Merge pull request #17 from warrickball/joss-editorial-fixes

Various editorial fixes following acceptance in JOSS

joss/paper.bib

@@ -24,7 +24,7 @@ @misc{david_grant_2022_7437681
 }
 
 @ARTICLE{bell_eureka_2022,
-    author = {{Bell}, Taylor and {Ahrer}, Eva-Maria and {Brande}, Jonathan and {Carter}, Aarynn and {Feinstein}, Adina and {Caloca}, Giannina and {Mansfield}, Megan and {Zieba}, Sebastian and {Piaulet}, Caroline and {Benneke}, Bj{\"o}rn and {Filippazzo}, Joseph and {May}, Erin and {Roy}, Pierre-Alexis and {Kreidberg}, Laura and {Stevenson}, Kevin},
+    author = {{Bell}, Taylor and {Ahrer}, Eva-Maria and {Brande}, Jonathan and {Carter}, Aarynn and {Feinstein}, Adina D. and {Caloca}, Giannina and {Mansfield}, Megan and {Zieba}, Sebastian and {Piaulet}, Caroline and {Benneke}, Bj{\"o}rn and {Filippazzo}, Joseph and {May}, Erin and {Roy}, Pierre-Alexis and {Kreidberg}, Laura and {Stevenson}, Kevin},
     title = "{Eureka!: An End-to-End Pipeline for JWST Time-Series Observations}",
     journal = {Journal of Open Source Software},
     keywords = {Cython, astronomy, exoplanets, JWST, Python, spectroscopy, HST, photometry, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Earth and Planetary Astrophysics},
@@ -203,13 +203,23 @@ @ARTICLE{Benneke2024
       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
 
-@misc{pacman2022,
-  author = {{Zieba}, Sebastian and {Kreidberg}, Laura},
-  title = {PACMAN},
-  year = 2022,
-  publisher = {GitHub},
-  journal = {GitHub repository},
-  url = {https://github.com/sebastian-zieba/PACMAN}
+@ARTICLE{pacman2022,
+       author = {{Zieba}, Sebastian and {Kreidberg}, Laura},
+        title = "{PACMAN: A pipeline to reduce and analyze Hubble Wide Field Camera 3 IR Grism data}",
+      journal = {The Journal of Open Source Software},
+     keywords = {astronomy, exoplanets, python, Python, spectroscopy, HST, photometry, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Earth and Planetary Astrophysics},
+         year = 2022,
+        month = dec,
+       volume = {7},
+       number = {80},
+          eid = {4838},
+        pages = {4838},
+          doi = {10.21105/joss.04838},
+archivePrefix = {arXiv},
+       eprint = {2212.11421},
+ primaryClass = {astro-ph.IM},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2022JOSS....7.4838Z},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
 
 @misc{tshirt2022,
@@ -222,7 +232,7 @@ @misc{tshirt2022
 }
 
 @misc{nirhiss2022,
-  author = {{Feinstein}, Adina},
+  author = {{Feinstein}, Adina D.},
   title = {nirHiss},
   year = 2022,
   publisher = {GitHub},
@@ -276,15 +286,19 @@ @article{exoplanet:joss
                 Brett M. and {Price-Whelan}, Adrian M. and {Savel}, Arjun B.},
         title = "{exoplanet: Gradient-based probabilistic inference for
                   exoplanet data \& other astronomical time series}",
-      journal = {arXiv e-prints},
+      journal = {The Journal of Open Source Software},
+     keywords = {Python, astronomy, Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Earth and Planetary Astrophysics},
          year = 2021,
-        month = may,
-          eid = {arXiv:2105.01994},
-        pages = {arXiv:2105.01994},
+        month = jun,
+       volume = {6},
+       number = {62},
+          eid = {3285},
+        pages = {3285},
+          doi = {10.21105/joss.03285},
 archivePrefix = {arXiv},
        eprint = {2105.01994},
  primaryClass = {astro-ph.IM},
-       adsurl = {https://ui.adsabs.harvard.edu/abs/2021arXiv210501994F},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2021JOSS....6.3285F},
       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
 

joss/paper.md

@@ -31,15 +31,15 @@ Finally, `exoTEDRF` has also been designed to be run in "batch" mode: simultaneo
 
 
 # Overview of exoTEDRF Stages
-Like similar pipelines (`Eureka!` [@bell_eureka_2022], `jwst` [@bushouse_howard_2022_7038885], etc.)
+Like similar pipelines [e.g. `Eureka!`, @bell_eureka_2022; `jwst`, @bushouse_howard_2022_7038885]
 `exoTEDRF` is divided up into four major stages which are summarized below:
 
 - Stage 1, Detector-level processing: Converts raw, 4D (integrations, groups, $x$-pixel, $y$-pixel) data frames to 3D (integrations, $x$-pixel, $y$-pixel) slope images. Steps include superbias subtractions, correction of 1/$f$ noise, ramp fitting, etc. 
 - Stage 2, Spectroscopic processing: Performs additional calibrations to prepare slope images for spectral extraction. Steps include, flat field correction, background subtraction, etc. 
 - Stage 3, Spectral extraction: Extract the 2D stellar spectra from the 3D slope images.
 - Stage 4, Light curve fitting: An optional stage for the fitting of extracted light curves.
 
-In `exoTEDRF`, Stage 4 is an optional installation which is currently built around the `exoUPRF` library [@michael_radica_2024_12628066], and incorporates tools such as `ExoTiC-LD` [@david_grant_2022_7437681] for the estimation of stellar limb darkening parameters. 
+In `exoTEDRF`, Stage 4 is an optional installation which is currently built around the `exoUPRF` library [@michael_radica_2024_12628066], and incorporates tools such as `ExoTiC-LD` [@david_grant_2022_7437681] for the estimation of stellar limb-darkening parameters. 
 In certain places (e.g., superbias subtraction, flat field correction), `exoTEDRF` simply provides a wrapper around the existing functionalities of the `jwst` package maintained by the Space Telescope Science Institute. 
 
 
@@ -86,8 +86,8 @@ The foundations of `exoTEDRF` are built upon many wonderful Python libraries, in
 MR acknowledges funding from the Natural Sciences and Engineering Research Council of Canada,
 the Fonds de Recherche du Québec -- Nature et Technologies, and the Trottier Institute for Research on Exoplanets. 
 He would also like to thank the JWST Transiting Exoplanet Community Early Release Science program for providing the 
-forum where much of the development of this pipeline occured, and in particular, Adina Feinstein, Louis-Philippe 
+forum where much of the development of this pipeline occurred, and in particular, Adina Feinstein, Louis-Philippe 
 Coulombe, Néstor Espinoza, and Lili Alderson for many helpful conversations. 
 
 
-# References
+# References