nexusim 0.1.0b2__tar.gz

nexusim-0.1.0b2/LICENSE

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+MIT License
+
+Copyright (c) 2025 Amogh Singh
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

nexusim-0.1.0b2/PKG-INFO

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+Metadata-Version: 2.4
+Name: nexusim
+Version: 0.1.0b2
+Summary: JAX-accelerated multi-scale simulator for biological control and causal discovery
+License-Expression: MIT
+Keywords: biology,simulator,jax,causal-discovery,multi-scale
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: fastexcel>=0.16.0
+Requires-Dist: hydra-core>=1.3.2
+Requires-Dist: imageio>=2.37.2
+Requires-Dist: jax>=0.6.2
+Requires-Dist: marimo>=0.17.0
+Requires-Dist: matplotlib>=3.10.7
+Requires-Dist: msgspec>=0.20.0
+Requires-Dist: networkx>=3.4.2
+Requires-Dist: numpy>=2.2.6
+Requires-Dist: optax>=0.2.6
+Requires-Dist: polars>=1.34.0
+Requires-Dist: pyyaml>=6.0.3
+Requires-Dist: requests>=2.32.5
+Requires-Dist: tiledb>=0.35.2
+Requires-Dist: tqdm>=4.67.1
+Dynamic: license-file
+
+# Nexus
+
+Nexus is a JAX-accelerated multi-scale simulator for biological control and causal discovery, capable of generating biologically-realistic data.
+
+## Table of contents
+
+- [Setup](#setup)
+- [Code Structure](#code-structure)
+- [Usage](#usage)
+- [Visualization](#visualization)
+
+## Setup
+
+Install [uv](https://docs.astral.sh/uv/getting-started/installation/) package manager before running the setup
+
+```bash
+# Install using pip
+pip install nexusim
+
+# (OR)
+# Clone repo and build the package in uv
+## Clone repository and 
+git clone https://github.com/AmoghSingh25/GeneProtSim.git
+
+## Create venv and download packages
+uv sync
+```
+
+## Code Structure
+
+- `src/nexus/`
+  - `simulator/` - Core simulation engine
+    - `dynamics/` - Mathematical models for simulator dynamics
+    - `noise_models/` - Noise processes, random seeds
+    - `utils/` - Utility functions for simulator
+    - `grn/` - Code and logs of the GRN simulator
+    - `spatial/` -  Code, model definitions and logs of the Spatial Sim
+    - `spatial_vec/` -  Code, model definitions and logs of the vectorized version of Spatial Sim
+    - `run_sim.py` - Run the GRN and Spatial Sim
+    - `run_linked_sim.py` - Run the GRN and Spatial Sim together, allowing diffusion between cells and fields
+  - `causal/` - Causal discovery and inference modules
+    - `identification/` - Algorithms for structure/parameter learning
+    - `evaluation/` - Evaluation scripts
+  - `experiments/` - Scripts for running experiments
+  - `dashboard/` - Plotting, analysis, dashboards
+    - `web/` - Next.JS website for visualization of simulator outputs
+    - `retrieve_logger_api.py` - Flask API to serve data to the website
+  - `tests/` - Unit & integration tests
+- `configs/` - Config files for runs
+- `notebooks/` - Exploratory analyses and demos
+- `docs/` - Documentation
+  - `config_desc.md` - Configuration parameters and their description
+  - `intervention_api.md` - Working of intervention API and its configuration
+  - `simulator.md` - Working of the GRN simulator
+  - `spatial_simulator.md` - Working of the spatial simulator
+- `examples/` - Examples scripts
+  - `marimo_example.py` - Marimo notebook containing example scripts
+  - `ipynb_example.py` - IPYNB notebook containing example scripts
+- `pyproject.toml` - For package/dependency management
+- `README.md`
+
+## Usage
+
+A short code snippet for using the simulator is given below.
+```py
+from nexus.simulator.grn.grnSim import GRNSim
+from nexus.simulator.spatial.spatialSim import SpatialSim
+from hydra import initialize_config_dir, compose
+
+ def get_config(config_name="test_config"): # Get config from Hydra config file
+    conf_path = os.path.join(os.getcwd(), "configs")
+    with initialize_config_dir(version_base=None, config_dir=conf_path):
+        cfg = compose(config_name=config_name)
+    return cfg
+
+cfg = get_config()
+
+sim = GRNSim(cfg.grn)
+sim.run_sim()
+
+spatial_sim = SpatialSim(cfg.spatial)
+spatial_sim.run_sim()
+```
+
+Examples for running the simulator are given in a [Marimo notebook](examples/marimo_example.py) and a [IPYNB notebook](examples/ipynb_example.ipynb). The simulator uses Hydra configs for the simulation parameters and the description of the config files are given in [Config Description](docs/config_desc.md).
+
+## Intervention API
+
+The simulator also supports interventions on the parameters that allows for generating interventional data for causal discovery and analysis. Guidance on using interventions is given in the [Intervention Doc](docs/intevention_api.md).
+
+## Visualization
+
+The visualization can be run by the running the two commands in seperate terminal windows.
+
+```bash
+## Runs the API for fetching the data from TileDB
+uv run src/dashboard/retrieve_logger_api.py
+
+## Runs the website to visualize the data
+cd dashboard/web/
+npm install # If the packages are not installed
+npm run dev
+```
+
+After running these two commands, open the link `http://localhost:3000` and select a log file from the dropdown. This log file should be present inside the relative directory `logs/`.
+
+Further instructions on using the dashboard is given in [README](dashboard/web/README.md)

nexusim-0.1.0b2/README.md

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+# Nexus
+
+Nexus is a JAX-accelerated multi-scale simulator for biological control and causal discovery, capable of generating biologically-realistic data.
+
+## Table of contents
+
+- [Setup](#setup)
+- [Code Structure](#code-structure)
+- [Usage](#usage)
+- [Visualization](#visualization)
+
+## Setup
+
+Install [uv](https://docs.astral.sh/uv/getting-started/installation/) package manager before running the setup
+
+```bash
+# Install using pip
+pip install nexusim
+
+# (OR)
+# Clone repo and build the package in uv
+## Clone repository and 
+git clone https://github.com/AmoghSingh25/GeneProtSim.git
+
+## Create venv and download packages
+uv sync
+```
+
+## Code Structure
+
+- `src/nexus/`
+  - `simulator/` - Core simulation engine
+    - `dynamics/` - Mathematical models for simulator dynamics
+    - `noise_models/` - Noise processes, random seeds
+    - `utils/` - Utility functions for simulator
+    - `grn/` - Code and logs of the GRN simulator
+    - `spatial/` -  Code, model definitions and logs of the Spatial Sim
+    - `spatial_vec/` -  Code, model definitions and logs of the vectorized version of Spatial Sim
+    - `run_sim.py` - Run the GRN and Spatial Sim
+    - `run_linked_sim.py` - Run the GRN and Spatial Sim together, allowing diffusion between cells and fields
+  - `causal/` - Causal discovery and inference modules
+    - `identification/` - Algorithms for structure/parameter learning
+    - `evaluation/` - Evaluation scripts
+  - `experiments/` - Scripts for running experiments
+  - `dashboard/` - Plotting, analysis, dashboards
+    - `web/` - Next.JS website for visualization of simulator outputs
+    - `retrieve_logger_api.py` - Flask API to serve data to the website
+  - `tests/` - Unit & integration tests
+- `configs/` - Config files for runs
+- `notebooks/` - Exploratory analyses and demos
+- `docs/` - Documentation
+  - `config_desc.md` - Configuration parameters and their description
+  - `intervention_api.md` - Working of intervention API and its configuration
+  - `simulator.md` - Working of the GRN simulator
+  - `spatial_simulator.md` - Working of the spatial simulator
+- `examples/` - Examples scripts
+  - `marimo_example.py` - Marimo notebook containing example scripts
+  - `ipynb_example.py` - IPYNB notebook containing example scripts
+- `pyproject.toml` - For package/dependency management
+- `README.md`
+
+## Usage
+
+A short code snippet for using the simulator is given below.
+```py
+from nexus.simulator.grn.grnSim import GRNSim
+from nexus.simulator.spatial.spatialSim import SpatialSim
+from hydra import initialize_config_dir, compose
+
+ def get_config(config_name="test_config"): # Get config from Hydra config file
+    conf_path = os.path.join(os.getcwd(), "configs")
+    with initialize_config_dir(version_base=None, config_dir=conf_path):
+        cfg = compose(config_name=config_name)
+    return cfg
+
+cfg = get_config()
+
+sim = GRNSim(cfg.grn)
+sim.run_sim()
+
+spatial_sim = SpatialSim(cfg.spatial)
+spatial_sim.run_sim()
+```
+
+Examples for running the simulator are given in a [Marimo notebook](examples/marimo_example.py) and a [IPYNB notebook](examples/ipynb_example.ipynb). The simulator uses Hydra configs for the simulation parameters and the description of the config files are given in [Config Description](docs/config_desc.md).
+
+## Intervention API
+
+The simulator also supports interventions on the parameters that allows for generating interventional data for causal discovery and analysis. Guidance on using interventions is given in the [Intervention Doc](docs/intevention_api.md).
+
+## Visualization
+
+The visualization can be run by the running the two commands in seperate terminal windows.
+
+```bash
+## Runs the API for fetching the data from TileDB
+uv run src/dashboard/retrieve_logger_api.py
+
+## Runs the website to visualize the data
+cd dashboard/web/
+npm install # If the packages are not installed
+npm run dev
+```
+
+After running these two commands, open the link `http://localhost:3000` and select a log file from the dropdown. This log file should be present inside the relative directory `logs/`.
+
+Further instructions on using the dashboard is given in [README](dashboard/web/README.md)

nexusim-0.1.0b2/pyproject.toml

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+[project]
+name = "nexusim"
+version = "0.1.0b2"
+description = "JAX-accelerated multi-scale simulator for biological control and causal discovery"
+keywords = [
+    "biology",
+    "simulator",
+    "jax",
+    "causal-discovery",
+    "multi-scale",
+]
+readme = "README.md"
+license = "MIT"
+license-files = [
+    "LICENSE",
+]
+requires-python = ">=3.10"
+dependencies = [
+    "fastexcel>=0.16.0",
+    "hydra-core>=1.3.2",
+    "imageio>=2.37.2",
+    "jax>=0.6.2",
+    "marimo>=0.17.0",
+    "matplotlib>=3.10.7",
+    "msgspec>=0.20.0",
+    "networkx>=3.4.2",
+    "numpy>=2.2.6",
+    "optax>=0.2.6",
+    "polars>=1.34.0",
+    "pyyaml>=6.0.3",
+    "requests>=2.32.5",
+    "tiledb>=0.35.2",
+    "tqdm>=4.67.1",
+]
+
+[dependency-groups]
+dev = [
+    "pytest>=8.4.2",
+    "ruff>=0.14.0",
+    "pre-commit>=4.3.0",
+    "dash>=3.3.0",
+    "dash-ag-grid>=32.3.2",
+    "dash-bootstrap-components>=2.0.4",
+    "flask-cors>=6.0.2",
+    "diffrax>=0.7.0",
+]
+
+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.ruff]
+exclude = ["notebooks/", "examples/"]
+
+[[tool.uv.index]]
+name = "testpypi"
+url = "https://test.pypi.org/simple/"
+publish-url = "https://test.pypi.org/legacy/"
+explicit = true
+
+[tool.setuptools.package-dir]
+nexus = "src/nexus"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+exclude = [
+    "tests*",
+    "outputs*",
+    "experiments*",
+    "simulator.archive*",
+    "*.egg-info*",
+    "dashboard*"
+]
+
+[tool.setuptools.exclude-package-data]
+simulator = ["archive/*", "outputs/*", "logs/*"]
+outputs=["*"]

nexusim-0.1.0b2/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+