From a3ebf3e183133bba5791488d15df639e7b0391a2 Mon Sep 17 00:00:00 2001 From: patnr Date: Fri, 1 Nov 2024 16:17:00 +0100 Subject: [PATCH] Dont escape all kinds of characters --- docs/bib/bib2md.py | 7 +++ docs/references.md | 120 ++++++++++++++++++++++----------------------- 2 files changed, 67 insertions(+), 60 deletions(-) diff --git a/docs/bib/bib2md.py b/docs/bib/bib2md.py index c6e3534f..4ef560ab 100644 --- a/docs/bib/bib2md.py +++ b/docs/bib/bib2md.py @@ -2,11 +2,18 @@ from pathlib import Path +import pybtex.backends.markdown as fmt from pybtex.database import parse_string from pybtex.richtext import Tag, Text from pybtex.style.formatting.unsrt import Style as UnsrtStyle from pybtex.style.formatting.unsrt import field, sentence +fmt.SPECIAL_CHARS.remove("[") +fmt.SPECIAL_CHARS.remove("]") +fmt.SPECIAL_CHARS.remove("(") +fmt.SPECIAL_CHARS.remove(")") +fmt.SPECIAL_CHARS.remove("-") + HERE = Path(__file__).parent diff --git a/docs/references.md b/docs/references.md index c580e9bb..806aa014 100644 --- a/docs/references.md +++ b/docs/references.md @@ -3,79 +3,79 @@ Patrick N\. Raanes\. *Improvements to Ensemble Methods for Data Assimilation in the Geosciences*\. PhD thesis, University of Oxford, January 2016\. -\\url https://ora\.ox\.ac\.uk/objects/uuid:9f9961f0\-6906\-4147\-a8a9\-ca9f2d0e4a12\. +\\url https://ora\.ox\.ac\.uk/objects/uuid:9f9961f0-6906-4147-a8a9-ca9f2d0e4a12\. ### `bocquet2010a` Marc Bocquet, Carlos A\. Pires, and Lin Wu\. `"Beyond Gaussian statistical modeling in geophysical data assimilation"`\. -*Monthly Weather Review*, 138\(8\):2997–3023, 2010\. +*Monthly Weather Review*, 138(8):2997–3023, 2010\. ### `bocquet2015` Marc Bocquet, Patrick N\. Raanes, and Alexis Hannart\. `"Expanding the validity of the ensemble Kalman filter without the intrinsic need for inflation"`\. -*Nonlinear Processes in Geophysics*, 22\(6\):645–662, 2015\. +*Nonlinear Processes in Geophysics*, 22(6):645–662, 2015\. ### `sakov2008a` Pavel Sakov and Peter R\. Oke\. `"Implications of the form of the ensemble transformation in the ensemble square root filters"`\. -*Monthly Weather Review*, 136\(3\):1042–1053, 2008\. +*Monthly Weather Review*, 136(3):1042–1053, 2008\. ### `wiljes2016` Jana de Wiljes, Walter Acevedo, and Sebastian Reich\. -`"Second\-order accurate ensemble transform particle filters"`\. +`"Second-order accurate ensemble transform particle filters"`\. *arXiv preprint arXiv:1608\.08179*, 2016\. ### `bocquet2011` Marc Bocquet\. `"Ensemble Kalman filtering without the intrinsic need for inflation"`\. -*Nonlinear Processes in Geophysics*, 18\(5\):735–750, 2011\. +*Nonlinear Processes in Geophysics*, 18(5):735–750, 2011\. ### `hoteit2015a` -I\. Hoteit, D\.\-T\. Pham, M\. E\. Gharamti, and X\. Luo\. +I\. Hoteit, D\.-T\. Pham, M\. E\. Gharamti, and X\. Luo\. `"Mitigating observation perturbation sampling errors in the stochastic EnKF"`\. -*Monthly Weather Review*, 143\(7\):2918–2936, 2015\. +*Monthly Weather Review*, 143(7):2918–2936, 2015\. ### `bocquet2013` Marc Bocquet and Pavel Sakov\. `"Joint state and parameter estimation with an iterative ensemble Kalman smoother"`\. -*Nonlinear Processes in Geophysics*, 20\(5\):803–818, 2013\. +*Nonlinear Processes in Geophysics*, 20(5):803–818, 2013\. ### `hunt2007` Brian R\. Hunt, Eric J\. Kostelich, and Istvan Szunyogh\. `"Efficient data assimilation for spatiotemporal chaos: a local ensemble transform Kalman filter"`\. -*Physica D: Nonlinear Phenomena*, 230\(1\):112–126, 2007\. +*Physica D: Nonlinear Phenomena*, 230(1):112–126, 2007\. ### `karspeck2007` Alicia R\. Karspeck and Jeffrey L\. Anderson\. `"Experimental implementation of an ensemble adjustment filter for an intermediate ENSO model"`\. -*Journal of Climate*, 20\(18\):4638–4658, 2007\. +*Journal of Climate*, 20(18):4638–4658, 2007\. ### `todter2015a` Julian Tödter and Bodo Ahrens\. -`"A second\-order exact ensemble square root filter for nonlinear data assimilation"`\. -*Monthly Weather Review*, 143\(4\):1347–1367, 2015\. +`"A second-order exact ensemble square root filter for nonlinear data assimilation"`\. +*Monthly Weather Review*, 143(4):1347–1367, 2015\. ### `chen2003` Zhe Chen\. `"Bayesian filtering: from Kalman filters to particle filters, and beyond"`\. -*Statistics*, 182\(1\):1–69, 2003\. +*Statistics*, 182(1):1–69, 2003\. ### `bocquet2012a` Marc Bocquet and Pavel Sakov\. -`"Combining inflation\-free and iterative ensemble Kalman filters for strongly nonlinear systems"`\. -*Nonlinear Processes in Geophysics*, 19\(3\):383–399, 2012\. +`"Combining inflation-free and iterative ensemble Kalman filters for strongly nonlinear systems"`\. +*Nonlinear Processes in Geophysics*, 19(3):383–399, 2012\. ### `doucet2001sequential` @@ -94,74 +94,74 @@ Springer, 2001\. Marc Bocquet and Pavel Sakov\. `"An iterative ensemble Kalman smoother"`\. -*Quarterly Journal of the Royal Meteorological Society*, 140\(682\):1521–1535, 2014\. +*Quarterly Journal of the Royal Meteorological Society*, 140(682):1521–1535, 2014\. ### `sakov2008b` Pavel Sakov and Peter R\. Oke\. `"A deterministic formulation of the ensemble Kalman filter: an alternative to ensemble square root filters"`\. -*Tellus A*, 60\(2\):361–371, 2008\. +*Tellus A*, 60(2):361–371, 2008\. ### `zupanski2005` Milija Zupanski\. `"Maximum likelihood ensemble filter: theoretical aspects"`\. -*Monthly Weather Review*, 133\(6\):1710–1726, 2005\. +*Monthly Weather Review*, 133(6):1710–1726, 2005\. ### `sakov2012a` Pavel Sakov, Dean S\. Oliver, and Laurent Bertino\. `"An iterative EnKF for strongly nonlinear systems\."`\. -*Monthly Weather Review*, 140\(6\):1988–2004, 2012\. +*Monthly Weather Review*, 140(6):1988–2004, 2012\. ### `evensen2009a` G\. Evensen\. `"The ensemble Kalman filter for combined state and parameter estimation"`\. -*Control Systems, IEEE*, 29\(3\):83–104, 2009\. +*Control Systems, IEEE*, 29(3):83–104, 2009\. ### `raanes2015a` Patrick Nima Raanes\. -`"On the ensemble Rauch\-Tung\-Striebel smoother and its equivalence to the ensemble Kalman smoother"`\. -*Quarterly Journal of the Royal Meteorological Society*, 142\(696\):1259–1264, 2016\. +`"On the ensemble Rauch-Tung-Striebel smoother and its equivalence to the ensemble Kalman smoother"`\. +*Quarterly Journal of the Royal Meteorological Society*, 142(696):1259–1264, 2016\. ### `anderson2010` Jeffrey L\. Anderson\. -`"A non\-Gaussian ensemble filter update for data assimilation\."`\. -*Monthly Weather Review*, 138\(11\):4186–4198, 2010\. +`"A non-Gaussian ensemble filter update for data assimilation\."`\. +*Monthly Weather Review*, 138(11):4186–4198, 2010\. ### `raanes2019` Patrick Nima Raanes, Andreas Størksen Stordal, and Geir Evensen\. `"Revising the stochastic iterative ensemble smoother"`\. -*Nonlinear Processes in Geophysics*, 26\(3\):325–338, 2019\. +*Nonlinear Processes in Geophysics*, 26(3):325–338, 2019\. ### `van2009` Peter Jan van Leeuwen\. `"Particle filtering in geophysical systems"`\. -*Monthly Weather Review*, 137\(12\):4089–4114, 2009\. +*Monthly Weather Review*, 137(12):4089–4114, 2009\. ### `raanes2019a` Patrick N\. Raanes, Marc Bocquet, and Alberto Carrassi\. `"Adaptive covariance inflation in the ensemble Kalman filter by Gaussian scale mixtures"`\. -*Quarterly Journal of the Royal Meteorological Society*, 145\(718\):53–75, 2019\. +*Quarterly Journal of the Royal Meteorological Society*, 145(718):53–75, 2019\. [doi:10\.1002/qj\.3386](https://doi.org/10.1002/qj.3386)\. ### `lei2011` Jing Lei and Peter Bickel\. -`"A moment matching ensemble filter for nonlinear non\-Gaussian data assimilation"`\. -*Monthly Weather Review*, 139\(12\):3964–3973, 2011\. +`"A moment matching ensemble filter for nonlinear non-Gaussian data assimilation"`\. +*Monthly Weather Review*, 139(12):3964–3973, 2011\. ### `wikle2007` C\. K\. Wikle and L\. M\. Berliner\. `"A Bayesian tutorial for data assimilation"`\. -*Physica D: Nonlinear Phenomena*, 230\(1\-2\):1–16, 2007\. +*Physica D: Nonlinear Phenomena*, 230(1-2):1–16, 2007\. ### `doucet2009` @@ -173,19 +173,19 @@ Arnaud Doucet and Adam M\. Johansen\. Marc Bocquet\. `"Localization and the iterative ensemble Kalman smoother"`\. -*Quarterly Journal of the Royal Meteorological Society*, 142\(695\):1075–1089, 2016\. +*Quarterly Journal of the Royal Meteorological Society*, 142(695):1075–1089, 2016\. ### `raanes2014` Patrick N\. Raanes, Alberto Carrassi, and Laurent Bertino\. `"Extending the square root method to account for model noise in the ensemble Kalman filter"`\. -*Monthly Weather Review*, 143\(10\):3857–3873, 2015\. +*Monthly Weather Review*, 143(10):3857–3873, 2015\. ### `lorenz1998` Edward N\. Lorenz and Kerry A\. Emanuel\. `"Optimal sites for supplementary weather observations: simulation with a small model"`\. -*Journal of the Atmospheric Sciences*, 55\(3\):399–414, 1998\. +*Journal of the Atmospheric Sciences*, 55(3):399–414, 1998\. ### `frei2013` @@ -203,24 +203,24 @@ Marco Frei and Hans R Künsch\. Takemasa Miyoshi\. `"The Gaussian approach to adaptive covariance inflation and its implementation with the local ensemble transform Kalman filter"`\. -*Monthly Weather Review*, 139\(5\):1519–1535, 2011\. +*Monthly Weather Review*, 139(5):1519–1535, 2011\. ### `mandel2016hybrid` J\. Mandel, E\. Bergou, S\. Gürol, S\. Gratton, and I\. Kasanický\. -`"Hybrid Levenberg\-Marquardt and weak\-constraint ensemble Kalman smoother method"`\. -*Nonlinear Processes in Geophysics*, 23\(2\):59–73, 2016\. +`"Hybrid Levenberg-Marquardt and weak-constraint ensemble Kalman smoother method"`\. +*Nonlinear Processes in Geophysics*, 23(2):59–73, 2016\. ### `anderson2009a` Jeffrey L\. Anderson\. `"Spatially and temporally varying adaptive covariance inflation for ensemble filters"`\. -*Tellus A*, 61\(1\):72–83, 2009\. +*Tellus A*, 61(1):72–83, 2009\. ### `bengtsson2003` Thomas Bengtsson, Chris Snyder, and Doug Nychka\. -`"Toward a nonlinear ensemble filter for high\-dimensional systems"`\. +`"Toward a nonlinear ensemble filter for high-dimensional systems"`\. *Journal of Geophysical Research: Atmospheres*, 2003\. ### `lorenz1996predictability` @@ -233,83 +233,83 @@ In *Proc\. ECMWF Seminar on Predictability*, volume 1, 1–18\. Reading, UK, 199 Daniel S\. Wilks\. `"Effects of stochastic parametrizations in the Lorenz'96 system"`\. -*Quarterly Journal of the Royal Meteorological Society*, 131\(606\):389–407, 2005\. +*Quarterly Journal of the Royal Meteorological Society*, 131(606):389–407, 2005\. ### `harty2021` Travis Harty, Matthias Morzfeld, and Chris Snyder\. -`"Eigenvector\-spatial localisation"`\. -*Tellus A: Dynamic Meteorology and Oceanography*, 73\(1\):1–18, 2021\. +`"Eigenvector-spatial localisation"`\. +*Tellus A: Dynamic Meteorology and Oceanography*, 73(1):1–18, 2021\. ### `rainwater2013` Sabrina Rainwater and Brian Hunt\. -`"Mixed\-resolution ensemble data assimilation"`\. -*Monthly weather review*, 141\(9\):3007–3021, 2013\. +`"Mixed-resolution ensemble data assimilation"`\. +*Monthly weather review*, 141(9):3007–3021, 2013\. ### `counillon2009a` François Counillon, Pavel Sakov, and Laurent Bertino\. -`"Application of a hybrid \`enkf\-oi\` to ocean forecasting"`\. -*Ocean Science*, 5\(4\):389–401, 2009\. +`"Application of a hybrid \`enkf-oi\` to ocean forecasting"`\. +*Ocean Science*, 5(4):389–401, 2009\. ### `pajonk2012a` Oliver Pajonk, Bojana V\. Rosić, Alexander Litvinenko, and Hermann G\. Matthies\. -`"A deterministic filter for non\-Gaussian Bayesian estimation—applications to dynamical system estimation with noisy measurements"`\. -*Physica D: Nonlinear Phenomena*, 241\(7\):775–788, 2012\. +`"A deterministic filter for non-Gaussian Bayesian estimation—applications to dynamical system estimation with noisy measurements"`\. +*Physica D: Nonlinear Phenomena*, 241(7):775–788, 2012\. ### `lorenz2005` Edward N\. Lorenz\. `"A look at some details of the growth of initial uncertainties"`\. -*Tellus A: Dynamic Meteorology and Oceanography*, 57\(1\):1–11, 2005\. +*Tellus A: Dynamic Meteorology and Oceanography*, 57(1):1–11, 2005\. ### `bocquet2019a` Marc Bocquet and Alban Farchi\. `"On the consistency of the local ensemble square root kalman filter perturbation update"`\. -*Tellus A: Dynamic Meteorology and Oceanography*, 71\(1\):1613142, 2019\. +*Tellus A: Dynamic Meteorology and Oceanography*, 71(1):1613142, 2019\. ### `lorenz1984` Edward N\. Lorenz\. `"Irregularity: a fundamental property of the atmosphere"`\. -*Tellus A*, 36\(2\):98–110, 1984\. +*Tellus A*, 36(2):98–110, 1984\. ### `vano2006` J\. A\. Vano, J\. C\. Wildenberg, M\. B\. Anderson, J\. K\. Noel, and J\. C\. Sprott\. -`"Chaos in low\-dimensional Lotka–Volterra models of competition"`\. -*Nonlinearity*, 19\(10\):2391, 2006\. +`"Chaos in low-dimensional Lotka–Volterra models of competition"`\. +*Nonlinearity*, 19(10):2391, 2006\. ### `emerick2012` Alexandre A\. Emerick and Albert C\. Reynolds\. -`"History matching time\-lapse seismic data using the ensemble Kalman filter with multiple data assimilations"`\. -*Computational Geosciences*, 16\(3\):639–659, 2012\. +`"History matching time-lapse seismic data using the ensemble Kalman filter with multiple data assimilations"`\. +*Computational Geosciences*, 16(3):639–659, 2012\. ### `pinheiro2019a` Flavia R\. Pinheiro, Peter J\. van Leeuwen, and Gernot Geppert\. `"Efficient nonlinear data assimilation using synchronization in a particle filter"`\. -*Quarterly Journal of the Royal Meteorological Society*, 145\(723\):2510–2523, 2019\. +*Quarterly Journal of the Royal Meteorological Society*, 145(723):2510–2523, 2019\. ### `vissio2020` Gabriele Vissio and Valerio Lucarini\. `"Mechanics and thermodynamics of a new minimal model of the atmosphere"`\. -*The European Physical Journal Plus*, 135\(10\):1–21, 2020\. +*The European Physical Journal Plus*, 135(10):1–21, 2020\. ### `grudzien2020a` Colin Grudzien, Marc Bocquet, and Alberto Carrassi\. -`"On the numerical integration of the lorenz\-96 model, with scalar additive noise, for benchmark twin experiments"`\. -*Geoscientific Model Development*, 13\(4\):1903–1924, 2020\. +`"On the numerical integration of the lorenz-96 model, with scalar additive noise, for benchmark twin experiments"`\. +*Geoscientific Model Development*, 13(4):1903–1924, 2020\. ### `lorenz2005a` Edward\. N\. Lorenz\. `"Designing chaotic models"`\. -*Journal of the Atmospheric Sciences*, 62\(5\):1574–1587, 2005\. +*Journal of the Atmospheric Sciences*, 62(5):1574–1587, 2005\.