jaxspec 0.1.3__py3-none-any.whl → 0.2.0__py3-none-any.whl

jaxspec/util/typing.py

@@ -1,68 +1,5 @@
-from typing import Any
-
 import numpyro.distributions as dist
 
-from jax import numpy as jnp
 from jax.typing import ArrayLike
-from pydantic import BaseModel, field_validator
 
 PriorDictType = dict[str, dict[str, dist.Distribution | ArrayLike]]
-
-
-def is_flat_dict(input_data: dict[str, Any]) -> bool:
-    """
-    Check if the input data is a flat dictionary with string keys and non-dictionary values.
-    """
-    return all(isinstance(k, str) and not isinstance(v, dict) for k, v in input_data.items())
-
-
-class PriorDictModel(BaseModel):
-    """
-    Pydantic model for a nested dictionary of NumPyro distributions or JAX arrays.
-    The top level keys are strings, and the values are dictionaries with string keys and values that are either
-    NumPyro distributions or JAX arrays (or convertible to JAX arrays).
-    """
-
-    nested_dict: PriorDictType
-
-    class Config:  # noqa D106
-        arbitrary_types_allowed = True
-
-    @classmethod
-    def from_dict(cls, input_prior: dict[str, Any]):
-        if is_flat_dict(input_prior):
-            nested_dict = {}
-
-            for key, obj in input_prior.items():
-                component, component_number, *parameter = key.split("_")
-
-                sub_dict = nested_dict.get(f"{component}_{component_number}", {})
-                sub_dict["_".join(parameter)] = obj
-
-                nested_dict[f"{component}_{component_number}"] = sub_dict
-
-            return cls(nested_dict=nested_dict)
-
-        return cls(nested_dict=input_prior)
-
-    @field_validator("nested_dict", mode="before")
-    def check_and_cast_nested_dict(cls, value: dict[str, Any]):
-        if not isinstance(value, dict):
-            raise ValueError("The top level must be a dictionary")
-
-        for key, inner_dict in value.items():
-            if not isinstance(inner_dict, dict):
-                raise ValueError(f'The value for key "{key}" must be a dictionary')
-
-            for inner_key, obj in inner_dict.items():
-                if not isinstance(obj, dist.Distribution):
-                    try:
-                        # Attempt to cast to JAX array
-                        value[key][inner_key] = jnp.array(obj, dtype=float)
-
-                    except Exception as e:
-                        raise ValueError(
-                            f'The value for key "{inner_key}" in {key} be a NumPyro '
-                            f"distribution or castable to JAX array. Error: {e}"
-                        )
-        return value

{jaxspec-0.1.3.dist-info → jaxspec-0.2.0.dist-info}/METADATA

@@ -1,43 +1,42 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: jaxspec
-Version: 0.1.3
+Version: 0.2.0
 Summary: jaxspec is a bayesian spectral fitting library for X-ray astronomy.
-Home-page: https://github.com/renecotyfanboy/jaxspec
 License: MIT
 Author: sdupourque
 Author-email: sdupourque@irap.omp.eu
-Requires-Python: >=3.10,<3.12
+Requires-Python: >=3.10,<3.13
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Dist: arviz (>=0.17.1,<0.20.0)
+Classifier: Programming Language :: Python :: 3.12
+Requires-Dist: arviz (>=0.17.1,<0.21.0)
 Requires-Dist: astropy (>=6.0.0,<7.0.0)
+Requires-Dist: catppuccin (>=2.3.4,<3.0.0)
 Requires-Dist: chainconsumer (>=1.1.2,<2.0.0)
 Requires-Dist: cmasher (>=1.6.3,<2.0.0)
-Requires-Dist: dm-haiku (>=0.0.12,<0.0.13)
-Requires-Dist: gpjax (>=0.8.0,<0.9.0)
+Requires-Dist: flax (>=0.10.1,<0.11.0)
 Requires-Dist: interpax (>=0.3.3,<0.4.0)
-Requires-Dist: jax (>=0.4.33,<0.5.0)
-Requires-Dist: jaxlib (>=0.4.30,<0.5.0)
-Requires-Dist: jaxns (<2.6)
+Requires-Dist: jax (>=0.4.37,<0.5.0)
+Requires-Dist: jaxns (>=2.6.7,<3.0.0)
 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: mendeleev (>=0.15,<0.20)
 Requires-Dist: networkx (>=3.1,<4.0)
 Requires-Dist: numpy (<2.0.0)
-Requires-Dist: numpyro (>=0.15.3,<0.16.0)
-Requires-Dist: optimistix (>=0.0.7,<0.0.8)
+Requires-Dist: numpyro (>=0.16.1,<0.17.0)
+Requires-Dist: optimistix (>=0.0.7,<0.0.10)
 Requires-Dist: pandas (>=2.2.0,<3.0.0)
 Requires-Dist: pooch (>=1.8.2,<2.0.0)
-Requires-Dist: pyzmq (<27)
 Requires-Dist: scipy (<1.15)
 Requires-Dist: seaborn (>=0.13.1,<0.14.0)
-Requires-Dist: simpleeval (>=0.9.13,<0.10.0)
-Requires-Dist: sparse (>=0.15.1,<0.16.0)
+Requires-Dist: simpleeval (>=0.9.13,<1.1.0)
+Requires-Dist: sparse (>=0.15.4,<0.16.0)
 Requires-Dist: tinygp (>=0.3.0,<0.4.0)
 Requires-Dist: watermark (>=2.4.3,<3.0.0)
 Project-URL: Documentation, https://jaxspec.readthedocs.io/en/latest/
+Project-URL: Homepage, https://github.com/renecotyfanboy/jaxspec
 Description-Content-Type: text/markdown
 
 <p align="center">
@@ -78,3 +77,24 @@ Once the environment is set up, you can install jaxspec directly from pypi
 pip install jaxspec --upgrade
 ```
 
+## Citation 
+
+If you use `jaxspec` in your research, please consider citing the following article 
+
+```
+@ARTICLE{2024A&A...690A.317D,
+       author = {{Dupourqu{\'e}}, S. and {Barret}, D. and {Diez}, C.~M. and {Guillot}, S. and {Quintin}, E.},
+        title = "{jaxspec: A fast and robust Python library for X-ray spectral fitting}",
+      journal = {\aap},
+     keywords = {methods: data analysis, methods: statistical, X-rays: general},
+         year = 2024,
+        month = oct,
+       volume = {690},
+          eid = {A317},
+        pages = {A317},
+          doi = {10.1051/0004-6361/202451736},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2024A&A...690A.317D},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+```
+

jaxspec-0.2.0.dist-info/RECORD

@@ -0,0 +1,34 @@
+jaxspec/__init__.py,sha256=Sbn02lX6Y-zNXk17N8dec22c5jeypiS0LkHmGfz7lWA,126
+jaxspec/_fit/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+jaxspec/_fit/_build_model.py,sha256=NgLobtysyhCoiRguAazYGRIpG75iW-pG0Ss_hQGuCT4,2019
+jaxspec/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+jaxspec/analysis/_plot.py,sha256=1VbWentCLHR8XzM3jZtGyppbQRFWnChNztrwpZ2reA4,6185
+jaxspec/analysis/compare.py,sha256=g2UFhmR9Zt-7cz5gQFOB6lXuklXB3yTyUvjTypOzoSY,725
+jaxspec/analysis/results.py,sha256=jgv-AuaxYK6xR5NuCrP4RuskGwfQzuaxynjxjJFF1Gw,24784
+jaxspec/data/__init__.py,sha256=aantcYKC9kZFvaE-V2SIwSuLhIld17Kjrd9CIUu___Y,415
+jaxspec/data/instrument.py,sha256=RDiG_LkucvnF2XE_ghTFME6d_2YirgQUcEY0gEle6dk,4775
+jaxspec/data/obsconf.py,sha256=r0deDgzpfKJZFMeiKQYUnkqQEmoDYTzl3eQFjb5xYjo,10263
+jaxspec/data/observation.py,sha256=dfb-hJFpeSPMS52oNmQl39CB9GD_MK1gG9vHlQXhhwU,7741
+jaxspec/data/ogip.py,sha256=57lfUgvMhM4j5tdfnOmwLI0ehx09pG7SvJx6VNIJFHE,9543
+jaxspec/data/util.py,sha256=gW9s5Yt9hpKmJ6XPSFsC9-KsFaBNqK7GWCjVAS0jrnU,7286
+jaxspec/fit.py,sha256=8efhb2giQGgdTJ4jb9lT0gApQaYiuIS1hkalAMHZDnE,23513
+jaxspec/model/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+jaxspec/model/_graph_util.py,sha256=hPvHYmAxb7P3nyIecaZ7RqWOjwcZ1WvUByt_yNANiaY,4552
+jaxspec/model/abc.py,sha256=sHaFKOGfpD1ocXKlzEMdsmGLluikmBSmX8FAu7duFMQ,15489
+jaxspec/model/additive.py,sha256=kJHyJgL8jlSduIWoIRHQBlfIiZOdJuGL_eq0QBzAx5A,20221
+jaxspec/model/background.py,sha256=INRuuHIYgfu2E1a8Ddqpr_gF1wnhPtOpciWCteZfVVg,7687
+jaxspec/model/list.py,sha256=0RPAoscVz_zM1CWdx_Gd5wfrQWV5Nv4Kd4bSXu2ayUA,860
+jaxspec/model/multiplicative.py,sha256=yErnav1lOg-CFM_ge7yEQ6TN2JeKNtZPkQPOtgjR6Ug,7894
+jaxspec/scripts/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+jaxspec/scripts/debug.py,sha256=qhyDtX4G5UdChmTLCM-5Wti4XZU-sU5S-wDb6TZjrvM,292
+jaxspec/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+jaxspec/util/abundance.py,sha256=fsC313taIlGzQsZNwbYsJupDWm7ZbqzGhY66Ku394Mw,8546
+jaxspec/util/integrate.py,sha256=_Ax_knpC7d4et2-QFkOUzVtNeQLX1-cwLvm-FRBxYcw,4505
+jaxspec/util/misc.py,sha256=O3qorCL1Y2X1BS2jdd36C1eDHK9QDXTSOr9kj3uqcJo,654
+jaxspec/util/online_storage.py,sha256=vm56RfcbFKpkRVfr0bXO7J9aQxuBq-I_oEgA26YIhCo,2469
+jaxspec/util/typing.py,sha256=ZQM_l68qyYnIBZPz_1mKvwPMx64jvVBD8Uj6bx9sHv0,140
+jaxspec-0.2.0.dist-info/LICENSE.md,sha256=2q5XoWzddts5IqzIcgYYMOL21puU3MfO8gvT3Ype1eQ,1073
+jaxspec-0.2.0.dist-info/METADATA,sha256=MRbKhSlcAJAJWzG5ZcujxPEjEFuWshv0WgLr5hSkKdY,4463
+jaxspec-0.2.0.dist-info/WHEEL,sha256=IYZQI976HJqqOpQU6PHkJ8fb3tMNBFjg-Cn-pwAbaFM,88
+jaxspec-0.2.0.dist-info/entry_points.txt,sha256=kzLG2mGlCWITRn4Q6zKG_idx-_RKAncvA0DMNYTgHAg,71
+jaxspec-0.2.0.dist-info/RECORD,,

{jaxspec-0.1.3.dist-info → jaxspec-0.2.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.9.0
+Generator: poetry-core 2.0.1
 Root-Is-Purelib: true
 Tag: py3-none-any

jaxspec/data/grouping.py

@@ -1,23 +0,0 @@
-import numpy as np
-from .observation import Observation
-
-
-def constant_rebin(obs: Observation, downfactor: int):
-    """
-    Create a grouping matrix for constant rebinning of the data.
-
-    Parameters:
-        obs: Observation object.
-        downfactor: Downfactor for the rebinning.
-
-    Returns:
-        A grouping matrix.
-    """
-    n_channels = len(obs.pha.channel)
-    n_bins = n_channels // downfactor + 1 * (n_channels % downfactor != 0)
-    grouping = np.zeros((n_bins, n_channels), dtype=bool)
-
-    for i in range(n_bins):
-        grouping[i, i * downfactor : (i + 1) * downfactor] = True
-
-    return grouping

jaxspec-0.1.3.dist-info/RECORD

@@ -1,31 +0,0 @@
-jaxspec/__init__.py,sha256=Sbn02lX6Y-zNXk17N8dec22c5jeypiS0LkHmGfz7lWA,126
-jaxspec/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-jaxspec/analysis/_plot.py,sha256=C4XljmuzQz8xQur_jQddgInrBDmKgTn0eugSreLoD5k,862
-jaxspec/analysis/compare.py,sha256=g2UFhmR9Zt-7cz5gQFOB6lXuklXB3yTyUvjTypOzoSY,725
-jaxspec/analysis/results.py,sha256=Kz3eryxS3N_hiajcFLTWS1dtgTQo5hlh-rDCnJ3A-3c,27811
-jaxspec/data/__init__.py,sha256=aantcYKC9kZFvaE-V2SIwSuLhIld17Kjrd9CIUu___Y,415
-jaxspec/data/grouping.py,sha256=hhgBt-voiH0DDSyePacaIGsaMnrYbJM_-ZeU66keC7I,622
-jaxspec/data/instrument.py,sha256=0pSf1p82g7syDMmKm13eVbYih-Veiq5DnwsyZe6_b4g,3890
-jaxspec/data/obsconf.py,sha256=gv14sL6azK2avRiMCWuTbyLBPulzm4PwvoLY6iWPEVE,9833
-jaxspec/data/observation.py,sha256=1UnFu5ihZp9z-vP_I7tsFY8jhhIJunv46JyuE-acrg0,6394
-jaxspec/data/ogip.py,sha256=sv9p00qHS5pzw61pzWyyF0nV-E-RXySdSFK2tUavokA,9545
-jaxspec/data/util.py,sha256=ycLPVE-cjn6VpUWYlBU1BGfw73ANXIBilyVAUOYOSj0,9540
-jaxspec/fit.py,sha256=hI0koMO4KsNpe9mLlaFm_tNLgm4BVAYVyiMb1E1eyZE,24553
-jaxspec/model/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-jaxspec/model/abc.py,sha256=wbzpKYB2sB-qdP1B0YaUw7VHEYeTegeDhaoJ1EHPWaQ,20924
-jaxspec/model/additive.py,sha256=wjY2wL3Io3F45GJpz-UB8xYVnA-W1OFBnZMbj5pWPbQ,22449
-jaxspec/model/background.py,sha256=QSFFiuyUEvuzXBx3QfkvVneUR8KKEP-VaANEVXcavDE,7865
-jaxspec/model/list.py,sha256=0RPAoscVz_zM1CWdx_Gd5wfrQWV5Nv4Kd4bSXu2ayUA,860
-jaxspec/model/multiplicative.py,sha256=GCQ6JRz92QqbzDBFwWxGZ9SUqTJZQpD7B6ji9VEFXWo,8135
-jaxspec/scripts/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-jaxspec/scripts/debug.py,sha256=RIRykBW_kzt8__PhOohQn2xtDW6oAz49E8rmuR5ewAU,293
-jaxspec/util/__init__.py,sha256=vKurfp7p2hxHptJjXhXqFAXAikAGXAqISMJUqPeiGTw,1259
-jaxspec/util/abundance.py,sha256=fsC313taIlGzQsZNwbYsJupDWm7ZbqzGhY66Ku394Mw,8546
-jaxspec/util/integrate.py,sha256=_Ax_knpC7d4et2-QFkOUzVtNeQLX1-cwLvm-FRBxYcw,4505
-jaxspec/util/online_storage.py,sha256=vm56RfcbFKpkRVfr0bXO7J9aQxuBq-I_oEgA26YIhCo,2469
-jaxspec/util/typing.py,sha256=8qK1aJlsqTcVKjYN-BxsDx20BTwtnS-wMw6Bdurpm-o,2459
-jaxspec-0.1.3.dist-info/LICENSE.md,sha256=2q5XoWzddts5IqzIcgYYMOL21puU3MfO8gvT3Ype1eQ,1073
-jaxspec-0.1.3.dist-info/METADATA,sha256=HF52McS84ujvKhSIWFHdlqrkTIukDcxUAmkMMhMDoJU,3708
-jaxspec-0.1.3.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-jaxspec-0.1.3.dist-info/entry_points.txt,sha256=kzLG2mGlCWITRn4Q6zKG_idx-_RKAncvA0DMNYTgHAg,71
-jaxspec-0.1.3.dist-info/RECORD,,