specsy 0.6.4__tar.gz → 0.9.dev1__tar.gz

{specsy-0.6.4/src/specsy.egg-info → specsy-0.9.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: specsy
-Version: 0.6.4
+Version: 0.9.dev1
 Summary: Model fitting package for the chemical analysis of astronomical spectra
 Author-email: Vital Fernández <vgf@umich.edu>
 License-Expression: GPL-3.0-or-later
@@ -8,30 +8,26 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Requires-Python: >=3.11
 Description-Content-Type: text/x-rst
-Requires-Dist: arviz~=0.21
+Requires-Dist: arviz~=0.23.4
 Requires-Dist: corner~=2.2
 Requires-Dist: h5netcdf~=1.3.0
-Requires-Dist: jax~=0.4
-Requires-Dist: jaxlib~=0.4
-Requires-Dist: lime-stable~=2.0.dev6
-Requires-Dist: lmfit~=1.3
-Requires-Dist: bokeh~=3.7
-Requires-Dist: matplotlib~=3.10
-Requires-Dist: numpy~=2.2
-Requires-Dist: pymc~=5.1
-Requires-Dist: scipy~=1.15
+Requires-Dist: jax~=0.9.2
+Requires-Dist: jaxlib~=0.9.2
+Requires-Dist: aspect-stable~=0.7.dev1
+Requires-Dist: lime-stable~=2.2.dev1
+Requires-Dist: innate-stable~=0.2.1
+Requires-Dist: pymc~=5.28
 Requires-Dist: toml~=0.10
-Requires-Dist: tomli>=2.0.0; python_version < "3.11"
-Requires-Dist: xarray~=2024.3.0
+Requires-Dist: xarray~=2026.2.0
 Provides-Extra: tensors
-Requires-Dist: pytensor~=2.20; extra == "tensors"
+Requires-Dist: pytensor~=2.38.2; extra == "tensors"
 Provides-Extra: docs
-Requires-Dist: nbsphinx~=0.9; extra == "docs"
-Requires-Dist: ipympl~=0.9; extra == "docs"
 Requires-Dist: sphinx-rtd-theme~=3.0; extra == "docs"
+Requires-Dist: ipympl~=0.9; extra == "docs"
+Requires-Dist: myst-nb~=1.3; extra == "docs"
 Provides-Extra: tests
-Requires-Dist: pytest~=8.3; extra == "tests"
-Requires-Dist: pytest-cov~=6.0; extra == "tests"
+Requires-Dist: pytest~=8.4; extra == "tests"
+Requires-Dist: pytest-cov~=7.0; extra == "tests"
 Requires-Dist: pytest-mpl~=0.17; extra == "tests"
 
 ###################

{specsy-0.6.4 → specsy-0.9.dev1}/pyproject.toml

@@ -4,42 +4,39 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "specsy"
-version = "0.6.4"
+version = "0.9.dev1"
 readme = "README.rst"
 requires-python = ">=3.11"
 license = "GPL-3.0-or-later"
 authors = [{name = "Vital Fernández", email = "vgf@umich.edu"}]
 description = "Model fitting package for the chemical analysis of astronomical spectra"
-dependencies = ["arviz~=0.21",
+dependencies = ["arviz~=0.23.4",
                 "corner~=2.2",
                 "h5netcdf~=1.3.0",
-                "jax~=0.4",
-                "jaxlib~=0.4",
-                "lime-stable~=2.0.dev6",
-                "lmfit~=1.3",
-                "bokeh~=3.7",
-                "matplotlib~=3.10",
-                "numpy~=2.2",
-                "pymc~=5.1",
-                "scipy~=1.15",
+                "jax~=0.9.2",
+                "jaxlib~=0.9.2",
+                "aspect-stable~=0.7.dev1",
+                "lime-stable~=2.2.dev1",
+                "innate-stable~=0.2.1",
+                "pymc~=5.28",
                 "toml~=0.10",
-                "tomli >= 2.0.0 ; python_version < '3.11'",
-                "xarray~=2024.3.0"]
+                "xarray~=2026.2.0"]
 
 classifiers = ["Programming Language :: Python :: 3",
                "Programming Language :: Python :: 3.11"]
 
 [project.optional-dependencies]
-tensors = ["pytensor~=2.20"]
+tensors = ["pytensor~=2.38.2"]
 
-docs = ["nbsphinx~=0.9",
+docs = ["sphinx-rtd-theme~=3.0",
         "ipympl~=0.9",
-        "sphinx-rtd-theme~=3.0"]
+        "myst-nb~=1.3"]
 
-tests = ["pytest~=8.3",
-         "pytest-cov~=6.0",
+tests = ["pytest~=8.4",
+         "pytest-cov~=7.0",
          "pytest-mpl~=0.17"]
 
+
 [tool.pytest.ini_options]
 pythonpath = ["src"]
 mpl-baseline-path = 'tests/baseline'

{specsy-0.6.4 → specsy-0.9.dev1}/src/specsy/__init__.py

@@ -1,7 +1,3 @@
-"""
-Specsy - A python package for the analysis of astronomical spectra
-"""
-
 import logging
 import tomllib
 
@@ -18,15 +14,14 @@ _logger.addHandler(consoleHandle)
 
 # Read lime configuration .toml
 _inst_dir = Path(__file__).parent
-_conf_path = _inst_dir/'config.toml'
+_conf_path = _inst_dir/'specsy.toml'
 with open(_conf_path, mode="rb") as fp:
     _setup_cfg = tomllib.load(fp)
 
 __version__ = _setup_cfg['metadata']['version']
 
-from .tools import flux_distribution
-from .innate import Innate, load_inference_data, save_inference_data
-from .treatement import SpectraSynthesizer, ChemicalModel
-from .models import *
-from .plotting.plots import plot_traces, plot_flux_grid, plot_corner_matrix, theme
-from .io import load_cfg, load_frame
+from lime import load_cfg as load_cfg, load_frame as load_frame, Line as Line, lines_frame as lines_frame, save_frame as save_frame
+from lime import Spectrum as Spectrum, Cube as Cube
+from innate import load_dataset as load_dataset
+from specsy.observations import Nebula
+from specsy.models.extinction import extinction_coeff_calc

{specsy-0.6.4/src/specsy/inference → specsy-0.9.dev1/src/specsy}/emission.py

@@ -2,10 +2,10 @@ import numpy as np
 import pymc
 import pytensor
 from pytensor import tensor as tt, function
-from ..models.fluxes_line import EmissionTensors
-from ..models.chemistry import TOIII_from_TSIII_relation, TOII_from_TOIII_relation
+from models.fluxes_line import EmissionTensors
+# from ..models.chemistry import TOIII_from_TSIII_relation, TOII_from_TOIII_relation
 from pymc.sampling.jax import sample_blackjax_nuts
-from ..innate import save_inference_data
+# from ..innate_old import save_inference_data
 import arviz as az
 import xarray as xr
 from warnings import catch_warnings, simplefilter

specsy-0.9.dev1/src/specsy/inference.py

@@ -0,0 +1,10 @@
+from specsy.models.chemistry import DirectMethod
+
+
+class ModelManager:
+
+    def __init__(self, lines_df, ion_struct):
+
+        self.direct_method = DirectMethod(lines_df=lines_df, ion_struct=ion_struct)
+
+        return

{specsy-0.6.4 → specsy-0.9.dev1}/src/specsy/io.py

@@ -2,15 +2,9 @@ import os
 import numpy as np
 import configparser
 from pathlib import Path
-
-import pandas as pd
-
-from lime.transitions import label_decomposition
-import lime
-from lime.io import load_cfg, save_cfg, save_frame, check_file_dataframe, check_fit_conf
 from collections.abc import Sequence
 from astropy.io import fits
-
+from innate import load_dataset
 
 FITS_INPUTS_EXTENSION = {'lines_list': '20A', 'line_fluxes': 'E', 'line_err': 'E'}
 
@@ -27,28 +21,6 @@ class SpecSyError(Exception):
     """SpecSy exception function"""
 
 
-# Load log
-def load_frame(file_address, page: str ='LINELOG', sample_levels: list =['id', 'line'], flux_type=None, lines_list=None,
-               norm_line=None):
-
-    # Return
-    if isinstance(file_address, pd.DataFrame):
-        log = file_address.copy()
-    else:
-        log = lime.load_frame(file_address, page, sample_levels)
-
-    extra_column = 'line_extract' if norm_line is not None else 'line_flux'
-
-    # Create new column for the lines flux with the requested type (None for user to introduce "line_flux")
-    if flux_type is not None:
-        lime.tools.extract_fluxes(log, flux_type=flux_type, column_name=extra_column)
-
-    # Check for requested lines and their normalization
-    if norm_line is not None:
-        lime.tools.normalize_fluxes(log, lines_list, norm_line, flux_column=extra_column, column_name='line_flux')
-
-    return log
-
 
 def load_HII_CHI_MISTRY_grid(log_scale=False, log_zero_value = -1000):
 
@@ -285,7 +257,7 @@ def fits_db(fits_address, model_db, ext_name='', header=None):
     return
 
 
-def save_trace(trace, prior_dict, line_labels, input_fluxes, input_err, inference_model):
+def pack_results(trace, prior_dict, line_labels, input_fluxes, input_err, inference_model):
 
     #  ---------------------------- Treat traces and store outputs
     model_params = []
@@ -344,3 +316,30 @@ def save_trace(trace, prior_dict, line_labels, input_fluxes, input_err, inferenc
     fit_results = {'models': inference_model, 'trace': trace, 'inputs': inputs, 'outputs': output_dict}
 
     return fit_results
+
+
+def load_emissivity_interp(fname, array_mode=False):
+
+    emis_set = load_dataset(fname)
+
+    interp_dict = {}
+    for trans, emis_matrix in emis_set[0].items():
+
+        temp_range = np.linspace(*emis_set[1][trans]['temp_range'])
+        den_range = np.linspace(*emis_set[1][trans]['den_range'])
+        log_emis = np.log10(emis_matrix)
+
+        interp = make_bilinear_interp(temp_range, den_range, log_emis)
+
+        if array_mode:
+            x_sym = tensor.dscalar("x")
+            y_sym = tensor.dscalar("y")
+            interp_dict[trans] = pt_function([x_sym, y_sym], interp(x_sym, y_sym))
+
+        else:
+            interp_dict[trans] = interp
+
+    return interp_dict
+
+
+    return

specsy-0.9.dev1/src/specsy/models/__init__.py

@@ -0,0 +1,2 @@
+from specsy.models.nebular_continuum import NebularContinua
+from specsy.models.literature import _TEM_FUNC_DICT, _DEN_FUNC_DICT