gp4c 0.0.9__tar.gz

gp4c-0.0.9/LICENSE

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+MIT License
+
+Copyright (c) 2026 Rodrigo Calderon
+
+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.

gp4c-0.0.9/MANIFEST.in

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+# Include Cython source files
+include gp4c/_core.pyx
+include gp4c/_core.c
+
+# Include C library files
+include gp4c/gp4c.c
+include gp4c/gp4c.h
+
+# Include installation script
+include install_library.sh
+
+# Include documentation
+include README.md
+include LICENSE
+
+# Include test data if any
+recursive-include tests *.py
+
+# Include examples
+recursive-include examples *.py *.c Makefile
+
+# Exclude build artifacts
+global-exclude __pycache__
+global-exclude *.py[co]
+global-exclude .DS_Store

gp4c-0.0.9/PKG-INFO

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+Metadata-Version: 2.4
+Name: gp4c
+Version: 0.0.9
+Summary: Fast joint GP sampling with integral and derivative relationships
+Author-email: Rodrigo Calderon <calderon.cosmology@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/rcalderonb6/gp4c
+Project-URL: Documentation, https://github.com/rcalderonb6/gp4c#readme
+Project-URL: Repository, https://github.com/rcalderonb6/gp4c
+Project-URL: Issues, https://github.com/rcalderonb6/gp4c/issues
+Keywords: gaussian-process,gp,sampling,integral,derivative,bayesian
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Cython
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.21
+Requires-Dist: typer>=0.9.0
+Requires-Dist: rich>=13.0.0
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: matplotlib>=3.5; extra == "dev"
+Requires-Dist: ipython; extra == "dev"
+Requires-Dist: pytest-cov>=4.0; extra == "dev"
+Requires-Dist: codespell>=2.2.0; extra == "dev"
+Requires-Dist: bump-my-version>=0.26.0; extra == "dev"
+Provides-Extra: viz
+Requires-Dist: matplotlib>=3.5; extra == "viz"
+Requires-Dist: seaborn>=0.12; extra == "viz"
+Provides-Extra: docs
+Requires-Dist: mkdocs<2.0,>=1.5; extra == "docs"
+Requires-Dist: mkdocs-material>=9.0; extra == "docs"
+Requires-Dist: mkdocs-marimo>=0.1.0; extra == "docs"
+Requires-Dist: mkdocstrings[python]>=0.27.0; extra == "docs"
+Requires-Dist: pymdown-extensions>=10.0; extra == "docs"
+Requires-Dist: codespell>=2.2.0; extra == "docs"
+Dynamic: license-file
+
+# gp4c
+
+High-performance C implementation with Python bindings for sampling from joint Gaussian Processes with integral and derivative relationships.
+
+## Overview
+
+Sample from joint GP $(f, g, h)$ where:
+
+- $f(x) \sim \mathcal{GP}(0, k_f)$ — original process with RBF kernel
+- $g(x) = \int_0^x f(t) dt$ — integrated process
+- $h(x) = f'(x)$ — derivative process
+
+All three are correlated through proper cross-covariance structures.
+
+## Key Features
+
+- **Fast C implementation** using GSL (GNU Scientific Library)
+- **Zero-copy Cython wrapper** for seamless NumPy integration
+- **Three-way joint sampling** of function, integral, and derivative
+- **Posterior sampling** conditioned on observed data
+- **Mixed observations** — observe f, predict h, or any combination
+- **Mathematically rigorous** covariance structure
+- **Fully tested** with comprehensive unit tests
+
+## Quick Install
+
+### Prerequisites
+
+Install GSL first:
+
+```bash
+# macOS
+brew install gsl
+
+# Ubuntu/Debian
+sudo apt-get install libgsl-dev
+
+# Fedora/RHEL
+sudo dnf install gsl-devel
+```
+
+### Install Package
+
+```bash
+pip install -e .
+```
+
+## Quick Start
+
+```python
+import numpy as np
+from gp4c import sample_joint_gp
+
+x = np.linspace(0, 5, 100)
+f_samples, g_samples = sample_joint_gp(
+    x, x,
+    sigma2=1.0,
+    ell=0.5,
+    n_samples=5,
+    seed=42
+)
+```
+
+## Documentation
+
+Full documentation is available at: **[https://yourusername.github.io/gp4c](https://yourusername.github.io/gp4c)**
+
+Or build locally:
+
+```bash
+pip install mkdocs-material
+mkdocs serve
+```
+
+### Quick Links
+
+- [Installation Guide](https://yourusername.github.io/gp4c/getting-started/installation/)
+- [Quick Start Tutorial](https://yourusername.github.io/gp4c/getting-started/quickstart/)
+- [API Reference](https://yourusername.github.io/gp4c/api/functions/)
+- [Mathematical Background](https://yourusername.github.io/gp4c/math/kernels/)
+- [Examples](https://yourusername.github.io/gp4c/examples/python/)
+
+## Examples
+
+Basic usage:
+
+```python
+# Sample f and its derivative h
+from gp4c import sample_gp, SamplingSpec
+
+spec = SamplingSpec(x_f=x, x_h=x)
+result = sample_gp(spec, sigma2=1.0, ell=0.5, n_samples=5)
+```
+
+Posterior sampling:
+
+```python
+# Condition on observations
+from gp4c import sample_gp_posterior, Observations
+
+x_train = np.array([0.0, 1.0, 2.0, 3.0, 4.0])
+y_train = np.sin(x_train)
+obs = Observations(x_f=x_train, y_f=y_train, noise_f=0.01)
+
+x_test = np.linspace(0, 5, 100)
+spec = SamplingSpec(x_f=x_test)
+
+result = sample_gp_posterior(obs, spec, ell=1.0, n_samples=10)
+```
+
+See the [examples/](examples/) directory and [documentation](https://yourusername.github.io/gp4c/examples/python/) for more.
+
+## Testing
+
+```bash
+pytest tests/ -v
+```
+
+## C Library
+
+The core can be used directly in C/C++ projects. See [C Integration Guide](https://yourusername.github.io/gp4c/examples/c-integration/).
+
+Quick install as system library:
+
+```bash
+./install_library.sh        # System-wide (requires sudo)
+./install_library.sh --user # User install (no sudo)
+```
+
+## Project Structure
+
+```
+gp4c/
+├── gp4c/                # Python package
+│   ├── _sampler.c       # C implementation
+│   ├── _core.pyx        # Cython wrapper
+│   └── types.py         # Type definitions
+├── docs/                # MkDocs documentation
+├── tests/               # Test suite
+├── examples/            # Example scripts
+├── notebooks/           # Jupyter notebooks
+└── mkdocs.yml           # Documentation config
+```
+
+## Contributing
+
+Contributions welcome! See [Contributing Guide](https://yourusername.github.io/gp4c/reference/contributing/).
+
+1. Fork the repository
+2. Create a feature branch
+3. Add tests for new functionality
+4. Submit a pull request
+
+## License
+
+MIT License - see LICENSE file for details.
+
+## Citation
+
+If you use this package in your research, please cite:
+
+```bibtex
+@software{gp4c,
+  title = {gp4c: Fast Joint Gaussian Process Sampling with integral and derivative information},
+  author = {Calderón, Rodrigo},
+  year = {2026},
+  url = {https://github.com/rcalderonb6/gp4c}
+}
+```
+
+## References
+
+1. Solak et al. (2003) - Derivative observations in Gaussian process models
+2. Rasmussen & Williams (2006) - Gaussian Processes for Machine Learning
+3. GSL Manual - https://www.gnu.org/software/gsl/doc/html/

gp4c-0.0.9/README.md

@@ -0,0 +1,175 @@
+# gp4c
+
+High-performance C implementation with Python bindings for sampling from joint Gaussian Processes with integral and derivative relationships.
+
+## Overview
+
+Sample from joint GP $(f, g, h)$ where:
+
+- $f(x) \sim \mathcal{GP}(0, k_f)$ — original process with RBF kernel
+- $g(x) = \int_0^x f(t) dt$ — integrated process
+- $h(x) = f'(x)$ — derivative process
+
+All three are correlated through proper cross-covariance structures.
+
+## Key Features
+
+- **Fast C implementation** using GSL (GNU Scientific Library)
+- **Zero-copy Cython wrapper** for seamless NumPy integration
+- **Three-way joint sampling** of function, integral, and derivative
+- **Posterior sampling** conditioned on observed data
+- **Mixed observations** — observe f, predict h, or any combination
+- **Mathematically rigorous** covariance structure
+- **Fully tested** with comprehensive unit tests
+
+## Quick Install
+
+### Prerequisites
+
+Install GSL first:
+
+```bash
+# macOS
+brew install gsl
+
+# Ubuntu/Debian
+sudo apt-get install libgsl-dev
+
+# Fedora/RHEL
+sudo dnf install gsl-devel
+```
+
+### Install Package
+
+```bash
+pip install -e .
+```
+
+## Quick Start
+
+```python
+import numpy as np
+from gp4c import sample_joint_gp
+
+x = np.linspace(0, 5, 100)
+f_samples, g_samples = sample_joint_gp(
+    x, x,
+    sigma2=1.0,
+    ell=0.5,
+    n_samples=5,
+    seed=42
+)
+```
+
+## Documentation
+
+Full documentation is available at: **[https://yourusername.github.io/gp4c](https://yourusername.github.io/gp4c)**
+
+Or build locally:
+
+```bash
+pip install mkdocs-material
+mkdocs serve
+```
+
+### Quick Links
+
+- [Installation Guide](https://yourusername.github.io/gp4c/getting-started/installation/)
+- [Quick Start Tutorial](https://yourusername.github.io/gp4c/getting-started/quickstart/)
+- [API Reference](https://yourusername.github.io/gp4c/api/functions/)
+- [Mathematical Background](https://yourusername.github.io/gp4c/math/kernels/)
+- [Examples](https://yourusername.github.io/gp4c/examples/python/)
+
+## Examples
+
+Basic usage:
+
+```python
+# Sample f and its derivative h
+from gp4c import sample_gp, SamplingSpec
+
+spec = SamplingSpec(x_f=x, x_h=x)
+result = sample_gp(spec, sigma2=1.0, ell=0.5, n_samples=5)
+```
+
+Posterior sampling:
+
+```python
+# Condition on observations
+from gp4c import sample_gp_posterior, Observations
+
+x_train = np.array([0.0, 1.0, 2.0, 3.0, 4.0])
+y_train = np.sin(x_train)
+obs = Observations(x_f=x_train, y_f=y_train, noise_f=0.01)
+
+x_test = np.linspace(0, 5, 100)
+spec = SamplingSpec(x_f=x_test)
+
+result = sample_gp_posterior(obs, spec, ell=1.0, n_samples=10)
+```
+
+See the [examples/](examples/) directory and [documentation](https://yourusername.github.io/gp4c/examples/python/) for more.
+
+## Testing
+
+```bash
+pytest tests/ -v
+```
+
+## C Library
+
+The core can be used directly in C/C++ projects. See [C Integration Guide](https://yourusername.github.io/gp4c/examples/c-integration/).
+
+Quick install as system library:
+
+```bash
+./install_library.sh        # System-wide (requires sudo)
+./install_library.sh --user # User install (no sudo)
+```
+
+## Project Structure
+
+```
+gp4c/
+├── gp4c/                # Python package
+│   ├── _sampler.c       # C implementation
+│   ├── _core.pyx        # Cython wrapper
+│   └── types.py         # Type definitions
+├── docs/                # MkDocs documentation
+├── tests/               # Test suite
+├── examples/            # Example scripts
+├── notebooks/           # Jupyter notebooks
+└── mkdocs.yml           # Documentation config
+```
+
+## Contributing
+
+Contributions welcome! See [Contributing Guide](https://yourusername.github.io/gp4c/reference/contributing/).
+
+1. Fork the repository
+2. Create a feature branch
+3. Add tests for new functionality
+4. Submit a pull request
+
+## License
+
+MIT License - see LICENSE file for details.
+
+## Citation
+
+If you use this package in your research, please cite:
+
+```bibtex
+@software{gp4c,
+  title = {gp4c: Fast Joint Gaussian Process Sampling with integral and derivative information},
+  author = {Calderón, Rodrigo},
+  year = {2026},
+  url = {https://github.com/rcalderonb6/gp4c}
+}
+```
+
+## References
+
+1. Solak et al. (2003) - Derivative observations in Gaussian process models
+2. Rasmussen & Williams (2006) - Gaussian Processes for Machine Learning
+3. GSL Manual - https://www.gnu.org/software/gsl/doc/html/

gp4c-0.0.9/examples/Makefile

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+# Makefile for GP Sampler C Examples
+#
+# Usage:
+#   make              # Build the C example
+#   make run          # Build and run
+#   make clean        # Remove build artifacts
+
+CC = gcc
+CFLAGS = -O3 -Wall -Wextra $(shell gsl-config --cflags)
+LDFLAGS = $(shell gsl-config --libs) -lm
+
+# Directories
+SRC_DIR = ..
+INCLUDES = -I$(SRC_DIR)
+
+# Targets
+TARGET = c_example
+SOURCES = c_integration_example.c $(SRC_DIR)/gp_sampler_core.c
+OBJECTS = $(SOURCES:.c=.o)
+HEADERS = $(SRC_DIR)/gp_sampler_core.h
+
+# Build rules
+all: $(TARGET)
+
+$(TARGET): $(OBJECTS)
+	$(CC) -o $@ $^ $(LDFLAGS)
+	@echo "Build successful! Run with: ./$(TARGET)"
+
+%.o: %.c $(HEADERS)
+	$(CC) $(CFLAGS) $(INCLUDES) -c $< -o $@
+
+run: $(TARGET)
+	./$(TARGET)
+
+clean:
+	rm -f $(OBJECTS) $(TARGET)
+	rm -f $(SRC_DIR)/gp_sampler_core.o
+	@echo "Cleaned build artifacts"
+
+# Static library (optional)
+libgp4c.a: $(SRC_DIR)/gp_sampler_core.o
+	ar rcs $@ $^
+	@echo "Created static library: libgp4c.a"
+
+.PHONY: all run clean

gp4c-0.0.9/gp4c/__init__.py

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+"""gp4c - Fast joint GP sampling with integral and derivative relationships.
+
+This package provides efficient sampling from joint Gaussian Processes where:
+- f(x) is a GP with RBF kernel
+- g(x) = integral of f from 0 to x
+- h(x) = f'(x), the derivative
+
+All functions maintain exact covariance structure through analytically-derived
+cross-covariance kernels.
+"""
+
+from ._core import (
+    sample_joint_gp,
+    sample_gp,
+    sample_and_integrate,
+    sample_gp_posterior,
+)
+from .types import (
+    MeanSpec,
+    SamplingSpec,
+    GPSamples,
+    Observations,
+    PosteriorSamples,
+)
+
+__version__ = "2.0.0"
+__all__ = [
+    "sample_joint_gp",
+    "sample_gp",
+    "sample_and_integrate",
+    "sample_gp_posterior",
+    "MeanSpec",
+    "SamplingSpec",
+    "GPSamples",
+    "Observations",
+    "PosteriorSamples",
+]