feat(paper):Publishing paper to JOSS

.github/workflows/cd.yml

@@ -1,4 +1,4 @@
-name: Production deployment
+name: 🚀 Production deployment
 
 on:
   push:

.github/workflows/draft-pdf.yml

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+name: 📖 Draft Paper
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - 'paper/**'
+  pull_request:
+    branches:
+      - main
+    paths:
+      - 'paper/**'
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v2
+        with:
+          name: paper
+          path: paper/paper.pdf

paper/paper.bib

@@ -0,0 +1,112 @@
+@article{article,
+author = {Pannier, Erwan and Laux, Christophe},
+year = {2018},
+month = {10},
+pages = {},
+title = {RADIS: A nonequilibrium line-by-line radiative code for CO2 and HITRAN-like database species},
+volume = {222},
+journal = {Journal of Quantitative Spectroscopy and Radiative Transfer},
+doi = {10.1016/j.jqsrt.2018.09.027}
+}
+
+@article{article,
+author = {Goldenstein, Christopher and Miller, Victor and Spearrin, Raymond and Strand, Christopher},
+year = {2017},
+month = {06},
+pages = {},
+title = {SpectraPlot.com: Integrated Spectroscopic Modeling of Atomic and Molecular Gases},
+volume = {200},
+journal = {Journal of Quantitative Spectroscopy and Radiative Transfer},
+doi = {10.1016/j.jqsrt.2017.06.007}
+}
+
+@article{article,
+author = {Gordon, Iouli and Rothman, L.S. and Hill, Christian and Kochanov, Roman and Tan, Yan and Bernath, P.F. and Birk, M. and Boudon, Vincent and Campargue, A. and Chance, Kelly and Drouin, B.J. and Flaud, J.-M and Gamache, Robert and Hodges, Joseph and Jacquemart, D. and Perevalov, Valery and Perrin, Agnes and Shine, K.P. and Smith, M.-A.H. and Zak, Emil},
+year = {2017},
+month = {07},
+pages = {},
+title = {The HITRAN2016 molecular spectroscopic database},
+volume = {203},
+journal = {Journal of Quantitative Spectroscopy and Radiative Transfer},
+doi = {10.1016/j.jqsrt.2017.06.038}
+}
+
+@article{article,
+author = {Kochanov, Roman and Gordon, Iouli and Rothman, L.S. and Wcislo, Piotr and Hill, Christian and Wilzewski, J.S.},
+year = {2016},
+month = {03},
+pages = {},
+title = {HITRAN Application Programming Interface (HAPI): A comprehensive approach to working with spectroscopic data},
+volume = {177},
+journal = {Journal of Quantitative Spectroscopy and Radiative Transfer},
+doi = {10.1016/j.jqsrt.2016.03.005}
+}
+
+@article{article,
+author = {Rothman, L.S. and Gordon, Iouli and Barber, R.J. and Dothe, Hoang and Gamache, Robert and Goldman, A. and Perevalov, Valery and Tashkun, Sergey and Tennyson, Jonathan},
+year = {2010},
+month = {10},
+pages = {2139-2150},
+title = {HITEMP, the high-temperature molecular spectroscopic database},
+volume = {111},
+journal = {Journal of Quantitative Spectroscopy and Radiative Transfer},
+doi = {10.1016/j.jqsrt.2010.05.001}
+}
+
+@article{GORDON2022107949,
+title = {The HITRAN2020 molecular spectroscopic database},
+journal = {Journal of Quantitative Spectroscopy and Radiative Transfer},
+volume = {277},
+pages = {107949},
+year = {2022},
+issn = {0022-4073},
+doi = {https://doi.org/10.1016/j.jqsrt.2021.107949},
+url = {https://www.sciencedirect.com/science/article/pii/S0022407321004416},
+author = {I.E. Gordon and L.S. Rothman and R.J. Hargreaves and R. Hashemi and E.V. Karlovets and F.M. Skinner and E.K. Conway and C. Hill and R.V. Kochanov and Y. Tan and P. Wcisło and A.A. Finenko and K. Nelson and P.F. Bernath and M. Birk and V. Boudon and A. Campargue and K.V. Chance and A. Coustenis and B.J. Drouin and J.–M. Flaud and R.R. Gamache and J.T. Hodges and D. Jacquemart and E.J. Mlawer and A.V. Nikitin and V.I. Perevalov and M. Rotger and J. Tennyson and G.C. Toon and H. Tran and V.G. Tyuterev and E.M. Adkins and A. Baker and A. Barbe and E. Canè and A.G. Császár and A. Dudaryonok and O. Egorov and A.J. Fleisher and H. Fleurbaey and A. Foltynowicz and T. Furtenbacher and J.J. Harrison and J.–M. Hartmann and V.–M. Horneman and X. Huang and T. Karman and J. Karns and S. Kassi and I. Kleiner and V. Kofman and F. Kwabia–Tchana and N.N. Lavrentieva and T.J. Lee and D.A. Long and A.A. Lukashevskaya and O.M. Lyulin and V.Yu. Makhnev and W. Matt and S.T. Massie and M. Melosso and S.N. Mikhailenko and D. Mondelain and H.S.P. Müller and O.V. Naumenko and A. Perrin and O.L. Polyansky and E. Raddaoui and P.L. Raston and Z.D. Reed and M. Rey and C. Richard and R. Tóbiás and I. Sadiek and D.W. Schwenke and E. Starikova and K. Sung and F. Tamassia and S.A. Tashkun and J. {Vander Auwera} and I.A. Vasilenko and A.A. Vigasin and G.L. Villanueva and B. Vispoel and G. Wagner and A. Yachmenev and S.N. Yurchenko},
+keywords = {HITRAN, Spectroscopic database, Molecular spectroscopy, Spectroscopic line parameters, Absorption cross-sections, Collision-induced absorption, Aerosols, Molecular opacities},
+abstract = {The HITRAN database is a compilation of molecular spectroscopic parameters. It was established in the early 1970s and is used by various computer codes to predict and simulate the transmission and emission of light in gaseous media (with an emphasis on terrestrial and planetary atmospheres). The HITRAN compilation is composed of five major components: the line-by-line spectroscopic parameters required for high-resolution radiative-transfer codes, experimental infrared absorption cross-sections (for molecules where it is not yet feasible for representation in a line-by-line form), collision-induced absorption data, aerosol indices of refraction, and general tables (including partition sums) that apply globally to the data. This paper describes the contents of the 2020 quadrennial edition of HITRAN. The HITRAN2020 edition takes advantage of recent experimental and theoretical data that were meticulously validated, in particular, against laboratory and atmospheric spectra. The new edition replaces the previous HITRAN edition of 2016 (including its updates during the intervening years). All five components of HITRAN have undergone major updates. In particular, the extent of the updates in the HITRAN2020 edition range from updating a few lines of specific molecules to complete replacements of the lists, and also the introduction of additional isotopologues and new (to HITRAN) molecules: SO, CH3F, GeH4, CS2, CH3I and NF3. Many new vibrational bands were added, extending the spectral coverage and completeness of the line lists. Also, the accuracy of the parameters for major atmospheric absorbers has been increased substantially, often featuring sub-percent uncertainties. Broadening parameters associated with the ambient pressure of water vapor were introduced to HITRAN for the first time and are now available for several molecules. The HITRAN2020 edition continues to take advantage of the relational structure and efficient interface available at www.hitran.org and the HITRAN Application Programming Interface (HAPI). The functionality of both tools has been extended for the new edition.}
+}
+
+@article{article,
+author = {ROTHMAN, L.S. and RINSLAND, C.P. and GOLDMAN, A. and MASSIE, S.T. and Edwards, D.P.A. and FLAUD, J-M and Perrin, Agnes and Camy-Peyret, Claude and DANA, V. and Mandin, J.Y. and SCHROEDER, J. and MCCANN, A. and Gamache, Robert and WATTSON, R.B. and YOSHINO, K. and Chance, Kelly and Jucks, K.W. and BROWN, L.R. and Nemtchinov, Vassilii and VARANASI, P.},
+year = {1998},
+month = {11},
+pages = {665-710},
+title = {The HITRAN molecular spectroscopic database and HAWKS (Hitran Atmospheric Workstation): 1996 edition},
+volume = {60},
+journal = {Journal of Quantitative Spectroscopy and Radiative Transfer},
+doi = {10.1016/S0022-4073(98)00078-8}
+}
+
+@article{article,
+author = {Rond, Cathy and Bultel, Arnaud and Boubert, P. and Cheron, B.G.},
+year = {2008},
+month = {12},
+pages = {16-26},
+title = {Spectroscopic measurements of nonequilibrium CO 2 plasma in RF torch},
+volume = {354},
+journal = {Chemical Physics - CHEM PHYS},
+doi = {10.1016/j.chemphys.2008.09.006}
+}
+
+@article{article,
+author = {Tajayanagi, Hiroki and Lemal, Adrien and Nomura, Satoshi and Fujita, Kazuhisa},
+year = {2018},
+month = {04},
+pages = {483-494},
+title = {Measurements of Carbon Dioxide Nonequilibrium Infrared Radiation in Shocked and Expanded Flows},
+volume = {32},
+journal = {Journal of Thermophysics and Heat Transfer},
+doi = {10.2514/1.T5200}
+}
+
+@article{article,
+author = {Lemal, Adrien and Tajayanagi, Hiroki and Nomura, Satoshi and Fujita, Kazuhisa},
+year = {2018},
+month = {01},
+pages = {184-195},
+title = {Simulations of Carbon-Dioxide Equilibrium Infrared Radiation Measurements},
+volume = {32},
+journal = {Journal of Thermophysics and Heat Transfer},
+doi = {10.2514/1.T5134}
+}

paper/paper.md

@@ -0,0 +1,67 @@
+---
+title: 'Radis app : web app for Radis high-resolution infrared molecular spectra'
+tags:
+  - python
+  - spectroscopy
+  - physics
+  - web app
+  - Radis
+  - molecular
+  - spectra
+authors:
+  - name: Arunava Basu
+    orcid: 0009-0000-2880-2142
+  - name: Susannah Klanecek
+    orcid: 0000-0002-3325-6569
+affiliations:
+date: 20 July 2023
+bibliography: paper.bib
+---
+# Summary
+
+**Radis App** is a web application for Radis high-resolution infrared molecular spectra. Instead of writing code, this project aims to create an intuitive user interface (UI).
+It uses Radis internally to produce spectrum, and the updated version and Radis algorithm makes it incredibly efficient to compute millions of lines in only a few minutes.
+Radis app leverages React 18 to offer the user interface, and FastApi on the backend. We are using react-hook-form for the fastest user experience and to maintain performance on the client slide. In the backend, we use FastApi to offer the fastest response.
+
+# Statement of need
+
+We build  **Radis App** to address an important need in the field of high-resolution infrared molecular spectroscopy. Traditional approaches for analyzing  molecular spectra often involve complex coding and lack intuitive user interfaces, leading to barriers for researchers and practitioners in effectively utilizing this valuable data.
+
+The Radis app fills this gap by providing a user-friendly web application that leverages the power of the Radis algorithm. By abstracting the need for coding, the Radis app enables researchers to efficiently generate high-resolution spectra with ease. This not only saves significant time and effort but also opens up opportunities for a wider range of users to explore and analyze molecular spectra.
+The ability of the Radis app to plot spectra, export them, and overlay multiple spectra for comparative analysis further enhances its usefulness. This comprehensive set of features caters to the diverse needs of researchers working in various fields, ranging from atmospheric science to chemical engineering.
+
+
+# App Architecture
+
+- **Radis Architecture -**
+![Radis  Architecture](./images/radis_architecture.png)
+
+- **Radis App Architecture -**
+![Radis App Architecture](./images/radisapp_architecture.png)
+
+
+# Features
+
+The Radis app offers several key features that enhance the user experience and facilitate efficient analysis of high-resolution infrared molecular spectra. These features includes -
+
+1. **Plotting Spectra**: The app allows users to plot the generated spectra visually. This feature provides a clear and concise representation of the spectral data, enabling researchers to easily analyze and interpret the results. Visualizations can be customized and adjusted to meet specific requirements, enhancing data comprehension and facilitating further analysis.
+
+![Plotting Spectra](./images/plotting_spectra.png)
+
+
+2. **Exporting Spectra**: The Radis app enables users to export the generated spectra in various formats, such as CSV and Spec files. This feature allows researchers to save and share the spectra for further analysis, publication, or collaboration with peers. The ability to export spectra enhances reproducibility and enables seamless integration with other tools and packages.
+
+![Exporting Spectra](./images/exporting_spectra.png)
+
+
+3. **Overlaying Spectra**: The app offers the capability to overlay multiple spectra for comparative analysis. Researchers can compare different spectra on a single plot, facilitating the identification of patterns, differences, and correlations between different molecular species or experimental conditions.
+
+![Overlaying Spectra](./images/overlaying_spectra.png)
+
+
+Overall, the combination of plotting spectra, exporting spectra, and overlaying spectra in the Radis app provides researchers with powerful tools to explore, analyze, and visualize high-resolution infrared molecular spectra effectively
+
+# Acknowledgements
+We acknowledge contributions and support from Erwan Pannier during the genesis of this project.
+
+# References