Adding Docs Website to the Project

.github/workflows/ci.yml

@@ -0,0 +1,26 @@
+name: CI
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - docs
+    tags: '*'
+jobs:
+  docs:
+    name: Documentation
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+      - run: |
+          julia --project=docs -e '
+            using Pkg
+            Pkg.instantiate()'
+      - run: julia --project=docs docs/make.jl
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

docs/Project.toml

@@ -0,0 +1,5 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
+Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"

docs/make.jl

@@ -0,0 +1,37 @@
+using Documenter
+using DocumenterCitations
+using Literate
+
+bib_filepath = joinpath(dirname(@__FILE__), "references.bib")
+bib = CitationBibliography(bib_filepath, style=:authoryear)
+
+makedocs(bib;
+    doctest  = false,
+    format   = Documenter.HTML(collapselevel=1,prettyurls=false),
+    authors  = "Nathanael Wong <[email protected]>",
+    sitename = "ConvectionIsotopes",
+    pages    = [
+        "Introduction"        => "index.md",
+        # "WTG Schemes"         => "schemes.md",
+        # "Experimental Setups" => "setups.md",
+        # "Comparing WTG Schemes" => [
+        #     "Results"                      => "comparison/results.md",
+        #     "Vertical Mode Decomposiition" => "comparison/verticalmodes.md",
+        #     "Gross Moist Stability"        => "comparison/grossmoist.md",
+        # ],
+        # "Idealized Radiation vs RRTM" => [
+        #     "Results"                           => "radiation/results.md",
+        #     "Implications for Self-Aggregation" => "radiation/selfaggregation.md",
+        # ],
+        # "Convectively Coupled Waves?"=> [
+        #     "Results"              => "ccw/results.md",
+        #     "Diurnal vs Perpetual" => "ccw/diurnalcycle.md",
+        # ],
+        "References"          => "references.md"
+    ]
+)
+
+deploydocs(
+    repo = "github.com/natgeo-wong/ConvectionIsotopes.git",
+    devbranch = "docs"
+)

docs/references.bib

@@ -0,0 +1,208 @@
+@article{Yoshimura2008,
+   author = {K. Yoshimura and M. Kanamitsu and D. Noone and T. Oki},
+   doi = {10.1029/2008JD010074},
+   issn = {0148-0227},
+   issue = {D19},
+   journal = {Journal of Geophysical Research},
+   month = {10},
+   pages = {D19108},
+   title = {Historical isotope simulation using Reanalysis atmospheric data},
+   volume = {113},
+   year = {2008},
+}
+@article{Gonzalo2004,
+   author = {Gonzalo Miguez-Macho and Georgiy L. Stenchikov and Alan Robock},
+   doi = {10.1029/2003JD004495},
+   issn = {01480227},
+   issue = {D13},
+   journal = {Journal of Geophysical Research: Atmospheres},
+   month = {7},
+   pages = {n/a-n/a},
+   title = {Spectral nudging to eliminate the effects of domain position and geometry in regional climate model simulations},
+   volume = {109},
+   year = {2004},
+}
+@article{Lamraoui2018,
+   abstract = {<p>The present study explores the ability of the Weather Research and Forecasting (WRF) Model to accurately reproduce the passage of extratropical cold fronts at the DOE ARM eastern North Atlantic (ENA) observation site on the Azores. An analysis of three case studies is performed in which the impact of the WRF domain size, position of the model boundary relative to the ENA site, grid spacing, and spectral nudging conditions are explored. The results from these case studies indicate that model biases in the timing and duration of cold front passages change with the distance between the model domain boundary and the ENA site. For these three cases, if the western model boundary is farther than 1500 km from the site, the front becomes too meridional and fails to reach the site, making 1000 or 1500 km the optimal distances. In contrast, integrations with small distances (e.g., 500 km) between the site and domain boundaries have inadequate spatial spinup (i.e., the domain is too small for the model to properly stabilize). For all three cases, regardless of domain size, the model has biases in its upper-level circulation that impact the position and timing of the front. However, this issue is most serious for 4000-km2 domains and larger. For these domains, prolonged spectral nudging can correct cold front biases. As such, this analysis provides a framework to optimize the WRF Model configuration necessary for a realistic hindcast of a cold front passage at a fixed location centered in a domain as large as computationally possible.</p>},
+   author = {Fayçal Lamraoui and James F. Booth and Catherine M. Naud},
+   doi = {10.1175/MWR-D-17-0281.1},
+   issn = {0027-0644},
+   issue = {8},
+   journal = {Monthly Weather Review},
+   month = {8},
+   pages = {2417-2432},
+   title = {WRF Hindcasts of Cold Front Passages over the ARM Eastern North Atlantic Site: A Sensitivity Study},
+   volume = {146},
+   year = {2018},
+}
+@article{Zhang2017,
+   abstract = {A high-resolution regional atmospheric model is employed to project the late twenty-first-century changes of tropical cyclone (TC) activity over the western North Pacific (WP) and southwest Pacific (SP). The model realistically reproduces the basic features of the TC climatology in the present-day simulation. Future projections under the representative concentration pathway 4.5 (RCP45) and 8.5 (RCP85) scenarios are investigated. The results show no significant change of TC genesis frequency (TCGF) in the WP by RCP45 due to the cancellation of the reduction over the western part and the increase over the eastern part together with a considerable decrease of TCGF by RCP85 due to the excessive TCGF reduction in the western part. The TCGF over the SP consistently decreases from RCP45 to RCP85. Despite the fact that the simulated maximum surface wind speeds are below 52 m s <sup>−1</sup> , the change with more strong TCs and fewer weak TCs is robust. The future changes in the TC genesis locations and translational speeds modulate the TC lifetime and frequency of occurrence. The TC genesis potential index (GPI) is used to evaluate the projected TCGF changes. The results show that low-level vorticity and midtropospheric vertical velocity largely contribute to the reduction of GPI in the western part of the WP, while vertical wind shear and midtropospheric vertical velocity mainly contribute to the decrease of GPI over the SP. The weakening of the monsoon trough is found to be responsible for the decreases of GPI and TCGF over the western part of the WP.},
+   author = {Chunxi Zhang and Yuqing Wang},
+   doi = {10.1175/JCLI-D-16-0597.1},
+   issn = {0894-8755},
+   issue = {15},
+   journal = {Journal of Climate},
+   month = {8},
+   pages = {5923-5941},
+   title = {Projected Future Changes of Tropical Cyclone Activity over the Western North and South Pacific in a 20-km-Mesh Regional Climate Model},
+   volume = {30},
+   year = {2017},
+}
+@article{Zavisa1994,
+   author = {Zaviša I. Janjić},
+   doi = {10.1175/1520-0493(1994)122<0927:TSMECM>2.0.CO;2},
+   issn = {0027-0644},
+   issue = {5},
+   journal = {Monthly Weather Review},
+   month = {5},
+   pages = {927-945},
+   title = {The Step-Mountain Eta Coordinate Model: Further Developments of the Convection, Viscous Sublayer, and Turbulence Closure Schemes},
+   volume = {122},
+   year = {1994},
+}
+@inproceedings{Tewari2004,
+   author = {Mukul Tewari and F Chen and W Wang and Jimy Dudhia and M A LeMone and Kieran Mitchell and M Ek and G Gayno and Jerry Wegiel and R H Cuenca},
+   issue = {6},
+   journal = {20th conference on weather analysis and forecasting/16th conference on numerical weather prediction},
+   pages = {2165-2170},
+   title = {Implementation and verification of the unified NOAH land surface model in the WRF model},
+   volume = {1115},
+   year = {2004},
+}
+@article{,
+   author = {Zaviša I Janjić},
+   title = {Nonsingular implementation of the Mellor-Yamada level 2.5 scheme in the NCEP Meso model},
+   year = {2001},
+}
+@article{Iacono2008,
+   author = {Michael J. Iacono and Jennifer S. Delamere and Eli J. Mlawer and Mark W. Shephard and Shepard A. Clough and William D. Collins},
+   doi = {10.1029/2008JD009944},
+   issn = {0148-0227},
+   issue = {D13},
+   journal = {Journal of Geophysical Research},
+   month = {7},
+   pages = {D13103},
+   title = {Radiative forcing by long-lived greenhouse gases: Calculations with the AER radiative transfer models},
+   volume = {113},
+   year = {2008},
+}
+@article{Moore2016,
+   author = {M. Moore and P. N. Blossey and A. Muhlbauer and Z. Kuang},
+   doi = {10.1002/2015JD023763},
+   issn = {2169-897X},
+   issue = {12},
+   journal = {Journal of Geophysical Research: Atmospheres},
+   month = {6},
+   pages = {7235-7253},
+   title = {Microphysical controls on the isotopic composition of wintertime orographic precipitation},
+   volume = {121},
+   year = {2016},
+}
+@article{Dee2011,
+   author = {D. P. Dee and S. M. Uppala and A. J. Simmons and P. Berrisford and P. Poli and S. Kobayashi and U. Andrae and M. A. Balmaseda and G. Balsamo and P. Bauer and P. Bechtold and A. C. M. Beljaars and L. van de Berg and J. Bidlot and N. Bormann and C. Delsol and R. Dragani and M. Fuentes and A. J. Geer and L. Haimberger and S. B. Healy and H. Hersbach and E. V. Hólm and L. Isaksen and P. Kållberg and M. Köhler and M. Matricardi and A. P. McNally and B. M. Monge-Sanz and J.-J. Morcrette and B.-K. Park and C. Peubey and P. de Rosnay and C. Tavolato and J.-N. Thépaut and F. Vitart},
+   doi = {10.1002/qj.828},
+   issn = {00359009},
+   issue = {656},
+   journal = {Quarterly Journal of the Royal Meteorological Society},
+   month = {4},
+   pages = {553-597},
+   title = {The ERA-Interim reanalysis: configuration and performance of the data assimilation system},
+   volume = {137},
+   year = {2011},
+}
+@article{Uppala2005,
+   author = {S. M. Uppala and P. W. Kallberg and A. J. Simmons and U. Andrae and V. Da Costa Bechtold and M. Fiorino and J. K. Gibson and J. Haseler and A. Hernandez and G. A. Kelly and X. Li and K. Onogi and S. Saarinen and N. Sokka and R. P. Allan and E. Andersson and K. Arpe and M. A. Balmaseda and A. C. M. Beljaars and L. Van De Berg and J. Bidlot and N. Bormann and S. Caires and F. Chevallier and A. Dethof and M. Dragosavac and M. Fisher and M. Fuentes and S. Hagemann and E. Hólm and B. J. Hoskins and L. Isaksen and P. A. E. M. Janssen and R. Jenne and A. P. Mcnally and J.-F. Mahfouf and J.-J. Morcrette and N. A. Rayner and R. W. Saunders and P. Simon and A. Sterl and K. E. Trenberth and A. Untch and D. Vasiljevic and P. Viterbo and J. Woollen},
+   doi = {10.1256/qj.04.176},
+   issn = {00359009},
+   issue = {612},
+   journal = {Quarterly Journal of the Royal Meteorological Society},
+   month = {10},
+   pages = {2961-3012},
+   title = {The ERA-40 re-analysis},
+   volume = {131},
+   year = {2005},
+}
+@article{Lavers2022,
+   author = {David A. Lavers and Adrian Simmons and Freja Vamborg and Mark J. Rodwell},
+   doi = {10.1002/qj.4351},
+   issn = {0035-9009},
+   issue = {748},
+   journal = {Quarterly Journal of the Royal Meteorological Society},
+   month = {10},
+   pages = {3152-3165},
+   title = {An evaluation of ERA5 precipitation for climate monitoring},
+   volume = {148},
+   year = {2022},
+}
+@article{FuchsStone2020,
+   author = {Z. Fuchs‐Stone and D. J. Raymond and S. Sentic},
+   doi = {10.1029/2020GL087564},
+   issn = {0094-8276},
+   issue = {11},
+   journal = {Geophysical Research Letters},
+   month = {6},
+   title = {OTREC2019: Convection Over the East Pacific and Southwest Caribbean},
+   volume = {47},
+   year = {2020},
+}
+@inproceedings{Konecky2014a,
+   author = {Bronwen L Konecky and D C Noone and Jesse M Nusbaumer and Kim M Cobb},
+   journal = {AGU Fall Meeting Abstracts},
+   pages = {PP31D-1169},
+   title = {Enso and Indo-Pacific water isotopes: Observations, modeling, and implications for proxy reconstructions},
+   volume = {2014},
+   year = {2014},
+}
+@inproceedings{Nusbaumer2014b,
+   author = {Jesse M Nusbaumer and Tony E Wong and D C Noone},
+   journal = {AGU Fall Meeting Abstracts},
+   pages = {PP33F-04},
+   title = {The Impact of Differing Land Surface Models and Water Isotopic Parameterizations to the Distribution of Water Isotopes in a Coupled Atmosphere-Land Global Climate Model.},
+   volume = {2014},
+   year = {2014},
+}
+@article{Nusbaumer2016,
+   author = {Jesse M Nusbaumer},
+   title = {An examination of atmospheric river moisture transport and hydrology using isotope-enabled CAM5},
+   year = {2016},
+}
+@article{Blossey2010,
+   author = {Peter N. Blossey and Zhiming Kuang and David M. Romps},
+   doi = {10.1029/2010JD014554},
+   issn = {01480227},
+   issue = {D24},
+   journal = {Journal of Geophysical Research: Atmospheres},
+   month = {12},
+   title = {Isotopic composition of water in the tropical tropopause layer in cloud-resolving simulations of an idealized tropical circulation},
+   volume = {115},
+   year = {2010},
+}
+@article{Aggarwal2007,
+   author = {Pradeep K. Aggarwal and Oleg Alduchov and Luis Araguás Araguás and Shawan Dogramaci and Gernot Katzlberger and Karel Kriz and Kshitij M. Kulkarni and Türker Kurttas and Brent D. Newman and Alexander Purcher},
+   doi = {10.1029/2007EO490002},
+   issn = {00963941},
+   issue = {49},
+   journal = {Eos, Transactions American Geophysical Union},
+   month = {12},
+   pages = {537-538},
+   title = {New capabilities for studies using isotopes in the water cycle},
+   volume = {88},
+   year = {2007},
+}
+@article{Schotterer1996,
+   author = {Ulrich Schotterer and Frank Oldfield and Klaus Froehlich},
+   title = {GNIP: Global Network for Isotopes in Precipitation},
+   year = {1996},
+}
+@article{Torri2017,
+   author = {Giuseppe Torri and Ding Ma and Zhiming Kuang},
+   doi = {10.1002/2016JD026154},
+   issn = {2169-897X},
+   issue = {7},
+   journal = {Journal of Geophysical Research: Atmospheres},
+   month = {4},
+   pages = {3703-3717},
+   title = {Stable water isotopes and large‐scale vertical motions in the tropics},
+   volume = {122},
+   year = {2017},
+}

docs/src/index.md

@@ -0,0 +1,4 @@
+# [ConvectionIsotopes](https://github.com/natgeo-wong/ConvectionIsotopes)
+*Linking Isotopic Depletion of Precipitation to the Vertical Profiles of Convective Heating in the East Pacific using both Station Observations and Convective-Permitting Simulations*
+
+Text

docs/src/references.md

@@ -0,0 +1,4 @@
+# References
+
+```@bibliography
+```