Merge pull request #25 from dawn-cph/update-ruby

update ruby

.github/workflows/jekyll-manual.yml

@@ -37,7 +37,7 @@ jobs:
         # uses: ruby/setup-ruby@0a29871fe2b0200a17a4497bae54fe5df0d973aa # v1.115.3
         with:
           bundler-cache: true # runs 'bundle install' and caches installed gems automatically
-          cache-version: 0 # Increment this number if you need to re-download cached gems
+          cache-version: 1 # Increment this number if you need to re-download cached gems
       - name: Setup Pages
         id: pages
         uses: actions/configure-pages@v2

.ruby-version

@@ -1 +1 @@
-2.7.6
+3.1.2

Gemfile

@@ -2,5 +2,4 @@ source "https://rubygems.org"
 
 gem "github-pages", group: :jekyll_plugins
 gem "jekyll-include-cache", group: :jekyll_plugins
-gem "jekyll-scholar", group: :jekyll_plugins
 gem "webrick", "~> 1.7", group: :jekyll_plugins

_config.yml

@@ -52,28 +52,4 @@ plugins:
     - jekyll-email-protect
     - jekyll-paginate
     - jemoji
-    - jekyll/scholar
 
-# Jekyll-Scholar
-scholar:
-
-  last_name:
-
-  style: apa
-  locale: en
-
-  sort_by: year
-  order: descending
-
-  source: /_bibliography/
-  bibliography: papers.bib
-  bibliography_template: bib
-
-  replace_strings: true
-  join_strings: true
-
-  details_dir: bibliography
-  details_layout: bibtex.html
-  details_link: Details
-
-  query: "@*"

_includes/bibliography/build.sh

@@ -0,0 +1,7 @@
+grep -v "@string" papers.bib | sed "s/.aap/Astronomy\\ \& Astrophysics/g" | sed "s/.apjs/ApJSS/g" | sed "s/.apjl/ApJL/g" | sed "s/.apj/ApJ/g" > papers-repl.bib
+
+pandoc -t markdown_strict --citeproc pandoc-bib.md -o pandoc-bib-output.md --bibliography papers-repl.bib 
+
+cat pandoc-bib-output.md | sed "s/<span class=\"nocase\">/\*\*/g" | sed "s/<\/span>/\*\*/g" > papers.md
+
+rm pandoc-bib-output.md papers-repl.bib

_includes/bibliography/pandoc-bib.md

@@ -0,0 +1,5 @@
+---
+bibliography: papers.bib
+nocite: "@*"
+csl: apa.csl
+---

_includes/bibliography/papers.md

@@ -0,0 +1,275 @@
+Abdurro’uf, Larson, R. L., Coe, D., Hsiao, T. Y.-Y., Álvarez-Márquez,
+J., Crespo Gómez, A., Adamo, A., Bhatawdekar, R., Bik, A., Bradley, L.
+D., Conselice, C. J., Dayal, P., Diego, J. M., Fujimoto, S., Furtak, L.
+J., Hutchison, T. A., Jung, I., Killi, M., Kokorev, V., … Zitrin, A.
+(2024). **JWST NIRSpec High-resolution Spectroscopy
+of MACS0647-JD at z=10.167: Resolved \[OII\] Doublet and Electron
+Density in an Early Galaxy**. *arXiv e-Prints*, arXiv:2404.16201.
+<https://doi.org/10.48550/arXiv.2404.16201>
+
+Austin, D., Conselice, C. J., Adams, N. J., Harvey, T., Duan, Q.,
+Trussler, J., Li, Q., Juodzbalis, I., Ormerod, K., Ferreira, L.,
+Westcott, L., Harris, H., Wilkins, S. M., Bhatawdekar, R., Caruana, J.,
+Coe, D., Cohen, S. H., Driver, S. P., D’Silva, J. C. J., … Zackrisson,
+E. (2024). **EPOCHS III: Unbiased UV continuum slopes
+at 6.5&lt;z&lt;13 from combined PEARLS GTO and public JWST NIRCam
+imaging**. *arXiv e-Prints*, arXiv:2404.10751.
+<https://doi.org/10.48550/arXiv.2404.10751>
+
+Barrufet, L., Oesch, P., Marques-Chaves, R., Arellano-Cordova, K.,
+Baggen, J. F. W., Carnall, A. C., Cullen, F., Dunlop, J. S.,
+Gottumukkala, R., Fudamoto, Y., Illingworth, G. D., Magee, D., McLure,
+R. J., McLeod, D. J., Michałowski, M. J., Stefanon, M., van Dokkum, P.
+G., & Weibel, A. (2024). **Quiescent or dusty?
+Unveiling the nature of extremely red galaxies at *z* &gt; 3**.
+*arXiv e-Prints*, arXiv:2404.08052.
+<https://doi.org/10.48550/arXiv.2404.08052>
+
+Boogaard, L. A., Gillman, S., Melinder, J., Walter, F., Colina, L.,
+Östlin, G., Caputi, K. I., Iani, E., Pérez-González, P., van der Werf,
+P., Greve, T. R., Wright, G., Alonso-Herrero, A., Álvarez-Márquez, J.,
+Annunziatella, M., Bik, A., Bosman, S., Costantin, L., Crespo Gómez, A.,
+… Henning, T. (2023). **MIDIS: JWST/MIRI reveals the
+Stellar Structure of ALMA-selected Galaxies in the Hubble-UDF at Cosmic
+Noon**. *arXiv e-Prints*, arXiv:2308.16895.
+<https://doi.org/10.48550/arXiv.2308.16895>
+
+Bradley, L. D., Adamo, A., Vanzella, E., Sharon, K., Brammer, G., Coe,
+D., Diego, J. M., Kokorev, V., Mahler, G., Oguri, M., Abdurro’uf,
+Bhatawdekar, R., Christensen, L., Fujimoto, S., Hashimoto, T., Y. -Y
+Hsiao, T., Inoue, A. K., Jiménez-Teja, Y., Messa, M., … Zitrin, A.
+(2024). **Unveiling the Cosmic Gems Arc at *z* ∼ 10.2
+with JWST**. *arXiv e-Prints*, arXiv:2404.10770.
+<https://doi.org/10.48550/arXiv.2404.10770>
+
+Cameron, A. J., Katz, H., Witten, C., Saxena, A., Laporte, N., & Bunker,
+A. J. (2023). **Nebular dominated galaxies in the
+early Universe with top-heavy stellar initial mass functions**.
+*arXiv e-Prints*, arXiv:2311.02051.
+<https://doi.org/10.48550/arXiv.2311.02051>
+
+Cutler, S. E., Whitaker, K. E., Weaver, J. R., Wang, B., Pan, R.,
+Bezanson, R., Furtak, L. J., Labbe, I., Leja, J., Price, S. H., Cheng,
+Y., Clausen, M., Cullen, F., Dayal, P., de Graaff, A., Dickinson, M.,
+Dunlop, J. S., Feldmann, R., Franx, M., … Suess, K. A. (2023).
+**Two Distinct Classes of Quiescent Galaxies at
+Cosmic Noon Revealed by JWST PRIMER and UNCOVER**. *arXiv
+e-Prints*, arXiv:2312.15012. <https://doi.org/10.48550/arXiv.2312.15012>
+
+de Graaff, A., Setton, D. J., Brammer, G., Cutler, S., Suess, K. A.,
+Labbe, I., Leja, J., Weibel, A., Maseda, M. V., Whitaker, K. E.,
+Bezanson, R., Boogaard, L. A., Cleri, N. J., De Lucia, G., Franx, M.,
+Greene, J. E., Hirschmann, M., Matthee, J., McConachie, I., … Williams,
+C. C. (2024). **Efficient formation of a massive
+quiescent galaxy at redshift 4.9**. *arXiv e-Prints*,
+arXiv:2404.05683. <https://doi.org/10.48550/arXiv.2404.05683>
+
+Duan, Q., Conselice, C. J., Li, Q., Harvey, T., Austin, D., Ormerod, K.,
+Trussler, J., & Adams, N. (2024). **Adding value to
+JWST spectra and photometry: stellar population and star formation
+properties of spectroscopically confirmed JADES and CEERS galaxies at z
+&gt; 7**. *529*(4), 4728–4744.
+<https://doi.org/10.1093/mnras/stae872>
+
+Fujimoto, S., Ouchi, M., Kohno, K., Valentino, F., Giménez-Arteaga, C.,
+Brammer, G. B., Furtak, L. J., Kohandel, M., Oguri, M., Pallottini, A.,
+Richard, J., Zitrin, A., Bauer, F. E., Boylan-Kolchin, M.,
+Dessauges-Zavadsky, M., Egami, E., Finkelstein, S. L., Ma, Z., Smail,
+I., … Yajima, H. (2024). **Primordial Rotating Disk
+Composed of ≥<!-- -->15 Dense Star-Forming Clumps at Cosmic Dawn**.
+*arXiv e-Prints*, arXiv:2402.18543.
+<https://doi.org/10.48550/arXiv.2402.18543>
+
+Giménez-Arteaga, C., Fujimoto, S., Valentino, F., Brammer, G. B., Mason,
+C. A., Rizzo, F., Rusakov, V., Colina, L., Prieto-Lyon, G., Oesch, P.
+A., Espada, D., Heintz, K. E., Knudsen, K. K., Dessauges-Zavadsky, M.,
+Laporte, N., Lee, M., Magdis, G. E., Ono, Y., Ao, Y., … Koekemoer, A. M.
+(2024). **Outshining in the Spatially Resolved
+Analysis of a Strongly-Lensed Galaxy at z=6.072 with JWST NIRCam**.
+*arXiv e-Prints*, arXiv:2402.17875.
+<https://doi.org/10.48550/arXiv.2402.17875>
+
+Giménez-Arteaga, C., Oesch, P. A., Brammer, G. B., Valentino, F., Mason,
+C. A., Weibel, A., Barrufet, L., Fujimoto, S., Heintz, K. E., Nelson, E.
+J., Strait, V. B., Suess, K. A., & Gibson, J. (2023).
+**Spatially Resolved Properties of Galaxies at 5 &lt;
+z &lt; 9 in the SMACS 0723 JWST ERO Field**. *ApJ*, *948*(2), 126.
+<https://doi.org/10.3847/1538-4357/acc5ea>
+
+Goulding, A. D., Greene, J. E., Setton, D. J., Labbe, I., Bezanson, R.,
+Miller, T. B., Atek, H., Bogdán, Á., Brammer, G., Chemerynska, I.,
+Cutler, S. E., Dayal, P., Fudamoto, Y., Fujimoto, S., Furtak, L. J.,
+Kokorev, V., Khullar, G., Leja, J., Marchesini, D., … Zitrin, A. (2023).
+**UNCOVER: The Growth of the First Massive Black
+Holes from JWST/NIRSpec-Spectroscopic Redshift Confirmation of an X-Ray
+Luminous AGN at z = 10.1**. *ApJL*, *955*(1), L24.
+<https://doi.org/10.3847/2041-8213/acf7c5>
+
+Hainline, K. N., Helton, J. M., Johnson, B. D., Sun, F., Topping, M. W.,
+Leisenring, J. M., Baker, W. M., Eisenstein, D. J., Hausen, R., Hviding,
+R. E., Lyu, J., Robertson, B., Tacchella, S., Williams, C. C., Willmer,
+C. N. A., & Roellig, T. L. (2024). **Brown Dwarf
+Candidates in the JADES and CEERS Extragalactic Surveys**. *ApJ*,
+*964*(1), 66. <https://doi.org/10.3847/1538-4357/ad20d1>
+
+Heintz, K. E., Brammer, G. B., Giménez-Arteaga, C., Strait, V. B., del
+P. Lagos, C., Vijayan, A. P., Matthee, J., Watson, D., Mason, C. A.,
+Hutter, A., Toft, S., Fynbo, J. P. U., & Oesch, P. A. (2023).
+**Dilution of chemical enrichment in galaxies 600 Myr
+after the Big Bang**. *Nature Astronomy*, *7*, 1517–1524.
+<https://doi.org/10.1038/s41550-023-02078-7>
+
+Heintz, K. E., Brammer, G. B., Watson, D., Oesch, P. A., Keating, L. C.,
+Hayes, M. J., Abdurro’uf, Arellano-Córdova, K. Z., Carnall, A. C.,
+Christiansen, C. R., Cullen, F., Davé, R., Dayal, P., Ferrara, A.,
+Finlator, K., Fynbo, J. P. U., Flury, S. R., Gelli, V., Gillman, S., …
+Witstok, J. (2024). **The JWST-PRIMAL Legacy Survey.
+A JWST/NIRSpec reference sample for the physical properties and
+Lyman-*α* absorption and emission of  ∼ 500 galaxies at
+*z* = 5.5 − 13.4**. *arXiv e-Prints*, arXiv:2404.02211.
+<https://doi.org/10.48550/arXiv.2404.02211>
+
+Heintz, K. E., Watson, D., Brammer, G., Vejlgaard, S., Hutter, A.,
+Strait, V. B., Matthee, J., Oesch, P. A., Jakobsson, P., Tanvir, N. R.,
+Laursen, P., Naidu, R. P., Mason, C. A., Killi, M., Jung, I., Hsiao, T.
+Y.-Y., Abdurro’uf, Coe, D., Arrabal Haro, P., … Toft, S. (2023).
+**Extreme damped Lyman-*α* absorption in young
+star-forming galaxies at *z* = 9 − 11**. *arXiv e-Prints*,
+arXiv:2306.00647. <https://doi.org/10.48550/arXiv.2306.00647>
+
+Jin, S., Sillassen, N. B., Magdis, G. E., Brinch, M., Shuntov, M.,
+Brammer, G., Gobat, R., Valentino, F., Carnall, A. C., Lee, M., Vijayan,
+A. P., Gillman, S., Kokorev, V., Le Bail, A., Greve, T. R., Gullberg,
+B., Gould, K. M. L., & Toft, S. (2024). **Cosmic
+Vine: A z = 3.44 large-scale structure hosting massive quiescent
+galaxies**. *Astronomy & Astrophysics*, *683*, L4.
+<https://doi.org/10.1051/0004-6361/202348540>
+
+Killi, M., Watson, D., Brammer, G., McPartland, C., Antwi-Danso, J.,
+Newshore, R., Coe, D., Allen, N., Fynbo, J. P. U., Gould, K., Heintz, K.
+E., Rusakov, V., & Vejlgaard, S. (2023).
+**Deciphering the JWST spectrum of a ’little red dot’
+at *z* ∼ 4.53: An obscured AGN and its star-forming host**. *arXiv
+e-Prints*, arXiv:2312.03065. <https://doi.org/10.48550/arXiv.2312.03065>
+
+Kokorev, V., Caputi, K. I., Greene, J. E., Dayal, P., Trebitsch, M.,
+Cutler, S. E., Fujimoto, S., Labbé, I., Miller, T. B., Iani, E.,
+Navarro-Carrera, R., & Rinaldi, P. (2024). **A Census
+of Photometrically Selected Little Red Dots at 4 &lt; z &lt; 9 in JWST
+Blank Fields**. *arXiv e-Prints*, arXiv:2401.09981.
+<https://doi.org/10.48550/arXiv.2401.09981>
+
+Langeroodi, D., & Hjorth, J. (2023). **Little Red
+Dots or Brown Dwarfs? NIRSpec Discovery of Three Distant Brown Dwarfs
+Masquerading as NIRCam-selected Highly Reddened Active Galactic
+Nuclei**. *ApJL*, *957*(2), L27.
+<https://doi.org/10.3847/2041-8213/acfeec>
+
+Lian, J., & Luo, L. (2024). **The Thickness of Galaxy
+Disks from z = 5 to 0 Probed by JWST**. *ApJL*, *960*(2), L10.
+<https://doi.org/10.3847/2041-8213/ad1492>
+
+Markov, V., Gallerani, S., Ferrara, A., Pallottini, A., Parlanti, E., Di
+Mascia, F., Sommovigo, L., & Kohandel, M. (2024).
+**Dust attenuation evolution in *z* ∼ 2-12 JWST
+galaxies**. *arXiv e-Prints*, arXiv:2402.05996.
+<https://doi.org/10.48550/arXiv.2402.05996>
+
+Nanayakkara, T., Glazebrook, K., Jacobs, C., Kawinwanichakij, L.,
+Schreiber, C., Brammer, G., Esdaile, J., Kacprzak, G. G., Labbe, I.,
+Lagos, C., Marchesini, D., Marsan, Z. C., Oesch, P. A., Papovich, C.,
+Remus, R.-S., & Tran, K.-V. H. (2024). **A population
+of faint, old, and massive quiescent galaxies at 3 &lt;z &lt;4 revealed
+by JWST NIRSpec Spectroscopy**. *Scientific Reports*, *14*, 3724.
+<https://doi.org/10.1038/s41598-024-52585-4>
+
+Setton, D. J., Khullar, G., Miller, T. B., Bezanson, R., Greene, J. E.,
+Suess, K. A., Whitaker, K. E., Antwi-Danso, J., Atek, H., Brammer, G.,
+Cutler, S. E., Dayal, P., Feldmann, R., Furtak, L. J., Fujimoto, S.,
+Glazebrook, K., Goulding, A. D., Kokorev, V., Labbe, I., … Williams, C.
+C. (2024). **UNCOVER NIRSpec/PRISM Spectroscopy
+Unveils Evidence of Early Core Formation in a Massive, Centrally Dusty
+Quiescent Galaxy at *z*<sub>*s**p**e**c*</sub> = 3.97**. *arXiv
+e-Prints*, arXiv:2402.05664. <https://doi.org/10.48550/arXiv.2402.05664>
+
+Sharma, G., Freundlich, J., van de Ven, G., Famaey, B., Salucci, P.,
+Martorano, M., & Renaud, F. (2023). **Dark Matter
+Fraction in Disk-Like Galaxies Over the Past 10 Gyr**. *arXiv
+e-Prints*, arXiv:2309.04541. <https://doi.org/10.48550/arXiv.2309.04541>
+
+Terp, C., Heintz, K. E., Watson, D., Brammer, G., Carnall, A., Witstok,
+J., Smit, R., & Vejlgaard, S. (2024). **Uncovering
+the physical origin of the prominent Lyman-*α* emission and absorption
+in GS9422 at *z* = 5.943**. *arXiv e-Prints*, arXiv:2404.06543.
+<https://doi.org/10.48550/arXiv.2404.06543>
+
+Triani, D. P., Di Stefano, R., & Kewley, L. J. (2024).
+**The significant contribution of supersoft X-ray
+Sources to the nebular HeII line emission**. *arXiv e-Prints*,
+arXiv:2405.08121. <https://doi.org/10.48550/arXiv.2405.08121>
+
+Valentino, F., Brammer, G., Gould, K. M. L., Kokorev, V., Fujimoto, S.,
+Jespersen, C. K., Vijayan, A. P., Weaver, J. R., Ito, K., Tanaka, M.,
+Ilbert, O., Magdis, G. E., Whitaker, K. E., Faisst, A. L., Gallazzi, A.,
+Gillman, S., Giménez-Arteaga, C., Gómez-Guijarro, C., Kubo, M., … Toft,
+S. (2023). **An Atlas of Color-selected Quiescent
+Galaxies at z &gt; 3 in Public JWST Fields**. *ApJ*, *947*(1), 20.
+<https://doi.org/10.3847/1538-4357/acbefa>
+
+Vikaeus, A., Zackrisson, E., Wilkins, S., Nabizadeh, A., Kokorev, V.,
+Abdurro’uf, Bradley, L. D., Coe, D., Dayal, P., & Ricotti, M. (2024).
+**To be, or not to be: Balmer breaks in high-z
+galaxies with JWST**. *529*(2), 1299–1307.
+<https://doi.org/10.1093/mnras/stae323>
+
+Wang, B., de Graaff, A., Davies, R. L., Greene, J. E., Leja, J.,
+Goulding, A. D., Williams, C. C., Brammer, G. B., Suess, K. A., Weibel,
+A., Bezanson, R., Boogaard, L. A., Cleri, N. J., Hirschmann, M., Katz,
+H., Labbe, I., Maseda, M. V., Matthee, J., McConachie, I., … Whitaker,
+K. E. (2024). **RUBIES: JWST/NIRSpec Confirmation of
+an Infrared-luminous, Broad-line Little Red Dot with an Ionized
+Outflow**. *arXiv e-Prints*, arXiv:2403.02304.
+<https://doi.org/10.48550/arXiv.2403.02304>
+
+Wang, B., Leja, J., de Graaff, A., Brammer, G. B., Weibel, A., van
+Dokkum, P., Baggen, J. F. W., Suess, K. A., Greene, J. E., Bezanson, R.,
+Cleri, N. J., Hirschmann, M., Labbe, I., Matthee, J., McConachie, I.,
+Naidu, R. P., Nelson, E., Oesch, P. A., Setton, D. J., & Williams, C. C.
+(2024). **RUBIES: Evolved Stellar Populations with
+Extended Formation Histories at *z* ∼ 7 − 8 in Candidate Massive
+Galaxies Identified with JWST/NIRSpec**. *arXiv e-Prints*,
+arXiv:2405.01473. <https://doi.org/10.48550/arXiv.2405.01473>
+
+Wang, T., Sun, H., Zhou, L., Xu, K., Cheng, C., Li, Z., Chen, Y., Mo, H.
+J., Dekel, A., Zheng, X., Cai, Z., Yang, T., Dai, Y.-S., Elbaz, D., &
+Huang, J.-S. (2024). **The true number density of
+massive galaxies in the early Universe revealed by JWST/MIRI**.
+*arXiv e-Prints*, arXiv:2403.02399.
+<https://doi.org/10.48550/arXiv.2403.02399>
+
+Weibel, A., Oesch, P. A., Barrufet, L., Gottumukkala, R., Ellis, R. S.,
+Santini, P., Weaver, J. R., Allen, N., Bouwens, R., Bowler, R. A. A.,
+Brammer, G., Carnall, A. C., Cullen, F., Dayal, P., Donnan, C. T.,
+Dunlop, J. S., Giavalisco, M., Grogin, N. A., Illingworth, G. D., …
+Xiao, M. (2024). **Galaxy Build-up in the first 1.5
+Gyr of Cosmic History: Insights from the Stellar Mass Function at
+*z* ∼ 4 − 9 from JWST NIRCam Observations**. *arXiv e-Prints*,
+arXiv:2403.08872. <https://doi.org/10.48550/arXiv.2403.08872>
+
+Withers, S., Muzzin, A., Ravindranath, S., Sarrouh, G. T. E., Abraham,
+R., Asada, Y., Bradač, M., Brammer, G., Desprez, G., Iyer, K., Martis,
+N., Mowla, L., Noirot, G., Sawicki, M., Strait, V., & Willott, C. J.
+(2023). **Spectroscopy from Photometry: A Population
+of Extreme Emission Line Galaxies at 1.7 ≲ z ≲ 6.7 Selected with JWST
+Medium Band Filters**. *ApJL*, *958*(1), L14.
+<https://doi.org/10.3847/2041-8213/ad01c0>
+
+Wright, L., Whitaker, K. E., Weaver, J. R., Cutler, S. E., Wang, B.,
+Carnall, A., Suess, K. A., Bezanson, R., Nelson, E., Miller, T. B., Ito,
+K., & Valentino, F. (2024). **Remarkably Compact
+Quiescent Candidates at 3 &lt; z &lt; 5 in JWST-CEERS**. *ApJL*,
+*964*(1), L10. <https://doi.org/10.3847/2041-8213/ad2b6d>
+
+Xu, D., & Yu, S.-Y. (2024). **JWST reveals a high
+fraction of disk breaks at 1 ≤ z ≤ 3**. *Astronomy & Astrophysics*,
+*682*, L17. <https://doi.org/10.1051/0004-6361/202449252>

_includes/bibliography/readme.md

@@ -0,0 +1,6 @@
+Workflow:
+=========
+
+  1. Add BibTeX entries to `papers.bib`
+  2. Run `bash build.sh` (requires pandocs)
+  3. Commit changes to papers.bib and ../_includes/papers.md

about/publications.md

@@ -7,4 +7,6 @@ navigation_weight: 14
 
 Are there more? Send them through a <a href="https://github.com/dawn-cph/dja/"> Pull Request </a>!
 
-{% bibliography %}
+<!-- Run `bash build.sh in _includes/bibliography/` to generate papers.md -->
+
+{% include bibliography/papers.md %}