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Merge dev branch #300

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merged 74 commits into from
Nov 1, 2024
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8bc62a0
Use importlib.resources instead of pkg_resources (from setuptools)
Apr 18, 2024
d53422f
Simplify feature bounds using np.nan instead of masking
jdtsmith May 9, 2024
3017dda
Add missing colon
jdtsmith May 9, 2024
ec97932
Remove BoundedMaskedColumn
jdtsmith May 9, 2024
afc0bc9
Fix bounded_is_missing arg usage
jdtsmith May 9, 2024
ef094af
features: doc improvements
jdtsmith May 9, 2024
4740c34
Merge pull request #278 from drvdputt/use_importlib
jdtsmith May 9, 2024
4fefb0a
Fix dtype var mention
jdtsmith May 9, 2024
3c9fb7a
_construct_table: fix dtypes formulation
jdtsmith May 9, 2024
2729f89
Make linter happier
jdtsmith May 9, 2024
ce49a70
_construct_table: hard-code str for column types for no-bounds cols
jdtsmith May 9, 2024
1cd8404
Fix dtype and format for structured array Features cells
jdtsmith May 9, 2024
cf180ee
Suppress mention of [val, min, max] in column headers
jdtsmith May 9, 2024
be7cca1
Features: Strip dtype from default __repr__
jdtsmith May 9, 2024
19e9c25
Allow meta['pahfit_format'] on table and columns
jdtsmith May 9, 2024
646ffd1
Mask unused value for linter
jdtsmith Oct 27, 2022
6bd5e1d
Expose KIND_PARAMS and PARAM_UNITS as module level constants
jdtsmith Mar 17, 2023
3d0aae5
UNITS: remove fwhm, add solid_angle
jdtsmith Dec 15, 2022
a274097
Bug: Enum members need .value to extract the unit value
jdtsmith Dec 15, 2022
548ded1
units: switch to simple module constants
jdtsmith Dec 16, 2022
8d637c4
Remove 'tied' param/group type (for another PR)
jdtsmith Mar 17, 2023
1157f89
_index_table: re-add
jdtsmith Mar 17, 2023
b4a5ba4
linter happiness
jdtsmith Mar 17, 2023
21c61f0
Set power unit to intensity_power amplitude for now
May 8, 2024
e7e5c70
Convert input spectrum to internal units, error if not ~ MJy sr-1
May 9, 2024
1a3360b
State that MJy / sr unit restriction is temporary
May 9, 2024
4573a35
Convert example spectra to MJy / sr (temporary fix)
May 9, 2024
6ec9596
Merge pull request #284 from drvdputt/units-standard
jdtsmith May 10, 2024
5ce6067
Replace Model.plot() implementation by method that uses tabulate()
May 7, 2024
1bbe11f
scalefac_resid argument for plot() and use it in plot_pahfit script
May 7, 2024
99dda28
Remove old plot from PAHFITBase
May 7, 2024
6a85e38
Fix accidentally removed pahfit.units import
May 13, 2024
50f232c
Tweaks to Model.plot() based on pull request #281 review
May 13, 2024
68ce437
Merge pull request #281 from drvdputt/plot_rewrite
jdtsmith May 13, 2024
58038bc
Merge branch 'simpler-bounded-params' into dev
jdtsmith May 13, 2024
c3abd93
Add Fitter API and APFitter implementation
May 13, 2024
a73dcb4
Delete base.py and use Fitter API in Model class implementation
May 14, 2024
87a6e18
Regular floats for Features _bounds_dtype to exactly match test
May 14, 2024
a5e370d
Fixes based on test cases
May 14, 2024
9ded572
Remove obsolete helpers.calculate_compounds, more formatting
May 14, 2024
c1a2665
Remove mentions of PAHFITBase
May 14, 2024
96757a6
Clarify Fitter API operation description
May 14, 2024
a9311cc
Array vs scalar arguments to determine fitted/fixed in Fitter
May 17, 2024
02cd40b
Remove clear() from Fitter and APFitter
May 17, 2024
45d1497
Rename register_* to add_feature_*, clean up APFitter var names
May 17, 2024
add53ab
Model and geometry keywords for add_feature_attenuation/absorption
May 20, 2024
7aed851
Replace xz, yz by lam, flux
May 20, 2024
edcbbf6
Docstring and formatting fixes
May 20, 2024
4057012
Add TODO in guess to replace fwhm guessing by sigma_v
May 21, 2024
8f4d2bc
Work with self.fitter directly instead fitter argument/return
May 21, 2024
ac2146f
Remove Fitter.components(), instead keep 'enabled' list in Model
May 21, 2024
2942c08
Don't copy when applying feature mask in tabulate
Jun 25, 2024
30b0c2e
Better documentation and variable names for _set_up_fitter
Jun 25, 2024
e241077
Replace wavelengths named w by lam
Jun 25, 2024
040798d
Fix instrument and redshift being swapped in Features metadata
Jun 25, 2024
032ed4b
Fix style issue
Jun 25, 2024
f53c8db
Put fitter modules in pahfit.fitters. Rename apfitter to ap_fitter.
Jun 25, 2024
a990b47
Fix astropy contribution guide link
drvdputt Jul 3, 2024
2dc3c80
Replace links to PAHFIT classic
drvdputt Jul 3, 2024
5d22489
Rephrase comment explaining redshift adjustment of fwhm
drvdputt Jul 3, 2024
da9ed24
Replace more cases of "wav" by "lam", fix redshift bug in plot
drvdputt Jul 8, 2024
4e16008
Use "is np.ma.masked" when interpreting fwhm column
drvdputt Jul 9, 2024
50c19b7
Merge pull request #289 from drvdputt/dev-fitterapi
jdtsmith Jul 9, 2024
f80c460
Add PowerDrude1D and PowerGaussian1D classes
Jun 25, 2024
76d1d20
Switch from amplitude to power units and adjust guess accordingly
Jun 25, 2024
ddec47b
Remove equation with nu0 from PowerDrude docstring
Jun 27, 2024
aa15514
Set power unit in Features table to intensity_power
drvdputt Jun 28, 2024
79cac6f
Change trapz to trapezoid to fix deprecation warning
drvdputt Jul 9, 2024
8310da1
Formatting
drvdputt Jul 9, 2024
c500ae8
Fix typo in PowerDrude1D docstring
drvdputt Aug 13, 2024
4c22207
Use scipy.integrate.trapezoid instead of np.trapezoid
drvdputt Aug 13, 2024
936a2fa
Access intensity_amplitude_factor via self in power features
drvdputt Aug 13, 2024
a643417
Clean up some more docstrings in ap_components
drvdputt Aug 13, 2024
6f6ead0
Merge pull request #295 from drvdputt/dev-powerfeatures
jdtsmith Aug 30, 2024
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2 changes: 1 addition & 1 deletion CHANGES.rst
Original file line number Diff line number Diff line change
Expand Up @@ -12,4 +12,4 @@
==================

- IDL versions
- http://tir.astro.utoledo.edu/jdsmith/research/pahfit.php
- https://github.com/PAHFIT/pahfit_classic
2 changes: 1 addition & 1 deletion README.rst
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ PAHFIT
======


``PAHFIT`` is a decomposition model and tool for astronomical infrared spectra, focusing on dust and gas emission features from the interstellar medium (see `Smith, J.D.T., Draine B.T., et al., 2007, ApJ, 656, 770 <http://tir.astro.utoledo.edu/jdsmith/research/pahfit.php>`_).
``PAHFIT`` is a decomposition model and tool for astronomical infrared spectra, focusing on dust and gas emission features from the interstellar medium (see `Smith, J.D.T., Draine B.T., et al., 2007, ApJ, 656, 770 <https://github.com/PAHFIT/pahfit_classic>`_).

This package provides an updated python implementation of ``PAHFIT``. While the original versions of ``PAHFIT`` (``v1.x``) were written in IDL and focused mainly on Spitzer/IRS spectroscopic observations, the newer python-based versions (``>=v2.0``) will expand instrument coverage to other existing (e.g., AKARI) and planned (e.g., JWST) facilities, and will offer a more flexible modeling framework suitable for modeling a wider range of astrophysical sources.

Expand Down
10 changes: 3 additions & 7 deletions docs/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ and a more flexible modeling framework suitable for modeling a wider range
of astrophysical sources.

For details for the IDL version of PAHFIT see
`Smith, J.D.T., Draine B.T., et al., 2007, ApJ, 656, 770 <http://tir.astro.utoledo.edu/jdsmith/research/pahfit.php>`_.
`Smith, J.D.T., Draine B.T., et al., 2007, ApJ, 656, 770 <https://github.com/PAHFIT/pahfit_classic>`_.

This package is potentially an
`astropy affiliated package <http://www.astropy.org/affiliated/>`_
Expand Down Expand Up @@ -77,7 +77,7 @@ contributors who will abide by the `Python Software Foundation Code of Conduct
`Astropy`_. The following pages will help you get started with contributing
fixes, code, or documentation (no git or GitHub experience necessary):

* `How to make a code contribution <https://docs.astropy.org/en/latest/development/workflow/development_workflow.html>`_
* `How to make a code contribution <https://docs.astropy.org/en/latest/index_dev.html#developer-docs>`_

* `Coding Guidelines <https://docs.astropy.org/en/latest/development/codeguide.html>`_

Expand All @@ -92,10 +92,6 @@ contributors page on Github
Reference API
=============

Base class for PAHFIT

.. automodapi:: pahfit.base

Component models not provided by astropy.models.

.. automodapi:: pahfit.component_models
.. automodapi:: pahfit.fitters.ap_components
2 changes: 1 addition & 1 deletion docs/version_description/version_description.rst
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ Version Description
v1.0 - v1.4
------------

The original IDL version of PAHFIT can be found in: `http://tir.astro.utoledo.edu/jdsmith/research/pahfit.php <http://tir.astro.utoledo.edu/jdsmith/research/pahfit.php>`_. For more details and background of ``PAHFIT``, see the `background <https://pahfit.readthedocs.io/en/latest/background.html>`_ page.
The original IDL version of PAHFIT can be found in: `https://github.com/PAHFIT/pahfit_classic <https://github.com/PAHFIT/pahfit_classic>`_. For more details and background of ``PAHFIT``, see the `background <https://pahfit.readthedocs.io/en/latest/background.html>`_ page.

v2.0
------------
Expand Down
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