jaxspec 0.1.0__tar.gz → 0.1.2__tar.gz

{jaxspec-0.1.0 → jaxspec-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: jaxspec
-Version: 0.1.0
+Version: 0.1.2
 Summary: jaxspec is a bayesian spectral fitting library for X-ray astronomy.
 Home-page: https://github.com/renecotyfanboy/jaxspec
 License: MIT
@@ -15,19 +15,18 @@ Requires-Dist: arviz (>=0.17.1,<0.20.0)
 Requires-Dist: astropy (>=6.0.0,<7.0.0)
 Requires-Dist: chainconsumer (>=1.1.2,<2.0.0)
 Requires-Dist: cmasher (>=1.6.3,<2.0.0)
-Requires-Dist: dm-haiku (>=0.0.11,<0.0.13)
+Requires-Dist: dm-haiku (>=0.0.12,<0.0.13)
 Requires-Dist: gpjax (>=0.8.0,<0.9.0)
 Requires-Dist: interpax (>=0.3.3,<0.4.0)
-Requires-Dist: jax (>=0.4.30,<0.5.0)
+Requires-Dist: jax (>=0.4.33,<0.5.0)
 Requires-Dist: jaxlib (>=0.4.30,<0.5.0)
-Requires-Dist: jaxns (>=2.5.1,<3.0.0)
+Requires-Dist: jaxns (<2.6)
 Requires-Dist: jaxopt (>=0.8.1,<0.9.0)
 Requires-Dist: matplotlib (>=3.8.0,<4.0.0)
 Requires-Dist: mendeleev (>=0.15,<0.18)
-Requires-Dist: mkdocstrings (>=0.24,<0.26)
 Requires-Dist: networkx (>=3.1,<4.0)
 Requires-Dist: numpy (<2.0.0)
-Requires-Dist: numpyro (>=0.15.2,<0.16.0)
+Requires-Dist: numpyro (>=0.15.3,<0.16.0)
 Requires-Dist: optimistix (>=0.0.7,<0.0.8)
 Requires-Dist: pandas (>=2.2.0,<3.0.0)
 Requires-Dist: pooch (>=1.8.2,<2.0.0)
@@ -41,7 +40,14 @@ Requires-Dist: watermark (>=2.4.3,<3.0.0)
 Project-URL: Documentation, https://jaxspec.readthedocs.io/en/latest/
 Description-Content-Type: text/markdown
 
-# jaxspec
+<p align="center">
+  <img src="https://raw.githubusercontent.com/renecotyfanboy/jaxspec/main/docs/logo/logo_small.svg" alt="Logo" width="100" height="100">
+</p>
+
+<h1 align="center">
+  jaxspec
+</h1>
+
 
 [![PyPI - Version](https://img.shields.io/pypi/v/jaxspec?style=for-the-badge&logo=pypi&color=rgb(37%2C%20150%2C%20190))](https://pypi.org/project/jaxspec/)
 [![Python package](https://img.shields.io/pypi/pyversions/jaxspec?style=for-the-badge)](https://pypi.org/project/jaxspec/)

{jaxspec-0.1.0 → jaxspec-0.1.2}/README.md

@@ -1,4 +1,11 @@
-# jaxspec
+<p align="center">
+  <img src="https://raw.githubusercontent.com/renecotyfanboy/jaxspec/main/docs/logo/logo_small.svg" alt="Logo" width="100" height="100">
+</p>
+
+<h1 align="center">
+  jaxspec
+</h1>
+
 
 [![PyPI - Version](https://img.shields.io/pypi/v/jaxspec?style=for-the-badge&logo=pypi&color=rgb(37%2C%20150%2C%20190))](https://pypi.org/project/jaxspec/)
 [![Python package](https://img.shields.io/pypi/pyversions/jaxspec?style=for-the-badge)](https://pypi.org/project/jaxspec/)

{jaxspec-0.1.0 → jaxspec-0.1.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "jaxspec"
-version = "0.1.0"
+version = "0.1.2"
 description = "jaxspec is a bayesian spectral fitting library for X-ray astronomy."
 authors = ["sdupourque <sdupourque@irap.omp.eu>"]
 license = "MIT"
@@ -11,13 +11,13 @@ documentation = "https://jaxspec.readthedocs.io/en/latest/"
 
 [tool.poetry.dependencies]
 python = ">=3.10,<3.12"
-jax = "^0.4.30"
+jax = "^0.4.33"
 jaxlib = "^0.4.30"
 numpy = "<2.0.0"
 pandas = "^2.2.0"
 astropy = "^6.0.0"
-numpyro = "^0.15.2"
-dm-haiku = ">=0.0.11,<0.0.13"
+numpyro = "^0.15.3"
+dm-haiku = "^0.0.12"
 networkx = "^3.1"
 matplotlib = "^3.8.0"
 arviz = ">=0.17.1,<0.20.0"
@@ -28,23 +28,22 @@ gpjax = "^0.8.0"
 jaxopt = "^0.8.1"
 tinygp = "^0.3.0"
 seaborn = "^0.13.1"
-mkdocstrings = ">=0.24,<0.26"
 sparse = "^0.15.1"
 optimistix = "^0.0.7"
 scipy = "<1.15"
 mendeleev = ">=0.15,<0.18"
 pyzmq = "<27"
-jaxns = "^2.5.1"
+jaxns = "<2.6"
 pooch = "^1.8.2"
 interpax = "^0.3.3"
 watermark = "^2.4.3"
 
 
 [tool.poetry.group.docs.dependencies]
-mkdocs = "^1.5.3"
+mkdocs = "^1.6.1"
 mkdocs-material = "^9.4.6"
-mkdocstrings = {extras = ["python"], version = ">=0.24,<0.26"}
-mkdocs-jupyter = "^0.24.6"
+mkdocstrings = {extras = ["python"], version = ">=0.24,<0.27"}
+mkdocs-jupyter = "^0.25.0"
 
 
 [tool.poetry.group.test.dependencies]
@@ -59,7 +58,7 @@ testbook = "^0.4.2"
 
 [tool.poetry.group.dev.dependencies]
 pre-commit = "^3.5.0"
-ruff = ">=0.2.1,<0.6.0"
+ruff = ">=0.2.1,<0.7.0"
 jupyterlab = "^4.0.7"
 notebook = "^7.0.6"
 ipywidgets = "^8.1.1"
@@ -118,4 +117,4 @@ requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
 
 [tool.poetry.scripts]
-jaxspec-debug-info = "jaxspec.scripts.debug:debug_info"
+jaxspec-debug-info = "jaxspec.scripts.debug:debug_info"

jaxspec-0.1.2/src/jaxspec/analysis/_plot.py

@@ -0,0 +1,35 @@
+import matplotlib.pyplot as plt
+import numpy as np
+
+from jax.typing import ArrayLike
+from scipy.stats import nbinom
+
+
+def _plot_poisson_data_with_error(
+    ax: plt.Axes,
+    x_bins: ArrayLike,
+    y: ArrayLike,
+    percentiles: tuple = (16, 84),
+):
+    """
+    Plot Poisson data with error bars. We extrapolate the intrinsic error of the observation assuming a prior rate
+    distributed according to a Gamma RV.
+    """
+    y_low = nbinom.ppf(percentiles[0] / 100, y, 0.5)
+    y_high = nbinom.ppf(percentiles[1] / 100, y, 0.5)
+
+    ax_to_plot = ax.errorbar(
+        np.sqrt(x_bins[0] * x_bins[1]),
+        y,
+        xerr=np.abs(x_bins - np.sqrt(x_bins[0] * x_bins[1])),
+        yerr=[
+            y - y_low,
+            y_high - y,
+        ],
+        color="black",
+        linestyle="none",
+        alpha=0.3,
+        capsize=2,
+    )
+
+    return ax_to_plot

{jaxspec-0.1.0 → jaxspec-0.1.2}/src/jaxspec/data/obsconf.py

@@ -229,5 +229,39 @@ class ObsConfiguration(xr.Dataset):
             attrs=observation.attrs | instrument.attrs,
         )
 
+    @classmethod
+    def mock_from_instrument(
+        cls,
+        instrument: Instrument,
+        exposure: float,
+        low_energy: float = 1e-20,
+        high_energy: float = 1e20,
+    ):
+        """
+        Create a mock observation configuration from an instrument object. The fake observation will have zero counts.
+
+        Parameters:
+            instrument: The instrument object.
+            exposure: The total exposure of the mock observation.
+            low_energy: The lower bound of the energy range to consider.
+            high_energy: The upper bound of the energy range to consider.
+        """
+
+        n_channels = len(instrument.coords["instrument_channel"])
+
+        observation = Observation.from_matrix(
+            np.zeros(n_channels),
+            sparse.eye(n_channels),
+            np.arange(n_channels),
+            np.zeros(n_channels, dtype=bool),
+            exposure,
+            backratio=np.ones(n_channels),
+            attributes={"description": "Mock observation"} | instrument.attrs,
+        )
+
+        return cls.from_instrument(
+            instrument, observation, low_energy=low_energy, high_energy=high_energy
+        )
+
     def plot_counts(self, **kwargs):
         return self.folded_counts.plot.step(x="e_min_folded", where="post", **kwargs)