Update JOSS paper

joss/paper.bib

@@ -398,3 +398,31 @@ @ARTICLE{2020SciPy-NMeth
     adsurl  = {https://rdcu.be/b08Wh},
     doi     = {10.1038/s41592-019-0686-2},
 }
+
+@ARTICLE{Cadieux2024,
+       author = {{Cadieux}, Charles and {Doyon}, Ren{\'e} and {MacDonald}, Ryan J. and {Turbet}, Martin and {Artigau}, {\'E}tienne and {Lim}, Olivia and {Radica}, Michael and {Fauchez}, Thomas J. and {Salhi}, Salma and {Dang}, Lisa and {Albert}, Lo{\"\i}c and {Coulombe}, Louis-Philippe and {Cowan}, Nicolas B. and {Lafreni{\`e}re}, David and {L'Heureux}, Alexandrine and {Piaulet}, Caroline and {Benneke}, Bj{\"o}rn and {Cloutier}, Ryan and {Charnay}, Benjamin and {Cook}, Neil J. and {Fournier-Tondreau}, Marylou and {Plotnykov}, Mykhaylo and {Valencia}, Diana},
+        title = "{Transmission Spectroscopy of the Habitable Zone Exoplanet LHS 1140 b with JWST/NIRISS}",
+      journal = {arXiv e-prints},
+     keywords = {Astrophysics - Earth and Planetary Astrophysics},
+         year = 2024,
+        month = jun,
+          eid = {arXiv:2406.15136},
+        pages = {arXiv:2406.15136},
+          doi = {10.48550/arXiv.2406.15136},
+archivePrefix = {arXiv},
+       eprint = {2406.15136},
+ primaryClass = {astro-ph.EP},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2024arXiv240615136C},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+@software{michael_radica_2024_12628066,
+  author       = {Michael Radica},
+  title        = {radicamc/exoUPRF: exoUPRF v1.0.0},
+  month        = jul,
+  year         = 2024,
+  publisher    = {Zenodo},
+  version      = {v1.0.0},
+  doi          = {10.5281/zenodo.12628066},
+  url          = {https://doi.org/10.5281/zenodo.12628066}
+}

joss/paper.md

@@ -13,7 +13,7 @@ authors:
 affiliations:
  - name: Trottier Institute for Research on Exoplanets (iREx), Université de Montréal, Montréal, Canada
    index: 1
-date: 30 April 2024
+date: 05 July 2024
 bibliography: paper.bib
 ---
 
@@ -25,7 +25,7 @@ it is imperative to ensure that the spectral features that drive atmosphere infe
 
 Here, I present the community with `exoTEDRF` (EXOplanet Transit and Eclipse Data Reduction Framework; formerly known as 
 `supreme-SPOON`), an end-to-end pipeline for data reduction and light curve analysis of time series observations (TSOs) of transiting exoplanets with JWST. The pipeline is highly modular and designed to produce reliable spectra from raw JWST exposures. 
-`exoTEDRF` consists of four stages, each of which are further subdivided into a series of steps. These steps can either be run individually, for example in a Jupyter notebook, or via the command line using the provided configuration files.
+`exoTEDRF` (pronounced exo-tedorf) consists of four stages, each of which are further subdivided into a series of steps. These steps can either be run individually, for example in a Jupyter notebook, or via the command line using the provided configuration files.
 The steps are highly tunable, allowing full control over every parameter in the reduction. Each step also produces diagnostic plots to allow the user to verify their results at each intermediate stage, and compare outputs with other pipelines if so desired.
 Finally, `exoTEDRF` has also been designed to be run in "batch" mode: simultaneously running multiple reductions, each tweaking a subset of parameters, to understand any impacts on the resulting atmosphere spectrum.
 
@@ -39,50 +39,52 @@ Like similar pipelines (`Eureka!` [@bell_eureka_2022], `jwst` [@bushouse_howard_
 - 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 excellent `juliet` library [@espinoza_juliet_2019], 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. 
 
 
 # Statement of Need
 Data analysis is a challenging process that is encountered by all observational studies. Ensuring that the resulting 
 atmosphere spectra are robust against particular choices made in the reduction process is critical, especially as we push to characterize the atmospheres of small rocky planets. 
 The modularity and tunability of `exoTEDRF` make it easy to run multiple reductions of a given dataset, and therefore robustly ascertain whether the spectral features driving atmosphere inferences are robust, or sensitive to the peculiarities of a given reduction.
-Moreover, `exoTEDRF` has full support for TSOs with NIRISS/SOSS [@Albert2023], an observing mode which is underserved by the current ecosystem of JWST reduction tools, including the ability to run the `ATOCA` extraction algorithm [@Darveau-Bernier2022; @Radica2022] to explicitly model the SOSS order overlap. 
+Moreover, `exoTEDRF` has full support for TSOs with NIRISS/SOSS [@Albert2023], an observing mode which is underserved by the current ecosystem of JWST reduction tools, including being the only pipeline with the ability to run the `ATOCA` extraction algorithm [@Darveau-Bernier2022; @Radica2022] to explicitly model the SOSS order overlap. 
 
 
 # Documentation
 Documentation for `exoTEDRF`, including example notebooks, is available at [https://exotedrf.readthedocs.io/en/latest/](https://exotedrf.readthedocs.io/en/latest/). 
 
 
 # Uses of exoTEDRF in Current Literature
-`exoTEDRF` (particulalry in its previous life as `supreme-SPOON`) has been widely applied to exoplanet TSOs. 
+`exoTEDRF` (particularly in its previous life as `supreme-SPOON`) has been widely applied to exoplanet TSOs. 
 A list of current literature which has made use of `exoTEDRF` includes: 
-@Feinstein2023, @Coulombe2023, @Radica2023, @Albert2023, @Lim2023, @Radica2024, @Fournier-Tondreau2024, and @Benneke2024.
+@Feinstein2023, @Coulombe2023, @Radica2023, @Albert2023, @Lim2023, @Radica2024, @Fournier-Tondreau2024, @Benneke2024, and @Cadieux2024.
 
 
 # Future Developments
-The current release of `exoTEDRF` (v1.4.0) currently supports the reduction of TSOs observed with JWST NIRISS/SOSS. 
-Support for observations with NIRSpec and MIRI/LRS are in development and will be added in the coming months.
-`exoTEDRF` has also been applied to exoplanet observations from the Hubble Space Telescope using the UVIS mode (Radica et al., 2024, in prep). This functionality will also be made available to the public.
-Finally, updates to the light curve fitting routines are underway to allow for more flexibility for the fitting of both astrophysical and systematics models.
+The current release of `exoTEDRF` (v2.0.0) currently supports the reduction of TSOs observed with JWST NIRISS/SOSS as well as NIRSpec/BOTS. 
+Support for observations MIRI/LRS is in development and will be added in the coming months.
+`exoTEDRF` has also been applied to exoplanet observations from the Hubble Space Telescope using the UVIS mode (Radica et al., 2024b, in prep). This functionality will also be made available to the public.
 
 Suggestions for additional features are always welcome!
 
 
 # Similar Tools
-The following is a list of other open source pipelines tailored to exoplanet observations with JWST:
-`Eureka!` [@bell_eureka_2022], `jwst` [@bushouse_howard_2022_7038885], `tshirt` [@tshirt2022], `PACMAN` [@pacman2022],
-`nirHiss` [@nirhiss2022], `ExoTiC-JEDI` [@jedi2022], `ExoTiC-MIRI` [@grant_david_2023_8211207], 
-and `transitspectroscopy` [@espinoza_nestor_2022_6960924].
-Packages like `exoplanet` [@exoplanet:joss] and `Eureka!` [@bell_eureka_2022] also enable similar light curve fitting. 
+The following is a list of other open source pipelines tailored to exoplanet observations with JWST, some of which general purpose, and others which are more tailored to specific instruments:
+- General purpose: `Eureka!` [@bell_eureka_2022], `jwst` [@bushouse_howard_2022_7038885], `transitspectroscopy` [@espinoza_nestor_2022_6960924]
+- NIRISS specific: `nirHiss` [@nirhiss2022]
+- NIRCam specific: `tshirt` [@tshirt2022]
+- MIRI specific:  `PACMAN` [@pacman2022], `ExoTiC-MIRI` [@grant_david_2023_8211207]
+- NIRSpec specific: `ExoTiC-JEDI` [@jedi2022]
+
+Packages like `exoplanet` [@exoplanet:joss], `Eureka!` [@bell_eureka_2022], and `juliet` [@espinoza_juliet_2019] also enable similar light curve fitting. 
 
 
 # Acknowledgements
 The foundations of `exoTEDRF` are built upon many wonderful Python libraries, including `numpy` [@harris2020array], `scipy` [@2020SciPy-NMeth], `astropy` [@astropy:2013; @astropy:2018], and `matplotlib` [@Hunter:2007].
 
 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. 
-MR would also like to thank the JWST Transiting Exoplanet Community Early Release Science program for providing the 
+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 
 Coulombe, Néstor Espinoza, and Lili Alderson for many helpful conversations.