PyPI - jaxspec - Versions diffs - 0.0.2__tar.gz → 0.0.4__tar.gz - Mend

jaxspec 0.0.2tar.gz → 0.0.4tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (44) hide show

{jaxspec-0.0.2 → jaxspec-0.0.4}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: jaxspec
-Version: 0.0.2
+Version: 0.0.4
 Summary: jaxspec is a bayesian spectral fitting library for X-ray astronomy.
 License: MIT
 Author: sdupourque
@@ -10,11 +10,11 @@ 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 (>=0.17.0,<0.18.0)
+Requires-Dist: arviz (>=0.17.1,<0.18.0)
 Requires-Dist: astropy (>=6.0.0,<7.0.0)
 Requires-Dist: chainconsumer (>=1.0.0,<2.0.0)
 Requires-Dist: cmasher (>=1.6.3,<2.0.0)
-Requires-Dist: dm-haiku (>=0.0.11,<0.0.12)
+Requires-Dist: dm-haiku (>=0.0.11,<0.0.13)
 Requires-Dist: gpjax (>=0.8.0,<0.9.0)
 Requires-Dist: jax (>=0.4.23,<0.5.0)
 Requires-Dist: jaxlib (>=0.4.23,<0.5.0)
@@ -23,15 +23,19 @@ Requires-Dist: matplotlib (>=3.8.0,<4.0.0)
 Requires-Dist: mkdocstrings (>=0.24.0,<0.25.0)
 Requires-Dist: networkx (>=3.1,<4.0)
 Requires-Dist: numpy (>=1.26.1,<2.0.0)
-Requires-Dist: numpyro (>=0.13.2,<0.14.0)
+Requires-Dist: numpyro (>=0.13.2,<0.15.0)
 Requires-Dist: pandas (>=2.2.0,<3.0.0)
+Requires-Dist: scipy (<1.13)
 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: tinygp (>=0.3.0,<0.4.0)
 Description-Content-Type: text/markdown
 # jaxspec
+[![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/)
 [![Read the Docs](https://img.shields.io/readthedocs/jaxspec?style=for-the-badge)](https://jaxspec.readthedocs.io/en/latest/)
 [![Codecov](https://img.shields.io/codecov/c/github/renecotyfanboy/jaxspec?style=for-the-badge)](https://app.codecov.io/gh/renecotyfanboy/jaxspec)
 [![Slack](https://img.shields.io/badge/Slack-4A154B?style=for-the-badge&logo=slack&logoColor=white)](https://join.slack.com/t/jaxspec/shared_invite/zt-2cuxkdl2f-t0EEAKP~HBEHKvIUZJL2sg)

{jaxspec-0.0.2 → jaxspec-0.0.4}/README.md RENAMED Viewed

@@ -1,5 +1,7 @@
 # jaxspec
+[![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/)
 [![Read the Docs](https://img.shields.io/readthedocs/jaxspec?style=for-the-badge)](https://jaxspec.readthedocs.io/en/latest/)
 [![Codecov](https://img.shields.io/codecov/c/github/renecotyfanboy/jaxspec?style=for-the-badge)](https://app.codecov.io/gh/renecotyfanboy/jaxspec)
 [![Slack](https://img.shields.io/badge/Slack-4A154B?style=for-the-badge&logo=slack&logoColor=white)](https://join.slack.com/t/jaxspec/shared_invite/zt-2cuxkdl2f-t0EEAKP~HBEHKvIUZJL2sg)

{jaxspec-0.0.2 → jaxspec-0.0.4}/pyproject.toml RENAMED Viewed

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "jaxspec"
-version = "0.0.2"
+version = "0.0.4"
 description = "jaxspec is a bayesian spectral fitting library for X-ray astronomy."
 authors = ["sdupourque <sdupourque@irap.omp.eu>"]
 license = "MIT"
@@ -13,11 +13,11 @@ jaxlib = "^0.4.23"
 numpy = "^1.26.1"
 pandas = "^2.2.0"
 astropy = "^6.0.0"
-numpyro = "^0.13.2"
-dm-haiku = "^0.0.11"
+numpyro = ">=0.13.2,<0.15.0"
+dm-haiku = ">=0.0.11,<0.0.13"
 networkx = "^3.1"
 matplotlib = "^3.8.0"
-arviz = "^0.17.0"
+arviz = "^0.17.1"
 chainconsumer = "^1.0.0"
 simpleeval = "^0.9.13"
 cmasher = "^1.6.3"
@@ -26,6 +26,8 @@ jaxopt = "^0.8.1"
 tinygp = "^0.3.0"
 seaborn = "^0.13.1"
 mkdocstrings = "^0.24.0"
+sparse = "^0.15.1"
+scipy = "<1.13"
 [tool.poetry.group.docs.dependencies]
@@ -39,7 +41,7 @@ mkdocs-jupyter = "^0.24.6"
 chex = "^0.1.83"
 mktestdocs = "^0.2.1"
 coverage = "^7.3.2"
-pytest-cov = "^4.1.0"
+pytest-cov = ">=4.1,<6.0"
 flake8 = "^7.0.0"
 pytest = "^8.0.0"
 testbook = "^0.4.2"
@@ -47,7 +49,7 @@ testbook = "^0.4.2"
 [tool.poetry.group.dev.dependencies]
 pre-commit = "^3.5.0"
-ruff = "^0.2.1"
+ruff = ">=0.2.1,<0.4.0"
 jupyterlab = "^4.0.7"
 notebook = "^7.0.6"
 ipywidgets = "^8.1.1"

{jaxspec-0.0.2 → jaxspec-0.0.4}/src/jaxspec/analysis/results.py RENAMED Viewed

@@ -343,7 +343,7 @@ class ChainResult:
                     folding_model.out_energies,
                     y_observed=folding_model.folded_background.data,
                     y_samples=bkg_count,
-                    denominator=denominator / folding_model.backratio.data,
+                    denominator=denominator * folding_model.folded_backratio.data,
                     color=(0.26787604, 0.60085972, 0.63302651),
                     percentile=percentile,
                 )

{jaxspec-0.0.2 → jaxspec-0.0.4}/src/jaxspec/data/__init__.py RENAMED Viewed

@@ -5,3 +5,6 @@ from .observation import Observation  # noqa: F401
 import astropy.units as u
 u.add_enabled_aliases({"counts": u.count})
+u.add_enabled_aliases({"channel": u.dimensionless_unscaled})
+# Arbitrary units are found in .rsp files , let's hope it is compatible with what we would expect as the rmf x arf
+# u.add_enabled_aliases({"au": u.dimensionless_unscaled})

jaxspec-0.0.4/src/jaxspec/data/example_data/fakeit.pha ADDED Viewed

@@ -0,0 +1,334 @@
+SIMPLE  =                    T / file does conform to FITS standard             BITPIX  =                    8 / number of bits per data pixel                  NAXIS   =                    0 / number of data axes                            EXTEND  =                    T / FITS dataset may contain extensions            COMMENT   FITS (Flexible Image Transport System) format is defined in 'AstronomyCOMMENT   and Astrophysics', volume 376, page 359; bibcode: 2001A&A...376..359H END                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             XTENSION= 'BINTABLE'           / binary table extension                         BITPIX  =                    8 / 8-bit bytes                                    NAXIS   =                    2 / 2-dimensional binary table                     NAXIS1  =                   12 / width of table in bytes                        NAXIS2  =                 4096 / number of rows in table                        PCOUNT  =                    0 / size of special data area                      GCOUNT  =                    1 / one data group (required keyword)              TFIELDS =                    4 / number of fields in each row                   TTYPE1  = 'CHANNEL '           / label for field   1                            TFORM1  = 'J       '           / data format of field: 4-byte INTEGER           TTYPE2  = 'COUNTS  '           / label for field   2                            TFORM2  = 'J       '           / data format of field: 4-byte INTEGER           TTYPE3  = 'QUALITY '           / label for field   3                            TFORM3  = 'I       '           / data format of field: 2-byte INTEGER           TTYPE4  = 'GROUPING'           / label for field   4                            TFORM4  = 'I       '           / data format of field: 2-byte INTEGER           EXTNAME = 'SPECTRUM'           / name of this binary table extension            HDUCLASS= 'OGIP    '           / format conforms to OGIP standard               HDUCLAS1= 'SPECTRUM'           / PHA dataset (OGIP memo OGIP-92-007)            HDUVERS = '1.2.1   '           / Version of format (OGIP memo OGIP-92-007a)     TELESCOP= 'XMM     '           / mission/satellite name                         INSTRUME= 'EPN     '           / instrument name                                DETNAM  = 'UNKNOWN '           / detector name                                  FILTER  = 'Medium  '           / filter name                                    STOKESPR= 'UNKNOWN '           / Stokes parameter(s)                            STOKESWT= 'UNKNOWN '           / Stokes weighting                               CHANTYPE= 'PI      '           / channel type (PHA, PI etc)                     DATE    = '2024-03-20T11:51:55' / file creation date (YYYY-MM-DDThh:mm:ss UT)   HISTORY Fake data file created by XSPEC version: 12.13.1 "fakeit" command       FKSRC001= 'cutoffpl'                                                            FKRSP001= 'PN.rmf  '                                                            FKARF001= 'PN.arf  '                                                            RESPFILE= 'PN.rmf  '           / associated redistrib matrix filename           ANCRFILE= 'PN.arf  '           / associated ancillary response filename         CORRFILE= '        '           / associated correction filename                 CORRSCAL=                   1. / correction file scaling factor                 BACKFILE= '        '           / associated background filename                 EXPOSURE=               10000. / exposure (in seconds)                          TLMIN1  =                    0 / Lowest legal channel number                    TLMAX1  =                 4095 / Highest legal channel number                   DETCHANS=                 4096 / total number possible channels                 POISSERR=                    T / Pois. err assumed ?                            AREASCAL=                   1. / area scaling factor                            BACKSCAL=                   1. / background file scaling factor                 END                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             �!�x�����a��$8	0�
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{jaxspec-0.0.2 → jaxspec-0.0.4}/src/jaxspec/data/instrument.py RENAMED Viewed

@@ -1,6 +1,7 @@
 import os
 import numpy as np
 import xarray as xr
+from matplotlib import colors
 from .ogip import DataARF, DataRMF
@@ -64,21 +65,26 @@ class Instrument(xr.Dataset):
         )
     @classmethod
-    def from_ogip_file(cls, arf_file: str | os.PathLike, rmf_file: str | os.PathLike, **kwargs):
+    def from_ogip_file(cls, rmf_path: str | os.PathLike, arf_path: str | os.PathLike = None):
         """
         Load the data from OGIP files.
         Parameters:
-            arf_file: The ARF file path.
-            rmf_file: The RMF file path.
+            rmf_path: The RMF file path.
+            arf_path: The ARF file path.
             exposure: The exposure time in second.
             grouping: The grouping matrix.
         """
-        arf = DataARF.from_file(arf_file)
-        rmf = DataRMF.from_file(rmf_file)
+        rmf = DataRMF.from_file(rmf_path)
-        return cls.from_matrix(rmf.matrix, arf.specresp, rmf.energ_lo, rmf.energ_hi, rmf.e_min, rmf.e_max)
+        if arf_path is not None:
+            specresp = DataARF.from_file(arf_path).specresp
+        else:
+            specresp = np.ones(rmf.energ_lo.shape)
+        return cls.from_matrix(rmf.sparse_matrix, specresp, rmf.energ_lo, rmf.energ_hi, rmf.e_min, rmf.e_max)
     def plot_redistribution(self, **kwargs):
         """
@@ -95,9 +101,8 @@ class Instrument(xr.Dataset):
             y="e_max_channel",
             xscale="log",
             yscale="log",
-            cmap=cmr.cosmic,
-            vmin=0,
-            vmax=0.075,
+            cmap=cmr.ember_r,
+            norm=colors.LogNorm(vmin=1e-6, vmax=1),
             add_labels=True,
             **kwargs,
         )

jaxspec 0.0.2__tar.gz → 0.0.4__tar.gz

jaxspec 0.0.2tar.gz → 0.0.4tar.gz