Merge pull request #213 from karllark/joss_paper

Joss paper

.github/workflows/draft-pdf.yml

@@ -0,0 +1,30 @@
+name: Draft PDF
+on:
+ push:
+ paths:
+ - paper/paper.md
+ - paper/paper.bib
+ - paper/*.png
+ - .github/workflows/draft-pdf.yml
+
+jobs:
+ paper:
+ runs-on: ubuntu-latest
+ name: Paper Draft
+ steps:
+ - name: Checkout
+ uses: actions/checkout@v4
+ - name: Build draft PDF
+ uses: openjournals/openjournals-draft-action@master
+ with:
+ journal: joss
+ # This should be the path to the paper within your repo.
+ paper-path: paper/paper.md
+ - name: Upload
+ uses: actions/upload-artifact@v4
+ with:
+ name: paper
+ # This is the output path where Pandoc will write the compiled
+ # PDF. Note, this should be the same directory as the input
+ # paper.md
+ path: paper/paper.pdf

docs/dust_extinction/references.rst

@@ -96,12 +96,13 @@ G21: `Gordon et al. 2021, ApJ, 916, 33
 <https://ui.adsabs.harvard.edu/abs/2021ApJ...916...33G>`_
 
 G23: `Gordon et al. 2023, ApJ, 950, 86
-<https://ui.adsabs.harvard.edu/abs/2023ApJ...950...86G/abstract>`_
+<https://ui.adsabs.harvard.edu/abs/2023ApJ...950...86G>`_
 
-G24: Gordon et al. 2024, ApJ, in press
+G24: `Gordon et al. 2024, ApJ, in press
+<https://ui.adsabs.harvard.edu/abs/2024arXiv240512792G>`_
 
 HD23: `Hensley & Draine 2023, ApJ, 948, 55
-<https://ui.adsabs.harvard.edu/abs/2023ApJ...948...55H/abstract>`_
+<https://ui.adsabs.harvard.edu/abs/2023ApJ...948...55H>`_
 
 I05: `Indebetouw et al. 2005, ApJ, 619, 931
 <https://ui.adsabs.harvard.edu/abs/2005ApJ...619..931I>`_

docs/index.rst

@@ -7,10 +7,13 @@ Interstellar Dust Extinction
 ``dust_extinction`` is a python package to provide models of interstellar dust
 extinction curves.
 
-Extinction describes the effects of dust on a single star. The dust along the
-line-of-sight to the stars removes flux by absorbing photons or scattering
-photons out of the line-of-sight. In general, extinction models are used to
-model or correct the effects of dust on observations a single star.
+Extinction describes the effects of dust on observations of single star due to
+the dust along the line-of-sight to a star removiong flux by absorbing photons
+and scattering photons out of the line-of-sight. The wavelength dependence of
+dust extinction (also know as extinction curves) provides fundamental
+information about the size, composition, and shape of interstellar dust grain.
+In general, extinction models are used to model or correct the effects of dust
+on observations.
 
 In contrast, dust attenuation refers to the effects of dust on the measurements
 of groups of stars mixed with dust or stars with circumstellar dust.

paper/paper.md

@@ -0,0 +1,82 @@
+---
+title: 'dust_extinction: Interstellar Dust Extinction Models'
+tags:
+ - Python
+ - astronomy
+ - milky way
+ - magellanic clouds
+ - dust
+ - extinction
+ - interstellar
+authors:
+ - name: Karl D. Gordon
+ orcid: 0000-0001-5340-6774
+ affiliation: 1
+affiliations:
+ - name: Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD, 21218, USA
+ index: 1
+date: 22 May 2024
+bibliography: paper.bib
+---
+
+# Summary
+
+Extinction describes the effects of dust on observations of single star due to
+the dust along the line-of-sight to a star removiong flux by absorbing photons
+and scattering photons out of the line-of-sight. The wavelength dependence of
+dust extinction (also know as extinction curves) provides fundamental
+information about the size, composition, and shape of interstellar dust grain.
+In general, models giving the wavelength dependence of extinction are used to
+model or correct the effects of dust on observations. This python astropy
+affiliated package [@Astropy22] provides many of the published extinction models
+in one place with a consistent interface.
+
+# Statement of need
+
+Many observational and theoretical based extinction curves have been presented
+in the literature. Having one python package providing these models ensures
+that they are straightforward to use and used within their valid wavelength
+and parameter (where appropriate) ranges.
+
+The types of extinction models supported are Averages, Parameter Averages, Grain
+Models, and Shapes. The Averages are averages of a set of measured extinction
+curves and examples are shown in Fig. \autoref{fig:averages}. The Parameter
+Averages are extinction curve averages that depend on a parameter, often $R(V) =
+A(V)/E(B-V)$ which is the ratio of total to selective extinction. Fig.
+\autoref{fig:parameter_averages} shows examples of such models. The Grain
+Models are those extinction curves computed using dust grain models. See Fig.
+\autoref{fig:grain} and note that these models provide dust extinction
+predictions from the X-ray through submm wavelengths. The final type of models
+are Shapes that provide flexible functional forms that fit selected wavelength
+ranges (see Fig. \autoref{fig:shapes} for an example).
+
+![Examples of Average models based on observations in the Milky Way, Large Magellanic Cloud (LMC), and Small Magellanic Cloud (SMC) [@Bastiaansen92; @Gordon03; @Gordon09; @Gordon21; @Gordon24].\label{fig:averages}](average_models_uv_nir.png){
+width=70% }
+
+![Examples of Parameter Average models [@Cardelli89; @ODonnell94; @Fitzpatrick99; @Fitzpatrick04; @Valencic04; @Gordon09; @MaizApellaniz14; @Fitzpatrick19; @Decleir22; @Gordon23].\label{fig:parameter_averages}](parameter_average_models.png)
+
+![Examples of Grain models that are based on fitting observed extinction curves as well as other dust observables (e.g., emission and polarization) [@Desert90; @Weingartner01; @Draine03; @Zubko04; @Compiegne11; @Jones13; @Hensley23].\label{fig:grain}](grain_models.png){ width=70% }
+
+![Example of a Shape model that is focused on decomposing the UV extinction curve [@Fitzpatrick90].\label{fig:shapes}](shape_models.png){ width=70% }
+
+The wavelength dependence of extinction for a model is computed by passing a
+wavelength or frequency vector with units. Each model has a valid wavelength
+range that is enforced as extrapolation is not supported. The model output is in
+the standard $A(\lambda)/A(V)$ units where $A(\lambda)$ is the extinction at
+wavelength $\lambda$ and $A(V)$ is the extinction in the V band. Every model has
+a helper `extinguish` function that alternatively provides the fractional
+effects of extinction for a specific dust column (e.g., $A(V)$ value). This
+allows for the effects of dust to be modeled for or removed from an observation.
+
+This package does not implement dust attenuation models. Dust attenuation
+results when observing more complex systems like a star with nearby,
+circumstellar dust or a galaxy with many stars extinguished by different amounts
+of dust. In both cases, the wavelength dependence of effects of dust are
+dependent not just on the dust grain properties, but also the effects of the
+dust radiative transfer [@Steinacker13]. Specifically, the averaging of sources
+extinguished by differing amount of dust and the inclusion of a significnat
+number of photons scattered into the observing beam.
+
+Any published dust extinction model is welcome for inclusion in this package.
+
+# References