages/app/README.md
+packages/app/lorax_app/__init__.py
+packages/app/lorax_app/app.py
+packages/app/lorax_app/cli.py
+packages/app/lorax_app/static/X.png
+packages/app/lorax_app/static/index.html
+packages/app/lorax_app/static/logo.png
+packages/app/lorax_app/static/lorax-logo.png
+packages/app/lorax_app/static/vite.svg
+packages/app/lorax_app/static/assets/index-BCEGlUFi.js
+packages/app/lorax_app/static/assets/index-iKjzUpA9.css
+packages/app/lorax_app/static/assets/localBackendWorker-BaWwjSV_.js
+packages/app/lorax_app/static/assets/renderDataWorker-BKLdiU7J.js
+packages/app/lorax_app/static/gestures/gesture-flick.ogv
+packages/app/lorax_app/static/gestures/gesture-two-finger-scroll.ogv
+packages/backend/lorax/buffer.py
+packages/backend/lorax/cli.py
+packages/backend/lorax/constants.py
+packages/backend/lorax/context.py
+packages/backend/lorax/handlers.py
+packages/backend/lorax/lineage.py
+packages/backend/lorax/lorax_app.py
+packages/backend/lorax/manager.py
+packages/backend/lorax/modes.py
+packages/backend/lorax/pg.py
+packages/backend/lorax/redis_utils.py
+packages/backend/lorax/routes.py
+packages/backend/lorax/session_manager.py
+packages/backend/lorax/utils.py
+packages/backend/lorax/cache/__init__.py
+packages/backend/lorax/cache/csv_tree_graph.py
+packages/backend/lorax/cache/disk.py
+packages/backend/lorax/cache/file_cache.py
+packages/backend/lorax/cache/file_context.py
+packages/backend/lorax/cache/lru.py
+packages/backend/lorax/cache/tree_graph.py
+packages/backend/lorax/cloud/__init__.py
+packages/backend/lorax/cloud/gcs_utils.py
+packages/backend/lorax/csv/__init__.py
+packages/backend/lorax/csv/config.py
+packages/backend/lorax/csv/layout.py
+packages/backend/lorax/csv/newick_tree.py
+packages/backend/lorax/loaders/__init__.py
+packages/backend/lorax/loaders/csv_loader.py
+packages/backend/lorax/loaders/loader.py
+packages/backend/lorax/loaders/tskit_loader.py
+packages/backend/lorax/metadata/__init__.py
+packages/backend/lorax/metadata/loader.py
+packages/backend/lorax/metadata/mutations.py
+packages/backend/lorax/sockets/__init__.py
+packages/backend/lorax/sockets/connection.py
+packages/backend/lorax/sockets/debug.py
+packages/backend/lorax/sockets/decorators.py
+packages/backend/lorax/sockets/file_ops.py
+packages/backend/lorax/sockets/lineage.py
+packages/backend/lorax/sockets/metadata.py
+packages/backend/lorax/sockets/mutations.py
+packages/backend/lorax/sockets/node_search.py
+packages/backend/lorax/sockets/tree_layout.py
+packages/backend/lorax/sockets/utils.py
+packages/backend/lorax/tree_graph/__init__.py
+packages/backend/lorax/tree_graph/tree_graph.py

lorax_arg-0.1/lorax_arg.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

lorax_arg-0.1/lorax_arg.egg-info/entry_points.txt

@@ -0,0 +1,4 @@
+[console_scripts]
+lorax = lorax_app.cli:main
+lorax-arg = lorax_app.cli:main
+lorax-backend = lorax.cli:main

lorax_arg-0.1/lorax_arg.egg-info/requires.txt

@@ -0,0 +1,31 @@
+fastapi>=0.100.0
+uvicorn>=0.20.0
+python-socketio>=5.0.0
+python-dotenv>=1.0.0
+click>=8.0.0
+aiofiles>=24.0.0
+aiohttp>=3.0.0
+numpy>=2.0.0
+pandas>=2.0.0
+pyarrow>=18.0.0
+tskit>=1.0.0
+tszip>=0.2.0
+redis>=5.0.0
+google-cloud-storage>=3.0.0
+starlette>=0.40.0
+psutil>=5.0.0
+ete3>=3.1.0
+numba>0.57.1
+python-multipart>=0.0.10
+
+[dev]
+pytest>=7.0.0
+pytest-asyncio>=0.21.0
+pytest-cov>=4.0.0
+httpx>=0.24.0
+locust>=2.15.0
+python-socketio[client]>=5.0.0
+msprime>=1.2.0
+
+[prod]
+gunicorn>=23.0.0

lorax_arg-0.1/lorax_arg.egg-info/top_level.txt

@@ -0,0 +1,2 @@
+lorax
+lorax_app

lorax_arg-0.1/packages/app/README.md

@@ -0,0 +1,92 @@
+# lorax-arg
+
+`lorax-arg` is a pip-installable distribution that runs Lorax as a **single-port app**.
+It ships the backend package in the same wheel so the install does not depend on a separate `lorax` PyPI release.
+CLI entrypoint: `lorax` (with `lorax-arg` as an alias).
+
+- React UI served at `/`
+- Backend API served at `/api/*`
+- Socket.IO served at `/api/socket.io/`
+
+## Development (monorepo)
+
+This package can run against the backend Python package from `packages/backend/` during development.
+
+### Build + sync UI assets (for wheel builds)
+
+Build the website with `VITE_API_BASE=/api`, then copy the `dist/` output into the Python package:
+
+```bash
+npm ci
+VITE_API_BASE=/api npm --workspace packages/website run build
+python packages/app/scripts/sync_ui_assets.py
+```
+
+### Run from source without copying assets
+
+```bash
+export LORAX_APP_STATIC_DIR=packages/website/dist
+python -m pip install -e .
+lorax
+```
+
+## Clean (remove build artifacts)
+
+```bash
+rm -rf build dist *.egg-info
+find packages/app -type d -name __pycache__ -prune -exec rm -rf {} +
+```
+
+## Production build (bundled UI)
+
+Build the UI and bundle it into the Python package, then build the wheel/sdist:
+
+```bash
+npm ci
+VITE_API_BASE=/api npm --workspace packages/website run build
+python packages/app/scripts/sync_ui_assets.py
+
+python -m pip install -U build
+python -m build .
+```
+
+You can also run:
+
+```bash
+lorax build
+```
+
+## Production install
+
+Install the built wheel locally (recommended for production verification):
+
+```bash
+python -m pip install --force-reinstall dist/lorax_arg-*.whl
+lorax
+```
+
+## Publish online (PyPI)
+
+1) Update `version` in the repo-root `pyproject.toml`.
+2) Build fresh artifacts:
+
+```bash
+rm -rf build dist *.egg-info
+npm ci
+VITE_API_BASE=/api npm --workspace packages/website run build
+python packages/app/scripts/sync_ui_assets.py
+python -m pip install -U build twine
+python -m build .
+```
+
+3) Upload to TestPyPI (recommended), then PyPI:
+
+```bash
+python -m twine upload --repository testpypi dist/*
+# verify: python -m pip install -i https://test.pypi.org/simple lorax-arg
+python -m twine upload dist/*
+```
+
+Notes:
+- You need PyPI credentials (or a token) configured in `~/.pypirc` or via `TWINE_USERNAME`/`TWINE_PASSWORD`.
+- Keep `README.md` and metadata in sync with what you want on PyPI.

lorax_arg-0.1/packages/app/lorax_app/__init__.py

@@ -0,0 +1,4 @@
+__all__ = ["__version__"]
+
+__version__ = "0.1.0"
+