Merge branch 'main' of github.com:BDNYC/sedkit into absolute_flux_patch

.github/workflows/ci.yml

@@ -1,4 +1,4 @@
-name: CI
+name: Run tests
 
 on: 
   pull_request:
@@ -10,12 +10,11 @@ jobs:
   SEDkit-CI:
 
     name: Python - ${{ matrix.python-version }}
+    runs-on: macos-latest    
     strategy:
       max-parallel: 5
       matrix:
-        os: ['macos-latest']
-        python-version: [ '3.11' ]
-    runs-on:  ${{ matrix.os }}
+        python-version: [ "3.13", "3.12", "3.11", ]
     steps:
       - name: Checkout code
         uses: actions/checkout@v4
@@ -26,10 +25,16 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies
-        run: |
+        run: |  
           python -m pip install --upgrade pip
-          pip install .[test]
+          pip install ".[test]"
 
-      - name: Test with pytest
+      - name: List packages
         run: |
+          pip list
+
+      - name: Test with pytest
+        # tb=no: no traceback
+        # disable-warnings: disable pytest warnings
+        run: |  
           pytest --tb=no --disable-warnings

.gitignore

@@ -65,3 +65,5 @@ target/
 .idea/
 .idea/*
 .vscode/settings.json
+
+sedkit/data/models/atmospheric/spexprismlibrary/index.p

CITATION.cff

@@ -0,0 +1,17 @@
+authors:
+- family-names: Filippazzo
+  given-names: Joseph
+  orcid: https://orcid.org/0000-0002-0201-8306
+- family-names: Alejandro Merchan
+  given-names: Sherelyn
+  orcid: https://orcid.org/0000-0003-0548-0093
+- family-names: Cruz
+  given-names: Kelle
+  orcid: https://orcid.org/0000-0002-1821-0650
+cff-version: 1.2.0
+doi: 10.5281/zenodo.14014658
+repository-code: https://github.com/BDNYC/sedkit/
+title: 'sedkit'
+type: software
+message: "If you use this software, please cite the Zenodo record"
+license: BSD-3-Clause

LICENSE

@@ -1,21 +1,11 @@
-The MIT License (MIT)
+Copyright (c) 2024, Joe Filippazzo, Sherelyn Alejandro Merchan, Kelle Cruz
 
-Copyright (c) 2019 Joe Filippazzo
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
+Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
 
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
+Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -3,27 +3,27 @@
 [![Build Status](https://github.com/hover2pi/sedkit/actions/workflows/ci.yml/badge.svg)](https://github.com/hover2pi/sedkit/actions/workflows/ci.yml)
 [![Coverage Status](https://coveralls.io/repos/github/hover2pi/sedkit/badge.svg?branch=master&service=github)](https://coveralls.io/github/hover2pi/sedkit?branch=master)
 [![Documentation Status](https://readthedocs.org/projects/sedkit/badge/?version=latest)](https://sedkit.readthedocs.io/en/latest/?badge=latest)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14014658.svg)](https://doi.org/10.5281/zenodo.14014658)
+
 
 ## Introduction
 
-`sedkit` is a collection of pure Python modules for simple SED construction and analysis. Users can create individual SEDs or SED catalogs from spectra and/or photometry and calculate fundamental parameters (f<sub>bol</sub>, M<sub>bol</sub>, L<sub>bol</sub>, T<sub>eff</sub>, mass, log(g)) using the methods presented in [Filippazzo et al. (2015)](http://adsabs.harvard.edu/abs/2015ApJ...810..158F).
+`sedkit` is a collection of pure Python modules for simple SED construction and analysis. Users can create individual SEDs or SED catalogs from spectra and/or photometry and calculate fundamental parameters (f<sub>bol</sub>, M<sub>bol</sub>, L<sub>bol</sub>, T<sub>eff</sub>, mass, log(g)) using the methods presented in [Filippazzo et al. (2015)](http://adsabs.harvard.edu/abs/2015ApJ...810..158F) and described in the documentation: https://sedkit.readthedocs.io/.
+
 
 ## Installation
 
-Install via PyPI with
+Install in an environment with Python 3.11, 3.12, 3.13.
 
 ```
 pip install sedkit
 ```
+### Developer Instructions
 
-or via `conda` with
+If you plan to modify and/or contribute to the code, clone the repository and then install an editable version of the package and the requirements for running the tests.
 
 ```
-git clone https://github.com/hover2pi/sedkit.git
-cd sedkit
-conda env create -f env/environment-3.11.yml --force
-conda activate sedkit
-python setup.py install
+pip install -e ".[test]"
 ```
 
 ## Demo
@@ -55,10 +55,10 @@ trap1.find_WISE()
 Spectrum arrays or ASCII/FITS files can also be added to the SED data.
 
 ```python
-from pkg_resources import resource_filename
-spec_file = resource_filename('sedkit', 'data/Trappist-1_NIR.fits')
+import importlib.resources
+spec_file = str(importlib.resources.files('sedkit')/ 'data/Trappist-1_NIR.fits')
 import astropy.units as u
-trap1.add_spectrum_file(spec_file, wave_units=u.um, flux_units=u.erg/u.s/q.cm**2/u.AA)
+trap1.add_spectrum_file(spec_file, wave_units=u.um, flux_units=u.erg/u.s/u.cm**2/u.AA)
 ```
 
 Other data which may affect the calculated and inferred fundamantal parameters can be set at any time.
@@ -201,20 +201,19 @@ trap1.evo_model = 'DUSTY00'
 trap1.infer_mass()
 ```
 
-<img src="https://github.com/hover2pi/sedkit/blob/master/sedkit/data/figures/Lbol_v_mass.png" height="400">
-
-A variety of atmospheric model grids can be fit to the data with or without MCMC analysis,
+<img src="sedkit/data/figures/Lbol_v_mass.png" height="400">
 
+<!-- A variety of atmospheric model grids can be fit to the data with or without MCMC analysis,
 ```python
 from sedkit import BTSettl
 trap1.fit_modelgrid(BTSettl(), mcmc=True)
-```
+``` -->
 
-And any arbitrary atlas of models can be applied as well.
+Any arbitrary atlas of models (stored in `data\models\atmospheric`) can be used to fit the data with or without MCMC analysis. 
 
 ```python
 from sedkit import SpexPrismLibrary
-trap1.fit_modelgrid(SpexPrismLibrary())
+trap1.fit_modelgrid(SpexPrismLibrary(), mcmc=True)
 ```
 
 Inspect the SED at any time with the interactive plotting method.
@@ -223,28 +222,22 @@ Inspect the SED at any time with the interactive plotting method.
 trap1.plot(integral=True, best_fit=True)
 ```
 
-<img src="https://github.com/hover2pi/sedkit/blob/master/sedkit/data/figures/sed_plot.png" height="500">
+<img src="sedkit/data/figures/sed_plot.png" height="500">
 
 References for all data can be accessed via the `refs` attribute.
 
 Entire catalogs of `SED` objects can also be created and their properties can be arbitrarily compared and analyzed with the `sedkit.catalog.Catalog()` object.
 
-<img src="https://github.com/hover2pi/sedkit/blob/master/sedkit/data/figures/Lbol_v_SpT.png" height="500">
+<img src="sedkit/data/figures/Lbol_v_SpT.png" height="500">
 
-Please read the full documentation for details on this functionality and much more.
+Please read the [full documentation](https://sedkit.readthedocs.io/en/latest/) for details on this functionality and much more.
 
-## Documentation
+## Documentation and Notebooks
 
-Full documentation for the latest build can be found on [ReadTheDocs](https://sedkit.readthedocs.io/en/latest/).
+Full documentation is available: https://sedkit.readthedocs.io/.
 
 The package also contains detailed Jupyter notebooks highlighting the core functionality of its primary classes, including
 
-- [sedkit.spectrum.Spectrum](https://github.com/hover2pi/sedkit/blob/master/sedkit/notebooks/working_with_spectra.ipynb)
-- [sedkit.sed.SED](https://github.com/hover2pi/sedkit/blob/master/sedkit/notebooks/create_sed.ipynb)
-- [sedkit.catalog.Catalog](https://github.com/hover2pi/sedkit/blob/master/sedkit/notebooks/create_catalog.ipynb)
-
-If you use or reference this software, please cite [Filippazzo et al. (submitted to PASP)]()
-
-## Licensed
-
-This project is Copyright (c) Joe Filippazzo and licensed under the terms of the BSD 3-Clause license. See the licenses folder for more information.
+- [sedkit.spectrum.Spectrum](sedkit/notebooks/working_with_spectra.ipynb)
+- [sedkit.sed.SED](sedkit/notebooks/create_sed.ipynb)
+- [sedkit.catalog.Catalog](sedkit/notebooks/create_catalog.ipynb)

pyproject.toml

@@ -15,25 +15,27 @@ description="Spectral energy distribution construction and analysis tools"
 keywords=['astronomy']
 classifiers=[
 	'Intended Audience :: Science/Research',
-	"License :: OSI Approved :: MIT License",
 	'Operating System :: OS Independent',
+	'License :: OSI Approved :: BSD License',
 	'Programming Language :: Python :: 3',
 	'Topic :: Scientific/Engineering :: Astronomy',
 	'Topic :: Software Development :: Libraries :: Python Modules',
 ]
-requires-python = ">=3.11"
+requires-python = ">=3.11,<=3.13"
 dependencies = [
-	"astropy>=5.3.1",
-	"astroquery>=0.4.6",
+	"astropy>=6.1.3",
+	"astroquery>=0.4.7",
+	"astropy>=6.1.3",
+	"astroquery>=0.4.7",
 	"bokeh>=3.2.1",
 	"dill>=0.3.4",
-	"dustmaps>=1.0.9",
-	"emcee>=3.1.1",
-	"numpy>=1.25.1",
-	"pandas>=1.3.5",
-	"scipy>=1.8.0",
+	"dustmaps>=1.0.13",
+	"emcee>=3.1.6",
+	"numpy>=2.1",
+	"pandas>=2.2.2",
+	"scipy>=1.14.1",
 	"svo-filters>=0.4.4",
-	"importlib-resources"
+	"setuptools>=64",
 ]
 dynamic = ["version"]
 readme = "README.md"

sedkit/catalog.py

@@ -10,7 +10,7 @@
 import dill
 import pickle
 from copy import copy
-import importlib_resources
+import importlib.resources
 import shutil
 
 from astropy.io import ascii
@@ -983,5 +983,5 @@ def __init__(self, **kwargs):
         super().__init__(name='M Dwarf Catalog', **kwargs)
 
         # Read the names from the file
-        file = importlib_resources.files('sedkit')/ 'data/sources.txt'
+        file = str(importlib.resources.files('sedkit')/ 'data/sources.txt')
         self.from_file(file, run_methods=['find_SDSS', 'find_2MASS', 'find_WISE'])

sedkit/helpers.py

@@ -9,7 +9,7 @@
 
 from glob import glob
 import os
-from pkg_resources import resource_filename
+import importlib.resources
 
 from astropy.io import ascii
 import astropy.table as at
@@ -19,7 +19,7 @@ def process_dmestar(dir=None, filename='dmestar_solar.txt'):
     """Combine all DMESTAR isochrones into one text file"""
     # Get the filenames
     if dir is None:
-        dir = resource_filename('sedkit', 'data/models/evolutionary/DMESTAR/')
+        dir = str(importlib.resources.files('sedkit')/ 'data/models/evolutionary/DMESTAR/')
 
     files = glob(os.path.join(dir, '*'))
 
@@ -40,7 +40,7 @@ def process_dmestar(dir=None, filename='dmestar_solar.txt'):
     if len(tables) > 0:
         table = at.vstack(tables)
         table.meta = None
-        path = resource_filename('sedkit', 'data/models/evolutionary/')
+        path = str(importlib.resources.files('sedkit')/ 'data/models/evolutionary/')
         table.write(os.path.join(path, filename), format='csv')
 
     else:

sedkit/isochrone.py

@@ -8,7 +8,7 @@
 
 import os
 import glob
-from pkg_resources import resource_filename
+import importlib.resources
 
 import astropy.units as q
 import astropy.constants as ac
@@ -33,7 +33,7 @@
 
 # A list of all supported evolutionary models
 try:
-    EVO_MODELS = [os.path.basename(m).replace('.txt', '') for m in glob.glob(resource_filename('sedkit', 'data/models/evolutionary/*'))]
+    EVO_MODELS = [os.path.basename(m).replace('.txt', '') for m in glob.glob(str(importlib.resources.files('sedkit')/ 'data/models/evolutionary/*'))]
 # Fails RTD build for some reason
 except:
     EVO_MODELS = ['COND03', 'dmestar_solar', 'DUSTY00', 'f2_solar_age', 'hybrid_solar_age', 'nc+03_age','nc+0.0_age', 'nc-03_age', 'nc_solar_age','nc+0.5_age','nc-0.5_age', 'parsec12_solar','ATMO_NEQ_strong','ATMO_NEQ_strong_MIRI','chaubrier_2022.txt']
@@ -54,7 +54,7 @@ def __init__(self, name, units=None, verbose=True, **kwargs):
 
         # Set the path
         self.name = name
-        self.path = resource_filename('sedkit', 'data/models/evolutionary/{}.txt'.format(self.name))
+        self.path = str(importlib.resources.files('sedkit')/ 'data/models/evolutionary/{}.txt').format(self.name)
         self._age_units = None
         self._mass_units = None
         self._radius_units = None

sedkit/modelgrid.py

@@ -14,7 +14,7 @@
 import pickle
 from functools import partial
 from multiprocessing import Pool
-import importlib_resources
+import importlib.resources
 from pathlib import Path
 
 import astropy.units as q
@@ -761,7 +761,7 @@ def __init__(self, root=None, **kwargs):
 
         # Load the model grid
         modeldir = 'data/models/atmospheric/btsettl'
-        root = root or importlib_resources.files('sedkit')/ modeldir
+        root = root or str(importlib.resources.files('sedkit')/ modeldir)
         self.load(root)
 
 
@@ -777,7 +777,7 @@ def __init__(self):
 
         # Load the model grid
         model_path = 'data/models/atmospheric/spexprismlibrary'
-        root = importlib_resources.files('sedkit')/ model_path
+        root = str(importlib.resources.files('sedkit')/ model_path)
         self.load(root)
 
         # Add numeric spectral type