adacs-australia / beans

2023A project lead by Adelle Goodwin

BEANSp

Bayesian Estimation of Accreting Neutron Star parameters

• Free software: MIT license
• Documentation: https://beans-7.readthedocs.io/en/latest/
• Repo: https://github.com/adellej/beans

Features

This software uses a Markov Chain Monte Carlo approach to match observations of an accreting neutron star in outburst with a simple ignition model to predict unobservable parameters such as neutron star mass, radius, surface gravity, distance and inclination of the source, and accreted fuel composition. The code is all written in Python 3, except for settle which is a c++ code with a python wrapper. It makes use of Dan Foreman-Mackey's python implementation of MCMC, emcee, available here - https://github.com/dfm/emcee.

Credits

Software written by Adelle Goodwin. See Goodwin et al. (2019) - https://arxiv.org/pdf/1907.00996.

This softwate (BEANSp) was based on code written by Duncan Galloway, and uses Dan Foreman-Mackey's python implementation of MCMC, emcee. It depends on pySettle (https://github.com/adellej/pysettle), which was forked from the original settle written by Andrew Cumming.

Package installation and usage

BEANSp is on pyPI (https://pypi.org/project/beansp/) so installation is easy - either straight or in virtual environment:

pip install beansp

from beansp.beans import Beans

(Please refer to this simple test script as an example.)

Build and installation from this github repository

Please refer to build instructions.

beans's Issues

wheel(s) for pySettle pip packages install

• beans version: N/A
• Python version: 3.8-3.10
• Operating System: Linux, Mac OS-X

Description

pip installable packages not only source, but wheels including binary of the libsettle.so lib

• Linux (Ubuntu 20.04LTS)
• Mac OS-X Apple silicaon (CPU Arm64)
• Mac OS-X Intel/AMD (64bit CPU)

Get working and run Duncan's benchmark

• beans version: 1.0
• Python version: 3.8
• Operating System: Ubuntu 20.04 LTS

Description

• add Duncans Jupyter notebook to repo, incl the test data file table1.mrt
• get it working with current ver of beans/settle
• add ellapsed time measurement

Dead code

• Operating System: All

Description

A lot of dead code - never used functions, often exust only as headers, no implementation. Guessing mostly NR (Numerical Recipies in C book code), but some exist in mathlib as well. Could be coincidently identical function indentifiers though.

example dead code headers in nr.h

#define float double
...
void addint(double **uf, double **uc, double **res, int nf);
void airy(float x, float *ai, float *bi, float *aip, float *bip);
void amebsa(float **p, float y[], int ndim, float pb[],	float *yb,
	float ftol, float (*funk)(float []), int *iter, float temptr);
void amoeba(float **p, float y[], int ndim, float ftol,
	float (*funk)(float []), int *iter);
float amotry(float **p, float y[], float psum[], int ndim,
	float (*funk)(float []), int ihi, float fac);
float amotsa(float **p, float y[], float psum[], int ndim, float pb[],
	float *yb, float (*funk)(float []), int ihi, float *yhi, float fac);
void anneal(float x[], float y[], int iorder[], int ncity);
double anorm2(double **a, int n);
void arcmak(unsigned long nfreq[], unsigned long nchh, unsigned long nradd,
	arithcode *acode);
void arcode(unsigned long *ich, unsigned char **codep, unsigned long *lcode,
	unsigned long *lcd, int isign, arithcode *acode);
void arcsum(unsigned long iin[], unsigned long iout[], unsigned long ja,
	int nwk, unsigned long nrad, unsigned long nc);
void asolve(unsigned long n, double b[], double x[], int itrnsp);
void atimes(unsigned long n, double x[], double r[], int itrnsp);
void avevar(float data[], unsigned long n, float *ave, float *var);
void balanc(float **a, int n);
void banbks(float **a, unsigned long n, int m1, int m2, float **al,
	unsigned long indx[], float b[]);
void bandec(float **a, unsigned long n, int m1, int m2, float **al,
	unsigned long indx[], float *d);
void banmul(float **a, unsigned long n, int m1, int m2, float x[], float b[]);
void bcucof(float y[], float y1[], float y2[], float y12[], float d1,
	float d2, float **c);
void bcuint(float y[], float y1[], float y2[], float y12[],
	float x1l, float x1u, float x2l, float x2u, float x1,
	float x2, float *ansy, float *ansy1, float *ansy2);
void beschb(double x, double *gam1, double *gam2, double *gampl,
	double *gammi);
float bessi(int n, float x);
float bessi0(float x);
float bessi1(float x);
void bessik(float x, float xnu, float *ri, float *rk, float *rip,
	float *rkp);
float bessj(int n, float x);
float bessj0(float x);
float bessj1(float x);
void bessjy(float x, float xnu, float *rj, float *ry, float *rjp,
	float *ryp);
float bessk(int n, float x);
float bessk0(float x);
float bessk1(float x);
float bessy(int n, float x);
float bessy0(float x);
float bessy1(float x);
float beta(float z, float w);
float betacf(float a, float b, float x);
float betai(float a, float b, float x);
float bico(int n, int k);
void bksub(int ne, int nb, int jf, int k1, int k2, float ***c);
float bnldev(float pp, int n, long *idum);
float brent(float ax, float bx, float cx,
	float (*f)(float), float tol, float *xmin);
void broydn(float x[], int n, int *check,
	void (*vecfunc)(int, float [], float []));
void bsstep(float y[], float dydx[], int nv, float *xx, float htry,
	float eps, float yscal[], float *hdid, float *hnext,
	void (*derivs)(float, float [], float []));
void caldat(long julian, int *mm, int *id, int *iyyy);
void chder(float a, float b, float c[], float cder[], int n);
float chebev(float a, float b, float c[], int m, float x);
void chebft(float a, float b, float c[], int n, float (*func)(float));
void chebpc(float c[], float d[], int n);
void chint(float a, float b, float c[], float cint[], int n);
float chixy(float bang);
void choldc(float **a, int n, float p[]);
void cholsl(float **a, int n, float p[], float b[], float x[]);
void chsone(float bins[], float ebins[], int nbins, int knstrn,
	float *df, float *chsq, float *prob);
void chstwo(float bins1[], float bins2[], int nbins, int knstrn,
	float *df, float *chsq, float *prob);
void cisi(float x, float *ci, float *si);
void cntab1(int **nn, int ni, int nj, float *chisq,
	float *df, float *prob, float *cramrv, float *ccc);
void cntab2(int **nn, int ni, int nj, float *h, float *hx, float *hy,
	float *hygx, float *hxgy, float *uygx, float *uxgy, float *uxy);
void convlv(float data[], unsigned long n, float respns[], unsigned long m,
	int isign, float ans[]);
void copy(double **aout, double **ain, int n);
void correl(float data1[], float data2[], unsigned long n, float ans[]);
void cosft(float y[], int n, int isign);
void cosft1(float y[], int n);
void cosft2(float y[], int n, int isign);
void covsrt(float **covar, int ma, int ia[], int mfit);
void crank(unsigned long n, float w[], float *s);
void cyclic(float a[], float b[], float c[], float alpha, float beta,
	float r[], float x[], unsigned long n);
void daub4(float a[], unsigned long n, int isign);
float dawson(float x);
float dbrent(float ax, float bx, float cx,
	float (*f)(float), float (*df)(float), float tol, float *xmin);
void ddpoly(float c[], int nc, float x, float pd[], int nd);
int decchk(char string[], int n, char *ch);
void derivs(float x, float y[], float dydx[]);
float df1dim(float x);
void dfour1(double data[], unsigned long nn, int isign);
void dfpmin(float p[], int n, float gtol, int *iter, float *fret,
	float (*func)(float []), void (*dfunc)(float [], float []));
float dfridr(float (*func)(float), float x, float h, float *err);
void dftcor(float w, float delta, float a, float b, float endpts[],
	float *corre, float *corim, float *corfac);
void dftint(float (*func)(float), float a, float b, float w,
	float *cosint, float *sinint);
void difeq(int k, int k1, int k2, int jsf, int is1, int isf,
	int indexv[], int ne, float **s, float **y);
void dlinmin(float p[], float xi[], int n, float *fret,
	float (*func)(float []), void (*dfunc)(float [], float[]));
double dpythag(double a, double b);
void drealft(double data[], unsigned long n, int isign);
void dsprsax(double sa[], unsigned long ija[], double x[], double b[],
	unsigned long n);
void dsprstx(double sa[], unsigned long ija[], double x[], double b[],
	unsigned long n);
void dsvbksb(double **u, double w[], double **v, int m, int n, double b[],
	double x[]);
void dsvdcmp(double **a, int m, int n, double w[], double **v);
void eclass(int nf[], int n, int lista[], int listb[], int m);
void eclazz(int nf[], int n, int (*equiv)(int, int));
float ei(float x);
void eigsrt(float d[], float **v, int n);
float elle(float phi, float ak);
float ellf(float phi, float ak);
float ellpi(float phi, float en, float ak);
void elmhes(float **a, int n);
float erfcc(float x);

float erffc(float x);
void eulsum(float *sum, float term, int jterm, float wksp[]);
float evlmem(float fdt, float d[], int m, float xms);
float expdev(long *idum);
float expint(int n, float x);
float f1(float x);
float f1dim(float x);
float f2(float y);
float f3(float z);
float factln(int n);
float factrl(int n);
void fasper(float x[], float y[], unsigned long n, float ofac, float hifac,
	float wk1[], float wk2[], unsigned long nwk, unsigned long *nout,
	unsigned long *jmax, float *prob);
void fdjac(int n, float x[], float fvec[], float **df,
	void (*vecfunc)(int, float [], float []));
void fgauss(float x, float a[], float *y, float dyda[], int na);
void fill0(double **u, int n);
void fit(float x[], float y[], int ndata, float sig[], int mwt,
	float *a, float *b, float *siga, float *sigb, float *chi2, float *q);
void fitexy(float x[], float y[], int ndat, float sigx[], float sigy[],
	float *a, float *b, float *siga, float *sigb, float *chi2, float *q);
void fixrts(float d[], int m);
void fleg(float x, float pl[], int nl);
void flmoon(int n, int nph, long *jd, float *frac);
float nr_fmin(float x[]);
void four1(float data[], unsigned long nn, int isign);
void fourew(FILE *file[5], int *na, int *nb, int *nc, int *nd);
void fourfs(FILE *file[5], unsigned long nn[], int ndim, int isign);
void fourn(float data[], unsigned long nn[], int ndim, int isign);
void fpoly(float x, float p[], int np);
void fred2(int n, float a, float b, float t[], float f[], float w[],
	float (*g)(float), float (*ak)(float, float));
float fredin(float x, int n, float a, float b, float t[], float f[], float w[],
	float (*g)(float), float (*ak)(float, float));
void frenel(float x, float *s, float *c);
void frprmn(float p[], int n, float ftol, int *iter, float *fret,
	float (*func)(float []), void (*dfunc)(float [], float []));
void ftest(float data1[], unsigned long n1, float data2[], unsigned long n2,
	float *f, float *prob);
float gamdev(int ia, long *idum);
float gammln(float xx);
float gammp(float a, float x);
float gammq(float a, float x);

#undef float

#define float double

void gaucof(int n, float a[], float b[], float amu0, float x[], float w[]);
void gauher(float x[], float w[], int n);
void gaujac(float x[], float w[], int n, float alf, float bet);
void gaulag(float x[], float w[], int n, float alf);
void gauleg(float x1, float x2, float x[], float w[], int n);
void gaussj(float **a, int n, float **b, int m);
void gcf(float *gammcf, float a, float x, float *gln);
float golden(float ax, float bx, float cx, float (*f)(float), float tol,
	float *xmin);
void gser(float *gamser, float a, float x, float *gln);
void hpsel(unsigned long m, unsigned long n, float arr[], float heap[]);
void hpsort(unsigned long n, float ra[]);
void hqr(float **a, int n, float wr[], float wi[]);
void hufapp(unsigned long index[], unsigned long nprob[], unsigned long n,
	unsigned long i);
void hufdec(unsigned long *ich, unsigned char *code, unsigned long lcode,
	unsigned long *nb, huffcode *hcode);
void hufenc(unsigned long ich, unsigned char **codep, unsigned long *lcode,
	unsigned long *nb, huffcode *hcode);
void hufmak(unsigned long nfreq[], unsigned long nchin, unsigned long *ilong,
	unsigned long *nlong, huffcode *hcode);
void hunt(float xx[], unsigned long n, float x, unsigned long *jlo);
void hypdrv(float s, float yy[], float dyyds[]);
fcomplex hypgeo(fcomplex a, fcomplex b, fcomplex c, fcomplex z);
void hypser(fcomplex a, fcomplex b, fcomplex c, fcomplex z,
	fcomplex *series, fcomplex *deriv);
unsigned short icrc(unsigned short crc, unsigned char *bufptr,
	unsigned long len, short jinit, int jrev);
unsigned short icrc1(unsigned short crc, unsigned char onech);
unsigned long igray(unsigned long n, int is);
void iindexx(unsigned long n, long arr[], unsigned long indx[]);
void indexx(unsigned long n, float arr[], unsigned long indx[]);
void interp(double **uf, double **uc, int nf);
int irbit1(unsigned long *iseed);
int irbit2(unsigned long *iseed);
void jacobi(float **a, int n, float d[], float **v, int *nrot);
void jacobn(float x, float y[], float dfdx[], float **dfdy, int n);
long julday(int mm, int id, int iyyy);
void kendl1(float data1[], float data2[], unsigned long n, float *tau, float *z,
	float *prob);
void kendl2(float **tab, int i, int j, float *tau, float *z, float *prob);
void kermom(double w[], double y, int m);
void ks2d1s(float x1[], float y1[], unsigned long n1,
	void (*quadvl)(float, float, float *, float *, float *, float *),
	float *d1, float *prob);
void ks2d2s(float x1[], float y1[], unsigned long n1, float x2[], float y2[],
	unsigned long n2, float *d, float *prob);
void ksone(float data[], unsigned long n, float (*func)(float), float *d,
	float *prob);
void kstwo(float data1[], unsigned long n1, float data2[], unsigned long n2,
	float *d, float *prob);
void laguer(fcomplex a[], int m, fcomplex *x, int *its);
void lfit(float x[], float y[], float sig[], int ndat, float a[], int ia[],
	int ma, float **covar, float *chisq, void (*funcs)(float, float [], int));
void linbcg(unsigned long n, double b[], double x[], int itol, double tol,
	 int itmax, int *iter, double *err);
void linmin(float p[], float xi[], int n, float *fret,
	float (*func)(float []));
void lnsrch(int n, float xold[], float fold, float g[], float p[], float x[],
	 float *f, float stpmax, int *check, float (*func)(float []));
void load(float x1, float v[], float y[]);
void load1(float x1, float v1[], float y[]);
void load2(float x2, float v2[], float y[]);
void locate(float xx[], unsigned long n, float x, unsigned long *j);
void lop(double **out, double **u, int n);
void lubksb(float **a, int n, int *indx, float b[]);
void ludcmp(float **a, int n, int *indx, float *d);
void machar(int *ibeta, int *it, int *irnd, int *ngrd,
	int *machep, int *negep, int *iexp, int *minexp, int *maxexp,
	float *eps, float *epsneg, float *xmin, float *xmax);
void matadd(double **a, double **b, double **c, int n);
void matsub(double **a, double **b, double **c, int n);
void medfit(float x[], float y[], int ndata, float *a, float *b, float *abdev);
void memcof(float data[], int n, int m, float *xms, float d[]);
int metrop(float de, float t);
void mgfas(double **u, int n, int maxcyc);
void mglin(double **u, int n, int ncycle);
float midexp(float (*funk)(float), float aa, float bb, int n);
float midinf(float (*funk)(float), float aa, float bb, int n);
float midpnt(float (*func)(float), float a, float b, int n);
float midsql(float (*funk)(float), float aa, float bb, int n);
float midsqu(float (*funk)(float), float aa, float bb, int n);
void miser(float (*func)(float []), float regn[], int ndim, unsigned long npts,
	float dith, float *ave, float *var);
void mmid(float y[], float dydx[], int nvar, float xs, float htot,
	int nstep, float yout[], void (*derivs)(float, float[], float[]));
void mnbrak(float *ax, float *bx, float *cx, float *fa, float *fb,
	float *fc, float (*func)(float));
void mnewt(int ntrial, float x[], int n, float tolx, float tolf);
void moment(float data[], int n, float *ave, float *adev, float *sdev,
	float *var, float *skew, float *curt);
void mp2dfr(unsigned char a[], unsigned char s[], int n, int *m);
void mpadd(unsigned char w[], unsigned char u[], unsigned char v[], int n);
void mpdiv(unsigned char q[], unsigned char r[], unsigned char u[],
	unsigned char v[], int n, int m);
void mpinv(unsigned char u[], unsigned char v[], int n, int m);
void mplsh(unsigned char u[], int n);
void mpmov(unsigned char u[], unsigned char v[], int n);
void mpmul(unsigned char w[], unsigned char u[], unsigned char v[], int n,
	int m);
void mpneg(unsigned char u[], int n);
void mppi(int n);
void mprove(float **a, float **alud, int n, int indx[], float b[],
	float x[]);
void mpsad(unsigned char w[], unsigned char u[], int n, int iv);
void mpsdv(unsigned char w[], unsigned char u[], int n, int iv, int *ir);
void mpsmu(unsigned char w[], unsigned char u[], int n, int iv);
void mpsqrt(unsigned char w[], unsigned char u[], unsigned char v[], int n,
	int m);
void mpsub(int *is, unsigned char w[], unsigned char u[], unsigned char v[],
	int n);
void mrqcof(float x[], float y[], float sig[], int ndata, float a[],
	int ia[], int ma, float **alpha, float beta[], float *chisq,
	void (*funcs)(float, float [], float *, float [], int));
void mrqmin(float x[], float y[], float sig[], int ndata, float a[],
	int ia[], int ma, float **covar, float **alpha, float *chisq,
	void (*funcs)(float, float [], float *, float [], int), float *alamda);

void odeint(float ystart[], int nvar, float x1, float x2,
	float eps, float h1, float hmin, int *nok, int *nbad,
	void (*derivs)(float, float [], float []),
	void (*rkqs)(float [], float [], int, float *, float, float,
	float [], float *, float *, void (*)(float, float [], float [])));
void odeint2(float ystart[], int nvar, float x1, float x2,
	float eps, float h1, float hmin, int *nok, int *nbad,
	void (*derivs)(float, float [], float []),
	void (*rkqs)(float [], float [], int, float *, float, float,
	float [], float *, float *, void (*)(float, float [], float [])));
void orthog(int n, float anu[], float alpha[], float beta[], float a[],
	float b[]);
void pade(double cof[], int n, float *resid);
void pccheb(float d[], float c[], int n);
void pcshft(float a, float b, float d[], int n);
void pearsn(float x[], float y[], unsigned long n, float *r, float *prob,
	float *z);
void period(float x[], float y[], int n, float ofac, float hifac,
	float px[], float py[], int np, int *nout, int *jmax, float *prob);
void piksr2(int n, float arr[], float brr[]);
void piksrt(int n, float arr[]);
void pinvs(int ie1, int ie2, int je1, int jsf, int jc1, int k,
	float ***c, float **s);
float plgndr(int l, int m, float x);
float poidev(float xm, long *idum);
void polcoe(float x[], float y[], int n, float cof[]);
void polcof(float xa[], float ya[], int n, float cof[]);
void poldiv(float u[], int n, float v[], int nv, float q[], float r[]);
void polin2(float x1a[], float x2a[], float **ya, int m, int n,
	float x1, float x2, float *y, float *dy);
void polint(float xa[], float ya[], int n, float x, float *y, float *dy);
void powell(float p[], float **xi, int n, float ftol, int *iter, float *fret,
	float (*func)(float []));
void predic(float data[], int ndata, float d[], int m, float future[], int nfut);
float probks(float alam);
void psdes(unsigned long *lword, unsigned long *irword);
void pwt(float a[], unsigned long n, int isign);
void pwtset(int n);
float pythag(float a, float b);
void pzextr(int iest, float xest, float yest[], float yz[], float dy[],
	int nv);
float qgaus(float (*func)(float), float a, float b);
void qrdcmp(float **a, int n, float *c, float *d, int *sing);
float qromb(float (*func)(float), float a, float b);
float qromo(float (*func)(float), float a, float b,
	float (*choose)(float (*)(float), float, float, int));
void qroot(float p[], int n, float *b, float *c, float eps);
void qrsolv(float **a, int n, float c[], float d[], float b[]);
void qrupdt(float **r, float **qt, int n, float u[], float v[]);
float qsimp(float (*func)(float), float a, float b);
double qtrap(double (*func)(double), double a, double b, double EPS);
float quad3d(float (*func)(float, float, float), float x1, float x2);
void quadct(float x, float y, float xx[], float yy[], unsigned long nn,
	float *fa, float *fb, float *fc, float *fd);
void quadmx(float **a, int n);
void quadvl(float x, float y, float *fa, float *fb, float *fc, float *fd);

#undef float
float ran0(long *idum);
float ran1(long *idum);
float ran2(long *idum);
float ran3(long *idum);
float ran4(long *idum);
#define float double

void rank(unsigned long n, unsigned long indx[], unsigned long irank[]);
void ranpt(float pt[], float regn[], int n);
void ratint(float xa[], float ya[], int n, float x, float *y, float *dy);
void ratlsq(double (*fn)(double), double a, double b, int mm, int kk,
	double cof[], double *dev);
double ratval(double x, double cof[], int mm, int kk);
float rc(float x, float y);
float rd(float x, float y, float z);
void realft(float data[], unsigned long n, int isign);
void rebin(float rc, int nd, float r[], float xin[], float xi[]);
void red(int iz1, int iz2, int jz1, int jz2, int jm1, int jm2, int jmf,
	int ic1, int jc1, int jcf, int kc, float ***c, float **s);
void relax(double **u, double **rhs, int n);
void relax2(double **u, double **rhs, int n);
void resid(double **res, double **u, double **rhs, int n);
float revcst(float x[], float y[], int iorder[], int ncity, int n[]);
void reverse(int iorder[], int ncity, int n[]);
float rf(float x, float y, float z);
float rj(float x, float y, float z, float p);
void rk4(float y[], float dydx[], int n, float x, float h, float yout[],
	void (*derivs)(float, float [], float []));
void rkck(float y[], float dydx[], int n, float x, float h,
	float yout[], float yerr[], void (*derivs)(float, float [], float []));
void rkdumb(float vstart[], int nvar, float x1, float x2, int nstep,
	void (*derivs)(float, float [], float []));
void rkqs(float y[], float dydx[], int n, float *x,
	float htry, float eps, float yscal[], float *hdid, float *hnext,
	void (*derivs)(float, float [], float []));
void rlft3(float ***data, float **speq, unsigned long nn1,
	unsigned long nn2, unsigned long nn3, int isign);
float rofunc(float b);
void rotate(float **r, float **qt, int n, int i, float a, float b);
void rsolv(float **a, int n, float d[], float b[]);
void rstrct(double **uc, double **uf, int nc);
float rtbis(float (*func)(float), float x1, float x2, float xacc);
float rtflsp(float (*func)(float), float x1, float x2, float xacc);
float rtnewt(void (*funcd)(float, float *, float *), float x1, float x2,
	float xacc);
float rtsafe(void (*funcd)(float, float *, float *), float x1, float x2,
	float xacc);
float rtsec(float (*func)(float), float x1, float x2, float xacc);
void rzextr(int iest, float xest, float yest[], float yz[], float dy[], int nv);
void savgol(float c[], int np, int nl, int nr, int ld, int m);
void score(float xf, float y[], float f[]);
void scrsho(float (*fx)(float));
float select(unsigned long k, unsigned long n, float arr[]);
float selip(unsigned long k, unsigned long n, float arr[]);
void shell(unsigned long n, float a[]);
void shoot(int n, float v[], float f[]);
void shootf(int n, float v[], float f[]);
void simp1(float **a, int mm, int ll[], int nll, int iabf, int *kp,
	float *bmax);
void simp2(float **a, int n, int l2[], int nl2, int *ip, int kp, float *q1);
void simp3(float **a, int i1, int k1, int ip, int kp);
void simplx(float **a, int m, int n, int m1, int m2, int m3, int *icase,
	int izrov[], int iposv[]);
void simpr(float y[], float dydx[], float dfdx[], float **dfdy,
	int n, float xs, float htot, int nstep, float yout[],
	void (*derivs)(float, float [], float []));
void sinft(float y[], int n);
void slvsm2(double **u, double **rhs);
void slvsml(double **u, double **rhs);
void sncndn(float uu, float emmc, float *sn, float *cn, float *dn);
double snrm(unsigned long n, double sx[], int itol);
void sobseq(int *n, float x[]);
void solvde(int itmax, float conv, float slowc, float scalv[],
	int indexv[], int ne, int nb, int m, float **y, float ***c, float **s);
void sor(double **a, double **b, double **c, double **d, double **e,
	double **f, double **u, int jmax, double rjac);
void sort(unsigned long n, float arr[]);
void sort2(unsigned long n, float arr[], float brr[]);
void sort3(unsigned long n, float ra[], float rb[], float rc[]);
void spctrm(FILE *fp, float p[], int m, int k, int ovrlap);
void spear(float data1[], float data2[], unsigned long n, float *d, float *zd,
	float *probd, float *rs, float *probrs);
void sphbes(int n, float x, float *sj, float *sy, float *sjp, float *syp);
void splie2(float x1a[], float x2a[], float **ya, int m, int n, float **y2a);
void splin2(float x1a[], float x2a[], float **ya, float **y2a, int m, int n,
	float x1, float x2, float *y);
void spline(float x[], float y[], int n, float yp1, float ypn, float y2[]);
void splint(float xa[], float ya[], float y2a[], int n, float x, float *y);
void spread(float y, float yy[], unsigned long n, float x, int m);
void sprsax(float sa[], unsigned long ija[], float x[], float b[],
	unsigned long n);
void sprsin(float **a, int n, float thresh, unsigned long nmax, float sa[],
	unsigned long ija[]);
void sprspm(float sa[], unsigned long ija[], float sb[], unsigned long ijb[],
	float sc[], unsigned long ijc[]);
void sprstm(float sa[], unsigned long ija[], float sb[], unsigned long ijb[],
	float thresh, unsigned long nmax, float sc[], unsigned long ijc[]);
void sprstp(float sa[], unsigned long ija[], float sb[], unsigned long ijb[]);
void sprstx(float sa[], unsigned long ija[], float x[], float b[],
	unsigned long n);
void stifbs(float y[], float dydx[], int nv, float *xx,
	float htry, float eps, float yscal[], float *hdid, float *hnext,
	void (*derivs)(float, float [], float []));
void stiff(float y[], float dydx[], int n, float *x,
	float htry, float eps, float yscal[], float *hdid, float *hnext,
	void (*derivs)(float, float [], float []));
void stoerm(float y[], float d2y[], int nv, float xs,
	float htot, int nstep, float yout[],
	void (*derivs)(float, float [], float []));
void svbksb(float **u, float w[], float **v, int m, int n, float b[],
	float x[]);
void svdcmp(float **a, int m, int n, float w[], float **v);
void svdfit(float x[], float y[], float sig[], int ndata, float a[],
	int ma, float **u, float **v, float w[], float *chisq,
	void (*funcs)(float, float [], int));
void svdvar(float **v, int ma, float w[], float **cvm);
void toeplz(float r[], float x[], float y[], int n);
void tptest(float data1[], float data2[], unsigned long n, float *t, float *prob);
void tqli(float d[], float e[], int n, float **z);
double trapzd(double (*func)(double), double a, double b, int n);
void tred2(float **a, int n, float d[], float e[]);
void tridag(float a[], float b[], float c[], float r[], float u[],
	unsigned long n);
float trncst(float x[], float y[], int iorder[], int ncity, int n[]);
void trnspt(int iorder[], int ncity, int n[]);
void ttest(float data1[], unsigned long n1, float data2[], unsigned long n2,
	float *t, float *prob);
void tutest(float data1[], unsigned long n1, float data2[], unsigned long n2,
	float *t, float *prob);
void twofft(float data1[], float data2[], float fft1[], float fft2[],
	unsigned long n);
void vander(double x[], double w[], double q[], int n);
void vegas(float regn[], int ndim, float (*fxn)(float [], float), int init,
	unsigned long ncall, int itmx, int nprn, float *tgral, float *sd,
	float *chi2a);
void voltra(int n, int m, float t0, float h, float *t, float **f,
	float (*g)(int, float), float (*ak)(int, int, float, float));
void wt1(float a[], unsigned long n, int isign,
	void (*wtstep)(float [], unsigned long, int));
void wtn(float a[], unsigned long nn[], int ndim, int isign,
	void (*wtstep)(float [], unsigned long, int));
void wwghts(float wghts[], int n, float h,
	void (*kermom)(double [], double ,int));
int zbrac(float (*func)(float), float *x1, float *x2);
void zbrak(float (*fx)(float), float x1, float x2, int n, float xb1[],
	float xb2[], int *nb);

void zrhqr(float a[], int m, float rtr[], float rti[]);
float zriddr(float (*func)(float), float x1, float x2, float xacc);
void zroots(fcomplex a[], int m, fcomplex roots[], int polish);

Content of header files for .cc (C++ source) files is copied in .cc files rather than #included from headers

• Operating System: All

Description

All headers: missing include guards (#ifdef/#define)

odeint.h.cc ... hard copy of class definition in both .cc and .h
spline.h.cc ... hard copy of class definition in both .cc and .h; discrepancy between the two class definitions
usefu.h ... missing #ifdef/#define
eos.h ... missing #ifdef/#define

modify automated pytest after settle repo split

• beans version: 0.9.1
• Python version: 3.X
• Operating System: Linux, Mac OS-X

Description

modify automated pytest action recipe - remove settle build and test.
Also add pytest action recipe into separeted pysettle repo

The 'for' loop in the settle mainer() function runs only once - return is inside the loop block

• Operating System: All

Description

The 'for' loop in the mainer() function runs only once - return is inside the loop block.
Is that intended behaviour?

Line numbers for reference, it is module setlle.cc

85  int mainer(double* flu, double* Z, double* X, double* mdo, int* docomp,
86         double* trec, double* alpha, double* fluen, double* radius, double*mass)

141  for (int ii=1; ii<=1; ii++) {

276  return 0;
277  } // loop through flux

Macros in nrutil.h with global static variables (NR heritage)

• Operating System: All

Description

Macros in nrutil.h with global static variables (NR book example code heritage?)

• use generic C mathlib functions / macros where possible, with the rest:
• convert to in-line functions (assuming need to run fast, which is the reason to use macros)

Code with macros

static float sqrarg;
#define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 : sqrarg*sqrarg)

static double dsqrarg;
#define DSQR(a) ((dsqrarg=(a)) == 0.0 ? 0.0 : dsqrarg*dsqrarg)

static double dmaxarg1,dmaxarg2;
#define DMAX(a,b) (dmaxarg1=(a),dmaxarg2=(b),(dmaxarg1) > (dmaxarg2) ?\
        (dmaxarg1) : (dmaxarg2))

static double dminarg1,dminarg2;
#define DMIN(a,b) (dminarg1=(a),dminarg2=(b),(dminarg1) < (dminarg2) ?\
        (dminarg1) : (dminarg2))

static float maxarg1,maxarg2;
#define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1) > (maxarg2) ?\
        (maxarg1) : (maxarg2))

static float minarg1,minarg2;
#define FMIN(a,b) (minarg1=(a),minarg2=(b),(minarg1) < (minarg2) ?\
        (minarg1) : (minarg2))

static long lmaxarg1,lmaxarg2;
#define LMAX(a,b) (lmaxarg1=(a),lmaxarg2=(b),(lmaxarg1) > (lmaxarg2) ?\
        (lmaxarg1) : (lmaxarg2))

static long lminarg1,lminarg2;
#define LMIN(a,b) (lminarg1=(a),lminarg2=(b),(lminarg1) < (lminarg2) ?\
        (lminarg1) : (lminarg2))

static int imaxarg1,imaxarg2;
#define IMAX(a,b) (imaxarg1=(a),imaxarg2=(b),(imaxarg1) > (imaxarg2) ?\
        (imaxarg1) : (imaxarg2))

static int iminarg1,iminarg2;
#define IMIN(a,b) (iminarg1=(a),iminarg2=(b),(iminarg1) < (iminarg2) ?\
        (iminarg1) : (iminarg2))

#define SIGN(a,b) ((b) >= 0.0 ? fabs(a) : -fabs(a))

Eliminate 'harmless' warnings

• Operating System: All

Description

Eliminate 'harmless' warnings

• unused variables
• ignored retval of fread() -> moved to issuse #12
• ignored retval of scanf/fscanf() -> moved to issuse #12

Examples

In file included from root.c:2:
At top level:
nrutil.h:51:21: warning: ‘iminarg2’ defined but not used [-Wunused-variable]
   51 | static int iminarg1,iminarg2;

Functions headers are defined in different module than the code (function implementation)

• Operating System: All

Description

Some C modules have function headers declared in different modules and misising header files

→ correct this. Function int foo1() implemented in module foo.c shall have header un it's header file foo.h

• odeint.cc - nr.h
• root.c - nr.h
• nrutil.c - nr.h

Examples in the code

nr.h:void odeint(float ystart[], int nvar, float x1, float x2,
...
odeint.cc:void Ode_Int::odeint(double ystart[], int nvar, double x1, double x2, 
...

Eliminate harmful warnings

• Operating System: Linux, later Mac

Description

retval missing in settle.cc: In function ‘int mainer(double*, double*, double*, double*, int*, double*, double*, double*, double*, double*)’:

"control reaches end of non-void function [-Wreturn-type]"
→ add "return 1;" at the end of the function

When calling void nrerror(char error_text[]);

ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
→ modify to void nrerror(const char error_text[]);

Refactor to eliminate #define float double

• Operating System: All

Description

The settle code thoroughly uses re-typing (C) functions parameters from float to double. This might cause confusion to the compiler in optimisation stage. Readability and maintainability of the code is reduced.

This is done even for functions that are "zombie" dead code - only headers exist in nr.h, no implementation.

There are equivalent functions with double as parameter - use these instead.
Note: This issue was mostly hidden by compiling C code with g++ compiler.

example code

nr.h 
#define float double
...
void odeint(float ystart[], int nvar, float x1, float x2,
	float eps, float h1, float hmin, int *nok, int *nbad,
	void (*derivs)(float, float [], float []),
	void (*rkqs)(float [], float [], int, float *, float, float,
	float [], float *, float *, void (*)(float, float [], float [])));
#undef float

while the function odeint() is actually implemented in odeiint.cc as

odeint.cc:void Ode_Int::odeint(double ystart[], int nvar, double x1, double x2,
    ...

example dead code headers in nr.h - retyped from float to double

#define float double
...
void addint(double **uf, double **uc, double **res, int nf);
void airy(float x, float *ai, float *bi, float *aip, float *bip);
void amebsa(float **p, float y[], int ndim, float pb[],	float *yb,
	float ftol, float (*funk)(float []), int *iter, float temptr);
void amoeba(float **p, float y[], int ndim, float ftol,
	float (*funk)(float []), int *iter);
float amotry(float **p, float y[], float psum[], int ndim,
	float (*funk)(float []), int ihi, float fac);
float amotsa(float **p, float y[], float psum[], int ndim, float pb[],
	float *yb, float (*funk)(float []), int ihi, float *yhi, float fac);
void anneal(float x[], float y[], int iorder[], int ncity);
double anorm2(double **a, int n);
void arcmak(unsigned long nfreq[], unsigned long nchh, unsigned long nradd,
	arithcode *acode);
void arcode(unsigned long *ich, unsigned char **codep, unsigned long *lcode,
	unsigned long *lcd, int isign, arithcode *acode);
void arcsum(unsigned long iin[], unsigned long iout[], unsigned long ja,
	int nwk, unsigned long nrad, unsigned long nc);
void asolve(unsigned long n, double b[], double x[], int itrnsp);
void atimes(unsigned long n, double x[], double r[], int itrnsp);
void avevar(float data[], unsigned long n, float *ave, float *var);
void balanc(float **a, int n);
void banbks(float **a, unsigned long n, int m1, int m2, float **al,
	unsigned long indx[], float b[]);
void bandec(float **a, unsigned long n, int m1, int m2, float **al,
	unsigned long indx[], float *d);
void banmul(float **a, unsigned long n, int m1, int m2, float x[], float b[]);
void bcucof(float y[], float y1[], float y2[], float y12[], float d1,
	float d2, float **c);
void bcuint(float y[], float y1[], float y2[], float y12[],
	float x1l, float x1u, float x2l, float x2u, float x1,
	float x2, float *ansy, float *ansy1, float *ansy2);
void beschb(double x, double *gam1, double *gam2, double *gampl,
	double *gammi);
float bessi(int n, float x);
float bessi0(float x);
float bessi1(float x);
void bessik(float x, float xnu, float *ri, float *rk, float *rip,
	float *rkp);
float bessj(int n, float x);
float bessj0(float x);
float bessj1(float x);
void bessjy(float x, float xnu, float *rj, float *ry, float *rjp,
	float *ryp);
float bessk(int n, float x);
float bessk0(float x);
float bessk1(float x);
float bessy(int n, float x);
float bessy0(float x);
float bessy1(float x);
float beta(float z, float w);
float betacf(float a, float b, float x);
float betai(float a, float b, float x);
float bico(int n, int k);
void bksub(int ne, int nb, int jf, int k1, int k2, float ***c);
float bnldev(float pp, int n, long *idum);
float brent(float ax, float bx, float cx,
	float (*f)(float), float tol, float *xmin);
void broydn(float x[], int n, int *check,
	void (*vecfunc)(int, float [], float []));
void bsstep(float y[], float dydx[], int nv, float *xx, float htry,
	float eps, float yscal[], float *hdid, float *hnext,
	void (*derivs)(float, float [], float []));
void caldat(long julian, int *mm, int *id, int *iyyy);
void chder(float a, float b, float c[], float cder[], int n);
float chebev(float a, float b, float c[], int m, float x);
void chebft(float a, float b, float c[], int n, float (*func)(float));
void chebpc(float c[], float d[], int n);
void chint(float a, float b, float c[], float cint[], int n);
float chixy(float bang);
void choldc(float **a, int n, float p[]);
void cholsl(float **a, int n, float p[], float b[], float x[]);
void chsone(float bins[], float ebins[], int nbins, int knstrn,
	float *df, float *chsq, float *prob);
void chstwo(float bins1[], float bins2[], int nbins, int knstrn,
	float *df, float *chsq, float *prob);
void cisi(float x, float *ci, float *si);
void cntab1(int **nn, int ni, int nj, float *chisq,
	float *df, float *prob, float *cramrv, float *ccc);
void cntab2(int **nn, int ni, int nj, float *h, float *hx, float *hy,
	float *hygx, float *hxgy, float *uygx, float *uxgy, float *uxy);
void convlv(float data[], unsigned long n, float respns[], unsigned long m,
	int isign, float ans[]);
void copy(double **aout, double **ain, int n);
void correl(float data1[], float data2[], unsigned long n, float ans[]);
void cosft(float y[], int n, int isign);
void cosft1(float y[], int n);
void cosft2(float y[], int n, int isign);
void covsrt(float **covar, int ma, int ia[], int mfit);
void crank(unsigned long n, float w[], float *s);
void cyclic(float a[], float b[], float c[], float alpha, float beta,
	float r[], float x[], unsigned long n);
void daub4(float a[], unsigned long n, int isign);
float dawson(float x);
float dbrent(float ax, float bx, float cx,
	float (*f)(float), float (*df)(float), float tol, float *xmin);
void ddpoly(float c[], int nc, float x, float pd[], int nd);
int decchk(char string[], int n, char *ch);
void derivs(float x, float y[], float dydx[]);
float df1dim(float x);
void dfour1(double data[], unsigned long nn, int isign);
void dfpmin(float p[], int n, float gtol, int *iter, float *fret,
	float (*func)(float []), void (*dfunc)(float [], float []));
float dfridr(float (*func)(float), float x, float h, float *err);
void dftcor(float w, float delta, float a, float b, float endpts[],
	float *corre, float *corim, float *corfac);
void dftint(float (*func)(float), float a, float b, float w,
	float *cosint, float *sinint);
void difeq(int k, int k1, int k2, int jsf, int is1, int isf,
	int indexv[], int ne, float **s, float **y);
void dlinmin(float p[], float xi[], int n, float *fret,
	float (*func)(float []), void (*dfunc)(float [], float[]));
double dpythag(double a, double b);
void drealft(double data[], unsigned long n, int isign);
void dsprsax(double sa[], unsigned long ija[], double x[], double b[],
	unsigned long n);
void dsprstx(double sa[], unsigned long ija[], double x[], double b[],
	unsigned long n);
void dsvbksb(double **u, double w[], double **v, int m, int n, double b[],
	double x[]);
void dsvdcmp(double **a, int m, int n, double w[], double **v);
void eclass(int nf[], int n, int lista[], int listb[], int m);
void eclazz(int nf[], int n, int (*equiv)(int, int));
float ei(float x);
void eigsrt(float d[], float **v, int n);
float elle(float phi, float ak);
float ellf(float phi, float ak);
float ellpi(float phi, float en, float ak);
void elmhes(float **a, int n);
float erfcc(float x);

float erffc(float x);
void eulsum(float *sum, float term, int jterm, float wksp[]);
float evlmem(float fdt, float d[], int m, float xms);
float expdev(long *idum);
float expint(int n, float x);
float f1(float x);
float f1dim(float x);
float f2(float y);
float f3(float z);
float factln(int n);
float factrl(int n);
void fasper(float x[], float y[], unsigned long n, float ofac, float hifac,
	float wk1[], float wk2[], unsigned long nwk, unsigned long *nout,
	unsigned long *jmax, float *prob);
void fdjac(int n, float x[], float fvec[], float **df,
	void (*vecfunc)(int, float [], float []));
void fgauss(float x, float a[], float *y, float dyda[], int na);
void fill0(double **u, int n);
void fit(float x[], float y[], int ndata, float sig[], int mwt,
	float *a, float *b, float *siga, float *sigb, float *chi2, float *q);
void fitexy(float x[], float y[], int ndat, float sigx[], float sigy[],
	float *a, float *b, float *siga, float *sigb, float *chi2, float *q);
void fixrts(float d[], int m);
void fleg(float x, float pl[], int nl);
void flmoon(int n, int nph, long *jd, float *frac);
float nr_fmin(float x[]);
void four1(float data[], unsigned long nn, int isign);
void fourew(FILE *file[5], int *na, int *nb, int *nc, int *nd);
void fourfs(FILE *file[5], unsigned long nn[], int ndim, int isign);
void fourn(float data[], unsigned long nn[], int ndim, int isign);
void fpoly(float x, float p[], int np);
void fred2(int n, float a, float b, float t[], float f[], float w[],
	float (*g)(float), float (*ak)(float, float));
float fredin(float x, int n, float a, float b, float t[], float f[], float w[],
	float (*g)(float), float (*ak)(float, float));
void frenel(float x, float *s, float *c);
void frprmn(float p[], int n, float ftol, int *iter, float *fret,
	float (*func)(float []), void (*dfunc)(float [], float []));
void ftest(float data1[], unsigned long n1, float data2[], unsigned long n2,
	float *f, float *prob);
float gamdev(int ia, long *idum);
float gammln(float xx);
float gammp(float a, float x);
float gammq(float a, float x);

#undef float

#define float double

void gaucof(int n, float a[], float b[], float amu0, float x[], float w[]);
void gauher(float x[], float w[], int n);
void gaujac(float x[], float w[], int n, float alf, float bet);
void gaulag(float x[], float w[], int n, float alf);
void gauleg(float x1, float x2, float x[], float w[], int n);
void gaussj(float **a, int n, float **b, int m);
void gcf(float *gammcf, float a, float x, float *gln);
float golden(float ax, float bx, float cx, float (*f)(float), float tol,
	float *xmin);
void gser(float *gamser, float a, float x, float *gln);
void hpsel(unsigned long m, unsigned long n, float arr[], float heap[]);
void hpsort(unsigned long n, float ra[]);
void hqr(float **a, int n, float wr[], float wi[]);
void hufapp(unsigned long index[], unsigned long nprob[], unsigned long n,
	unsigned long i);
void hufdec(unsigned long *ich, unsigned char *code, unsigned long lcode,
	unsigned long *nb, huffcode *hcode);
void hufenc(unsigned long ich, unsigned char **codep, unsigned long *lcode,
	unsigned long *nb, huffcode *hcode);
void hufmak(unsigned long nfreq[], unsigned long nchin, unsigned long *ilong,
	unsigned long *nlong, huffcode *hcode);
void hunt(float xx[], unsigned long n, float x, unsigned long *jlo);
void hypdrv(float s, float yy[], float dyyds[]);
fcomplex hypgeo(fcomplex a, fcomplex b, fcomplex c, fcomplex z);
void hypser(fcomplex a, fcomplex b, fcomplex c, fcomplex z,
	fcomplex *series, fcomplex *deriv);
unsigned short icrc(unsigned short crc, unsigned char *bufptr,
	unsigned long len, short jinit, int jrev);
unsigned short icrc1(unsigned short crc, unsigned char onech);
unsigned long igray(unsigned long n, int is);
void iindexx(unsigned long n, long arr[], unsigned long indx[]);
void indexx(unsigned long n, float arr[], unsigned long indx[]);
void interp(double **uf, double **uc, int nf);
int irbit1(unsigned long *iseed);
int irbit2(unsigned long *iseed);
void jacobi(float **a, int n, float d[], float **v, int *nrot);
void jacobn(float x, float y[], float dfdx[], float **dfdy, int n);
long julday(int mm, int id, int iyyy);
void kendl1(float data1[], float data2[], unsigned long n, float *tau, float *z,
	float *prob);
void kendl2(float **tab, int i, int j, float *tau, float *z, float *prob);
void kermom(double w[], double y, int m);
void ks2d1s(float x1[], float y1[], unsigned long n1,
	void (*quadvl)(float, float, float *, float *, float *, float *),
	float *d1, float *prob);
void ks2d2s(float x1[], float y1[], unsigned long n1, float x2[], float y2[],
	unsigned long n2, float *d, float *prob);
void ksone(float data[], unsigned long n, float (*func)(float), float *d,
	float *prob);
void kstwo(float data1[], unsigned long n1, float data2[], unsigned long n2,
	float *d, float *prob);
void laguer(fcomplex a[], int m, fcomplex *x, int *its);
void lfit(float x[], float y[], float sig[], int ndat, float a[], int ia[],
	int ma, float **covar, float *chisq, void (*funcs)(float, float [], int));
void linbcg(unsigned long n, double b[], double x[], int itol, double tol,
	 int itmax, int *iter, double *err);
void linmin(float p[], float xi[], int n, float *fret,
	float (*func)(float []));
void lnsrch(int n, float xold[], float fold, float g[], float p[], float x[],
	 float *f, float stpmax, int *check, float (*func)(float []));
void load(float x1, float v[], float y[]);
void load1(float x1, float v1[], float y[]);
void load2(float x2, float v2[], float y[]);
void locate(float xx[], unsigned long n, float x, unsigned long *j);
void lop(double **out, double **u, int n);
void lubksb(float **a, int n, int *indx, float b[]);
void ludcmp(float **a, int n, int *indx, float *d);
void machar(int *ibeta, int *it, int *irnd, int *ngrd,
	int *machep, int *negep, int *iexp, int *minexp, int *maxexp,
	float *eps, float *epsneg, float *xmin, float *xmax);
void matadd(double **a, double **b, double **c, int n);
void matsub(double **a, double **b, double **c, int n);
void medfit(float x[], float y[], int ndata, float *a, float *b, float *abdev);
void memcof(float data[], int n, int m, float *xms, float d[]);
int metrop(float de, float t);
void mgfas(double **u, int n, int maxcyc);
void mglin(double **u, int n, int ncycle);
float midexp(float (*funk)(float), float aa, float bb, int n);
float midinf(float (*funk)(float), float aa, float bb, int n);
float midpnt(float (*func)(float), float a, float b, int n);
float midsql(float (*funk)(float), float aa, float bb, int n);
float midsqu(float (*funk)(float), float aa, float bb, int n);
void miser(float (*func)(float []), float regn[], int ndim, unsigned long npts,
	float dith, float *ave, float *var);
void mmid(float y[], float dydx[], int nvar, float xs, float htot,
	int nstep, float yout[], void (*derivs)(float, float[], float[]));
void mnbrak(float *ax, float *bx, float *cx, float *fa, float *fb,
	float *fc, float (*func)(float));
void mnewt(int ntrial, float x[], int n, float tolx, float tolf);
void moment(float data[], int n, float *ave, float *adev, float *sdev,
	float *var, float *skew, float *curt);
void mp2dfr(unsigned char a[], unsigned char s[], int n, int *m);
void mpadd(unsigned char w[], unsigned char u[], unsigned char v[], int n);
void mpdiv(unsigned char q[], unsigned char r[], unsigned char u[],
	unsigned char v[], int n, int m);
void mpinv(unsigned char u[], unsigned char v[], int n, int m);
void mplsh(unsigned char u[], int n);
void mpmov(unsigned char u[], unsigned char v[], int n);
void mpmul(unsigned char w[], unsigned char u[], unsigned char v[], int n,
	int m);
void mpneg(unsigned char u[], int n);
void mppi(int n);
void mprove(float **a, float **alud, int n, int indx[], float b[],
	float x[]);
void mpsad(unsigned char w[], unsigned char u[], int n, int iv);
void mpsdv(unsigned char w[], unsigned char u[], int n, int iv, int *ir);
void mpsmu(unsigned char w[], unsigned char u[], int n, int iv);
void mpsqrt(unsigned char w[], unsigned char u[], unsigned char v[], int n,
	int m);
void mpsub(int *is, unsigned char w[], unsigned char u[], unsigned char v[],
	int n);
void mrqcof(float x[], float y[], float sig[], int ndata, float a[],
	int ia[], int ma, float **alpha, float beta[], float *chisq,
	void (*funcs)(float, float [], float *, float [], int));
void mrqmin(float x[], float y[], float sig[], int ndata, float a[],
	int ia[], int ma, float **covar, float **alpha, float *chisq,
	void (*funcs)(float, float [], float *, float [], int), float *alamda);

void odeint(float ystart[], int nvar, float x1, float x2,
	float eps, float h1, float hmin, int *nok, int *nbad,
	void (*derivs)(float, float [], float []),
	void (*rkqs)(float [], float [], int, float *, float, float,
	float [], float *, float *, void (*)(float, float [], float [])));
void odeint2(float ystart[], int nvar, float x1, float x2,
	float eps, float h1, float hmin, int *nok, int *nbad,
	void (*derivs)(float, float [], float []),
	void (*rkqs)(float [], float [], int, float *, float, float,
	float [], float *, float *, void (*)(float, float [], float [])));
void orthog(int n, float anu[], float alpha[], float beta[], float a[],
	float b[]);
void pade(double cof[], int n, float *resid);
void pccheb(float d[], float c[], int n);
void pcshft(float a, float b, float d[], int n);
void pearsn(float x[], float y[], unsigned long n, float *r, float *prob,
	float *z);
void period(float x[], float y[], int n, float ofac, float hifac,
	float px[], float py[], int np, int *nout, int *jmax, float *prob);
void piksr2(int n, float arr[], float brr[]);
void piksrt(int n, float arr[]);
void pinvs(int ie1, int ie2, int je1, int jsf, int jc1, int k,
	float ***c, float **s);
float plgndr(int l, int m, float x);
float poidev(float xm, long *idum);
void polcoe(float x[], float y[], int n, float cof[]);
void polcof(float xa[], float ya[], int n, float cof[]);
void poldiv(float u[], int n, float v[], int nv, float q[], float r[]);
void polin2(float x1a[], float x2a[], float **ya, int m, int n,
	float x1, float x2, float *y, float *dy);
void polint(float xa[], float ya[], int n, float x, float *y, float *dy);
void powell(float p[], float **xi, int n, float ftol, int *iter, float *fret,
	float (*func)(float []));
void predic(float data[], int ndata, float d[], int m, float future[], int nfut);
float probks(float alam);
void psdes(unsigned long *lword, unsigned long *irword);
void pwt(float a[], unsigned long n, int isign);
void pwtset(int n);
float pythag(float a, float b);
void pzextr(int iest, float xest, float yest[], float yz[], float dy[],
	int nv);
float qgaus(float (*func)(float), float a, float b);
void qrdcmp(float **a, int n, float *c, float *d, int *sing);
float qromb(float (*func)(float), float a, float b);
float qromo(float (*func)(float), float a, float b,
	float (*choose)(float (*)(float), float, float, int));
void qroot(float p[], int n, float *b, float *c, float eps);
void qrsolv(float **a, int n, float c[], float d[], float b[]);
void qrupdt(float **r, float **qt, int n, float u[], float v[]);
float qsimp(float (*func)(float), float a, float b);
double qtrap(double (*func)(double), double a, double b, double EPS);
float quad3d(float (*func)(float, float, float), float x1, float x2);
void quadct(float x, float y, float xx[], float yy[], unsigned long nn,
	float *fa, float *fb, float *fc, float *fd);
void quadmx(float **a, int n);
void quadvl(float x, float y, float *fa, float *fb, float *fc, float *fd);

#undef float
float ran0(long *idum);
float ran1(long *idum);
float ran2(long *idum);
float ran3(long *idum);
float ran4(long *idum);
#define float double

void rank(unsigned long n, unsigned long indx[], unsigned long irank[]);
void ranpt(float pt[], float regn[], int n);
void ratint(float xa[], float ya[], int n, float x, float *y, float *dy);
void ratlsq(double (*fn)(double), double a, double b, int mm, int kk,
	double cof[], double *dev);
double ratval(double x, double cof[], int mm, int kk);
float rc(float x, float y);
float rd(float x, float y, float z);
void realft(float data[], unsigned long n, int isign);
void rebin(float rc, int nd, float r[], float xin[], float xi[]);
void red(int iz1, int iz2, int jz1, int jz2, int jm1, int jm2, int jmf,
	int ic1, int jc1, int jcf, int kc, float ***c, float **s);
void relax(double **u, double **rhs, int n);
void relax2(double **u, double **rhs, int n);
void resid(double **res, double **u, double **rhs, int n);
float revcst(float x[], float y[], int iorder[], int ncity, int n[]);
void reverse(int iorder[], int ncity, int n[]);
float rf(float x, float y, float z);
float rj(float x, float y, float z, float p);
void rk4(float y[], float dydx[], int n, float x, float h, float yout[],
	void (*derivs)(float, float [], float []));
void rkck(float y[], float dydx[], int n, float x, float h,
	float yout[], float yerr[], void (*derivs)(float, float [], float []));
void rkdumb(float vstart[], int nvar, float x1, float x2, int nstep,
	void (*derivs)(float, float [], float []));
void rkqs(float y[], float dydx[], int n, float *x,
	float htry, float eps, float yscal[], float *hdid, float *hnext,
	void (*derivs)(float, float [], float []));
void rlft3(float ***data, float **speq, unsigned long nn1,
	unsigned long nn2, unsigned long nn3, int isign);
float rofunc(float b);
void rotate(float **r, float **qt, int n, int i, float a, float b);
void rsolv(float **a, int n, float d[], float b[]);
void rstrct(double **uc, double **uf, int nc);
float rtbis(float (*func)(float), float x1, float x2, float xacc);
float rtflsp(float (*func)(float), float x1, float x2, float xacc);
float rtnewt(void (*funcd)(float, float *, float *), float x1, float x2,
	float xacc);
float rtsafe(void (*funcd)(float, float *, float *), float x1, float x2,
	float xacc);
float rtsec(float (*func)(float), float x1, float x2, float xacc);
void rzextr(int iest, float xest, float yest[], float yz[], float dy[], int nv);
void savgol(float c[], int np, int nl, int nr, int ld, int m);
void score(float xf, float y[], float f[]);
void scrsho(float (*fx)(float));
float select(unsigned long k, unsigned long n, float arr[]);
float selip(unsigned long k, unsigned long n, float arr[]);
void shell(unsigned long n, float a[]);
void shoot(int n, float v[], float f[]);
void shootf(int n, float v[], float f[]);
void simp1(float **a, int mm, int ll[], int nll, int iabf, int *kp,
	float *bmax);
void simp2(float **a, int n, int l2[], int nl2, int *ip, int kp, float *q1);
void simp3(float **a, int i1, int k1, int ip, int kp);
void simplx(float **a, int m, int n, int m1, int m2, int m3, int *icase,
	int izrov[], int iposv[]);
void simpr(float y[], float dydx[], float dfdx[], float **dfdy,
	int n, float xs, float htot, int nstep, float yout[],
	void (*derivs)(float, float [], float []));
void sinft(float y[], int n);
void slvsm2(double **u, double **rhs);
void slvsml(double **u, double **rhs);
void sncndn(float uu, float emmc, float *sn, float *cn, float *dn);
double snrm(unsigned long n, double sx[], int itol);
void sobseq(int *n, float x[]);
void solvde(int itmax, float conv, float slowc, float scalv[],
	int indexv[], int ne, int nb, int m, float **y, float ***c, float **s);
void sor(double **a, double **b, double **c, double **d, double **e,
	double **f, double **u, int jmax, double rjac);
void sort(unsigned long n, float arr[]);
void sort2(unsigned long n, float arr[], float brr[]);
void sort3(unsigned long n, float ra[], float rb[], float rc[]);
void spctrm(FILE *fp, float p[], int m, int k, int ovrlap);
void spear(float data1[], float data2[], unsigned long n, float *d, float *zd,
	float *probd, float *rs, float *probrs);
void sphbes(int n, float x, float *sj, float *sy, float *sjp, float *syp);
void splie2(float x1a[], float x2a[], float **ya, int m, int n, float **y2a);
void splin2(float x1a[], float x2a[], float **ya, float **y2a, int m, int n,
	float x1, float x2, float *y);
void spline(float x[], float y[], int n, float yp1, float ypn, float y2[]);
void splint(float xa[], float ya[], float y2a[], int n, float x, float *y);
void spread(float y, float yy[], unsigned long n, float x, int m);
void sprsax(float sa[], unsigned long ija[], float x[], float b[],
	unsigned long n);
void sprsin(float **a, int n, float thresh, unsigned long nmax, float sa[],
	unsigned long ija[]);
void sprspm(float sa[], unsigned long ija[], float sb[], unsigned long ijb[],
	float sc[], unsigned long ijc[]);
void sprstm(float sa[], unsigned long ija[], float sb[], unsigned long ijb[],
	float thresh, unsigned long nmax, float sc[], unsigned long ijc[]);
void sprstp(float sa[], unsigned long ija[], float sb[], unsigned long ijb[]);
void sprstx(float sa[], unsigned long ija[], float x[], float b[],
	unsigned long n);
void stifbs(float y[], float dydx[], int nv, float *xx,
	float htry, float eps, float yscal[], float *hdid, float *hnext,
	void (*derivs)(float, float [], float []));
void stiff(float y[], float dydx[], int n, float *x,
	float htry, float eps, float yscal[], float *hdid, float *hnext,
	void (*derivs)(float, float [], float []));
void stoerm(float y[], float d2y[], int nv, float xs,
	float htot, int nstep, float yout[],
	void (*derivs)(float, float [], float []));
void svbksb(float **u, float w[], float **v, int m, int n, float b[],
	float x[]);
void svdcmp(float **a, int m, int n, float w[], float **v);
void svdfit(float x[], float y[], float sig[], int ndata, float a[],
	int ma, float **u, float **v, float w[], float *chisq,
	void (*funcs)(float, float [], int));
void svdvar(float **v, int ma, float w[], float **cvm);
void toeplz(float r[], float x[], float y[], int n);
void tptest(float data1[], float data2[], unsigned long n, float *t, float *prob);
void tqli(float d[], float e[], int n, float **z);
double trapzd(double (*func)(double), double a, double b, int n);
void tred2(float **a, int n, float d[], float e[]);
void tridag(float a[], float b[], float c[], float r[], float u[],
	unsigned long n);
float trncst(float x[], float y[], int iorder[], int ncity, int n[]);
void trnspt(int iorder[], int ncity, int n[]);
void ttest(float data1[], unsigned long n1, float data2[], unsigned long n2,
	float *t, float *prob);
void tutest(float data1[], unsigned long n1, float data2[], unsigned long n2,
	float *t, float *prob);
void twofft(float data1[], float data2[], float fft1[], float fft2[],
	unsigned long n);
void vander(double x[], double w[], double q[], int n);
void vegas(float regn[], int ndim, float (*fxn)(float [], float), int init,
	unsigned long ncall, int itmx, int nprn, float *tgral, float *sd,
	float *chi2a);
void voltra(int n, int m, float t0, float h, float *t, float **f,
	float (*g)(int, float), float (*ak)(int, int, float, float));
void wt1(float a[], unsigned long n, int isign,
	void (*wtstep)(float [], unsigned long, int));
void wtn(float a[], unsigned long nn[], int ndim, int isign,
	void (*wtstep)(float [], unsigned long, int));
void wwghts(float wghts[], int n, float h,
	void (*kermom)(double [], double ,int));
int zbrac(float (*func)(float), float *x1, float *x2);
void zbrak(float (*fx)(float), float x1, float x2, int n, float xb1[],
	float xb2[], int *nb);

void zrhqr(float a[], int m, float rtr[], float rti[]);
float zriddr(float (*func)(float), float x1, float x2, float xacc);
void zroots(fcomplex a[], int m, fcomplex roots[], int polish);

re-typing

#define float double
...
float **matrix(long nrl, long nrh, long ncl, long nch);
...

Use of the function

#define float double
...
void Ode_Int::simpr(float y[], float dydx[], float dfdx[], float **dfdy, int n,
	float xs, float htot, int nstep, float yout[],
	void (*derivs)(float, float [], float []))
{
	int i,j,nn,*indx;
	float d,h,x,**a,*del,*ytemp;

	indx=ivector(1,n);
	**a=matrix(1,n,1,n);**
...

re-typing mathlib functions in nr.h

(Dangerous - compiled as C++ can cause floating point resolution issues !)

#define float double
...
/* use matlib's double erf( double arg ) instead" */
float erff(float x);

Killed 9 on Mac

• beans version: N/A
• Python version: 0.1.2
• Operating System: OS-X

Description

Running a short functional test of settle after libsettle re-install results in a strange failure.

What I Did

python tests/test_settle_sft.py 
Killed: 9

Makefile: modify to use a correct compiler for C

• Operating System: Linux Ubuntu 20.04 LTS

Description

Modify makefile to use gcc to compile C code, not g++ for all code.

Note: this was actually anabling C++ functionality in supposedlt C language code, particularly overloading functions

What I Did

linux: settle.o 
	gcc -Ofast -fPIC -c *.c
	g++ -Ofast -fPIC -c *.cc

Make sure settle compiles and installs on OS-X

• beans version:
• Python version:
• Operating System: OS-X

Description

settle:

• compile
• install
• make pip package

What I Did

Original nrutil.h.c files from Numerical Recipes book modified and mixed up with own code

• Operating System: All

Description

Start from scratch with the generic nrutil.h.c files.
Keep code modular.
Put own code (even though derived from NR book examples) into separate modules, eg gasdev.h.c

Possibly uninitialised variables

• Operating System: All

Description

in modules root.c, settle.cc and odeint.cc, there are possibly initialised variables.
(in case of specific execution flow, these variables can contain random/whatever number, practically artefact what was in the memory earlier)

warnings reported with -Ofast

root.c: In function ‘zbrent’:
root.c:52:18: warning: ‘e’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   52 |       min2=fabs(e*q);
      |                 ~^~
root.c: In function ‘lnsrch’:
root.c:225:8: warning: ‘tmplam’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  225 |   test,tmplam;
      |        ^~~~~~
root.c:254:12: warning: ‘fold2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  254 |     rhs2=f2-fold2-alam2*slope;
      |          ~~^~~~~~
root.c:254:12: warning: ‘f2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
root.c:256:14: warning: ‘alam2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  256 |     b=(-alam2*rhs1/(alam*alam)+alam*rhs2/(alam2*alam2))/(alam-alam2);
      |        ~~~~~~^~~~~
root.c: In function ‘ludcmp’:
root.c:336:10: warning: ‘imax’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  336 |     dum=a[imax][k];
      |          ^
g++ -g -Wall -Wno-unused-but-set-variable -Wno-unused-parameter -Wno-unused-variable -Ofast -fPIC -c *.cc
odeint.cc: In member function ‘void Ode_Int::ludcmp(double**, int, int*, double*)’:
odeint.cc:721:11: warning: ‘imax’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  721 |     dum=a[imax][k];
      |           ^~~~
odeint.cc: In member function ‘void Ode_Int::stifbs(double*, double*, int, double*, double, double, double*, double*, double*, void (*)(double, double*, double*))’:
odeint.cc:597:10: warning: ‘scale’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  597 |  *hnext=h/scale;
      |         ~^~~~~~
odeint.cc:493:28: warning: ‘red’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  493 |  double eps1,errmax,fact,h,red,scale,work,wrkmin,xest;
      |                            ^~~
odeint.cc: In member function ‘void Ode_Int::odeint(double*, int, double, double, double, double, double, int*, int*, void (*)(double, double*, double*))’:
odeint.cc:131:45: warning: ‘xsav’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  131 |     if (kmax > 0 && kount < kmax-1 && fabs(x-xsav) > fabs(this->dxsav)) {
      |                                            ~^~~~~
settle.cc: In function ‘int mainer(double*, double*, double*, double*, int*, double*, double*, double*, double*, double*)’:
settle.cc:90:14: warning: ‘y’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   90 |   double yb, y, dummy, Xbar;
      |              ^
settle.cc: In function ‘double doint(double)’:
settle.cc:397:25: warning: ‘F’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  397 |   if (G.COMPRESS) printf("flux/Fb= %lg; flux/Ft=%lg\n", F/G.Fb, F/G.Ft);
      |                   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Unhandled retvals of file manipulation functions

• Operating System: All

Description

Unhandled rerurn values of fread(), scanf() and fscanf().
Can result in hard to analyze issues in case of eg file access issues.

Recommended: check retvals, in case of unsuccessful execution, report err code.

compilation log

settle.cc: In function ‘double doint(double)’:
settle.cc:397:25: warning: ‘F’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  397 |   if (G.COMPRESS) printf("flux/Fb= %lg; flux/Ft=%lg\n", F/G.Fb, F/G.Ft);
      |                   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spline.cc: In member function ‘void Spline::init(FILE*, int, int, int)’:
spline.cc:170:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  170 |     fread(&(this->xtab[i]),1,DSIZE,fp);
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spline.cc:172:32: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  172 |     while (++col != ycol) fread(&dummy,1,DSIZE,fp);
      |                           ~~~~~^~~~~~~~~~~~~~~~~~~
spline.cc:173:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  173 |     fread(&(this->ytab[i]),1,DSIZE,fp);
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
spline.cc:174:32: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  174 |     while (col++ != ncol) fread(&dummy,1,DSIZE,fp);
      |                           ~~~~~^~~~~~~~~~~~~~~~~~~
useful.cc: In function ‘double askd(char*)’:
useful.cc:18:8: warning: ignoring return value of ‘int scanf(const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
   18 |   scanf("%lg", &var);
      |   ~~~~~^~~~~~~~~~~~~
useful.cc: In function ‘int aski(char*)’:
useful.cc:27:8: warning: ignoring return value of ‘int scanf(const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
   27 |   scanf("%d", &var);
      |   ~~~~~^~~~~~~~~~~~
useful.cc: In function ‘int flines(char*)’:
useful.cc:41:18: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
   41 |     while (fscanf(fp, "%c", &dummy), dummy != '\n');
      |            ~~~~~~^~~~~~~~~~~~~~~~~~

Split beans and settle repo

• beans version: 0.9
• Python version: 0.1.2
• Operating System: N/A

Description

Based on Adelle request, split the two packages into separate github repos.

• create new repo for settle (pySettle)
• if possible, transfer rhe history of changes - not just clear cut from zero fro settle.

make beans pip package

• beans version: 0.9
• Python version: 3.10 (test others as well !!!)
• Operating System: Linux, OS-X

Description

make beans pip package
Including wheels
(see issue #29, for reference, which covers pySettle wheels)

What I Did

make settle pip package

• beans version:
• Python version:
• Operating System: Linux, OS-X

Description

make settle pip package
Including the embedded C/C++ library

What I Did

Update Readme documentaion - build, installation, packaged

• beans version: 0.9
• Python version: 0.1.2
• Operating System: Linux, Mac OS-X

Description

Update documentation - README.rst for both beans and settle
include

• build instructions
• installation/local
• publishing on PyPI

What I Did