quasar-models 0.1.0__tar.gz

quasar_models-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: quasar-models
+Version: 0.1.0
+Author-email: Liam <liam_deburca@me.com>
+Project-URL: Repository, https://github.com/liamdeburca/quasar-models
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+Requires-Dist: quasar-typing==0.1.0
+Requires-Dist: quasar-utils==0.1.0
+Requires-Dist: matplotlib==3.10.0
+Requires-Dist: pydantic==2.12
+Requires-Dist: astropy==7.0
+Requires-Dist: numpy==1.26
+Requires-Dist: scipy==1.16
+Requires-Dist: click==8.5.0
+Requires-Dist: emcee==3.1.6
+Requires-Dist: lazy-imports==1.2.0
+Provides-Extra: dev
+Requires-Dist: pytest==9.1.1; extra == "dev"
+Requires-Dist: pytest-cov==7.1.0; extra == "dev"
+Requires-Dist: black==26.10.1; extra == "dev"
+Requires-Dist: isort==9.0.2; extra == "dev"

quasar_models-0.1.0/pyproject.toml

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+[build-system]
+requires = [
+    "wheel", 
+    "setuptools==72.1.0",
+    "Cython==3.0.12", 
+    "numpy==1.26",
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "quasar-models"
+authors = [{name = "Liam", email = "liam_deburca@me.com"}]
+version = "0.1.0"
+readme = "README.md"
+requires-python = ">=3.12"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.12",
+]
+dependencies = [
+    "quasar-typing==0.1.0",
+    "quasar-utils==0.1.0",
+
+    "matplotlib==3.10.0",
+    "pydantic==2.12",
+    "astropy==7.0",
+    "numpy==1.26",
+    "scipy==1.16",
+    "click==8.5.0",
+    "emcee==3.1.6",
+    "lazy-imports==1.2.0",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest==9.1.1",
+    "pytest-cov==7.1.0",
+    "black==26.10.1",
+    "isort==9.0.2",
+]
+
+[project.urls]
+Repository = "https://github.com/liamdeburca/quasar-models"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.ruff]
+line-length = 79
+
+[lint.pyupgrade]
+keep-runtime-typing = true
+
+[tool.pytest.ini_options]
+markers = [
+    "benchmark: test benchmarks different methods",
+]

quasar_models-0.1.0/setup.cfg

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

quasar_models-0.1.0/setup.py

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+from Cython.Build import cythonize
+from numpy import get_include
+from setuptools import Extension, find_packages, setup
+
+setup(
+    name="quasar_models",
+    packages=find_packages(where="src"),
+    package_dir={"": "src"},
+    ext_modules=cythonize(
+        [
+            # Array utils
+            Extension(
+                "quasar_models._core.utils",
+                sources=["src/quasar_models/_core/utils.pyx"],
+            ),
+            # Powerlaw
+            Extension(
+                "quasar_models._core.modeling.powerlaw.evaluate",
+                sources=["src/quasar_models/_core/modeling/powerlaw/evaluate.pyx"],
+            ),
+            Extension(
+                "quasar_models._core.modeling.powerlaw.fit_deriv",
+                sources=["src/quasar_models/_core/modeling/powerlaw/fit_deriv.pyx"],
+            ),
+            # Gaussian
+            Extension(
+                "quasar_models._core.modeling.gaussian.evaluate",
+                sources=["src/quasar_models/_core/modeling/gaussian/evaluate.pyx"],
+            ),
+            Extension(
+                "quasar_models._core.modeling.gaussian.fit_deriv",
+                sources=["src/quasar_models/_core/modeling/gaussian/fit_deriv.pyx"],
+            ),
+            # VProfileCopy
+            Extension(
+                "quasar_models._core.modeling.vprofilecopy.evaluate",
+                sources=["src/quasar_models/_core/modeling/vprofilecopy/evaluate.pyx"],
+            ),
+            Extension(
+                "quasar_models._core.modeling.vprofilecopy.fit_deriv",
+                sources=["src/quasar_models/_core/modeling/vprofilecopy/fit_deriv.pyx"],
+            ),
+            # Convolution
+            Extension(
+                "quasar_models._core.convolution.utils",
+                sources=["src/quasar_models/_core/convolution/utils.pyx"],
+            ),
+            # Template
+            Extension(
+                "quasar_models._core.modeling.template.evaluate",
+                sources=["src/quasar_models/_core/modeling/template/evaluate.pyx"],
+            ),
+            Extension(
+                "quasar_models._core.modeling.template.fit_deriv",
+                sources=["src/quasar_models/_core/modeling/template/fit_deriv.pyx"],
+            ),
+            Extension(
+                "quasar_models._core.modeling.template.cytemplate",
+                sources=["src/quasar_models/_core/modeling/template/cytemplate.pyx"],
+            ),
+            # Host
+            Extension(
+                "quasar_models._core.modeling.host.evaluate",
+                sources=["src/quasar_models/_core/modeling/host/evaluate.pyx"],
+            ),
+            Extension(
+                "quasar_models._core.modeling.host.fit_deriv",
+                sources=["src/quasar_models/_core/modeling/host/fit_deriv.pyx"],
+            ),
+            # Split
+            Extension(
+                "quasar_models._core.modeling.split.evaluate",
+                sources=["src/quasar_models/_core/modeling/split/evaluate.pyx"],
+            ),
+            Extension(
+                "quasar_models._core.modeling.split.fit_deriv",
+                sources=["src/quasar_models/_core/modeling/split/fit_deriv.pyx"],
+            ),
+            # Iron
+            Extension(
+                "quasar_models._core.modeling.iron.evaluate",
+                sources=["src/quasar_models/_core/modeling/iron/evaluate.pyx"],
+            ),
+            Extension(
+                "quasar_models._core.modeling.iron.fit_deriv",
+                sources=["src/quasar_models/_core/modeling/iron/fit_deriv.pyx"],
+            ),
+            # Balmer - Continuum
+            Extension(
+                "quasar_models._core.modeling.balmer.continuum.evaluate",
+                sources=[
+                    "src/quasar_models/_core/modeling/balmer/continuum/evaluate.pyx"
+                ],
+            ),
+            # Balmer - Series
+            Extension(
+                "quasar_models._core.modeling.balmer.series.evaluate",
+                sources=["src/quasar_models/_core/modeling/balmer/series/evaluate.pyx"],
+            ),
+            # Balmer
+            Extension(
+                "quasar_models._core.modeling.balmer.evaluate",
+                sources=["src/quasar_models/_core/modeling/balmer/evaluate.pyx"],
+            ),
+            Extension(
+                "quasar_models._core.modeling.balmer.fit_deriv",
+                sources=["src/quasar_models/_core/modeling/balmer/fit_deriv.pyx"],
+            ),
+        ],
+        language_level=3,
+        compiler_directives={
+            "boundscheck": False,
+            "wraparound": False,
+            "cdivision": True,
+            "warn.undeclared": False,
+            "warn.unreachable": False,
+        },
+        force=True,  # Tabula rasa
+        include_path=["src"],  # Necessary for cimporing .pxd files
+    ),
+    include_dirs=[get_include()],
+    package_data={"quasar_models._core": ["**/*.pxd"]},
+)

quasar_models-0.1.0/src/quasar_models/__init__.py

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+import sys
+from typing import TYPE_CHECKING
+
+from lazy_imports import LazyImporter
+
+_import_structure: dict[str, list[str]] = {
+    "balmer": [
+        "BalmerModel", 
+        "BaModel",
+    ],
+    "continuum": [
+        "PlModel", 
+        "PowerLawModel",
+    ],
+    "host": [
+        "HgModel", 
+        "HostGalaxyModel",
+    ],
+    "iron": [
+        "FeModel", 
+        "IronModel",
+    ],
+    "line": [
+        "EmModel", 
+        "GaussianModel", 
+        "VProfileCopy",
+    ],
+}
+
+if TYPE_CHECKING:
+    from .balmer import BalmerModel, BaModel  # noqa: F401
+    from .continuum import PlModel, PowerLawModel  # noqa: F401
+    from .host import HgModel, HostGalaxyModel  # noqa: F401
+    from .iron import FeModel, IronModel  # noqa: F401
+    from .line import EmModel, GaussianModel, VProfileCopy  # noqa: F401
+
+else:
+    sys.modules[__name__] = LazyImporter(
+        __name__,
+        __file__,
+        _import_structure,
+    )

quasar_models-0.1.0/src/quasar_models/_core/convolution/__init__.py

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+from quasar_typing.numpy import FloatMatrix, FloatVector
+
+from .utils import convolve as _convolve
+from .utils import convolve_deriv as _convolve_deriv
+from .utils import convolve_signal as _convolve_signal
+from .utils import convolve_signal2d as _convolve_signal2d
+from .utils import identify_closest_idx as _identify_closest_idx
+from .utils import (
+    identify_closest_idx_for_deriv as _identify_closest_idx_for_deriv,
+)
+from .utils import kernel as _kernel
+from .utils import kernel_deriv as _kernel_deriv
+from .utils import pixels as _pixels
+from .utils import scale as _scale
+
+
+def scale(fwhm: float, sigma_res: float) -> float:
+    """
+    Parameters
+    ----------
+    fwhm : float
+        FWHM (km/s) of the template.
+    sigma_res : float
+        Velocity resolution (c) of the spectrum.
+    
+    Returns
+    -------
+    float
+    """
+    return _scale(fwhm, sigma_res)
+
+
+def pixels(scale: float, n_scales: float) -> FloatVector:
+    """
+    Parameters
+    ----------
+    scale : float
+    n_scales : float
+
+    Returns
+    -------
+    FloatVector
+    """
+    return _pixels(scale, n_scales)
+
+
+def kernel(fwhm: float, sigma_res: float, n_scales: float) -> FloatVector:
+    """
+    Calculate the Gaussian kernel used for convolution.
+
+    Parameters
+    ----------
+    fwhm : float
+        FWHM (km/s) of the template.
+    sigma_res : float
+        Velocity resolution (c) of the spectrum.
+    n_scales : float
+
+    Returns
+    -------
+    FloatVector
+    """
+    return _kernel(fwhm, sigma_res, n_scales)
+
+
+def kernel_deriv(
+    fwhm: float, sigma_res: float, n_scales: float
+) -> FloatVector:
+    """
+    Calculate the derivative of the Gaussian kernel used for convolution w.r.t. 
+    FWHM.
+
+    Parameters
+    ----------
+    fwhm : float
+        FWHM (km/s) of the template.
+    sigma_res : float
+        Velocity resolution (c) of the spectrum.
+    n_scales : float
+
+    Returns
+    -------
+    FloatVector
+    """
+    return _kernel_deriv(fwhm, sigma_res, n_scales)
+
+
+def convolve_signal(signal: FloatVector, kernel: FloatVector) -> FloatVector:
+    """
+    Convolve a signal with a kernel.
+
+    Parameters
+    ----------
+    signal : FloatVector
+        Signal to be convolved.
+    kernel : FloatVector
+        Kernel to convolve with the signal.
+
+    Returns
+    -------
+    FloatVector
+        Convolved signal.
+    """
+    return _convolve_signal(signal, kernel)
+
+
+def convolve_signal2d(
+    signal2d: FloatMatrix, kernel: FloatVector
+) -> FloatVector:
+    """
+    Convolve a 2D signal with a kernel.
+
+    Parameters
+    ----------
+    signal2d : FloatMatrix
+        2D signal to be convolved.
+    kernel : FloatVector
+        Kernel to convolve with the signal.
+
+    Returns
+    -------
+    FloatVector
+        Convolved signal.
+    """
+    return _convolve_signal2d(signal2d, kernel)
+
+
+def identify_closest_idx(fwhm: FloatVector, fwhm_final: float) -> int:
+    """
+    Find the index of the closest FWHM value in an array to a given FWHM value.
+
+    Parameters
+    ----------
+    fwhm : FloatVector
+        Array of FWHM values.
+    fwhm_final : float
+        Target FWHM value to find the closest index for.
+
+    Returns
+    -------
+    int
+        Index of the closest element.
+    """
+    return _identify_closest_idx(fwhm, fwhm_final)
+
+
+def identify_closest_idx_for_deriv(
+    fwhm: FloatVector, fwhm_final: float
+) -> int:
+    """
+    Find the index of the closest FWHM value in an array to a given FWHM value.
+
+    This function is specifically used for derivative calculations as it ensures 
+    that if 'fwhm_final' lies in the 'fwhm' array, the index is shifted 
+    downwards to guarantee convolution.
+
+    Parameters
+    ----------
+    fwhm : FloatVector
+        Array of FWHM values.
+    fwhm_final : float
+        Target FWHM value to find the closest index for.
+
+    Returns
+    -------
+    int
+        Index of the element.
+    """
+    return _identify_closest_idx_for_deriv(fwhm, fwhm_final)
+
+
+def convolve(
+    data: FloatMatrix,
+    fwhm: FloatVector,
+    fwhm_final: float,
+    sigma_res: float,
+    n_scales: float,
+) -> FloatVector:
+    """
+    Find the index of the closest FWHM value and convolve the corresponding data 
+    array.
+
+    Parameters
+    ----------
+    data : FloatMatrix
+        2D array of data to be convolved.
+    fwhm : FloatVector
+        Array of FWHM values corresponding to the data.
+    fwhm_final : float
+        Target FWHM value for convolution.
+    sigma_res : float
+        Velocity resolution (c) of the spectrum.
+    n_scales : float
+
+    Returns
+    -------
+    FloatVector
+        Convolved data array.
+    """
+    return _convolve(data, fwhm, fwhm_final, sigma_res, n_scales)
+
+
+def convolve_deriv(
+    data: FloatMatrix,
+    fwhm: FloatVector,
+    fwhm_final: float,
+    sigma_res: float,
+    n_scales: float,
+) -> FloatVector:
+    """
+    Find the index the closest FWHM value and calculate the derivative of the 
+    convolved data array w.r.t. FWHM.
+
+    Parameters
+    ----------
+    data : FloatMatrix
+        2D array of data to be convolved.
+    fwhm : FloatVector
+        Array of FWHM values corresponding to the data.
+    fwhm_final : float
+        Target FWHM value for convolution.
+    sigma_res : float
+        Velocity resolution (c) of the spectrum.
+    n_scales : float
+
+    Returns
+    -------
+    FloatVector
+        Derivative of the convolved data array w.r.t. FWHM.
+    """
+    return _convolve_deriv(data, fwhm, fwhm_final, sigma_res, n_scales)