text:
@string{PR =   "Phys. Rev."}
@string{PRL =   "Phys. Rev. Lett."}
@string{PRE =   "Phys. Rev. E"}
@string{PoP =   "Phys. Plasmas"}
@string{PoF =   "Phys. Fluids"}
@string{PFB =   "Phys. Fluids B"}
@string{NF =   "Nucl. Fusion"}
@string{PPCF =   "Plasma Phys. Controlled Fusion"}
@string{RMP =   "Rev. Mod. Phys."}
@string{CPP =   "Contrib. Plasma Phys."}
@string{CPP =   "Comp. Phys. Comm."}

@book{Jeff,
 author="{Freidberg, J.}",
 title="Plasma Physics and Fusion Energy",
 publisher="Cambridge University Press",
 address="Cambridge",
 year=2007
}

@book{Wakatani,
 author="{M. Wakatani}",
 title="Stellarator and Heliotron Devices",
 publisher="Oxford University Press",
 address="Oxford",
 year=1998
}

@book{PerBook,
 author="P Helander and D J Sigmar",
 title="Collisional Transport in Magnetized Plasmas",
 publisher="Cambridge University Press",
 address="Cambridge",
 year=2002
}

@Article{LHD,
 author="A Iiyoshi and M Fujiwara and O Motojima and N Ohyabu and K Yamazaki",
 journal =      "Fusion Tech.",
 year =         1990,
 volume =       17,
 pages =        169
}

@Article{W7X1,
 author="C D Beidler and G Grieger and F Herrnegger and W Harmeyer and J Kisslinger and W Lotz and H Maassberg and P Merkel and J {N\"{u}henberg} and F Rau and J Sapper and F Sardei and R Scardovelli and A {Schl\"{u}ter} and H Wobig",
 journal =      "Fusion Tech.",
 year =         1990,
 volume =       17,
 pages =        148
}

@Article{W7X2,
 author="G Grieger and C D Beidler and E Harmeyer and W Lotz and J Kisslinger and P Merkel and J N{\"{u}}hrenberg and F Rau and E Strumberger and H Wobig",
 journal =      "Fusion Tech.",
 year =         1992,
 volume =       21,
 pages =        1767
}

@Article{JOSE,
 author="J M {Garc\'{i}a-Rega\~{n}a} and R Kleiber and C D Beidler and Y Turkin and H Maassberg and P Helander",
 journal =      PPCF,
 year =         2013,
 volume =       55,
 pages =        074008
}

@Article{Turkin,
 author="Y Turkin and C D Beidler and H Maassberg and S Murakami and V Tribalos and A Wakasa",
 journal =      PoP,
 year =         2011,
 volume =       18,
 pages =        022505
}

@Article{Braun,
 author="S Braun and P Helander",
 journal =      PoP,
 year =         2010,
 volume =       17,
 pages =        072514
}

@Article{Galeev,
 author="A A Galeev and R Z Sagdeev and H P Furth and M N Rosenbluth",
 journal =      PRL,
 year =         1969,
 volume =       22,
 pages =        511
}

@Article{SnyderWilson,
 author="{Snyder P B and Wilson H R}",
 journal =      PPCF,
 year =         2003,
 volume =       45,
 pages =        1671
}
% title="Ideal magnetohydrodynamic constraints on the pedestal temperature in tokamaks",

@Article{NEOFP,
 author="E A Belli and J Candy",
 journal =      PPCF,
 year =         2012,
 volume =       54,
 pages =        015015
}
% title="Full linearized {F}okker-{P}lanck collisions in neoclassical transport simulations",

@Article{NEO1,
 author="{Belli E A and Candy J}",
 journal =      {AIP Conf. Prof.},
 volume = 1069,
 year =         2008,
 pages =        "15"
}
%@Article{NEO1,
% author="{Belli E A and Candy J}",
% journal =      {Theory of Fusion Plasmas, Joint Varenna-Lausanne Intl. Workshop},
% year =         2008,
% pages =        "CP1069"
%}
% title="Drift-kinetic simulations of neoclassical transport",

@Article{NEO2,
 author="{Belli E A and Candy J}",
 journal =      PPCF,
 year =         2008,
 volume =       50,
 pages =        095010
}
% title="Kinetic calculation of neoclassical transport including self-consistent electron and impurity dynamics",

@Article{NEO3,
 author="{Belli E A and Candy J}",
 journal =      PPCF,
 year =         2009,
 volume =       51,
 pages =        075018
}
% title="An {E}ulerian method for the solution of the multi-species drift-kinetic equation",

@Article{Kernbichler1,
 author="W Kernbichler and S V Kasilov and G O Leitold and V V Nemov and K Allmaier K",
 journal =      {33rd EPS Conference on Plasma Phys., Rome},
 year =         2006,
 volume =       {30I},
 pages =        {P-2.189}
}
% title="Computation of neoclassical transport in stellarators using the full linearized Coulomb collision operator",

@Article{Kernbichler2,
 author="W Kernbichler and S V Kasilov and G O Leitold and V V  Nemov  and K Allmaier",
 journal =      {Plasma Fusion Res.},
 year =         2008,
 volume =       3,
 pages =        "S1061"
}
% title="Computation of neoclassical transport in stellarators using the full linearized Coulomb collision operator",

@Article{HirshmanSigmar,
 author="{Hirshman S P and Sigmar D J}",
 journal =      PoF,
 year =         1976,
 volume =       19,
 pages =        1532
}
% title="Approximate {F}okker-{P}lanck collision operator for transport theory applications",

@Article{NCLASS,
 author="{Houlberg W A, Shaing K C, Hirshman S P and Zarnstorff M C}",
 journal =      PoP,
 year =         1997,
 volume =       4,
 pages =        3230
}
% title="Bootstrap current and neoclassical transport in tokamaks of arbitrary collisionality and aspect ratio",

@Article{DarinNotch,
 author="{Ernst D R, Bell M G, Bell R E, Bush C E, Chang Z, Fredrickson E, Grisham L R, Hill K W, Jassby D L, Mansfield D K, McCune D C, Park H K, Ramsey A T, Scott D S, Strachan J D, Synakowski E J, Taylor G, Thompson M and Weiland R M}",
 journal =      PoP,
 year =         1998,
 volume =       5,
 pages =        665
}
% title="Notched velocity profiles and the radial electric field in high ion temperature plasmas in the Tokamak Fusion Test Reactor",

@Article{GENESource,
 author="{Lapillonne X, McMillan B F, Gorler T, Brunner S, Dannert T, Jenko F, Merz F and Villard L}",
 journal =      PoP,
 year =         2010,
 volume =       17,
 pages =        112321
}
% title="Nonlinear quasisteady state benchmark of global gyrokinetic codes",

@Article{globalGENE,
 author="T Gorler and X Lapillonne and S Brunner and T Dannert and F Jenko and F Merz and D Told",
 journal =      JCP,
 year =         2011,
 volume =       230,
 pages =        7053
}
% title="Nonlinear quasisteady state benchmark of global gyrokinetic codes",

@Article{CattoTsang,
 author="{Catto P J and Tsang K T}",
 journal =      PoF,
 year =         1977,
 volume =       20,
 pages =        396
}
% title="Linearized gyro-kinetic equation with collisions",

@Article{Abel,
 author="{Abel I G, Barnes M, Cowley S C, Dorland W and Schekochihin A A}",
 journal =      PoP,
 year =         2008,
 volume =       15,
 pages =        122509
}
% title="Linearized model {F}okker-{P}lanck collision operators for gyrokinetic simulations. {I. T}heory",

@Article{Lin1,
 author="{Lin Z, Tang W M and Lee W W}",
 journal =      PoP,
 year =         1995,
 volume =       2,
 pages =        2975
}
% title="",

@Article{Lin2,
 author="{Lin Z, Tang W M and Lee W W}",
 journal =      PRL,
 year =         1997,
 volume =      78,
 pages =        456
}
% title="",

@Article{Wang1,
 author="{Wang W X, Hinton F L and Wong S K}",
 journal =      PRL,
 year =         2001,
 volume =      87,
 pages =        055002
}
% title="",

@Article{CSChang1,
 author="{Chang C S, Ku S and Weitzner H}",
 journal =      PoP,
 year =         2004,
 volume =      11,
 pages =        2649
}
% title="",

@Article{Wang2,
 author="{Wang W X, Tang W M, Hinton F L, Zakharov L E, White R B and Manickam J}",
 journal =      {Comp. Phys. Comm.},
 year =         2004,
 volume =      164,
 pages =        178
}
% title="",

@Article{CSChang2,
 author="{Chang C S and Ku S}",
 journal =      CPP,
 year =         2006,
 volume =      46,
 pages =        496
}
% title="",

@Article{Wang3,
 author="{Wang W X, Rewoldt G, Tang W M, Hinton F L, Manickam J, Zakharov L E, White R B and Kaye S}",
 journal =      PoP,
 year =         2006,
 volume =      13,
 pages =        082501
}
% title="",

@Article{Kolesnikov,
 author="{Kolesnikov R A, Wang W X, Hinton F L, Rewoldt G and Tang W M}",
 journal =      PoP,
 year =         2010,
 volume =      17,
 pages =        022506
}
% title="",

@Article{ORB5,
 author="{Vernay T, Brunner S, Villard L, McMillan B F, Jollier S, Tran T M, Bottino A and Graves J P}",
 journal =      PoP,
 year =         2010,
 volume =      17,
 pages =        122301
}
% title="Neoclassical equilibria as starting point for global gyrokinetic microturbulence simulations",

@Article{Xu1,
 author="{Xu X Q, Xiong Z, Dorr M R, Hittinger J A, Bodi K, Candy J, Cohen B I, Cohen R H, Colella P, Kerbel G D, Krasheninnikov S, Nevins W M, Qin H, Rognlien T D, Snyder P B and Umansky M V}",
 journal =      NF,
 year =         2007,
 volume =       47,
 pages =        809
}
% title="",

@Article{Xu2,
 author="{Xu X Q}",
 journal =      PRE,
 year =         2008,
 volume =       78,
 pages =        016406
}
% title="",

@Article{COGENT,
 author="{Cohen R H, Dorf M, Compton J C, Dorr M, Rognlien T D, Colella P, McCorquodale P, Angus J and Krasheninnikov S}",
 journal =      {Bull. Am. Phys. Soc},
 year =         2012,
 volume =       57,
 number = 3,
 pages =        {BAPS.2012.APR.S1.38}
}
% title="Neoclassical and Initial Divertor-Geometry Tests of COGENT",

@MISC{FelixPersonalCommunication,
  author =       "{Parra F I}",
  howpublished = {Personal communication},
}

@Article{JeffParker,
 author="{Parker J B and Catto P J}",
 journal = PPCF,
 volume = 54,
 pages = "085011",
 year=2012
}
% title="Variational Calculation of Neoclassical Ion Heat Flux in the Banana Regime for Arbitrary Magnetic Geometry",
% journal =      PoF,
% year =         1970,
% volume =       13,
% pages =        482

@Article{Rutherford,
 author="{Rutherford P H}",
 journal =      PoF,
 year =         1970,
 volume =       13,
 pages =        482
}
% title="Collisional diffusion in an axisymmetric torus",

@Article{Solomon,
 author="{Solomon W M, Burrell K H, Andre R, Baylor L R, Budny R, Gohil P, Groebner R J, Holcomb C T, Houlberg W A and Wade M R}",
 journal =      PoP,
 year =         2006,
 volume =       13,
 pages =        056116
}
% title="Experimental test of the neoclassical theory of impurity poloidal rotation in tokamaks",

@Article{NSTXFlowComparisons,
 author="{Bell R E, Andre R, Kaye S M, Kolesnikov R A, LeBlanc B P, Rewoldt G, Wang W X and Sabbagh S A}",
 journal =      PoP,
 year =         2010,
 volume =       17,
 pages =        082507
}
% title="Comparison of poloidal velocity measurements to neoclassical theory on the National Spherical Torus Experiment",

@Article{Kenny2,
 author="{Kagan G, Marr K D, Catto P J, Landreman M, Lipschultz B and McDemott R}",
 journal =      PPCF,
 year =         2011,
 volume =       53,
 pages =        025008
}
% title="The effect of the radial electric field on neoclassical flows in a tokamak pedestal",

@Article{Kenny1,
 author="{Marr K D, Lipschultz B, Catto P J, McDermott R M, Reinke M L and Simakov A N}",
 journal =      PPCF,
 year =         2010,
 volume =       52,
 pages =        055010
}
% title="Comparison of neoclassical predictions with measured flows and evaluation of a poloidal impurity density asymmetry",

@Article{OldDIIIDFlows,
 author="{Kim J, Burrell K H, Gohil P, Groebner R J, Kim Y-B, St John H E, Seraydarian R P and Wade M R}",
 journal =      PRL,
 year =         1994,
 volume =       72,
 pages =        2199
}
% title="Rotation characteristics of main ions and impurity ions in {H}-mode tokamak plasma",

@Article{JETFlows,
 author="{Crombe K, Andrew Y, Brix M, Giroud C, Hacquin S, Hawkes N C, Murari A, Nave M F F, Ongena J, Parail V, Van Oost G, Voitsekhovitch I and Zastrow K-D}",
 journal =      PRL,
 year =         2005,
 volume =       95,
 pages =        155003
}
% title="Poloidal Rotation Dynamics, Radial Electric Field, and Neoclassical Theory in the {JET} Internal-Transport-Barrier Region",

@Article{SimakovCattoSecondOrderDKE,
 author="A N Simakov and P J Catto",
 journal =      PoP,
 year =         2005,
 volume =       12,
 pages =        012105
}
% title="Drift kinetic equation exact through second order in gyroradius expansion",

@Article{RMJ,
 author="M N Rosenbluth and W M MacDonald and D L Judd",
 journal =      PR,
 year =         1957,
 volume =       107,
 pages =        1
}
% title="{F}okker-{P}lanck equation for an inverse-square force",

@Article{Felix,
 author="{Parra F I and Catto P J}",
 journal =      PPCF,
 year =         2008,
 volume =       50,
 pages =        065014
}
% title="Limitations of gyrokineics on transport time scales",

@Article{WongChan,
 author="S K Wong and V S Chan",
 journal =      PPCF,
 year =         2011,
 volume =       53,
 pages =        095005
}
% title="Numerical solution of neoclassical ion transport using the {F}okker-{P}lanck operator for Coulomb collisions",

@Article{ChangHinton,
 author="{Chang C S and Hinton F L}",
 journal =      PoF,
 year =         1982,
 volume =       25,
 pages =        1493
}
% title="Effect of finite aspect ratio on the neoclassical ion thermal conductivity in the banana regime",

@Article{Sauter0,
 author="O Sauter and R W Harvey and F L Hinton",
 journal =      "Contrib. Plasma Phys.",
 year =         1994,
 volume =       34,
 pages =        169
}
% title="A 3{D} {F}okker-{P}lanck code for studying parallel transport in tokamak geometry with arbitrary collisionalities and application to neoclassical resistivity",

@Article{Sauter1,
 author="{Sauter O, Lin-Liu Y R, Hinton F L and Vaclavik J}",
 journal =      {Proceedings of the Theory of Fusion Plasmas workshop, Varenna (Editrice Compositori E. Sindoni, Bologna)},
 year =         1994,
 pages =        337
}
% title="3{D} {F}okker-{P}lanck code valid for arbitrary collisionality and adjoint function for bootstrap current calculation",

@Article{Sauter,
 author="O Sauter and C Angioni and Y R Lin-Liu",
 journal =      PoP,
 year =         1999,
 volume =       6,
 pages =        2834
}
% title="Neoclassical conductivity and bootstrap current formulas for general axisymmetric equilibria and arbitrary collisionality regime",

@Article{Lyons,
 author="{Lyons B C, Jardin S C, and Ramos J J}",
 journal =      PoP,
 year =         2012,
 volume =       19,
 pages =        {082515}
}

@Article{LyonsAPS,
 author="{Lyons B C, Jardin S C, and Ramos J J}",
 journal =      "Bull. Am. Phys. Soc",
 year =         2011,
 volume =       56,
 pages =        {JP9.146}
}
% title="Numerical calculation of the neoclassical electron distribution function in an axisymmetric torus",

@Article{BoDarin,
 author="{Li B and Ernst D R }",
 journal =      PRL,
 year =         2011,
 volume =       106,
 pages =        195002
}
% title="Gyrokinetic {F}okker-{P}lanck Collision Operator",

@Article{CattoErnst,
 author="{Catto P J and Ernst D R }",
 journal =      PPCF,
 year =         2009,
 volume =       51,
 pages =        062001
}
% title="Alternate form of model like particle collision operator",

@Article{Grisha1,
 author="G Kagan G and P J Catto",
 journal =      PPCF,
 year =         2008,
 volume =       50,
 pages =        085010
}
% title="Arbitrary poloidal gyroradius effects in tokamak pedestals and transport barriers",

@Article{GrishaZF,
 author="{Kagan G and Catto P J}",
 journal =      PoP,
 year =         2009,
 volume =       16,
 pages =        056105
}
% title="Zonal flow in a tokamak pedestal",

@Article{GrishaNeo,
 author="G Kagan and P J Catto",
 journal =      PPCF,
 year =         2010,
 volume =       52,
 pages =        055004
}
% title="Neoclassical ion heat flux and poloidal flow in a tokamak pedestal",

@Article{GrishaNeoErratum,
 author="{Kagan G and Catto P J}",
 journal =      PPCF,
 year =         2010,
 volume =       52,
 pages =        079801
}
% title="Corrigendum: {N}eoclassical ion heat flux and poloidal flow in a tokamak pedestal",

@Article{GrishaPRL,
 author="{Kagan G and Catto P J}",
 journal =      PRL,
 year =         2010,
 volume =       105,
 pages =        045002
}
% title="Enhancement of the Bootstrap Current in a Tokamak Pedestal",

@Article{Istvan,
 author="{Pusztai I and Catto P J}",
 journal =      PPCF,
 year =         2010,
 volume =       52,
 pages =        075016
}
% title="Neoclassical plateau regime transport in a tokamak pedestal",

@Article{IstvanErratum,
 author="{Pusztai I and Catto P J}",
 journal =      PPCF,
 year =         2010,
 volume =       52,
 pages =        119801
}
% title="Corrigendum: {N}eoclassical plateau regime transport in a tokamak pedestal",

@Article{SugamaNishimura,
 author="H Sugama and S Nishimura",
 journal =      PoP,
 year =         2002,
 volume =       9,
 pages =        4637
}
% title="How to calculate the neoclassical viscosity, diffusion, and current coefficients in general toroidal plasmas",

@Article{SugamaNishimura2,
 author="H Sugama and S Nishimura",
 journal =      PoP,
 year =         2008,
 volume =       15,
 pages =        042502
}
% title="Moment-equation methods for calculating neoclassical transport coefficients in general toroidal plasmas",

@Article{PerAndreiPRL,
 author="P Helander and A N Simakov",
 journal =      PRL,
 year =         2008,
 volume =       101,
 pages =        145003
}
% title="Intrinsic Ambipolarity and Rotation in Stellarators",

@Article{CSPRL,
 author="{J. R. Cary and S. G. Shasharina}",
 journal =      PRL,
 year =         1997,
 volume =       78,
 pages =        647
}
% title="Helical Plasma Confinement Devices with Good Confinement Properties",

@Article{CSPoP,
 author="{J. R. Cary and S. G. Shasharina}",
 journal =      PoP,
 year =         1997,
 volume =       4,
 pages =        3323
}
% title="Omnigenity and quasihelicity in helical plasma confinement systems",

@Article{Subbotin,
 author="{A. A. Subbotin, M. I. Mikhailov, V. D. Shafranov, M. Yu. Isaev, C. N\"{u}hrenberg, J. N\"{u}hrenberg, R. Zille, V. V. Nemov, S. V. Kasilov, V. N. Kalyuzhnyj, and W. A. Cooper}",
 journal =      NF,
 year =         2006,
 volume =       46,
 pages =        921
}
% title=         "Integrated physics optimization of a quasi-isodynamic stellarator with poloidally closed contours of the magnetic field strength",

@Article{Gori,
 author="{Gori, S., Lotz, W., and N\"{u}hrenberg, J.}",
 journal =      "Theory of Fusion Plasmas (Bologna: Editrice Compositori)",
 year =         1996,
 pages =        335
}

@Article{Mikhailov,
 author="{Mikhailov, M. I., Shafranov, V. D.,  and N\"{u}hrenberg, J.}",
 journal =      "Plasma Phys. Rep.",
 year =         2009,
 volume =       35,
 pages =        529
}

@Article{hn,
 author="{P. Helander, and J. N\"{u}hrenberg}",
 journal =      PPCF,
 year =         2009,
 volume =       51,
 pages =        055004
}
% title="Bootstrap current and neoclassical transport in quasi-isodynamic stellarators",

@Article{HallMcNamara,
 author="{Hall, L. S., and McNamara, B.}",
 journal =      PoF,
 year =         1975,
 volume =       18,
 pages =        552
}
% title="Three-Dimensional Equilibrium of the Anisotropic, Finite-Pressure Guiding-Center Plasma: Theory of the Magnetic Plasma",

@Article{Boozer81,
 author="{A. H. Boozer}",
 journal =      PoF,
 year =         1981,
 volume =       24,
 pages =        1999
}

@Article{Boozer95,
 author="{A. H. Boozer}",
 journal =      PPCF,
 year =         1995,
 volume =       37,
 pages =        "A103"
}
% title="Quasi-Helical Symmetry in Stellarators",

@Article{Boozer98,
 author="{Boozer, A. H.}",
 journal =      PoP,
 year =         1998,
 volume =       5,
 pages =        1647
}
% title="What is a stellarator?",

@Article{Zille,
 author="{J. N\"{u}hrenberg and R. Zille}",
 journal =      "Phys. Lett. A",
 year =         1988,
 volume =       129,
 pages =        113
}
% title="Quasi-helically symmetric toroidal stellarators",

@Article{Boozer80,
 author="{Boozer, A. H.}",
 journal =      PoF,
 year =         1980,
 volume =       23,
 pages =        904
}
% title="Guiding center drift equations",

@Article{Pytte,
 author="{A. Pytte and A. H. Boozer}",
 journal =      PoF,
 year =         1981,
 volume =       24,
 pages =        88
}
% title="Neoclassical transport in helically symmetric plasmas",

@Article{Boozer82,
 author="{Boozer, A. H.}",
 journal =      PoF,
 year =         1982,
 volume =       25,
 pages =        520
}
% title="Establishment of Magnetic Coordinates for a Given Magnetic Field",

@Article{Boozer83,
 author="{A. H. Boozer}",
 journal =      PoF,
 year =         1983,
 volume =       26,
 pages =        496
}
% title="Transport and Isomorphic Equilibria",

@Article{Garren1,
 author="{Garren, D. A., and Boozer, A. H.}",
 journal =      PFB,
 year =         1991,
 volume =       3,
 pages =        2805
}
% title="Magnetic field strength of toroidal plasma equilibria",

@Article{Garren2,
 author="{Garren, D. A., and Boozer, A. H.}",
 journal =      PFB,
 year =         1991,
 volume =       3,
 pages =        2822
}
% title="Existence of Quasihelically Symmetric Stellarators",

% author="{M. C. Zarnstorff, L. A. Berry, A. Brooks, E. Fredrickson, G.-Y. Fu, S. Hirshman, S. Hudson, L.-P. Ku, E. Lazarus, D. Mikkelsen, D. Monticello, G. H. Neilson,
% N. Pomphrey, A. Reiman, D. Spong, D. Strickler, A. Boozer, W. A. Cooper, R. Goldston, R. Hatcher, M. Isaev, C. Kessel, J. Lewandowski, J. F. Lyon, P. Merkel,
% H. Mynick, B. E. Nelson, C. Nhrenberg, M. Redi, W. Reiersen, P. Rutherford, R. Sanchez, J. Schmidt, and R. B. White}",
@Article{NCSX,
 author = "{M. C. Zarnstorff, L. A. Berry, A. Brooks, E. Fredrickson, G.-Y. Fu, S. Hirshman, S. Hudson, L.-P. Ku,
 E. Lazarus, D. Mikkelsen, et al.}",
 journal =      PPCF,
 year =         2001,
 volume =       43,
 pages =        "A237"
}
% title=         "Physics of the compact advanced stellarator {NCSX}",

@Article{HSX,
 author="{F. Anderson, A. Almagri, D. Anderson, P. Matthews, J. Talmadge, and J. Shohet}",
 journal =      "Fusion Tech.",
 year =         1995,
 volume =       27,
 pages =        273
}

@Article{Briesemeister,
 author="A Briesemeister and  K Zhai and D T Anderson and F S B Anderson and J N Talmadge",
 journal =      PPCF,
 year =         2013,
 volume =       55,
 pages =        014002
}

@Book{Lotz,
 author="{Lotz, W., N\"{u}hrenberg, J., and Schwab, C.}",
 publisher="Proc. 13th Int. Conf. on Plasma Physics and Controlled Nuclear Fusion Research (Washington), Paper IAEA-CN-53-C-III-5, IAEA, Vienna",
 year=1991
}

@Article{Grieger,
 author="{Grieger, G., et al.}",
 journal =      PFB,
 year =         1992,
 volume =       4,
 pages =        2081
}
% title="Physics optimization of stellarators",

@Article{CattoHazeltine,
 author="{Catto, P. J., and Hazeltine, R. D.}",
 journal =      PFB,
 year =         1992,
 volume =       4,
 pages =        2081
}
% title="Omnigenous Equilibria",

@Article{Hirsch,
 author="{Hirsch, M., et al.}",
 journal =      PPCF,
 year =         2008,
 volume =       50,
 pages =        053001
}
% title="Major results from the stellarator {W}endelstein 7-{AS}",

@Article{HoKulsrud,
 author="D D-M Ho and R M Kulsrud",
 journal =      PoF,
 year =         1987,
 volume =       30,
 pages =        442
}
% title="Neoclassical transport in stellarators",

@Article{HelanderRotation,
 author="{P. Helander}",
 journal =      PoP,
 year =         2007,
 volume =       14,
 pages =        104501
}
% title="On rapid plasma rotation",

@Article{AndreiPer2011,
 author="A N Simakov and P Helander",
 journal =      PPCF,
 year =         2011,
 volume =       53,
 pages =        024005
}
% title="Plasma rotation in a quasi-symmetric stellarator",

@Article{AndreiPer2009,
 author="A N Simakov and P Helander",
 journal =      PoP,
 year =         2009,
 volume =       16,
 pages =        042503
}
% title="Neoclassical momentum transport in a collisional stellarator and a rippled tokamak",

@Article{Johnson,
 author="{J. L. Johnson, K. Ichiguchi, Y. Nakamura, M. Okamoto, M. Wakatani, and N. Nakajima}",
 journal =      PoP,
 year =         1999,
 volume =       6,
 pages =        2513
}
% title="External kink modes in a Large Helical Device {(LHD)} equilibrium with self-consistent bootstrap current",

@Article{JurgenQI,
 author="{J. N\"{u}hrenberg}",
 journal =      PPCF,
 year =         2010,
 volume =       52,
 pages =        124003
}
% title="Development of quasi-isodynamic stellarators",

@Article{Isaev,
 author="{Isaev, M. Yu., Mikhailov, M. I., and Shafranov, V. D.}",
 journal =      "Plasma Phys. Rep.",
 year =         1994,
 volume =       20,
 pages =        319
}
% title="Quasi-symmetric toroidal magnetic systems",

@Article{meQS,
 author="{M. Landreman and P. J. Catto}",
 journal =      PPCF,
 year =         2011,
 volume =       53,
 pages =        015004
}
% title="Effects of the radial electric field in a quasisymmetric stellarator",

@Article{meQI,
 author="{M. Landreman, and P. J. Catto}",
 journal =      PPCF,
 year =         2011,
 volume =       53,
 pages =        035016
}
% title="Neoclassical flow, current, and electric field in a quasi-isodynamic stellarator",

@Article{meMonoenergetic,
 author="{M Landreman}",
 journal =      PPCF,
 year =         2011,
 volume =       53,
 pages =        082003
}
% title="The monoenergetic approximation in stellarator neoclassical calculations",

@Article{Lore,
 author="J Lore and W Guttenfelder and A Briesemeister and D T Anderson and F S B Anderson and C B Deng and K M Likin and D A Spong and J N Talmadge and K Zhai",
 journal =      PoP,
 year =         2010,
 volume =       17,
 pages =        056101
}
% title="Internal electron transport barrier due to neoclassical ambipolarity in the {H}elically {S}ymmetric {E}xperiment",

@Article{Canik,
 author="{Canik, J. M. et al}",
 journal =      PRL,
 year =         2007,
 volume =       98,
 pages =        085002
}
% title="Experimental Demonstration of Improved Neoclassical Transport with Quasihelical Symmetry",

@Article{Gerhardt,
 author="{Gerhardt, S. P., Talmadge, J. N., Canik, J. M., and Anderson, D. T.}",
 journal =      PoP,
 year =         2005,
 volume =       12,
 pages =        056116
}
% title="Measurements and modeling of plasma flow damping in the {H}elically {S}ymmetric e{X}periment",

@Article{MynickReview,
 author="{H. E. Mynick}",
 journal =      PoP,
 year =         2006,
 volume =       13,
 pages =        058102
}
% title="Transport optimization in stellarators",

@Article{Garabedian1,
 author="{Garabedian, P. R.}",
 journal =      PoP,
 year =         1996,
 volume =       3,
 pages =        2483
}
% title="Stellarators with the magnetic symmetry of a tokamak",

@Article{Garabedian2,
 author="{Garabedian, P. R.}",
 journal =      PoP,
 year =         1997,
 volume =       4,
 pages =        1617
}
% title="Recent progress in the design of stellarator experiments",

@Article{Wobig,
 author="{Wobig, H.}",
 journal =      PPCF,
 year =         1999,
 volume =       41,
 pages =        "A159"
}
% title="Theory of advanced stellarators",

@Article{DKES1,
 author="S P Hirshman and K C Shaing and W I van Rij and C O {Beasley Jr.} and E C {Crume Jr.}",
 journal =      PoF,
 year =         1986,
 volume =       29,
 pages =        2951
}
% title="Plasma transport coefficients for nonsymmetric toroidal confinement systems",

@Article{DKES2,
 author="W I van Rij and S P Hirshman",
 journal =      PFB,
 year =         1989,
 volume =       1,
 pages =        563
}
% title="Variational bounds for transport coefficients in three-dimensional toroidal plasmas",

@Article{PENTA,
 author="D A Spong",
 journal =      PoP,
 year =         2005,
 volume =       12,
 pages =        056114
}
% title="Generation and damping of neoclassical plasma flows in stellarators",

@Article{QPS,
 author="{Spong, D. A., Hirshman, S. P., Berry, L. A., Lyon, J. F., Fowler, R. H., Strickler, D. J., Cole, M. J., Nelson, B., N., Williamson, D. E., Ware, A. S., Alban, D., Sanchez, R., Fu, G. Y., Monticello, D. A., Miner, W. H., and Valanju, P. M.}",
 journal =      NF,
 year =         2001,
 volume =       41,
 pages =        711
}
% title="Physics issues of compact drift optimized stellarators",

@Article{Maassberg,
 author="H Maassberg and C D Beidler and Y Turkin",
 journal =      PoP,
 year =         2009,
 volume =       16,
 pages =        072504
}
% title="Momentum correction techniques for neoclassical transport in stellarators",

@Article{Beidler,
 author="C D Beidler and M Yu Isaev and  S V Kasilov and  W Kernbichler and H Maassberg and S Murakami and V V Nemov and D A Spong V Tribaldos",
 journal =      "Proceedings of the 17th {I}nternational {T}oki {C}onference and 16th {I}nternational {S}tellarator/{H}eliotron {W}orkshop, {T}oki",
 year =         2007
}
% title="{ICNTS} - Impact of Incompressible {$\vect{E}\times\vect{B}$} Flow in Estimating Mono-Energetic Transport Coefficients",

@Article{Talmadge,
 author="{Talmadge, J. N., et al.}",
 journal =      "Plasma Fusion Res.",
 year =         2008,
 volume =       3,
 pages =        "S1002"
}
% title="Experimental tests of quasisymmetry in {HSX}",

@Article{TalmadgeGerhardt,
 author="{Talmadge, J. N., and Garhardt, S. P.}",
 journal =      PoP,
 year =         2005,
 volume =       12,
 pages =        072513
}
% title="Numerical calculation of the {H}amada basis vectors for three-dimensional toroidal magnetic configurations",

@Article{BeidlerW7X,
 author="{Beidler, C., et al.}",
 journal =      "Fusion Tech.",
 year =         1990,
 volume =       17,
 pages =        148
}
% title="Physics and engineering design for {W}endelstein {VII-X}",

@Article{HintonHazeltine,
 author="{Hinton F L and Hazeltine R D}",
 journal =      "Rev. Mod. Phys.",
 year =         1976,
 volume =       48,
 pages =        239
}
% title="Theory of plasma transport in toroidal confinement systems",

@Article{HintonWong,
 author="{Hinton, F. L., and Wong, S. K.}",
 journal =      PoF,
 year =         1985,
 volume =       28,
 pages =        3082
}
% title="Neoclassical ion transport in rotating axisymmetric plasmas",

@Article{CattoBernsteinTessarotto,
 author="{Catto P J, Bernstein I B and Tessarotto M}",
 journal =      PoF,
 year =         1987,
 volume =       30,
 pages =        2784
}
% title="Ion transport in toroidally rotating tokamak plasmas",

@Article{HazeltineHinton,
 author="{Hazeltine R D and Hinton F L}",
 journal =      PoP,
 year =         2005,
 volume =       12,
 pages =        102506
}
% title="Kinetic theory of flowing, magnetized plasma",

@Article{Brizard,
 author="{Brizard, A. J.}",
 journal =      PoP,
 year =         1995,
 volume =       2,
 pages =        459
}
% title="Nonlinear gyrokinetic {V}lasov equation for toroidally rotating axisymmetric tokamaks",

@Article{CaryBrizard,
 author="{Cary, J. R., and Brizard, A. J.}",
 journal =      RMP,
 year =         2009,
 volume =       81,
 pages =        693
}
% title="Hamiltonian theory of guiding-center motion",

@Article{Ramos,
 author="{Ramos, J. J.}",
 journal =      PoP,
 year =         2008,
 volume =       15,
 pages =        082106
}
% title="Finite-{L}armor-radius kinetic theory of a magnetized plasma in the macroscopic flow reference frame",

@Article{Taguchi,
 author="M Taguchi",
 journal =      PPCF,
 year =         1988,
 volume =       30,
 pages =        1897
}
% title="Ion thermal conductivity and ion distribution function in the banana regime",

@Article{Taguchi2,
 author="M Taguchi",
 journal =      PFB,
 year =         1992,
 volume =       4,
 pages =        3638
}
% title="A method for calculating neoclassical transport coefficients with momentum conserving collision operator",

@Article{RHH,
 author="{Rosenbluth M N, Hazeltine R D and Hinton F L}",
 journal =      PoF,
 year =         1972,
 volume =       15,
 pages =        116
}
% title="Plasma transport in toroidal confinement systems",

@Article{HR,
 author="{Hinton F L and Rosenbluth M N}",
 journal =      PoF,
 year =         1973,
 volume =       16,
 pages =        836
}
% title="Transport properties of a toroidal plasma at low to intermediate collision frequencies",

@Article{YokoyamaCERC,
 author="M Yokoyama and H Maassberg and C D Beidler and V Tribaldos and K Ida and T Estrada and F Castejon and A Fujisawa and T Minami and T Shimozuma and Y Takeiri and A Dinklage and S Murakami and H Yamada",
 journal =      NF,
 year =         2007,
 volume =       47,
 pages =        1213
}
% title="Core electron-root confinement ({CERC}) in helical plasmas",

@Article{Wagner,
 author="{Wagner, F., Hirsch, M., Hartfuss, H.-J., Laqua, H. P., and Maassberg, H.}",
 journal =      PPCF,
 year =         2006,
 volume =       48,
 pages =        "A217"
}
% title="H-mode and transport barriers in helical systems",

@Article{Akiyama,
 author="{Akiyama, T., Hirsch, M., Estrada, T., Hidalgo, C., and Mizuuchi, T.}",
 journal =      CPP,
 year =         2010,
 volume =       50,
 pages =        590
}
% title="Status of a Stellarator/Heliotron {H}-mode Database",

@Article{BoozerRMP,
 author="{Boozer, A.}",
 journal =      RMP,
 year =         2004,
 volume =       76,
 pages =        1071
}
% title="Physics of magnetically confined plasmas",

@Book{Bateman,
 author="{Bateman, G.}",
 title="MHD Instabilities",
 year =         1978,
 publisher =        "MIT Press",
 address="Cambridge, Mass."
}

@Article{Tribaldos2001,
 author="V Tribaldos",
 journal =      PoP,
 year =         2001,
 volume =       8,
 pages =        1229
}
% title="Monte Carlo estimation of neoclassical transport for the TJ-II stellarator",

@Article{Tribaldos,
 author="{Tribaldos, V., and Guasp, J.}",
 journal =      PPCF,
 year =         2005,
 volume =       47,
 pages =        545
}
% title="Neoclassical global flux simulations in stellarators",

@Article{Hazeltine,
 author="R D Hazeltine",
 journal =      "Plasma Phys.",
 year =         1973,
 volume =       15,
 pages =        77
}
% title="Recursive derivation of drift-kinetic equation",

@INPROCEEDINGS{tamm,
  AUTHOR =       {Tamm, I. E.},
  YEAR =         {1961},
  editor =       {M. A. Leontovich},
  volume =       {1},
  series =       {Plasma Physics and the problem of controlled thermonuclear reactions},
  pages =        {35},
  address =      {New York},
  publisher =    {Pergamon},
}

@Article{diamond,
 author="{Diamond, P. H., Itoh, S.-I., Itoh, K., and Hahm, T. S.}",
 journal =      PPCF,
 year =         2005,
 volume =       47,
 pages =        R35
}
% title="Zonal flows in plasma - a review",

@Article{rwm,
 author="{Fitzpatrick, R., and Aydemir, A. Y.}",
 journal =      NF,
 year =         1996,
 volume =       36,
 pages =        11
}
% title="Stabilization of the resistive shell mode in tokamaks",

@Article{sugama11,
 author="{H. Sugama, T. H. Watanabe, M. Nunami, and S. Nishimura}",
 journal =      PPCF,
 year =         2011,
 volume =       53,
 pages =        024004
}

@Article{SugamaHighFlow,
 author="H Sugama and T H Watanabe and M Nunami and S Nishimura",
 journal =      PPCF,
 year =         2011,
 volume =       53,
 pages =        024004
}

@Article{ISS04,
 author = "{H. Yamada, J.H. Harris, A. Dinklage, E. Ascasibar, F. Sano,
S. Okamura, J. Talmadge, U. Stroth, A. Kus, S. Murakami,
M.Yokoyama, C.D. Beidler, V. Tribaldos, K.Y. Watanabe
and Y. Suzuki}",
 journal = NF,
 year = 2005,
 volume = 45,
 pages = 1684
}

@Article{BoozerBootstrap,
 author="{A. H. Boozer and H. J. Gardner}",
 journal =      PFB,
 year =         1990,
 volume =       2,
 pages =        2408
}

@Article{ShaingCallen,
 author="{K. C. Shaing and J. D. Callen}",
 journal =      PoF,
 year =         1983,
 volume =       26,
 pages =        3315
}

@Article{ShaingRipple,
 author = "K. C. Shaing",
 journal = PoP,
 year = 2003,
 volume = 10,
 pages = 1443
 }

@Article{BeidlerBigBenchmarking,
 author="C. D. Beidler and K. Allmaier and M. Yu. Isaev and S. V. Kasilov and W. Kernbichler and G. O. Leitold and H. Maassberg and D. R. Mikkelsen and S. Murakami and M. Schmidt and D. A. Spong and V. Tribaldos and A. Wakasa",
 journal = NF,
 year=2011,
 volume=51,
 pages=076001
 }

@Article{ConnorHastie,
 author="{J. W. Connor and R. J. Hastie}",
 journal = NF,
 year = 1973,
 volume = 13,
 pages = 221
 }

@Article{MynickChuBoozer,
 author="{H. E. Mynick, T. K. Chu, and A. H. Boozer}",
 journal=PRL,
 year=1982,
 volume=48,
 pages=322
 }

@Article{Asakura,
 author="{N. Asakura, K. Shimizu, H. Shirai, Y. Koide and T. Takizuka}",
 journal=PPCF,
 year=1997,
 volume=39,
 pages=1295
 note = "Fig. 5c."
 }

@Article{GroebnerOsborne,
 author="{R. J. Groebner and T. H. Osborne}",
 journal=PoP,
 year=1998,
 volume=5,
 pages=1800,
 note = "Fig. 2."
 }

@Article{Maggi,
 author="{C.F. Maggi, R.J. Groebner, N. Oyama, R. Sartori, L.D. Horton, A.C.C. Sips,W. Suttrop and the ASDEX Upgrade Team, A. Leonard, T.C. Luce, M.R.Wade and the DIII-D Team, et al}",
 journal=NF,
 year=2007,
 volume=47,
 pages=535
 note = "Fig. 9."
 }
% author="{C.F. Maggi, R.J. Groebner, N. Oyama, R. Sartori, L.D. Horton, A.C.C. Sips,W. Suttrop and the ASDEX Upgrade Team,
% A. Leonard, T.C. Luce, M.R.Wade and the DIII-D Team, Y. Kamada, H. Urano and the JT-60U Team, Y. Andrew, C. Giroud, E. Joffrin, E. de la Luna and EFDA-JET Contributorsa for the Pedestal and Edge Physics and the Steady State Operation Topical Groups of the ITPA}",

@Article{Corre,
 author="{Y Corre, E Joffrin, P Monier-Garbet, Y Andrew, G Arnoux, M Beurskens, S Brezinsek, M Brix, R Buttery, I Coffey, et al}",
 journal=PPCF,
 year=2008,
 volume=50,
 pages=115012
 note = "Figs. 6, 8-9."
 }
% author="{Y Corre, E Joffrin, P Monier-Garbet, Y Andrew, G Arnoux, M Beurskens, S Brezinsek, M Brix, R Buttery, I Coffey, K Crombe, E de La Luna,
%R Felton, C Giroud, S Hacquin, J Hobirk, A Huber, F Imbeaux, S Jachmich, M Kempenaars, X Litaudon, H Leggate, T Loarer, G Maddison, E Rachlew, J Rapp, O Sauter, A Savchkov, G Telesca, A Widdowson, K D Zastrow, O Zimmermann and JET-EFDA collaborators}",

@Article{Sontag,
 author="{A.C. Sontag, J.M. Canik, R. Maingi, J. Manickam, P.B. Snyder, R.E. Bell, S.P. Gerhardt, S. Kubota, B.P. LeBlanc, D. Mueller, T.H. Osborne and K.L. Tritz}",
 journal=NF,
 year=2011,
 volume=51,
 pages=103022
 note = "Fig. 5."
 }

@Article{SauterProfiles,
 author="{P. Sauter, T. Putterich, F. Ryter, E. Viezzer, E. Wolfrum, G.D. Conway, R. Fischer, B. Kurzan, R.M. McDermott, S.K. Rathgeber and the ASDEX Upgrade Team}",
 journal=NF,
 year=2012,
 volume=52,
 pages=012001
 note = "Fig. 2."
 }

@Article{Maingi,
 author="{R. Maingi, D.P. Boyle, J.M. Canik, S.M. Kaye, C.H. Skinner, J.P. Allain, M.G. Bell, R.E. Bell, S.P. Gerhardt, T.K. Gray, et al}",
 journal=NF,
 year=2012,
 volume=52,
 pages=083001
 note = "Fig. 2a-2e."
 }
% author="{R. Maingi, D.P. Boyle, J.M. Canik, S.M. Kaye, C.H. Skinner, J.P. Allain, M.G. Bell, R.E. Bell, S.P. Gerhardt, T.K. Gray, M.A. Jaworski, R. Kaita, H.W. Kugel,
% B.P. LeBlanc, J. Manickam, D.K. Mansfield, J.E. Menard, T.H. Osborne, R. Raman, A.L. Roquemore, S.A. Sabbagh, P.B. Snyder and V.A. Soukhanovskii}",

@Article{Rachel,
 author="{R. M. McDermott, B. Lipschultz, J. W. Hughes, P. J. Catto, A. E. Hubbard, I. H. Hutchinson, R. S. Granetz, M. Greenwald, B. LaBombard, K. Marr, et al}",
 journal=PoP,
 year=2009,
 volume=16,
 pages=056103
 }

@Article{Putterich,
 author="{T. P\"utterich, E. Viezzer, R. Dux, R. M. McDermott, and the ASDEX Upgrade team}",
 journal=NF,
 volume=52,
 pages=083013,
 year=2012
 }

@Article{Groebner,
 author="{R. J. Groebner, T. H. Osborne, A. W. Leonard, and M. E. Fenstermacher1}",
 journal=NF,
 volume=49,
 pages=045013,
 year=2009
 }

@Article{Diallo,
 author="{A. Diallo, R. Maingi, S. Kubota, A. Sontag, T. Osborne, M. Podesta, R. E. Bell, B. P. LeBlanc, J. Menard, and S. Sabbagh}",
 journal=NF,
 volume=51,
 pages=103031,
 year=2011
 }

@INPROCEEDINGS{Morgan,
 author="{T. W. Morgan, H. Meyer, D. Temple, and G. J. Tallents}",
 BOOKTITLE="37th EPS Conf. Plasma Phys.",
 address="Dublin",
 pages={P5.122},
 year=2010
 }

@Article{Meyer,
 author="{H. Meyer, M. F. M. De Bock, N. J. Conway, S. J. Freethy, K. Gibson, J. Hiratsuka, A. Kirk, C. A. Michael, T. Morgan, R. Scannell, et al}",
 journal=NF,
 volume=51,
 pages=113011,
 year=2011
 }

@Article{Evans,
 author="{T. E. Evans, M. E. Fenstermacher, R. A. Moyer, T. H. Osborne, J. G. Watkins, P. Gohil, I. Joseph, M. J. Schaffer, L. R. Baylor, M. B\'ecoulet, et al}",
 journal=NF,
 volume=48,
 pages=024002,
 year=2008
 }
@Article{usPedestal,
 author="M Landreman and D R Ernst",
 journal=PPCF,
 title="Local and global {Fokker-Planck} neoclassical calculations showing flow and bootstrap current modification in a pedestal",
 volume="54",
 pages="115006",
 year=2012
 }

@Article{speedGrids,
 author="M Landreman and D R Ernst",
 journal=JCP,
 title="New velocity-space discretization for continuum kinetic calculations and Fokker-Planck collisions",
 volume = 243,
 pages="130-150",
 year=2013
 }

@Article{PERFECT,
 author="M Landreman and F I Parra and P J Catto and D R Ernst and I Pusztai",
 journal=PPCF,
 year=2014,
 volume=56,
 pages=045005
 }
% title="",

@book{Trefethen,
 author="L N Trefethen",
 title="Spectral methods in Matlab",
 publisher="SIAM",
 address="Philadelphia",
 year=2000
}

@Article{Miller,
 author="R L Miller and M S Chu and J M Greene and Y R Lin-Liu and R E Waltz",
 journal = PoP,
 volume = 5,
 pages = "973-978",
 year=1998
}
% title = "Noncircular, finite aspect ratio, local equilibrium model",

@Article{PerPotato,
 author="P Helander",
 journal = PoP,
 volume = 7,
 pages = 2878,
 year=2000
}

@Article{Felix2010,
 author="F I Parra and P J Catto",
 journal = PPCF,
 volume = 52,
 pages = 045004,
 year=2010
}

@Article{Dorf,
 author="M A Dorf and R H Cohen and M Dorr and T Rognlien and J Hittinger and J Compton and P Colella and D Martin and P McCorquodale",
 journal = PoP,
 volume = 20,
 pages = 012513,
 year=2013
}
% title = "Simulation of neoclassical transport with the continuum gyrokinetic code {COGENT}",

@Article{DorfEr,
 author="M Dorf and R H Cohen and A N Simakov and I Joseph",
 journal =      PoP,
 year =         2013,
 volume =       20,
 pages =        082515
}
% title="On the applicability of the standard approaches for evaluating a neoclassical radial electric field in a tokamak edge region",

@Article{Peter,
 author="P J Catto and Felix I Parra and Grigory Kagan and Jeffrey B Parker and Istvan Pusztai and Matt Landreman",
 journal = PPCF,
 volume=55,
 pages=045009,
 year=2013
}
% title = "",

@Article{finiteErOmnigenous,
 author="M Landreman and P J Catto",
 journal = PPCF,
 volume=55,
 pages=095017,
 year=2013
}
% title = "Conservation of energy and magnetic moment in neoclassical calculations for optimized stellarators",

@Article{XGCBootstrap,
 author="S Koh and C S Chang and S Ku and J E Menard and H Weitzner and W Choe",
 journal = PoP,
 volume=19,
 pages="072505",
 year=2012
}
% title = "",

@Article{FORTEC_PFR,
 author="S Satake and R Kanno and H Sugama",
 journal = "Plasma Fusion Res.",
 volume=3,
 pages="S1062",
 year=2008
}
% title = "",

@Article{FORTEC_CPC,
 author="S Satake and Y Idomura and H Sugama and T-H Watanabe",
 journal = CPC,
 volume=181,
 pages=1069,
 year=2010
}
% title = "",

@Article{GSRAKE,
 author="C D Beidler and W D D'haeseleer",
 journal = PPCF,
 volume=37,
 pages=463,
 year=1995
}
% title = "",

@Article{Baldzuhn,
 author="J Baldzuhn and M Kick and H Maassberg and {the W7-AS Team}",
 journal = PPCF,
 volume=40,
 pages=967,
 year=1998
}
% title = "",

@Article{GYROSources,
 author="R E Waltz and J M Candy and M N Rosenbluth",
 journal = PoP,
 volume=9,
 pages=1938,
 year=2002
}
% title = "",

@Article{BICGstabl,
 author="Gerard L. G. Sleijpen and Diederik R. Fokkema",
 journal="{Electr. Trans. Num. Anal.}",
 title="BICGstab(L) for linear equations involving unsymmetric matrices with complex spectrum",
 volume=1,
 pages="11-32",
 year=1993
 }

@Article{GMRES,
 author="Youcef Saad and Martin H Schultz",
 journal="{SIAM J. Sci. and Stat. Comput.}",
 volume=7,
 pages="856-869",
 year=1986
 }

 @article{MUMPS:1,
   author  = "P. R. Amestoy and I. S. Duff and J. Koster and J.-Y. L'Excellent",
   title   = {A Fully Asynchronous Multifrontal Solver Using Distributed Dynamic Scheduling},
   journal = {SIAM Journal on Matrix Analysis and Applications},
   volume  = {23},
   number  = {1},
   year    = {2001},
   pages   = {15-41}
 }

@article{MUMPS:2,
   author  = {P. R. Amestoy and A. Guermouche and J.-Y. L'Excellent and S. Pralet},
   title   = {Hybrid scheduling for the parallel solution of linear systems},
   journal = {Parallel Computing},
   volume  = {32},
   number  = {2},
   year    = {2006},
   pages   = {136-156}
}

   @Misc{petsc-web-page,
            Author = "Satish Balay and Jed Brown and Kris Buschelman and William D. Gropp and Dinesh Kaushik and Matthew G. Knepley and Lois Curfman McInnes and Barry F. Smith and Hong Zhang",
            Title = "{PETSc} {W}eb page",
            Note = "{http://www.mcs.anl.gov/petsc}",
            Year = "Accessed October 6, 2012"
          }

          @TechReport{petsc-user-ref,
            Author = "Satish Balay and Jed Brown and and Kris Buschelman and Victor Eijkhout and William D.  Gropp and Dinesh Kaushik and Matthew G. Knepley and Lois Curfman McInnes and Barry F. Smith and Hong Zhang",
            Title = "{PETS}c Users Manual",
            Number = "ANL-95/11 - Revision 3.3",
            Institution = "Argonne National Laboratory",
            Year = "2012"
          }

          @InProceedings{petsc-efficient,
            Author = "Satish Balay and William D. Gropp and Lois Curfman McInnes and Barry F.  Smith",
            Title = "Efficient Management of Parallelism in Object Oriented Numerical Software Libraries",
            Booktitle = "Modern Software Tools in Scientific Computing",
            Editor = "E. Arge and A. M. Bruaset and H. P. Langtangen",
            Pages = "163--202",
            Publisher = "Birkh{\"{a}}user Press",
            Year = "1997"
          }

@article{superlu2,
     author = {Xiaoye S. Li and James W. Demmel},
     title = {{SuperLU_DIST}: A Scalable Distributed-Memory Sparse Direct
              Solver for Unsymmetric Linear Systems},
     journal = {ACM Trans. Mathematical Software},
     month = {June},
     volume = {29},
     number = {2},
     pages = {110-140},
     year = 2003
}

@techreport{superlu1,
     AUTHOR = {X.S. Li and J.W. Demmel and J.R. Gilbert and L. Grigori and M. Shao and
          I. Yamazaki},
     INSTITUTION = {Lawrence Berkeley National Laboratory},
     NUMBER = {LBNL-44289},
     TITLE = {{SuperLU Users' Guide}},
     MONTH = {September},
     YEAR = {1999},
     NOTE = "\url{http://crd.lbl.gov/~xiaoye/SuperLU/}.
             Last update: August 2011"
}

repository: landreman/sfincs

repo_name: landreman/sfincs

gha_language: Fortran


text:
@article{del2011emerging,
 author = {del Campo, Javier and Massana, Ramon},
 journal = {Protist},
 number = {3},
 pages = {435--448},
 publisher = {Urban & Fischer},
 title = {Emerging Diversity within Chrysophytes, Choanoflagellates and Bicosoecids Based on Molecular Surveys},
 volume = {162},
 year = {2011}
}

license: MIT

repository: delCampoLab/academic-kickstart

license_type: permissive

repo_name: delCampoLab/academic-kickstart

branch_name: refs/heads/master

gha_license_id: MIT

extension: bib


text:
require zziplib.inc

SRC_URI += "file://zziplib-buildfix.patch"

SRC_URI[md5sum] = "4943ab7aa141af2c339266cd66b05c74"
SRC_URI[sha256sum] = "5cc1a53bb909922596bdd0fa967b654fe1bfbe0dcf1d34608f0b7c90e0c27867"

extension: bb


text:
require busybox.inc

SRC_URI = "http://www.busybox.net/downloads/busybox-${PV}.tar.bz2;name=tarball \
           file://get_header_tar.patch \
           file://busybox-appletlib-dependency.patch \
           file://busybox-udhcpc-no_deconfig.patch \
           file://find-touchscreen.sh \
           file://busybox-cron \
           file://busybox-httpd \
           file://busybox-udhcpd \
           file://default.script \
           file://simple.script \
           file://hwclock.sh \
           file://mount.busybox \
           file://syslog \
           file://syslog-startup.conf \
           file://syslog.conf \
           file://busybox-syslog.default \
           file://mdev \
           file://mdev.conf \
           file://mdev-mount.sh \
           file://umount.busybox \
           file://defconfig \
           file://busybox-syslog.service.in \
           file://busybox-klogd.service.in \
           file://fail_on_no_media.patch \
           file://run-ptest \
           file://inetd.conf \
           file://inetd \
           file://login-utilities.cfg \
           file://recognize_connmand.patch \
           file://busybox-cross-menuconfig.patch \
           file://CVE-2014-9645_busybox_reject_module_names_with_slashes.patch \
"

SRC_URI[tarball.md5sum] = "7925683d7dd105aabe9b6b618d48cc73"
SRC_URI[tarball.sha256sum] = "05a6f9e21aad8c098e388ae77de7b2361941afa7157ef74216703395b14e319a"

EXTRA_OEMAKE += "V=1 ARCH=${TARGET_ARCH} CROSS_COMPILE=${TARGET_PREFIX} SKIP_STRIP=y"

do_install_ptest () {
        cp -r ${B}/testsuite ${D}${PTEST_PATH}/
        cp ${B}/.config      ${D}${PTEST_PATH}/
        ln -s /usr/local/bin/busybox   ${D}${PTEST_PATH}/busybox
}

repository: openpch/openpch

repo_name: openpch/openpch


text:
#
# Base recipe: meta/recipes-graphics/xorg-app/xprop_1.2.2.bb
# Base branch: daisy
#

require xorg-app-common.inc

SUMMARY = "Utility to display window and font properties of an X server"

DESCRIPTION = "The xprop utility is for displaying window and font \
properties in an X server. One window or font is selected using the \
command line arguments or possibly in the case of a window, by clicking \
on the desired window. A list of properties is then given, possibly with \
formatting information."

PR = "${INC_PR}.0"

LIC_FILES_CHKSUM = "file://COPYING;md5=e226ab8db88ac0bc0391673be40c9f91"

DEPENDS += " libxmu"

DPN = "x11-utils"

# Apply debian patch by quilt
DEBIAN_PATCH_TYPE = "quilt"

S = "${DEBIAN_UNPACK_DIR}/${PN}"

repository: nghiaht-tsdv/meta-debian

repo_name: nghiaht-tsdv/meta-debian

branch_name: refs/heads/jethro

gha_language: BitBake


text:
package main

import (
	"context"
	"net"
	"net/http"

	"github.com/sirupsen/logrus"
	"github.com/spf13/viper"
)

// HTTPServerHandler encapsulates all required objects to manage an HTTP server instance.
type HTTPServerHandler struct {
	config    *viper.Viper
	dbHandler *DBHandler
	server    *http.Server
}

// NewHTTPServerHandler creates a new HTTPServerHandler with the supplied config and dbHandlers.
func NewHTTPServerHandler(config *viper.Viper, dbHandler *DBHandler) *HTTPServerHandler {
	instance := new(HTTPServerHandler)
	instance.config = config
	instance.dbHandler = dbHandler

	return instance
}

// StartServer creates and configures a new instance of an HTTP server to handle health check requests.
func (s *HTTPServerHandler) StartServer() {
	socket := net.JoinHostPort(s.config.GetString("http.addr"), s.config.GetString("http.port"))
	path := s.config.GetString("http.path")

	logrus.Debugf("Registering health check endpoint at URI path %s", path)

	router := http.NewServeMux()
	router.HandleFunc(path, s.serveHTTPHealthCheck)

	s.server = &http.Server{
		Addr:    socket,
		Handler: router,
	}

	logrus.Info("Starting HTTP server.")

	if err := s.server.ListenAndServe(); err != http.ErrServerClosed {
		logrus.Fatalf("Error opening HTTP socket: %v", err)
	}
}

// StopServer signals to the running HTTP server to complete existing requests and shut down gracefully.
func (s *HTTPServerHandler) StopServer() {
	ctx, cancel := context.WithTimeout(context.Background(), httpTimeout)
	defer cancel()

	s.server.SetKeepAlivesEnabled(false)

	if err := s.server.Shutdown(ctx); err != nil {
		logrus.Fatalf("Could not gracefully shutdown the HTTP server: %v", err)
	}

	logrus.Info("HTTP server stopped.")
}

func (s *HTTPServerHandler) serveHTTPHealthCheck(w http.ResponseWriter, req *http.Request) {
	if req.URL.Path != s.config.GetString("http.path") {
		http.NotFound(w, req)
		return
	}

	logrus.Debugf("Processing health check request from %s", req.RemoteAddr)
	w.Header().Add("Connection", "close")

	ready, msg := RunStatusCheck(s.dbHandler)
	if !ready {
		w.WriteHeader(http.StatusServiceUnavailable)
	}

	_, err := w.Write([]byte(msg))
	if err != nil {
		logrus.Errorf("Error writing data to HTTP response: %v", err)
	}
}

repository: YuhuaDeng/mysql-healthcheck

repo_name: YuhuaDeng/mysql-healthcheck

extension: go


text:
// Package app

// Copyright © 2021 zc2638 <zc2638@qq.com>.
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
//     http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
package app

import (
	"errors"
	"os"
	"path/filepath"

	"github.com/99nil/arceus/handler/resource"
	"github.com/spf13/cobra"
)

func applyCommand() *cobra.Command {
	var filePath string
	cmd := &cobra.Command{
		Use:   "apply",
		Short: "Apply arceus resources",
		RunE: func(cmd *cobra.Command, args []string) error {
			if filePath == "" {
				return errors.New("resource path not found")
			}
			stat, err := os.Stat(filePath)
			if err != nil {
				return err
			}

			if err := initConfig(); err != nil {
				return err
			}

			var fileURLs []string
			if stat.IsDir() {
				// 处理目录下所有文件
				dirs, err := os.ReadDir(filePath)
				if err != nil {
					return err
				}
				for _, dir := range dirs {
					if dir.IsDir() {
						continue
					}
					fileURLs = append(fileURLs, filepath.Join(filePath, dir.Name()))
				}
			} else {
				fileURLs = append(fileURLs, filePath)
			}
			return apply(fileURLs)
		},
	}
	cmd.Flags().StringVarP(&filePath, "file", "f", "", "resource file path")
	return cmd
}

// TODO 支持quickstart资源使用
// TODO 新增create替代，与quickstart命令相对应
// TODO 兼容API和CMD，定义interface
func apply(fileURLs []string) error {
	for _, url := range fileURLs {
		fileData, err := os.ReadFile(url)
		if err != nil {
			return err
		}
		if err := resource.UploadResource(fileData); err != nil {
			return err
		}
	}
	return nil
}

branch_name: refs/heads/main


text:
# Copyright (c) 2021 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

if(NOT WIN32 OR NOT MSVC)
    return()
endif()

include(ExternalProject)

set(DIRENT_PROJECT "extern_dirent")
set(DIRENT_PREFIX_DIR    ${THIRD_PARTY_PATH}/dirent)
set(DIRENT_INSTALL_ROOT  ${THIRD_PARTY_PATH}/install/dirent)
set(DIRENT_INC_DIR       ${DIRENT_INSTALL_ROOT}/include)
set(DIRENT_DOWNLOAD_DIR    ${DIRENT_PREFIX_DIR}/src/${DIRENT_PROJECT})

include_directories(${DIRENT_INC_DIR})

set(DIRENT_URL "http://paddle-inference-dist.bj.bcebos.com/PaddleLite_ThirdParty%2Fdirent-1.23.2.zip")
ExternalProject_Add(
    ${DIRENT_PROJECT}
    ${EXTERNAL_PROJECT_LOG_ARGS}
    DEPENDS             ""
    GIT_TAG             "v1.23.2"  # 9 May 2018
    URL                 ${DIRENT_URL}
    DOWNLOAD_DIR        ${DIRENT_DOWNLOAD_DIR}
    DOWNLOAD_NAME       "dirent-1.23.2.zip"
    DOWNLOAD_NO_PROGRESS 1
    PREFIX              ${DIRENT_PREFIX_DIR}
    UPDATE_COMMAND      ""
    CONFIGURE_COMMAND   ""
    BUILD_COMMAND       ""
    INSTALL_COMMAND
        ${CMAKE_COMMAND} -E copy_directory ${DIRENT_DOWNLOAD_DIR}/include ${DIRENT_INC_DIR}
)

add_library(dirent INTERFACE)
add_dependencies(dirent ${DIRENT_PROJECT})

repository: PaddlePaddle/Paddle-Lite

repo_name: PaddlePaddle/Paddle-Lite

branch_name: refs/heads/develop

extension: cmake


text:
package bq

import (
	"context"
	"fmt"
	"github.com/pkg/errors"
	"github.com/viant/bqtail/base"
	"github.com/viant/bqtail/shared"
	"google.golang.org/api/bigquery/v2"
	"time"
)

//Patch patch temp table
func (s *service) Patch(ctx context.Context, request *PatchRequest) (*bigquery.Table, error) {
	if err := request.Init(s.projectID); err != nil {
		return nil, err
	}
	if err := request.Validate(); err != nil {
		return nil, err
	}
	tableRef, err := base.NewTableReference(request.Table)
	if err != nil {
		return nil, errors.Wrapf(err, "invalid table: %v", request.Table)
	}
	if tableRef.ProjectId == "" {
		tableRef.ProjectId = s.ProjectID
	}

	if request.TemplateTable == nil {
		templateRef, err := base.NewTableReference(request.Template)
		if err != nil {
			return nil, errors.Wrapf(err, "invalid template table: %v", request.Template)
		}
		request.TemplateTable, err = s.Table(ctx, templateRef)
		if err != nil {
			return nil, errors.Wrapf(err, "invalid get template table: %v", request.Table)
		}
	}

	call := s.Service.Tables.Patch(tableRef.ProjectId, tableRef.DatasetId, tableRef.TableId, request.TemplateTable)
	call.Context(ctx)
	var table *bigquery.Table
	for i := 0; i < shared.MaxRetries; i++ {
		call.Context(ctx)
		if table, err = call.Do(); err == nil {
			return nil, err
		}
		if base.IsRetryError(err) {
			//do extra sleep before retrying
			time.Sleep(shared.RetrySleepInSec * time.Second)
			continue
		}
		break
	}
	return table, err
}

//PatchRequest represents an export request
type PatchRequest struct {
	Template      string
	Table         string
	TemplateTable *bigquery.Table
	ProjectID     string
}

//Init initialises request
func (r *PatchRequest) Init(projectID string) (err error) {
	if r.ProjectID != "" {
		projectID = r.ProjectID
	} else {
		r.ProjectID = projectID
	}
	return nil
}

//Validate checks if request is valid
func (r *PatchRequest) Validate() error {
	if r.Template == "" && r.TemplateTable == nil {
		return fmt.Errorf("template was empty")
	}
	if r.Table == "" {
		return fmt.Errorf("destination was empty")
	}
	return nil
}

repository: fhoffa/bqtail

repo_name: fhoffa/bqtail


text:
/*
 * Content Delivery Network
 *
 * No description provided (generated by Openapi Generator https://github.com/openapitools/openapi-generator)
 *
 * API version: 1.0.0
 * Generated by: OpenAPI Generator (https://openapi-generator.tech)
 */

package cdn

import (
	"encoding/json"
)

// CdnSiteCertificate An SSL certificate and its relationship with its associated site
type CdnSiteCertificate struct {
	// Whether or not a site's SSL certificate is valid  An SSL certificate is valid when a hostname associated with the site is covered by the certificate.
	Valid *bool `json:"valid,omitempty"`
	Certificate *CdnCertificate `json:"certificate,omitempty"`
}

// NewCdnSiteCertificate instantiates a new CdnSiteCertificate object
// This constructor will assign default values to properties that have it defined,
// and makes sure properties required by API are set, but the set of arguments
// will change when the set of required properties is changed
func NewCdnSiteCertificate() *CdnSiteCertificate {
	this := CdnSiteCertificate{}
	return &this
}

// NewCdnSiteCertificateWithDefaults instantiates a new CdnSiteCertificate object
// This constructor will only assign default values to properties that have it defined,
// but it doesn't guarantee that properties required by API are set
func NewCdnSiteCertificateWithDefaults() *CdnSiteCertificate {
	this := CdnSiteCertificate{}
	return &this
}

// GetValid returns the Valid field value if set, zero value otherwise.
func (o *CdnSiteCertificate) GetValid() bool {
	if o == nil || o.Valid == nil {
		var ret bool
		return ret
	}
	return *o.Valid
}

// GetValidOk returns a tuple with the Valid field value if set, nil otherwise
// and a boolean to check if the value has been set.
func (o *CdnSiteCertificate) GetValidOk() (*bool, bool) {
	if o == nil || o.Valid == nil {
		return nil, false
	}
	return o.Valid, true
}

// HasValid returns a boolean if a field has been set.
func (o *CdnSiteCertificate) HasValid() bool {
	if o != nil && o.Valid != nil {
		return true
	}

	return false
}

// SetValid gets a reference to the given bool and assigns it to the Valid field.
func (o *CdnSiteCertificate) SetValid(v bool) {
	o.Valid = &v
}

// GetCertificate returns the Certificate field value if set, zero value otherwise.
func (o *CdnSiteCertificate) GetCertificate() CdnCertificate {
	if o == nil || o.Certificate == nil {
		var ret CdnCertificate
		return ret
	}
	return *o.Certificate
}

// GetCertificateOk returns a tuple with the Certificate field value if set, nil otherwise
// and a boolean to check if the value has been set.
func (o *CdnSiteCertificate) GetCertificateOk() (*CdnCertificate, bool) {
	if o == nil || o.Certificate == nil {
		return nil, false
	}
	return o.Certificate, true
}

// HasCertificate returns a boolean if a field has been set.
func (o *CdnSiteCertificate) HasCertificate() bool {
	if o != nil && o.Certificate != nil {
		return true
	}

	return false
}

// SetCertificate gets a reference to the given CdnCertificate and assigns it to the Certificate field.
func (o *CdnSiteCertificate) SetCertificate(v CdnCertificate) {
	o.Certificate = &v
}

func (o CdnSiteCertificate) MarshalJSON() ([]byte, error) {
	toSerialize := map[string]interface{}{}
	if o.Valid != nil {
		toSerialize["valid"] = o.Valid
	}
	if o.Certificate != nil {
		toSerialize["certificate"] = o.Certificate
	}
	return json.Marshal(toSerialize)
}

type NullableCdnSiteCertificate struct {
	value *CdnSiteCertificate
	isSet bool
}

func (v NullableCdnSiteCertificate) Get() *CdnSiteCertificate {
	return v.value
}

func (v *NullableCdnSiteCertificate) Set(val *CdnSiteCertificate) {
	v.value = val
	v.isSet = true
}

func (v NullableCdnSiteCertificate) IsSet() bool {
	return v.isSet
}

func (v *NullableCdnSiteCertificate) Unset() {
	v.value = nil
	v.isSet = false
}

func NewNullableCdnSiteCertificate(val *CdnSiteCertificate) *NullableCdnSiteCertificate {
	return &NullableCdnSiteCertificate{value: val, isSet: true}
}

func (v NullableCdnSiteCertificate) MarshalJSON() ([]byte, error) {
	return json.Marshal(v.value)
}

func (v *NullableCdnSiteCertificate) UnmarshalJSON(src []byte) error {
	v.isSet = true
	return json.Unmarshal(src, &v.value)
}

repository: kraney/stackpath

repo_name: kraney/stackpath


text:
package main

import (
	"fmt"
	"math/rand"
	"net"
	"strconv"

	"flag"
	"time"

	"sync"

	"bytes"

	"github.com/wudaoluo/dcache/internal"
	"github.com/wudaoluo/dcache/socket"
)

var typ, server, operation string
var total, valueSize, threads, keyspacelen, pipelen int

func init() {
	//flag.StringVar(&typ, "type", "redis", "cache server type")
	flag.StringVar(&server, "h", "localhost", "cache server address")
	flag.IntVar(&total, "n", 1000, "total number of requests")
	flag.IntVar(&valueSize, "d", 1000, "data size of SET/GET value in bytes")
	flag.IntVar(&threads, "c", 1, "number of parallel connections")
	flag.StringVar(&operation, "t", "put", "test set, could be get/put/del")
	flag.IntVar(&keyspacelen, "r", 10000000000, "keyspacelen, use random keys from 0 to keyspacelen-1")
	//flag.IntVar(&pipelen, "P", 1, "pipeline length")
	flag.Parse()
	//fmt.Println("type is", typ)
	fmt.Println("server is", server)
	fmt.Println("total", total, "requests")
	fmt.Println("data size is", valueSize)
	fmt.Println("we have", threads, "connections")
	fmt.Println("operation is", operation)
	fmt.Println("keyspacelen is", keyspacelen)
	//fmt.Println("pipeline length is", pipelen)

	rand.Seed(time.Now().UnixNano())
}

func main() {
	ch := make(chan int, 100)
	go func() {
		for i := 0; i < total; i++ {
			ch <- i
		}
		close(ch)
	}()

	var wg = sync.WaitGroup{}
	start := time.Now()
	for i := 0; i < threads; i++ {
		wg.Add(1)
		go process(ch, &wg)
	}

	wg.Wait()
	d := time.Now().Sub(start)

	fmt.Printf("%f seconds total\n", d.Seconds())
	fmt.Printf("rps is %f\n", float64(total)/float64(d.Seconds()))
	fmt.Printf("throughput is %f MB/s\n", +float64(total*valueSize)/1e6/d.Seconds())
}

func process(ch chan int, wg *sync.WaitGroup) {
	defer wg.Done()
	conn, err := net.Dial("tcp", server)
	if err != nil {
		panic(err)
	}

	c := socket.NewTcpConn(conn)

	var op byte
	switch operation {
	case "put":
		op = internal.OP_REQ_PUT
	case "get":
		op = internal.OP_REQ_GET
	case "del":

		op = internal.OP_REQ_DEL

	}

	var data = &internal.Data{}
	value := bytes.Repeat([]byte("a"), valueSize)
	sig := make(chan struct{}, 100)

	go func(ch chan int) {
		defer func() {
			//sig <- struct{}{}
			close(sig)
		}()
		var d = &internal.Data{}
		for {
			_, ok := <-ch
			if !ok {
				//c.Close()
				//golog.Warn("ch close")
				return
			}

			d.Op = op
			d.Key = []byte(strconv.Itoa(rand.Intn(keyspacelen)))
			d.Value = value
			_, err = c.WriteMsg(d)
			if err != nil {
				fmt.Println("err", err)
				return
			}

			sig <- struct{}{}
		}

	}(ch)

	for range sig {
		err = c.ReadMsg(data)
		if err != nil {
			fmt.Println("err1", err)
			return
		}
	}

}

repository: wudaoluo/dcache

repo_name: wudaoluo/dcache


text:
@InProceedings{fromont12,
  title = {Kernels Based Tests with Non-asymptotic Bootstrap Approaches for Two-sample Problems},
  author = {Magalie   Fromont and BÃ©atrice Laurent and Matthieu Lerasle and Patricia Reynaud-Bouret},
  pages = {23.1--23.23},
  abstract = {Considering either two independent i.i.d. samples, or two independent samples generated from a heteroscedastic regression model, or two independent Poisson processes, we address the question of testing equality of their respective distributions. We first propose single testing procedures based on a general symmetric kernel. The corresponding critical values are chosen from a wild or permutation bootstrap approach, and the obtained tests are exactly (and not just asymptotically) of level. We then introduce an aggregation method, which enables to overcome the difficulty of choosing a kernel and/or the parameters of the kernel. We derive non-asymptotic properties for the aggregated tests, proving that they may be optimal in a classical statistical sense.},
  pdf = {http://jmlr.org/proceedings/papers/v23/fromont12/fromont12.pdf},
}

repository: mreid/papersite

repo_name: mreid/papersite

gha_language: TeX


text:
package main

import "time"

type Post struct {
	ID     int64
	Text   string
	Images []string

	CreatedAt time.Time
}

repository: JedBeom/ttom

repo_name: JedBeom/ttom


text:
package main

import "testing"

type testpair struct {
	value int
	want  bool
}

// func Test(t *testing.T) {
// 	pairs := []testpair{
// 		{111111, true},
// 		{223450, false},
// 		{123789, false},
// 		{777770, false},
// 	}
//
// 	for _, p := range pairs {
// 		is := isValid(p.value, false)
// 		if is != p.want {
// 			t.Errorf("%d: Wanted %v but got %v", p.value, p.want, is)
// 		}
//
// 	}
// }

func TestExtendet(t *testing.T) {
	pairs := []testpair{
		// {112233, true},
		// {123444, false},
		// {111122, true},
		{667789, true},
	}

	for _, p := range pairs {
		is := isValid(p.value, true)
		if is != p.want {
			t.Errorf("%d: Wanted %v but got %v", p.value, p.want, is)
		}

	}
}


text:
% This file was created with JabRef 2.8.1.
% Encoding: UTF8

 %entre 5 et 10 références (avec au moins 5 références qui ne sont pas des liens de pages Web, mais plutôt des articles ou livres, de préférence à valeur scientifique cad publiés dans une conférence ou journal scientifique)

@Book{trilles02,
author={F. TRILLES},
publisher={CNFPT},
title={Les techniques et méthodes de l’entraînement sportif},
year={2002}
}

@Book{platonov88,
author={V. PLATONOV},
publisher={Revue EPS},
title={L'entraînement sportif, théorie et méthodologie},
year={1988}
}

@Book{ferre98,
author={J. FERRE,  B. PHILIPPE, P. LEROUX AND B. SANOU},
publisher={Amphora},
title={Dictionnaire des APS},
year={1998}
}

@Book{cazorlal97,
author={G. CAZORLA, E. THILL, R. THOMAS AND J. CAJA},
publisher={Vigot},
title={Manuel de l’Educateur Sportif, préparation au brevet d’Etat 1er et 2ème degrés},
year={1997}
}

@Book{whitaker14,
author={T. WHITAKER AND R. HAWORTH},
publisher={Routledge},
title={What Great Coaches Do Differently: 11 Elements of Effective Coaching},
year={2014}
}

@article{guerci12,
    author  = "B. GUERCI",
    title   = "Le glucose dans le liquide interstitiel",
    year    = "2012",
    journal = " Diabète \& Obésité",
    volume  = "7",
    number  = "57",
    pages   = "81--88"
}

@article{samuel08,
    author  = "C. SAMUEL",
    title   = "Sleep, Recovery, and Performance: The New Frontier in High-Performance Athletics",
    year    = "2008",
    journal = " Neurologic Clinics",
    number  = "26",
    pages   = "169–-180"
}

@misc{cerisier15,
  author = "N. CERISIER",
  title = "Gérer la récupération immédiate",
  note   = "\url{http://www.autourdutrail.com/2015/12/gerer-la-recuperation-immediate.html}",
  month = "Decembre",
  year = "2015"
}

@misc{ziane,
  author = {R. ZIANE},
  title = {L’entraînement invisible : qu’est-ce que c’est ?},
  note={\url{https://www.valdemarne.fr/newsletters/lettre-sport-sante-et-preparation-physique/lentrainement-invisible-quest-ce-que-cest}}
}

@misc{franck17,
  author = {C. FRANCK},
  title = {L’entrainement invisible mais permanent},
  note={\url{https://www.e-s-c.fr/entrainement-invisible.php}},
  month = "Juin",
  year = "2017"
}

@Book{lerner07,
author={K.L. LERNER, B.W. LERNER},
publisher={Gale},
title={World of Sports Science},
year={2007}
}

@mastersthesis{leuregans17,
author={C. LEUREGANS},
title={La technologie dans le cadre de
l’entraînement de natation},
school = "Université Paris Nanterre",
year={2017}
}

@misc{mathieu15,
  author = {C. MATHIEU},
  title = {Les filières énergétiques : Aérobie, Anaérobie Alactique et Lactique},
  note   = {\url{http://couloir4.com/les-filieres-energetiques-aerobie-anaerobie-lactique-et-alactique/}},
  month = "Janvier",
  year = "2015"
}

@misc{sporTech,
  author = {SporTech},
  title = {Energie de l'effort physique},
  note   = {\url{http://sportech.online.fr/sptc_idx.php?pge=spfr_src.html}}
}

@misc{ffdd,
  author = {Fédération Française Des Diabétiques},
  title = {La glycémie},
   note   = "\url{https://www.federationdesdiabetiques.org/information/glycemie}"
}

@misc{diabete,
  author = {Diabète \& Nutrition},
  title = {La glycémie qu'est ce que c'est ?},
  note   = "\url{https://diabetnutrition.ch/quest-ce-que-le-diabete/quest-ce-que-la-glycemie/}"
}

@article{denux,
    author  = "N. DENUX ",
    title   = "Les glucides et l'indice glycémique",
    journal = "Nutrition sportive",
    number  = "3",
}

@article{hirvonen92,
    author  = "J. HIRVONEN, A. NUMMELA, H. RUSKO, S. REHUNEN AND M. HÄRKÖNEN ",
    title   = "Fatigue and changes of ATP, creatine phosphate, and lactate during the 400-m sprint.",
    year    = "1992",
    journal = "Canadian journal of sport sciences",
    volume  = "17",
    number  = "2",
    pages   = "141--144"
}

@article{lacour90,
    author  = "J.R. LACOUR, E. BOUVAT AND J.C. BARTHELEMY",
    title   = "Post-competition blood lactate concentrations as indicators of anaerobic energy expenditure during 400-m and 800-m races",
    year    = "1990",
    journal = " European Journal of Applied Physiology and Occupational Physiology",
    volume  = "61",
    pages   = "172–176"
}

@article{bang36,
    author  = "O. BANG",
    title   = "The lactate content of the blood during and after
    muscular exercise in man.",
    year    = "1936",
    journal = "Scand. Arch. Physiol.",
    number = "Suppl 10",
    volume  = "74",
    pages   = "51--82"
}

@article{fahey12,
    author  = "A.J. FAHEY, N. PARAMALINGAM, R.J. DAVEY, E.A. DAVIS, T.W. JONES AND P. A. FOURNIER",
    title   = "The Effect of a Short Sprint on Postexercise Whole-Body Glucose Production and Utilization Rates in Individuals with Type 1 Diabetes Mellitus",
    year    = "2012",
    journal = "Journal of Clinical Endocrinology and Metabolism",
    number = "11",
    volume  = "97",
    pages   = "4193–-4200"
}

@article{goodwin07,
    author  = "M.L. GOODWIN, J.E. HARRIS, A. HERNANDEZ AND L.B GLADDEN",
    title   = "Blood Lactate Measurements and Analysis during Exercise: A Guide for Clinicians",
    year    = "2007",
    journal = "Journal of Diabetes Science and Technology",
    number = "4",
    volume  = "1",
    pages   = "558--569"
}

@article{graham84,
    author  = "T.E. GRAHAM",
    title   = "Mechanisms of Blood Lactate Increase During Exercise",
    year    = "1984",
    journal = "The Physiologist",
    number = "4",
    volume  = "27",
    pages   = "299--303"
}

@article{chassain86,
    author  = "A.P. CHASSAIN",
    title   = "Méthode d'appréciation objective de la tolérance de l'organisme à l'effort : application à la mesure des puissances critiques de la fréquence cardiaque et de la lactatémie",
    year    = "1986",
    journal = "Science \& Sports",
    volume  = "1",
    pages   = "41--48"
}

@article{cazorla01,
    author  = "G. CAZORLA, C. PETIBOIS, L. BOSQUET AND L. LEGER",
    title   = "Lactate et exercice : mythes et réalités",
    year    = "2001",
    journal = "Bioenergétique et activités physiques et sportives",
    volume  = "54",
    pages   = "63--76"
}

@article{justice15,
    author  = "T.D. JUSTICE, G.L. HAMMER, R.J. DAVEY, N. PARAMALINGAM, K.J. GUELFI, L. LEWIS, E.A. DAVIS, T.W. JONES AND P.A. FOURNIER,",
    title   = "Physiological Reports",
    year    = "2015",
    journal = "Journal of Clinical Endocrinology and Metabolism",
    number = "5",
    volume  = "3",
    pages   = "1--10"
}

@article{peronnet13,
    author  = "F. PERONNET",
    title   = "Signification de la concentration de lactate plasmatique au cours de l’exercice",
    year    = "2013",
    journal = "Movement \& Sport Sciences",
    number = "79",
    pages   = "	23--32"
}

@InProceedings{lain13,
    author = {D. LAIN, W. GRANGER},
    title = {{FOCUS}: OXYGEN SATURATION AND HEART RATE DURING EXERCISE PERFORMANCE},
    booktitle = {Anesthesia \& Analgesia},
    month = oct,
    year = 2013,
    publisher = {International Anesthesia Research Society}
}

@InProceedings{tabatabaei00,
    author  = "H. TABATABAEI",
    title   = "Evaluate the change of \%SpO2 (saturation percent oxygen) and heart rate at lactate threshold in male elite athletes during sport until exhaustion",
    year    = "2000"
}

@mastersthesis{sow08,
author={H. SOW},
publisher={Gale},
title={Etude de la concentration sanguine de lactate (lactatemie) après deux épreuves (200metres et  400metres plats) chez des athlètes sénégalais de niveau national spécialisés dans ces deux distances},
school = "Université CHEIKH ANTA DIOP
DE DAKAR",
year={2008}
}

@misc{lcornec,
    author  = "A.LE CORNEC-BOUTINEAU",
    title   = "Qu'est ce que l'acide lactique",
    journal = "SDPO-mag",
    note   ="\url{http://sdpo.com/quest-ce-lacide-lactique-amandine-cornec-2/}"

}

@misc{geonaute,
    author  = "GEONAUTE",
    title   = "Comment fonctionne un cardio optique?",
    note   = "\url{https://www.geonaute.fr/conseils/comment-fonctionne-un-cardio-optique-tp_1368}"
}

@misc{oxymetre,
    title   = {L’oxymètre de pouls ou saturomètre : principe et usage},
    year = "2015",
    note   = "\url{https://saintesante.com/diagnostic/dispositif/oxymetre-de-pouls-ou-saturometre}"
}

@misc{chauzi18,
    author = "B. CHAUZI",
    title   = {Cardiofréquencemètre et entraînement physique},
    year = "2018",
    note   = "\url{https://entrainement-sportif.fr/cardiofrequencemetre.htm}"
}

@misc{baudoin17,
    author = "P. BAUDOIN",
    title   = {Comment s'entraîner avec un cardio-fréquencemètre ?},
    year = "2017",
    note   = "\url{http://www.sport-passion.fr/conseils/cardio-frequencemetre.htm}"
}

@article{info12,
    title   = "Comment et pourquoi acheter un oxymètre de poul?",
    month = "Juin",
    year    = "2012",
    journal = "Info Respiration",
    number  = "109",
    pages   = "9--12",
    note   = "\url{http://www.automesure.com/library/pdf/acheter-un-oxymetre-de_pouls.pdf}"
}

repository: Jmedjid/MemoireFinal

repo_name: Jmedjid/MemoireFinal


text:
@InProceedings{williamson13,
  pdf = {http://jmlr.org/proceedings/papers/v28/williamson13.pdf},
  supplementary = {Supplementary:williamson13-supp.pdf},
  title = {Parallel {M}arkov Chain {M}onte {C}arlo for Nonparametric Mixture Models},
  number = {1},
  section = {cycle-1},
  author = {Williamson, Sinead and Dubey, Avinava and Xing, Eric},
  pages = {98-106},
  abstract = {Nonparametric mixture models based on the Dirichlet process are an elegant alternative to finite models when the number of underlying components is unknown, but inference in such models can be slow. Existing attempts to parallelize inference in such models have relied on introducing approximations, which can lead to inaccuracies in the posterior estimate. In this paper, we describe auxiliary variable representations for the Dirichlet process and the hierarchical Dirichlet process that allow us to perform MCMC using the correct equilibrium distribution, in a distributed manner. We show that our approach allows scalable inference without the deterioration in estimate quality that accompanies existing methods.},
}


text:
/*
Copyright 2019 The saiki Authors

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

    http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
*/

package purger

import (
	"context"
	"time"

	"github.com/trinchan/saiki/pkg/controller/cache"
	"github.com/trinchan/saiki/pkg/store"
	"k8s.io/klog"
)

type Purger interface {
	Queue(rev store.Revision)
	Stop()
}

func purgeKeyFunc(rev store.Revision) string {
	return rev.Key()
}

type Purge struct {
	s             store.Storer
	c             cache.RevisionCacher
	purgeInterval *time.Ticker
	ctx           context.Context
}

func New(ctx context.Context, s store.Storer, interval time.Duration) *Purge {
	purgeInterval := time.NewTicker(interval)
	f := &Purge{
		s:             s,
		c:             cache.New(purgeKeyFunc),
		purgeInterval: purgeInterval,
		ctx:           ctx,
	}
	go func() {
		klog.Infof("starting purger")
		// TODO wait group to wait for flush all on Close()?
		for range f.purgeInterval.C {
			f.purge(ctx)
		}
	}()
	return f
}

func (p *Purge) Queue(rev store.Revision) {
	klog.V(3).Infof("queueing for purge: %s", rev)
	p.c.Cache(rev)
}

func (p *Purge) Stop() {
	if p != nil && p.purgeInterval != nil {
		p.purgeInterval.Stop()
	}
}

func (p *Purge) purge(ctx context.Context) {
	toPurge := p.c.SafeCopy()
	purgeStart := time.Now()
	klog.Infof("purge starting [%d objects]", len(toPurge))
	defer func() { klog.Infof("purged %d objects in %s", len(toPurge), time.Since(purgeStart)) }()
	if len(toPurge) == 0 {
		return
	}
	revsToPurge := make(store.RevisionList, len(toPurge))
	i := 0
	for _, rev := range toPurge {
		revsToPurge[i] = rev
		i++
	}
	deletedRevs, err := p.s.PurgeRevisions(ctx, revsToPurge)
	if err != nil {
		klog.Warningf("error purging revisions: %v", err)
	}
	for _, obj := range deletedRevs {
		p.c.Delete(obj)
	}
}

repository: trinchan/saiki

repo_name: trinchan/saiki


text:
// +build nocrypto

package main

import (
	"io"
)

func maybeCrypt(r io.Reader) io.Reader {
	return r
}

func initCrypto() {
}

repository: couchbase-fs/cbfsd-go

repo_name: couchbase-fs/cbfsd-go


text:
//go:build linux || windows

// Copyright Amazon.com Inc. or its affiliates. All Rights Reserved.
//
// Licensed under the Apache License, Version 2.0 (the "License"). You may
// not use this file except in compliance with the License. A copy of the
// License is located at
//
//	http://aws.amazon.com/apache2.0/
//
// or in the "license" file accompanying this file. This file is distributed
// on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either
// express or implied. See the License for the specific language governing
// permissions and limitations under the License.

package execcmd

import (
	"context"
	"errors"
	"fmt"
	"path/filepath"
	"strconv"
	"time"

	"github.com/aws/amazon-ecs-agent/ecs-agent/logger"
	"github.com/aws/amazon-ecs-agent/ecs-agent/logger/field"

	"github.com/docker/docker/api/types"

	apicontainer "github.com/aws/amazon-ecs-agent/agent/api/container"
	"github.com/aws/amazon-ecs-agent/agent/api/container/status"
	apitask "github.com/aws/amazon-ecs-agent/agent/api/task"
	"github.com/aws/amazon-ecs-agent/agent/dockerclient"
	"github.com/aws/amazon-ecs-agent/agent/dockerclient/dockerapi"
	"github.com/aws/amazon-ecs-agent/ecs-agent/utils/retry"
)

// RestartAgentIfStopped restarts the ExecCommandAgent in the container passed as parameter, only for ExecCommandAgent-enabled containers.
// The status of the ExecCommandAgent in the container is retrieved using a docker exec inspect call, using the dockerExecID
// stored in the AgentMetadata.DockerExecID.
//
// If the ExecCommandAgent is still running (or has never started), no action is taken.
// To actually restart the ExecCommandAgent, this function invokes this instance's StartAgent method.
func (m *manager) RestartAgentIfStopped(ctx context.Context, client dockerapi.DockerClient, task *apitask.Task, container *apicontainer.Container, containerId string) (RestartStatus, error) {
	if !IsExecEnabledContainer(container) {
		logger.Warn("Attempt to restart ExecCommandAgent for a non ExecCommandAgent-enabled container was made", logger.Fields{
			field.TaskID:    task.GetID(),
			field.Container: container.Name,
		})
		return NotRestarted, nil
	}
	ma, _ := container.GetManagedAgentByName(ExecuteCommandAgentName)
	metadata := MapToAgentMetadata(ma.Metadata)
	if !m.isAgentStarted(ma) {
		return NotRestarted, nil
	}
	res, err := m.inspectExecAgentProcess(ctx, client, metadata)
	if err != nil || res == nil {
		// We don't want to report InspectContainerExec errors, just that we don't know what the status of the agent is
		return Unknown, nil
	}
	if res.Running { // agent still running, nothing to do
		return NotRestarted, nil
	}
	// Restart if not running
	//TODO: [ecs-exec] retry only for certain exit codes?
	logger.Warn("ExecCommandAgent Process stopped for container, restarting...", logger.Fields{
		field.TaskID:    task.GetID(),
		field.Container: container.Name,
		field.RuntimeID: containerId,
		"exitCode":      res.ExitCode,
	})
	container.UpdateManagedAgentByName(ExecuteCommandAgentName, apicontainer.ManagedAgentState{
		ID: ma.ID,
	})
	err = m.StartAgent(ctx, client, task, container, containerId)
	if err != nil {
		return NotRestarted, err
	}
	return Restarted, nil
}

func (m *manager) inspectExecAgentProcess(ctx context.Context, client dockerapi.DockerClient, metadata AgentMetadata) (*types.ContainerExecInspect, error) {
	backoff := retry.NewExponentialBackoff(m.retryMinDelay, m.retryMaxDelay, retryJitterMultiplier, retryDelayMultiplier)
	ctx, cancel := context.WithTimeout(ctx, m.inspectRetryTimeout)
	defer cancel()
	var (
		inspectRes *types.ContainerExecInspect
		inspectErr error
	)
	retry.RetryNWithBackoffCtx(ctx, backoff, maxRetries, func() error {
		inspectRes, inspectErr = client.InspectContainerExec(ctx, metadata.DockerExecID, dockerclient.ContainerExecInspectTimeout)
		if inspectErr != nil {
			retryable := true
			if _, ok := inspectErr.(*dockerapi.DockerTimeoutError); ok {
				retryable = false
			}
			return StartError{
				error:     inspectErr,
				retryable: retryable,
			}
		}
		return nil
	})
	return inspectRes, inspectErr
}

// StartAgent idempotently starts the ExecCommandAgent in the container passed as parameter, only for ExecCommandAgent-enabled containers.
// If no error is returned, it can be assumed the ExecCommandAgent is started.
func (m *manager) StartAgent(ctx context.Context, client dockerapi.DockerClient, task *apitask.Task, container *apicontainer.Container, containerId string) error {
	if !IsExecEnabledContainer(container) {
		logger.Warn("An attempt to start ExecCommandAgent for a non ExecCommandAgent-enabled container was made", logger.Fields{
			field.TaskID:    task.GetID(),
			field.Container: container.Name,
			field.RuntimeID: containerId,
		})
		return nil
	}
	ma, _ := container.GetManagedAgentByName(ExecuteCommandAgentName)
	existingMetadata := MapToAgentMetadata(ma.Metadata)
	if ma.ID == "" {
		return errors.New("container has not been initialized: missing UUID")
	}
	// Guarantee idempotency if the container already has been started
	if m.isAgentStarted(ma) {
		res, err := m.inspectExecAgentProcess(ctx, client, existingMetadata)
		if err != nil {
			logger.Warn("Could not verify if the ExecCommandAgent was already running for container", logger.Fields{
				field.TaskID:    task.GetID(),
				field.Container: container.Name,
				field.RuntimeID: containerId,
				field.Error:     err,
			})
		} else if res.Running { // agent is already running, nothing to do
			logger.Warn("An attempt was made to start the ExecCommandAgent but it was already running", logger.Fields{
				field.TaskID:    task.GetID(),
				field.Container: container.Name,
				field.RuntimeID: containerId,
			})
			return nil
		}
	}

	backoff := retry.NewExponentialBackoff(m.retryMinDelay, m.retryMaxDelay, retryJitterMultiplier, retryDelayMultiplier)
	ctx, cancel := context.WithTimeout(ctx, m.startRetryTimeout)
	defer cancel()
	var startErr error

	var execMD *AgentMetadata
	retry.RetryNWithBackoffCtx(ctx, backoff, maxRetries, func() error {
		execMD, startErr = m.doStartAgent(ctx, client, task, ma, containerId)
		if startErr != nil {
			logger.Warn("Exec command agent failed to start for container", logger.Fields{
				field.TaskID:    task.GetID(),
				field.Container: container.Name,
				field.RuntimeID: containerId,
				field.Error:     startErr,
			})
		}
		return startErr
	})
	if startErr != nil {
		container.UpdateManagedAgentByName(ExecuteCommandAgentName, apicontainer.ManagedAgentState{
			ID:     ma.ID,
			Status: status.ManagedAgentStopped,
			Reason: startErr.Error(),
		})
		return startErr
	}
	container.UpdateManagedAgentByName(ExecuteCommandAgentName, apicontainer.ManagedAgentState{
		ID:            ma.ID,
		Status:        status.ManagedAgentRunning,
		LastStartedAt: time.Now(),
		Metadata:      execMD.ToMap(),
	})
	return nil
}

func (m *manager) doStartAgent(ctx context.Context, client dockerapi.DockerClient, task *apitask.Task, ma apicontainer.ManagedAgent, containerId string) (*AgentMetadata, error) {
	execAgentCmdBinDir := getExecAgentCmdBinDir(&ma)
	execAgentCmd := filepath.Join(execAgentCmdBinDir, SSMAgentBinName)
	execCfg := types.ExecConfig{
		User:   execAgentCmdUser,
		Detach: true,
		Cmd:    []string{execAgentCmd},
	}
	newMD := &AgentMetadata{}
	execRes, err := client.CreateContainerExec(ctx, containerId, execCfg, dockerclient.ContainerExecCreateTimeout)
	if err != nil {
		return newMD, StartError{error: fmt.Errorf("unable to start ExecuteCommandAgent [create]: %v", err), retryable: true}
	}

	logger.Debug("Created ExecCommandAgent for container", logger.Fields{
		field.TaskID:    task.GetID(),
		field.RuntimeID: containerId,
		"execResId":     execRes.ID,
	})

	err = client.StartContainerExec(ctx, execRes.ID, types.ExecStartCheck{Detach: true, Tty: false}, dockerclient.ContainerExecStartTimeout)
	if err != nil {
		return newMD, StartError{error: fmt.Errorf("unable to start ExecuteCommandAgent [pre-start]: %v", err), retryable: true}
	}
	logger.Debug("Sent ExecCommandAgent start signal for container", logger.Fields{
		field.TaskID:    task.GetID(),
		field.RuntimeID: containerId,
		"execResId":     execRes.ID,
	})

	inspect, err := client.InspectContainerExec(ctx, execRes.ID, dockerclient.ContainerExecInspectTimeout)
	if err != nil {
		return newMD, StartError{error: fmt.Errorf("unable to start ExecuteCommandAgent [inspect]: %v", err), retryable: true}
	}
	logger.Debug("Inspect ExecCommandAgent for container", logger.Fields{
		field.TaskID:    task.GetID(),
		field.RuntimeID: containerId,
		"pid":           inspect.Pid,
		"exitCode":      inspect.ExitCode,
		"running":       inspect.Running,
	})

	if !inspect.Running { //TODO: [ecs-exec] retry only for certain exit codes?
		return newMD, StartError{
			error:     fmt.Errorf("ExecuteCommandAgent process exited with exit code: %d", inspect.ExitCode),
			retryable: true,
		}
	}
	logger.Info("Started ExecCommandAgent for container", logger.Fields{
		field.TaskID:    task.GetID(),
		field.RuntimeID: containerId,
		"execResId":     inspect.Pid,
	})
	newMD.PID = strconv.Itoa(inspect.Pid)
	newMD.DockerExecID = execRes.ID
	newMD.CMD = execAgentCmd
	return newMD, nil
}

repository: aws/amazon-ecs-agent

repo_name: aws/amazon-ecs-agent

gha_language: Go


text:
package rand

import(
    "math"
)

// Pois A variable following a normal distribution
type Pois struct{
    lambda float64
}

// NewPois Generate a new variable following a Gaussian law
func NewPois(lambda float64) (x *Pois){
    x = &Pois{lambda}
    return
}

// NewStdPois Generate a new variable following a centered, reduced Gaussian law
// (mu=0, sigma=1)
func NewStdPois() (x *Pois){
    x = &Pois{1.}
    return
}

// R Generate a random value following the same Pois distribution as x
func (x Pois) R() (res int){
    var lambda = x.lambda;
    var power = math.Log10(lambda);
    var scale = 10e-3
    // if lambda < 0.1, we do some scaling so that lambda/scale is an integer over 1
    if (power < 0){
        scale = scale*math.Pow(10, power)
    }
    // TODO : here is a HUGE approximation
    // plus it does work bad (results get underestimated) if lambda is under 10e-3
    // a complete process to simulate Pois is harder to implement but possible,
    // and as been don  e
    var binom = NewBinom(int(math.Ceil(lambda/scale)), scale)
    res = binom.R()
    return
}
// Rn Generate an array of random values following the same Pois distribution as x
func (x Pois) Rn(n int) (res []int){
    res = make([]int, n)
    for i := 0; i < n; i++ {
        res[i] = x.R()
    }
    return
}

// D Density probability function of the the Pois distribution
func (x Pois) D(k int) (f float64){
    norm := math.Exp(-x.lambda)
    // this syntax avoid explosion, we multiply result by lambda, then divide it,
    // so that mult is neither too small nor too big after each step
    mult := 1. // lambda^0/0!
    for i := 1; i <= int(k) ; i++{
        mult *= x.lambda
        mult /= float64(i)
    }
    f = norm*mult
    return
}

repository: eric-burel/rgo

repo_name: eric-burel/rgo


text:
package alsa

import (
	"fmt"
	"reflect"
)

type swParams struct {
	TstampMode int32
	PeriodStep uint32
	SleepMin   uint32

	AvailMin         uint
	XferAlign        uint
	StartThreshold   uint
	StopThreshold    uint
	SilenceThreshold uint
	SilenceSize      uint
	Boundary         uint

	Proto         pVersion
	TstampType    uint32
	Reserved      [56]byte
	padding_for_c [4]byte
}

func (s *swParams) String() string {
	return s.Diff(&swParams{})
}

func (s *swParams) Diff(w *swParams) string {
	r := ""

	v1 := reflect.ValueOf(*s)
	v2 := reflect.ValueOf(*w)

	typ := reflect.TypeOf(*s)

	for i := 0; i < typ.NumField(); i++ {
		field := typ.Field(i)
		if field.Name == "Reserved" || field.Name == "padding_for_c" {
			continue
		}

		v1v := v1.Field(i)
		v2v := v2.Field(i)
		d := ""

		switch v1v.Type().Kind() {
		case reflect.Uint32:
			if v1v.Uint() != v2v.Uint() {
				d = fmt_uint(uint32(v1v.Uint())) + fmt.Sprintf(" (%d)", v1v.Uint())
			}
		case reflect.Uint:
			fallthrough
		case reflect.Uint8:
			fallthrough
		case reflect.Uint16:
			fallthrough
		case reflect.Uint64:
			if v1v.Uint() != v2v.Uint() {
				d = fmt.Sprintf("%d", v1v.Uint())
			}
		case reflect.Int:
			fallthrough
		case reflect.Int8:
			fallthrough
		case reflect.Int16:
			fallthrough
		case reflect.Int32:
			fallthrough
		case reflect.Int64:
			if v1v.Int() != v2v.Int() {
				d = fmt.Sprintf("%d", v1v.Int())
			}
		case reflect.String:
			if v1v.String() != v2v.String() {
				d = v1v.String()
			}
		default:
			d = v1v.Type().Kind().String()
		}
		if d != "" {
			r += fmt.Sprintf("%20s %s\n", field.Name, d)
		}
	}

	if r == "" {
		r += "  No changes\n"
	}
	return r
}

repository: metakeule/alsa

repo_name: metakeule/alsa


text:
FILESEXTRAPATHS_prepend_centriq2400-rep := "${THISDIR}/${PN}:"
LICENSE = "Apache-2.0"
LIC_FILES_CHKSUM = "file://${COREBASE}/meta/files/common-licenses/Apache-2.0;md5=89aea4e17d99a7cacdbeed46a0096b10"

SRC_URI += "file://centriq-2400rep-console-client.sh"

do_install() {
        install -d ${D}${bindir}
        install -m 0755 ${WORKDIR}/centriq-2400rep-console-client.sh ${D}${bindir}/centriq-2400rep-console-client.sh
}

repository: ibm-openbmc/openbmc

repo_name: ibm-openbmc/openbmc

gha_license_id: NOASSERTION

gha_language: Python


text:
# libdvdnav.bb build file
HOMEPAGE="http://dvdnav.mplayerhq.hu"
DESCRIPTION="DVD navigation multimeda library"
LICENSE = "GPL"
DEPENDS = "libdvdread"
RDEPENDS_${PN} = "libdvdread"
SECTION = "libs/multimedia"

PR = "r0"

SRC_URI = "http://dvdnav.mplayerhq.hu/releases/libdvdnav-${PV}.tar.bz2"

inherit autotools pkgconfig

SRC_URI[md5sum] = "53be8903f9802e101929a3451203bbf6"
SRC_URI[sha256sum] = "8c971b08276c89ddcecd26fc44204460fd250dc57346f03476d3077188c47550"

gha_language: C


text:
SUMMARY = "A set of tools using pywbem"
DESCRIPTION = "A set of tools using pywbem to communicate with WBEM servers"
HOMEPAGE = "https://pywbemtools.readthedocs.io/en/stable/"
LICENSE = "Apache-2.0"
LIC_FILES_CHKSUM = "file://LICENSE.txt;md5=e23fadd6ceef8c618fc1c65191d846fa"

SRC_URI[sha256sum] = "921fb57ea2ae3ae2806e18895bb0457697f27221b345c8b05afa4cb304a7f939"

inherit pypi setuptools3

RDEPENDS:${PN}:class-target += "\
    ${PYTHON_PN}-ply \
    ${PYTHON_PN}-pyyaml \
    ${PYTHON_PN}-six \
    ${PYTHON_PN}-pywbem \
    ${PYTHON_PN}-click \
    ${PYTHON_PN}-requests \
    ${PYTHON_PN}-prompt-toolkit \
    ${PYTHON_PN}-mock \
    ${PYTHON_PN}-packaging \
    ${PYTHON_PN}-nocasedict \
    ${PYTHON_PN}-yamlloader \
    ${PYTHON_PN}-click-repl \
    ${PYTHON_PN}-click-spinner \
    ${PYTHON_PN}-asciitree \
    ${PYTHON_PN}-tabulate \
    ${PYTHON_PN}-pydicti \
    ${PYTHON_PN}-nocaselist \
    ${PYTHON_PN}-custom-inherit \
"

BBCLASSEXTEND = "native"

repository: openembedded/meta-openembedded

repo_name: openembedded/meta-openembedded


text:
// Copyright 2022 Fraunhofer AISEC
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
//     http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
//           $$\                           $$\ $$\   $$\
//           $$ |                          $$ |\__|  $$ |
//  $$$$$$$\ $$ | $$$$$$\  $$\   $$\  $$$$$$$ |$$\ $$$$$$\    $$$$$$\   $$$$$$\
// $$  _____|$$ |$$  __$$\ $$ |  $$ |$$  __$$ |$$ |\_$$  _|  $$  __$$\ $$  __$$\
// $$ /      $$ |$$ /  $$ |$$ |  $$ |$$ /  $$ |$$ |  $$ |    $$ /  $$ |$$ | \__|
// $$ |      $$ |$$ |  $$ |$$ |  $$ |$$ |  $$ |$$ |  $$ |$$\ $$ |  $$ |$$ |
// \$$$$$$\  $$ |\$$$$$   |\$$$$$   |\$$$$$$  |$$ |  \$$$   |\$$$$$   |$$ |
//  \_______|\__| \______/  \______/  \_______|\__|   \____/  \______/ \__|
//
// This file is part of Clouditor Community Edition.

package service

import (
	"clouditor.io/clouditor/api"
	"clouditor.io/clouditor/internal/util"
	"google.golang.org/grpc/codes"
	"google.golang.org/grpc/status"
	"google.golang.org/protobuf/proto"
)

// ValidateRequest validates an incoming request according to different criteria:
//   - If the request is nil, [api.ErrEmptyRequest] is returned
//   - The request is validated according to the generated validation method
//   - Lastly, if the request is a [api.PaginatedRequest], an additional check is performed to ensure only valid columns are listed
//
// Note: This function already returns a gRPC error, so the error can be returned directly without any wrapping in a
// request function.
func ValidateRequest(req IncomingRequest) (err error) {
	// Check, if request is nil. We need to check whether the interface itself is nil (untyped nil); this happens if
	// someone is directly setting nil to a variable of the interface IncomingRequest. Furthermore, we need to check,
	// whether the *value* of the interface is nil. This can happen if nil is first assigned to a variable of a struct
	// (pointer) that implements the interface. If this variable is then passed to the validate function, the req
	// parameter is not nil, but the value of the interface representing it is.
	if util.IsNil(req) {
		return status.Errorf(codes.InvalidArgument, "%s", api.ErrEmptyRequest)
	}

	// Validate request
	err = req.Validate()
	if err != nil {
		return status.Errorf(codes.InvalidArgument, "%v: %v", api.ErrInvalidRequest, err)
	}

	return nil
}

type IncomingRequest interface {
	Validate() error
	proto.Message
}

repository: clouditor/clouditor

repo_name: clouditor/clouditor


text:
@InProceedings{mnihb16,
  supplementary = {Supplementary:mnihb16-supp.pdf},
  title = {Variational Inference for Monte Carlo Objectives},
  author = {Andriy Mnih and Danilo Rezende},
  pages = {2188-2196},
  abstract = {Recent progress in deep latent variable models has largely been driven by the development of flexible and scalable variational inference methods. Variational training of this type involves maximizing a lower bound on the log-likelihood, using samples from the variational posterior to compute the required gradients. Recently, Burda et al. (2016) have derived a tighter lower bound using a multi-sample importance sampling estimate of the likelihood and showed that optimizing it yields models that use more of their capacity and achieve higher likelihoods. This development showed the importance of such multi-sample objectives and explained the success of several related approaches. We extend the multi-sample approach to discrete latent variables and analyze the difficulty encountered when estimating the gradients involved. We then develop the first unbiased gradient estimator designed for importance-sampled objectives and evaluate it at training generative and structured output prediction models. The resulting estimator, which is based on low-variance per-sample learning signals, is both simpler and more effective than the NVIL estimator proposed for the single-sample variational objective, and is competitive with the currently used biased estimators.},
}